Barriers and facilitators to perinatal care of women with disabilities in lower- and middle-income countries: a study protocol for scoping review of qualitative studies.

BACKGROUND: The Sustainable Development Goals have put emphasis on equitable healthcare access for marginalised groups and communities. The number of women with disabilities (WWD) to marry and have children is rapidly increasing in low- and middle-income countries (LMICs). However, these women experience multifaceted challenges to seeking perinatal care in LMICs. The objective of this scoping review is to document key facilitators and barriers to seeking perinatal care by WWD. We also will propose strategies for inclusive perinatal healthcare services for women with disabilities in LMICs. METHODS: We will conduct a scoping review of peer-reviewed and grey literature (published reports) of qualitative and mixed-methods studies on facilitators and barriers to seeking perinatal care for women with functional disabilities from 2010 to 2023 in LMICs. An electronic search will be conducted on Medline/PubMed, Scopus and Google Scholar databases. Two researchers will independently assess whether studies meet the eligibility criteria for inclusion based on the title, abstract and a full-text review. ETHICS AND DISSEMINATION: This scoping review is based on published literature and does not require ethics approval. Findings will be published in peer-reviewed journals and presented at conferences related to reproductive health, disability and inclusive health forums.

Mucosal organs exhibit distinct response signatures to hydrogen sulphide in Atlantic salmon (Salmo salar).

Hydrogen sulphide (H2S) is considered an immunotoxicant, and its presence in the water can influence the mucosal barrier functions of fish. However, there is a significant knowledge gap on how fish mucosa responds to low environmental H2S levels. The present study investigated the consequences of prolonged exposure to sub-lethal levels of H2S on the mucosal defences of Atlantic salmon (Salmo salar). Fish were continuously exposed to two levels of H2S (low: 0.05 µM; and high: 0.12 µM) for 12 days. Unexposed fish served as control. Molecular and histological profiling focused on the changes in the skin, gills and olfactory rosette. In addition, metabolomics and proteomics were performed on the skin and gill mucus. The gene expression profile indicated that the gills and olfactory rosette were more sensitive to H2S than the skin. The olfactory rosette showed a dose-dependent response, but not the gills. Genes related to stress responses were triggered at mucosal sites by H2S. Moreover, H2S elicited strong inflammatory responses, particularly in the gills. All mucosal organs demonstrated the key molecular repertoire for sulphide detoxification, but their temporal and spatial expression was not substantially affected by sub-lethal H2S levels. Mucosal barrier integrity was not considerably affected by H2S. Mucus metabolomes of the skin and gills were unaffected, but a matrix-dependent response was identified. Comparing the high-concentration group's skin and gills mucus metabolomes identified altered amino acid biosynthesis and metabolism pathways. The skin and gill mucus exhibited distinct proteomic profiles. Enrichment analysis revealed that proteins related to immunity and metabolism were affected in both mucus matrices. The present study expands our knowledge of the defence mechanisms against H2S at mucosal sites in Atlantic salmon. The findings offer insights into the health and welfare consequences of sub-lethal H2S, which can be incorporated into the risk assessment protocols in salmon land-based farms.

Atypical haemolytic uremic syndrome in a patient with severe Babesiosis.

Babesiosis is a tick-borne parasitic infection that can result in various haematological complications. This case report discusses a patient with severe Babesiosis complicated by an unorthodox presentation of Babesiosis-associated haemolytic uremic syndrome. Discussed here is the patient's clinical course and the management strategies employed, with an emphasis on early recognition and treatment of renal failure in the context of severe Babesiosis. Haematologic manifestations of Babesia are common and the severity of disease is dependent on parasite load. While treatment options such as red blood cell exchange have been proposed for severe cases, their impact on clinical outcomes is limited and they may not be readily available in resource-limited settings. Traditional management using antimicrobials has been proposed but there is limited discussion about managing unique presentations such as renal failure in Babesiosis. Hence, understanding the pathophysiology, early recognition and aggressive treatment strategies can optimise clinical outcomes and reduce mortality.

Negative Pressure Wound Therapy in Pharyngocutaneous Fistula.

