Characterization of meningitis-causing bacteria, with focus on genomic and pangenomic study of multi-drug resistant Streptococcus pneumoniae from cerebrospinal fluid.

Streptococcus pneumoniae is a major cause of meningitis in under developed countries with low vaccination rates and high antibiotic resistance. This study aimed to analyze 83 suspected meningitis patients in Karachi for the detection of S. pneumoniae followed by its whole genome sequencing and Pan Genome analysis. Out of the 83 samples collected, 33 samples with altered physical (turbidity), cytological (white blood cell count) and biochemical (total protein and total glucose concentrations) parameters indicated potential meningitis cases, while these parameters were within normal healthy ranges in remaining 50 samples. Latex particle agglutination (LPA) was performed on the 33 samples, revealing 20 positive cases of bacterial meningitis. The PCR and culturing methods revealed 5 S. pneumoniae isolates. Antibiotic susceptibility tests showed that one S. pneumoniae strain was resistant to erythromycin, levofloxacin, and tetracycline. Whole-genome sequencing of this resistant strain was performed and S. pneumoniae was confirmed with MLST analysis, while it had > 2.3 Mb genome and a single repUS43 plasmid. In CARD analysis, the strain had tet(M), ermB, RlmA(II), patB, pmrA, and patA ARGs, which could provide resistance against tetracycline, macrolide, fluoroquinolone, and glycopeptide antibiotics. Phylogenetic analysis revealed that the isolate was closely related to strains from Hungary and the USA. Pan-genome analysis with 144 genome assemblies from NCBI database showed that 1101 non-redundant core genes were shared between all strains. This study gives valuable understanding into the prevalence and characterization of meningitis-causing bacteria in Karachi, Pakistan  with prime focus on multi-drug resistant S. pneumoniae.

Navigating the triple threat: Management of post-ESWL urinoma, steinstrasse, and obstructive uropathy: A challenging case report.

Urinoma (collection of urine) formation secondary to extracorporeal shock wave lithotripsy (ESWL) is one of the rare complications encountered postprocedure and co-existence of urinoma with steinstrasse is a rare and challenging scenario to manage in the setting of obstructive uropathy. ESWL is known for being noninvasive for breaking kidney and ureteric stones. Urinoma is a collection of urine outside the collecting system in the retroperitoneum or perirenal space. Early detection and management are necessary to prevent complications related to urinoma and steinstrasse. This case report is about a patient who developed urinoma and steinstrasse in the setting of obstructive uropathy after sessions of ESWL on the right side and was managed with a nephrostomy tube and trans-ureteral lithotripsy on the right side and percutaneous nephrolithotomy on the left side after 1 month.

On the Synthesis of Graphene Oxide/Titanium Dioxide (GO/TiO2) Nanorods and Their Application as Saturable Absorbers for Passive Q-Switched Fiber Lasers.

We report passively Q-switched pulse operation through an erbium-doped fiber laser (EDFL) utilizing graphene oxide/titania (GO/TiO2) nanorods as a saturable absorber. The GO/TiO2 nanorods were fabricated using a Sol-gel-assisted hydrothermal method. The optical and physical characterization of the GO/TiO2 was then characterized using a field-emission-scanning electron microscope (FE-SEM), energy-dispersive X-ray spectroscopy (EDS), and diffuses reflectance spectroscopy (DRS). To investigate the performance of the Q-switched EDFL based on the GO/TiO2 SA, the prepared nanorods were mechanically deposited on the fiber ferrule employing adhesion effects of in-dex-matching gel. This integration of the nanorod SA resulted in a self-starting Q-switching opera-tion initiated at a pump power of 17.5 mW and sustained up to 306.9 mW. When the pump range was tuned from 17.5 to 306.9 mW, the emission wavelength varied from 1564.2 to 1562.9 nm, pulse repetition rates increased from 13.87 kHz to 83.33 kHz, and pulse width decreased from 30.27 µs to 3.75 µs. Moreover, at the maximum pump power of 306.9 mW, the laser exhibited an average output power of 0.74 mW, a peak power of 1.54 mW, and a pulse energy of 8.88 nJ. Furthermore, this study investigates the GO/TiO2 damage threshold and prolonged stability of the proposed EDFL system.

Methodology comparison of environmental sediment fungal community analysis.

Fungi play important roles in ecosystems. Analyzing fungal communities in environments has long been a challenge due to the large difference in compositions retrieved using different methods or sequencing regions, obscuring the true abundance and species information. Our study aimed to compare and determine more accurate approach for evaluating fungal populations in river sediment. To achieve this, different primer sets in the internal transcribed spacer (ITS) (ITS5/ITS1R, ITS1F/ITS2), 18S rRNA gene (0817F/1196R) for High-throughput sequencing (HTS), metagenomic shotgun sequencing (MS) directly from environmental samples, and HTS using ITS primers for the fungal samples collected from plate cultivation were used to characterize the fungal communities. We calculated diversity index and used FungalTraits to analyze methods preferences for fungal species. The study revealed that when analyzing the fungal species directly from environmental samples, amplification and sequencing of ITS region demonstrated more accuracy than MS and 18S rRNA gene sequencing methods, but displayed significant primer preference. Over 30 % fungal species from HTS after plate cultivation were not present in HTS from the environmental samples. NMDS analysis demonstrated significant disparities in species diversity among different methods, suggesting potential complementarity between them. Over 85% species identified by HTS using ITS primers belonged to filamentous fungi, while the MS mostly identified yeast (62%). Therefore, to get more accurate fungal community information in sediment, multiple methods were recommended by using cultivation, molecular biological methods dependent on PCR techniques like ITS1F/ITS2 primer for HTS and PCR independent method such as metagenomic shotgun sequencing techniques.

Transcription factors LvBBX24 and LvbZIP44 coordinated anthocyanin accumulation in response to light in lily petals.

Lily (Lilium spp.), a horticultural crop serving both ornamental and edible functions, derives its coloration primarily from anthocyanins. However, limited studies have been conducted on the accumulation of anthocyanins within lilies. In this study, we cloned a light-induced transcription factor named as LvBBX24 in lilies. Through genetic and biochemical analysis, we determined that LvBBX24 could upregulate the transcription of LvMYB5 and facilitate anthocyanin synthesis. Moreover, we identified that darkness promoted the degradation of LvBBX24 protein. Through screening a yeast library, we identified LvbZIP44 acts as its interacting partner. Genetic testing confirmed that LvbZIP44 also plays a role in promoting lily anthocyanin synthesis. This indicates a potential synergistic regulatory effect between LvBBX24 and LvbZIP44. Our study indicates that LvBBX24 and LvbZIP44 cooperate to regulate anthocyanin accumulation in lily petals. These findings provide compelling evidence supporting the idea that LvBBX24 and LvbZIP44 may form a looped helix surrounding the LvMYB5 promoter region to regulate anthocyanin biosynthesis.

Intra-ampullary and Periampullary Carcinoma: Clinicopathological Comparison and Survival Outcomes.

Introduction The ampulla of Vater is a structure in the duodenal wall in which the biliary and pancreatic ducts open. Malignant epithelial tumors arising at this site are commonly referred to as ampullary adenocarcinomas. In this study, we compared the clinicopathological features of intra-ampullary and periampullary carcinomas, including survival outcomes. Methods This retrospective cross-sectional study was conducted at the Department of Pathology, Liaquat National Hospital. All radiologically suspected cases or biopsy-proven (endoscopic biopsy) cases of intra-ampullary/periampullary carcinoma were included in the study. All patients underwent surgical resection (Whipple's procedure/pancreatoduodenectomy). The classification of intra-ampullary and periampullary carcinomas was performed according to the College of American Pathologists (CAP) guidelines. Results Among the 188 case studies, most (61.7%, n = 116) were males, with a median age of 55 years. Most tumors were of the pancreatobiliary subtype (57.4%, n = 108). Similarly, intra-ampullary carcinoma was more common than periampullary carcinoma (61.7% vs. 38.3%). Intra-ampullary carcinoma showed a higher extent of involvement of adjacent structures, a higher frequency of perineural invasion, and a higher nodal stage than periampullary carcinoma. Similarly, the median disease-specific survival of intra-ampullary carcinoma was significantly lower (46 months) than that of periampullary carcinoma (53.5 months). Conclusion We found a higher incidence of intra-ampullary carcinoma in our study. In addition, intra-ampullary carcinoma had a worse survival rate and was associated with poorer pathological parameters, such as perineural invasion and higher nodal and tumor stages than periampullary carcinoma.