Pharyngocutaneous fistula (PCF) is an abnormal connection between the pharynx and skin that can occur after laryngectomy surgery. It can have a significant negative impact on patient recovery, delaying wound healing, requiring prolonged nil-per-oral (NPO) status, and reducing quality of life. Traditionally, the management of PCF has relied on conservative measures or surgical intervention. However, negative pressure wound therapy (NPWT) offers a promising alternative approach. This case study involves three patients who underwent laryngectomy and developed postoperative PCF. All patients received NPWT with a modified suction catheter and low negative pressure (20-40 mmHg). With NPWT, all patients achieved complete wound closure, with healing times ranging from two weeks to six weeks. This suggests that NPWT may significantly accelerate PCF healing compared to traditional methods. However, maintaining an airtight dressing on the neck region can be challenging. This study highlights the potential of NPWT for faster PCF closure after laryngectomy. Further research is needed to optimize NPWT application techniques, explore the impact on long-term outcomes, and establish guidelines for broader clinical use.

Efficacy and Safety of Rivaroxaban Versus Enoxaparin in Prevention of Recurrence of Venous Thrombo-Embolism Events in Cancer Patients: A Meta-Analysis.

OBJECTIVE: To examine the effectiveness of rivaroxaban compared to enoxaparin in patients diagnosed with cancer and venous thromboembolism. METHODS: A search of Pub Med, Scopus, and Google Scholar, from inception through April 2023 was conducted. Articles comparing rivaroxaban with enoxaparin in patients with cancer and VTE/PE/DVT were included. Review Manager Version 5.2 was utilised for the analysis of the following outcomes; VTE, PE, DVT, major bleeding, and mortality. RESULTS: A total of 8 articles and 2276 patients were included in the final analysis. Pooled analysis showed that rivaroxaban had a statistically insignificant reduced association with VTE occurrence (RR:0.83, 95% CI:0.58-1.18, P:0.3) as well as a statically insignificant reduction in major bleeding (RR:0.79, 95% CI:0.53-1.18, P:0.25). Analysis showcased that there was an insignificant reduction of mortality rivaroxaban as compared to enoxaparin (RR:0.74, 95% CI: 0.46-1.20, P:0.23). CONCLUSION: Rivaroxaban can serve as a viable alternative to enoxaparin, with no appreciable drawbacks, for preventing and managing VTE in patients with malignancy.

Impact of public-private partnerships investment and FDI on CO2 emissions: A study of six global investment countries.

This study investigates the impact of public-private partnerships investment in energy and FDI on environmental quality in global investment countries during 1995-2018. Economic growth, technological innovations and consumption of clean energy are also considered as additional determinants of environmental quality. The study applied advanced panel econometric models. Our empirical results affirm the evidence of a long-run association between environmental quality and its determinants. Specifically, economic growth as well as clean energy use improves quality of environment by lowering carbon emissions. Public-private partnerships investment in energy, FDI and technological innovations decrease carbon emissions. Energy consumption (generated from fossil fuel) increases carbon emissions. Heterogeneous causality evidence indicates the presence of a unidirectional causality relation from carbon emissions to public-private partnerships investment in energy and a feedback causality occurs between consumption of clean energy and CO2 emissions. This empirical evidence provides new insights for both policymakers and governments to support public-private partnership investments in energy for the improvement of quality of environment in global investment countries.

Managing energy transition alongside environmental protection by making use of AI-led butanol powered SI engine optimization in compliance with SDGs.

Enormous consumption of fossil fuel resources has risked energy accessibility in the upcoming years. The price fluctuation and depletion rate of fossil fuels instigate the urgent need for searching their reliable substitute. The current study tries to address these issues by presenting butanol as a replacement for gasoline in SI engines at various speeds and loading conditions. The emission and performance parameters were ascertained for eight distinct butanol-gasoline fuel blends. The oxygenated butanol substantially increases engine efficiency and boosts power with lower fuel consumption. The carbon emissions were also observed to be lower in comparison with gasoline. Furthermore, the Artificial Intelligence (AI) approach was used in predicting engine performance running on the butanol blends. The correlation coefficients for the data training, validation, and testing were found to be 0.99986, 0.99942, and 0.99872, respectively. It was confirmed that the ANN predicted results were in accordance with the established statistical criteria. ANN was paired with Response Surface Methodology (RSM) technique to comprehend the influence of the sole design parameters along with their statistical interactions controlling the responses. Similarly, the R2 value of responses in case of RSM were close to unity and mean relative errors (MRE) were confined under specified range. A comparative study between ANN and RSM models unveiled that the ANN model should be preferred. Therefore, a joint utilization of the RSM and ANN can be more effective for reliable statistical interactions and predictions.