Evaluation of the Hypoglycemic and Hypolipidemic Potential of Extract Fraction of Quercus baloot Griff Seeds in Alloxan-induced Diabetic Mice.

INTRODUCTION: The discovery and development of new phytomedicines can be greatly aided by plants because of their tremendous therapeutic benefits, efficiency, cost-effectiveness, lack of side effects, and cheaper therapies. In this regard, Quercus baloot, generally known as oak, is used in folkloric medicine for treating and preventing various human disorders, including diabetes. AIM: For this purpose, the present study aimed to evaluate crude methanolic extract and various fractions of Quercus baloot for antihyperlipidemic and antihyperglycemic potential followed by the analysis of active compounds. METHODS: The hypoglycemic and hypolipidemic activity was evaluated in Swiss male Albino mice by administering an oral dose of 150-300 mg/kg of Q. baloot extracts in alloxan induced diabetic mice for 14 days. RESULTS: The results revealed that crude methanolic extract at a dose of 300 mg/kg exhibited a significant reduction in the blood glucose level (198.50 ± 1.99 mg/dl) at day 14 and the same treatment significantly increased the body weight (31.26 ± 0.27 g) at day 14 in comparison to the control group. Moreover, the biochemical parameters were investigated which presented an increase in high-density lipids (HDL) (30.33 ± 0.33 mg/dl), whereas low-density lipids (LDL) showed a significant decrease (105.66 ± 0.26 mg/dl). Additionally, triglyceride levels 104.83 ± 0.70 mg/dl, and total cholesterol 185.50 ± 0.76 mg/dl are significantly decreased. In serum biochemical analysis creatinine and hepatic enzyme markers, like serum glutamate pyruvate transaminase (32.00 ± 0.36 U/mg), serum glutamate oxaloacetate transaminase (34.33 ± 0.61 U/mg), and alkaline phosphatase (157.00 ± 0.73 U/mg), were significantly reduced by the crude methanolic extract at a dose of 300 mg/kg as compared to the control group. The antioxidant enzymes like Superoxide dismutase (4.57 ± 0.011), peroxidases dismutase (6.53 ± 0.014, and catalase (8.38 ± 0.014) at a dosage of 300 mg/kg of methanolic extract exhibited a significant increase. The histopathological study of the diabetic heart, liver, and pancreas showed substantial restoration of damaged tissues in the methanolic extract 150 and 300 mg/kg treated group, which supports the effectiveness of Q. baloot seeds. The gas chromatography-mass spectrometry analysis of methanolic extract identified 10 antidiabetic active compounds in the Q. baloot seeds, validating the antihyperglycemic activity. Thus, methanolic crude extract at the doses 150 and 300 mg/kg of Q. baloot showed significant antihyperlipidemic and antihyperglycemic activities, which validate the folkloric utilization of Q. baloot as a remedy in diabetes. CONCLUSION: In conclusion, the 300 mg/kg methanolic extract of Q. baloot has notable hypoglycemic and hypolipidemic potential, supporting the plant's traditional medicinal usage in the treatment of diabetes and its complications. Further studies are needed for the purification, characterization, and structural clarification of bioactive compounds.

Complete genome sequences of four representative Corynebacterium belfantii strains.

This report describes the complete genome sequence assemblies from four representative isolates of the human pathogen Corynebacterium belfantii. These data provide necessary references to aid accurate sequence-based species discrimination among closely related Corynebacterium spp. pathogens.

Pseudochrobactrum asaccharolyticum mitigates arsenic induced oxidative stress of maize plant by enhancing water status and antioxidant defense system.

BACKGROUND: Oxidative stress mediated by reactive oxygen species (ROS) is a common denominator in arsenic toxicity. Arsenic stress in soil affects the water absorption, decrease stomatal conductance, reduction in osmotic, and leaf water potential, which restrict water uptake and osmotic stress in plants. Arsenic-induced osmotic stress triggers the overproduction of ROS, which causes a number of germination, physiological, biochemical, and antioxidant alterations. Antioxidants with potential to reduce ROS levels ameliorate the arsenic-induced lesions. Plant growth promoting rhizobacteria (PGPR) increase the total soluble sugars and proline, which scavenging OH radicals thereby prevent the oxidative damages cause by ROS. The main objective of this study was to evaluate the potential role of Arsenic resistant PGPR in growth of maize by mitigating arsenic stress. METHODOLOGY: Arsenic tolerant PGPR strain MD3 (Pseudochrobactrum asaccharolyticum) was used to dismiss the 'As' induced oxidative stress in maize grown at concentrations of 50 and 100 mg/kg. Previously isolated arsenic tolerant bacterial strain MD3 "Pseudochrobactrum asaccharolyticum was used for this experiment. Further, growth promoting potential of MD3 was done by germination and physio-biochemical analysis of maize seeds. Experimental units were arranged in Completely Randomized Design (CRD). A total of 6 sets of treatments viz., control, arsenic treated (50 & 100 mg/kg), bacterial inoculated (MD3), and arsenic stress plus bacterial inoculated with three replicates were used for Petri plates and pot experiments. After treating with this MD3 strain, seeds of corn were grown in pots filled with or without 50 mg/kg and 100 mg/kg sodium arsenate. RESULTS: The plants under arsenic stress (100 mg/kg) decreased the osmotic potential (0.8 MPa) as compared to control indicated the osmotic stress, which caused the reduction in growth, physiological parameters, proline accumulation, alteration in antioxidant enzymes (Superoxide dismutase-SOD, catalase-CAT, peroxidase-POD), increased MDA content, and H2O2 in maize plants. As-tolerant Pseudochrobactrum asaccharolyticum improved the plant growth by reducing the oxidation stress and antioxidant enzymes by proline accumulation. PCA analysis revealed that all six treatments scattered differently across the PC1 and PC2, having 85.51% and 9.72% data variance, respectively. This indicating the efficiency of As-tolerant strains. The heatmap supported the As-tolerant strains were positively correlated with growth parameters and physiological activities of the maize plants. CONCLUSION: This study concluded that Pseudochrobactrum asaccharolyticum reduced the 'As' toxicity in maize plant through the augmentation of the antioxidant defense system. Thus, MD3 (Pseudochrobactrum asaccharolyticum) strain can be considered as bio-fertilizer.

Risk Factors of Oral Squamous Cell Carcinoma with Special Emphasis on Areca Nut Usage and Its Association with Clinicopathological Parameters and Recurrence.

Introduction: Oral squamous cell carcinoma (OSCC) is the most prevalent type of head and neck cancer and is associated with high mortality, particularly in Southeast Asian countries. Areca nut usage, smoking, and alcohol consumption are the most common risk factors for OSCC. Areca nut chewing is highly prevalent in Pakistan and has been attributed to an increase in OSCC cases. This study aimed to determine the association between areca nut usage and various clinicopathological features of OSCC and further evaluate the association of clinicopathological parameters of OSCC with tumor recurrence. Materials and Methods: The study was conducted using the data of 228 patients with OSCC resected at Liaquat National Hospital, Karachi, Pakistan, over 5 years between 2018 and 2022. Clinicopathological data were collected from hospital archives, and associations between various risk factors and clinicopathological parameters were determined. Results: Males were more commonly affected (77.2%), and the most common age group was <50 years (54.4%). Areca nut usage was reported in 59.6% of cases, and the buccal mucosa was the most common site (62.7%). Areca nut usage was significantly associated with male gender, greater tumor size, greater depth of invasion (DOI), higher tumor stage, nodal stage, presence of perineural invasion (PNI), and recurrence. In addition, multivariate analysis revealed that OSCC recurrence was significantly associated with older age, larger tumor size and DOI, nodal metastasis, and areca nut usage. Conclusion: Areca nut-related OSCCs were associated with poor prognosis and recurrence in our study population. Furthermore, OSCC recurrence was associated with various clinicopathological parameters, such as larger tumor size, a higher DOI, and nodal metastasis.