Experiences of Participation in a Study Investigating Feasibility of the Implantable Doppler Probe in Kidney Transplantation: An Embedded Qualitative Study.

OBJECTIVES: Kidney transplant survival can be improved with better graft surveillance postoperatively. In the quest to explore new technologies, we explored the feasibility of an implantable Doppler probe as a blood flow monitoring device in kidney transplant patients. This qualitative study was embeddedin a feasibility trial and aimed to test the device's clinical acceptability and obtain suggestions for the development of the intervention. Objectives included exploring the experiences of feasibility study participants and identifying barriers to the implementation of implantable Doppler probes in clinical practice. MATERIALS AND METHODS: We conducted semi-structured interviews containing open-ended questions with 12 feasibility study participants recruited by purposive sampling. All interviews were audio-recorded with verbatim transcription. Thematic data analysis was performed at the latent level by using an inductive approach with a previously published 6-phase guide. RESULTS: Three key themes emerged: (1) perceived value of the intervention in clinical practice, (2) challenges and barriers to implementation of the intervention, and (3) suggestions forthe development of the intervention. Due to functional limitations and lack of research, medical professional participants revealed clinical equipoise regarding the utility of implantable Doppler probes. However,the device was well received by patient participants. Challenges included device training needs for medical professionals and educational sessions for patients. Innovative ideas for development included the insertion of a display screen, adopting disposable units to reduce overall cost, online access allowing remote monitoring, decreasing external monitoring unit size, and integrating a wireless connection with the probe to reduce signal errors and increase patient safety. CONCLUSIONS: The clinical need for blood flow sensing technology in kidney transplants has been widely acknowledged. Implantable Doppler probes may be a beneficial adjunct in the early postoperative surveillance of kidney transplant patients. However, the device's technical limitations are the main challenges to its acceptance in clinical practice.

Effects of curcumin in patients with non-alcoholic fatty liver disease: A systematic review and meta-analysis.

Background: Curcumin is an anti-inflammatory that is proposed to have a positive impact on patients with non-alcoholic fatty liver disease (NAFLD). We aim to assess the effects of curcumin in patients with NAFLD. Methods: Clinical trials from PubMed, Scopus, the Web of Science, and Cochrane CENTRAL with variables alanine transferase, aspartate transaminase, alkaline phosphatase, glycated hemoglobin (HBA1c), BMI, waist circumference, total cholesterol, total glycerides, high-density lipoproteins, and low-density lipoproteins were included. Homogeneous and heterogeneous were analyzed under a fixed-effects model and the random-effects model, respectively. Results: Fourteen clinical trials found that curcumin has no statistically significant effect on alanine transferase (MD = -2.20 [-6.03, 1.63], p = 0.26], aspartate transaminase (MD = 1.37 [-4.56, 1.81], p = 0.4), alkaline phosphatase (MD = 3.06 [-15.85, 9.73], p = 0.64), glycated hemoglobin (HBA1c), (MD = -0.06 [-0.13, 0.02], p = 0.16], and BMI (MD = 0.04 [-0.38, 0.46], p = 0.86). Curcumin reduced the waist circumference (MD = -4.87 [-8.50, -1.25], p = 0.008). Lipid profile parameters were not significant, except the total glycerides (MD = -13.22 [-24.19, -2.24], p = 0.02). Conclusions: Curcumin significantly reduces total glycerides and waist circumference in NAFLD.

Acute toxicity appraisal of Saussurea heteromalla extract and development of its chemotherapeutic herbal dosage form.