Exploring the therapeutic potential of cannabinoids in cancer by modulating signaling pathways and addressing clinical challenges.

For centuries, cannabinoids have been utilized for their medicinal properties, particularly in Asian and South-Asian countries. Cannabis plants, known for their psychoactive and non-psychoactive potential, were historically used for spiritual and remedial healing. However, as cannabis became predominantly a recreational drug, it faced prohibition. Recently, the therapeutic potential of cannabinoids has sparked renewed research interest, extending their use to various medical conditions, including cancer. This review aims to highlight current data on the involvement of cannabinoids in cancer signaling pathways, emphasizing their potential in cancer therapy and the need for further investigation into the underlying mechanisms. A comprehensive literature review was conducted using databases such as PubMed/MedLine, Google Scholar, Web of Science, Scopus, and Embase. The search focused on peer-reviewed articles, review articles, and clinical trials discussing the anticancer properties of cannabinoids. Inclusion criteria included studies in English on the mechanisms of action and clinical efficacy of cannabinoids in cancer. Cannabinoids, including Δ9-THC, CBD, and CBG, exhibit significant anticancer activities such as apoptosis induction, autophagy stimulation, cell cycle arrest, anti-proliferation, anti-angiogenesis, and metastasis inhibition. Clinical trials have demonstrated cannabinoids' efficacy in tumor regression and health improvement in palliative care. However, challenges such as variability in cannabinoid composition, psychoactive effects, regulatory barriers, and lack of standardized dosing remain. Cannabinoids show promising potential as anticancer agents through various mechanisms. Further large-scale, randomized controlled trials are essential to validate these findings and establish standardized therapeutic protocols. Future research should focus on elucidating detailed mechanisms, optimizing dosing, and exploring cannabinoids as primary chemotherapeutic agents.

Phytosociology and ecological framework of forest tree species in the Toormang Valley, Dir Lower, Hindu Kush Range, Pakistan.

The phytosociological survey was conducted during 2018-2020. The research area was classified into five ecological zones based on habitat, physiognomy and species composition. Pc-Ord software was used for cluster analysis and four vegetation communities were established. The Quercus baloot-Quercus incana community is situated in Sair at an altitude of 1196 (mean ± SE) m altitude with a 14.1 ± 0 slope angle and contains eleven tree species. The Pinus wallichiana- Ailanthus altissima community had a relatively small number of tree species reported in Shakawlie at 1556 (mean ± SE) with a 17.5 ± 0 slope angle. The Pinus wallichiana- Quercus incana community is distributed in Wali Kandao and Mangi Kandao at altitudes of 2030.5 (mean ± SE) m and the slope angle was 19.2 ± 1.4. This community possesses a total of twenty-one tree species and is highly diverse. Similarly, the Populus alba - Platanus orientalis group was present in Banr Pate, with an altitude of 1613 (mean ± SE) m and a 16.3 slope angle. The principal component analysis (PCA) and non-metric multidimensional scaling (NMS) ordination methods were applied to study the relationships between ecological and soil variables with trees species. The NMS ordination of axis 1 was significantly correlated with Sand% (p<0.2), Nitrogen% (p<0.1) and Pb (mg/kg) (r= 0.876751, p<0.05), while the ordination of axis 2 was significantly correlated with Silt% (p<0.2), Sand% (p<0.2), Organic matter% (p<0.2), K (mg/kg) (r=0.882433, p<0.02), Fe (mg/kg)(r=0.614833, p<0.2), Ca (mg/kg) (r=0.721712, p< 0.2) and Zn (mg/kg) (r=0.609545, p<0.2). Similarly, the PCA ordination of axis 1 revealed that it was significantly correlated with phosphorus, calcium and slope angle, while that of axis 2 was significantly correlated with altitude, zinc and manganese.