Ethnopharmacological relevance of Saussurea species for anti-cancer compounds instigated us to develop chemotherapeutic herbal tablets. This study was an ongoing part of our previous research based on the scientific evaluation of Saussurea heteromalla (S. heteromalla) for anti-cancer lead compounds. In the current study, S. heteromalla herbal tablets (500 /800 mg) were designed and evaluated for anti-cancer activity. Arctigenin was found as a bioactive lead molecule with anti-cancer potential for cervical cancer. The in vitro results on the HeLa cell line supported the ethnopharmacological relevance and traditional utilization of S. heteromalla and provided the scientific basis for the management of cervical cancer as proclaimed by traditional practitioners in China. LD50 of the crude extract was established trough oral acute toxicity profiling in mice, wherein the minimum lethal dose was noticed as higher than 1000 mg/kg body weight orally. Chromatographic fingerprint analysis ensured the identity and consistency of S. heteromalla in herbal tablets in terms of standardization of the herbal drug. About 99.15% of the drug (S. heteromalla crude extract) was recovered in herbal tablets (RSD: 0.45%). In vitro drug release profile was found to be more than 87% within 1 h, which was also correlated with different mathematical kinetic models of drug release (r2 = 0.992), indicating that drug release from matrix tablets into the blood is constant throughout the delivery. The dosage form was found stable after an accelerated stability parameters study which may be used for anti-cervical cancer therapy in the future, if it qualifies successful preclinical investigation parameters.

Association of latent autoimmune diabetes of adults with type 3 polyglandular autoimmune syndrome-a diagnostic challenge.

Autoimmune polyendocrine syndromes (APS) encompass m ultiple e ndocrin e gland ins ufficiencies asso ci ated wit h auto immune disease. This c as e report underscores the importance of recognising the association between latent auto immune di a betes of ad ults (LADA) and type 3 polyglandular syndrome. A 42-year-old man belonging to R awalpi ndi, Pakistan, p resented to th e out patient department (OPD) of Ali Medi cal Centre, Islamab ad, i n Januar y 2023 with the complaints o f e xtreme thirs t and frequent urination. The patient reported consistently raised app etite an d eating four to five meals a day along with abrupt weight loss, dry mouth, fatigue occasional dizziness, an d dyspnoea. He was diagno s ed with type 3 polygla ndular syndrome w ith associat io n of LADA. Daily administration of 10 units of glargine insulin, along with six units of rapid-acting insulin, was prescribed. The patient's H bA1c level reduce d in a few months afte r succe ssive follow-up. Patients who exhi bit uncontrol led diabe tes despite dietar y and oral hypoglycaemic management should be further investigated for multiple au toimmune endocrine disorders.

Microorganism-mediated biodegradation for effective management and/or removal of micro-plastics from the environment: a comprehensive review.

Micro- plastics (MPs) pose significant global threats, requiring an environment-friendly mode of decomposition. Microbial-mediated biodegradation and biodeterioration of micro-plastics (MPs) have been widely known for their cost-effectiveness, and environment-friendly techniques for removing MPs. MPs resistance to various biocidal microbes has also been reported by various studies. The biocidal resistance degree of biodegradability and/or microbiological susceptibility of MPs can be determined by defacement, structural deformation, erosion, degree of plasticizer degradation, metabolization, and/or solubilization of MPs. The degradation of microplastics involves microbial organisms like bacteria, mold, yeast, algae, and associated enzymes. Analytical and microbiological techniques monitor microplastic biodegradation, but no microbial organism can eliminate microplastics. MPs can pose environmental risks to aquatic and human life. Micro-plastic biodegradation involves fragmentation, assimilation, and mineralization, influenced by abiotic and biotic factors. Environmental factors and pre-treatment agents can naturally degrade large polymers or induce bio-fragmentation, which may impact their efficiency. A clear understanding of MPs pollution and the microbial degradation process is crucial for mitigating its effects. The study aimed to identify deteriogenic microorganism species that contribute to the biodegradation of micro-plastics (MPs). This knowledge is crucial for designing novel biodeterioration and biodegradation formulations, both lab-scale and industrial, that exhibit MPs-cidal actions, potentially predicting MPs-free aquatic and atmospheric environments. The study emphasizes the urgent need for global cooperation, research advancements, and public involvement to reduce micro-plastic contamination through policy proposals and improved waste management practices.

Exploring mosquito abundance and Plasmodium infection through nested-PCR: implications for disease surveillance and control.

The Plasmodium is responsible for malaria which poses a major health threat, globally. This study is based on the estimation of the relative abundance of mosquitoes, and finding out the correlations of meteorological parameters (temperature, humidity and rainfall) with the abundance of mosquitoes. In addition, this study also focused on the use of nested PCR (species-specific nucleotide sequences of 18S rRNA genes) to explore the Plasmodium spp. in female Anopheles. In the current study, the percentage relative abundance of Culex mosquitoes was 57.65% and Anopheles 42.34% among the study areas. In addition, the highest number of mosquitoes was found in March in district Mandi Bahauddin at 21 °C (Tmax = 27, Tmin = 15) average temperature, 69% average relative humidity and 131 mm rainfall, and these climatic factors were found to affect the abundance of the mosquitoes, directly or indirectly. Molecular analysis showed that overall, 41.3% of the female Anopheles pools were positive for genus Plasmodium. Among species, the prevalence of Plasmodium (P.) vivax (78.1%) was significantly higher than P. falciparum (21.9%). This study will be helpful in the estimation of future risk of mosquito-borne diseases along with population dynamic of mosquitoes to enhance the effectiveness of vector surveillance and control programs.

Molecular Mechanisms of Ischemic Stroke: A Review Integrating Clinical Imaging and Therapeutic Perspectives.

Ischemic stroke poses a significant global health challenge, necessitating ongoing exploration of its pathophysiology and treatment strategies. This comprehensive review integrates various aspects of ischemic stroke research, emphasizing crucial mechanisms, therapeutic approaches, and the role of clinical imaging in disease management. It discusses the multifaceted role of Netrin-1, highlighting its potential in promoting neurovascular repair and mitigating post-stroke neurological decline. It also examines the impact of blood-brain barrier permeability on stroke outcomes and explores alternative therapeutic targets such as statins and sphingosine-1-phosphate signaling. Neurocardiology investigations underscore the contribution of cardiac factors to post-stroke mortality, emphasizing the importance of understanding the brain-heart axis for targeted interventions. Additionally, the review advocates for early reperfusion and neuroprotective agents to counter-time-dependent excitotoxicity and inflammation, aiming to preserve tissue viability. Advanced imaging techniques, including DWI, PI, and MR angiography, are discussed for their role in evaluating ischemic penumbra evolution and guiding therapeutic decisions. By integrating molecular insights with imaging modalities, this interdisciplinary approach enhances our understanding of ischemic stroke and offers promising avenues for future research and clinical interventions to improve patient outcomes.

ProtTrans and multi-window scanning convolutional neural networks for the prediction of protein-peptide interaction sites.

This study delves into the prediction of protein-peptide interactions using advanced machine learning techniques, comparing models such as sequence-based, standard CNNs, and traditional classifiers. Leveraging pre-trained language models and multi-view window scanning CNNs, our approach yields significant improvements, with ProtTrans standing out based on 2.1 billion protein sequences and 393 billion amino acids. The integrated model demonstrates remarkable performance, achieving an AUC of 0.856 and 0.823 on the PepBCL Set_1 and Set_2 datasets, respectively. Additionally, it attains a Precision of 0.564 in PepBCL Set 1 and 0.527 in PepBCL Set 2, surpassing the performance of previous methods. Beyond this, we explore the application of this model in cancer therapy, particularly in identifying peptide interactions for selective targeting of cancer cells, and other fields. The findings of this study contribute to bioinformatics, providing valuable insights for drug discovery and therapeutic development.

Efficacy and safety of laparoscopic Heller's myotomy versus pneumatic dilatation for achalasia: A systematic review and meta-analysis of randomized controlled trials.