Diethylenetriaminepentaacetic Acid-based Conducting Solid Polymer Electrolytes Impede Lithium Dendrites and Impart Antioxidant Capacity in Lithium-Ion Batteries.

In the development of lithium-ion batteries (LIBs), cheaper and safer solid polymer electrolytes are expected to replace combustible organic liquid electrolytes to meet the larger market demand. However, low ionic conductivity and inadequate cycling stability impede their commercial viability. Herein, a novel flexible conducting solid polymer electrolytes (CSPEs) based on polyvinyl alcohol (PVA) and ion-polarized diethylenetriaminepentaacetic acid (P-DETP) is developed for the first time and applied in LIBs. PVA and P-DETP form a compact polymer network through hydrogen bonding, enhancing the thermomechanical stability of CSPE while restricting the migration of larger anions. Furthermore, density functional theory calculations confirm that P-DETP can facilitate the dissociation of Li+-TFSI- via electrostatic attraction, resulting in increased mobility of lithium ions. Additionally, P-DETP contributes to the formation of a stable electrode-electrolyte interface layer, effectively suppressing the growth of lithium dendrites and improving antioxidant capacity. These synergistic effects enable CSPE to exhibit remarkable properties including high ionic conductivity (2.8 × 10-4 S cm-1), elevated electrochemical potential (5.1 V), and excellent lithium transference number (0.869). Notably, the P-DETP/LiTFSI CSPE demonstrates stable performance not only in LiFePO4 batteries but also adapts to high-nickel ternary LiNi0.88Co0.06Mn0.06O2 cathode, highlighting its immense potential for application in high energy density LIBs.

Bacterial Extracellular Vesicles: Potential Therapeutic Applications, Challenges, and Future Prospects.

Almost all cell types naturally secret extracellular vesicles (EVs) in the extracellular space with variable metabolic cargo facilitating intracellular communication, posing immune-modulation capacity. Thus, "bacterial extracellular vesicles" (BEVs), with their great immunoregulatory, immune response stimulation and disease condition-altering potential, have gained importance in the medical and therapeutic industry. Various subtypes of BEVs were observed and reported in the literature, such as exosomes (30-150 nm), microvesicles (100-1000 nm), apoptotic bodies (1000-5000 nm), and oncosomes (1000-10,000 nm). As biological systems are complex entities, inserting BEVs requires extra high purity. Various techniques for BEV isolation have been employed alone or with other strategies, such as ultracentrifugation, precipitation, size-exclusion chromatography, affinity-based separation, ultrafiltration, and field-flow fractionation. But to date, no BEV isolation method is considered perfect as the lack of standard protocols limits their scale-up. Medical research has focused on BEVs to explore their diverse therapeutic potential. This review particularly focused on the recent advancements in the potential medical application of BEVs, current challenges, and prospects associated with their scale-up.

Effect of Workplace Harassment on Organizational Cynicism with the Mediation of Perceived Incivility and the Moderating Role of Perceived Organizational Obstruction.

Workplace harassment is the most disliked behavior; it is about entering others' private space. It has dangerous consequences if the organizations do not control it. Perceived Incivility is a low-intensity deviant behavior that tends to apply damaging behavior; it may cause a wide range of mistreatment. This study investigates the effect of workplace harassment on organizational Cynicism in Pakistan, with the mediation of perceived Incivility and the moderating role of perceived organizational obstruction. Based on a sample of research students from various fields and institution types, the analysis supports the hypothesis that workplace harassment is positively related to perceived Incivility and organizational Cynicism. Furthermore, perceived Incivility is positively related to organizational cynicism and may mediate the relationship between workplace harassment and organizational cynicism. However, contrary to expectations, perceived organizational obstruction appears to weaken rather than strengthen the relationship between perceived Incivility and organizational cynicism. The findings have important implications for understanding the complex interplay between workplace harassment, Incivility, organizational obstruction, and Cynicism and for developing interventions to mitigate the negative impact of harassment on employees and organizations.