BACKGROUND AND OBJECTIVES: Achalasia has several treatment modalities. We aim to compare the efficacy and safety of laparoscopic Heller myotomy (LHM) with those of pneumatic dilatation (PD) in adult patients suffering from achalasia. METHODS: We searched Cochrane CENTRAL, PubMed, Web of Science, SCOPUS and Embase for related clinical trials about patients suffering from achalasia. The quality appraisal and assessment of risk of bias were conducted with GRADE and Cochrane's risk of bias tool, respectively. Homogeneous and heterogeneous data was analyzed under fixed and random-effects models, respectively. RESULTS: The pooled analysis of 10 studies showed that PD was associated with a higher rate of remission at three months, one year, three years and five years (RR = 1.25 [1.09, 1.42] (p = 0.001); RR = 1.13 [1.05, 1.20] (p = 0.0004); RR = 1.48 [1.19, 1.82] (p = 0.0003); RR = 1.49 [1.18, 1.89] (p = 0.001)), respectively. LHM was associated with lower number of cases suffering from adverse events, dysphagia and relapses (RR = 0.50 [0.25, 0.98] (p = 0.04); RR = 0.33 [0.16, 0.71] (p = 0.004); RR = 0.38 [0.15, 0.97] (p = 0.04)), respectively. There is no significant difference between both groups regarding the lower esophageal pressure, perforations, remission rate at two years, Eckardt score after one year and reflux. CONCLUSION: PD had higher remission rates than LHM at three months, one year and three years, but not at two years or five years. More research is needed to determine whether PD has a significant advantage over LHM in terms of long-term remission rates.

Modulating plant-soil microcosm with green synthesized ZnONPs in arsenic contaminated soil.

Biogenic nanoparticle (NP), derived from plant sources, is gaining prominence as a viable, cost-effective, sustainable, and biocompatible alternative for mitigating the extensive environmental impact of arsenic on the interplay between plant-soil system. Herein, the impact of green synthesized zinc oxide nanoparticles (ZnONPs) was assessed on Catharanthus roseus root system-associated enzymes and their possible impact on microbiome niches (rhizocompartments) and overall plant performance under arsenic (As) gradients. The application of ZnONPs at different concentrations successfully modified the arsenic uptake in various plant parts, with the root arsenic levels increasing 1.5 and 1.4-fold after 25 and 50 days, respectively, at medium concentration compared to the control. Moreover, ZnONPs gradients regulated the various soil enzyme activities. Notably, urease and catalase activities showed an increase when exposed to low concentrations of ZnONPs, whereas saccharase and acid phosphatase displayed the opposite pattern, showing increased activities under medium concentration which possibly in turn influence the plant root system associated microflora. The use of nonmetric multidimensional scaling ordination revealed a significant differentiation (with a significance level of p < 0.05) in the structure of both bacterial and fungal communities under different treatment conditions across root associated niches. Bacterial and fungal phyla level analysis showed that Proteobacteria and Basidiomycota displayed a significant increase in relative abundance under medium ZnONPs concentration, as opposed to low and high concentrations, respectively. Similarly, in depth genera level analysis revealed that Burkholderia, Halomonas, Thelephora and Sebacina exhibited a notably high relative abundance in both the rhizosphere and rhizoplane (the former refers to the soil region influenced by root exudates, while the latter is the root surface itself) under medium concentrations of ZnONPs, respectively. These adjustments to the plant root-associated microcosm likely play a role in protecting the plant from oxidative stress by regulating the plant's antioxidant system and overall biomass.

Efficacy and safety of terlipressin and albumin vs. noradrenaline and albumin in adult patients with hepatorenal syndrome: A systematic review and meta-analysis.

INTRODUCTION AND OBJECTIVES: Hepatorenal syndrome (HRS) is a serious complication of cirrhosis treated with various medications. We aim to evaluate terlipressin and albumin's effectiveness and safety compared to albumin and noradrenaline in adult hepatorenal disease patients. MATERIALS AND METHODS: Clinical trials from four databases were included. Cochrane's approach for calculating bias risk was utilized. We rated the quality evaluation by Grading of Recommendations Assessment, Development, and Evaluation (GRADE). We included the following outcomes: serum creatinine (mg/dl), urine output (ml/24 h), mean arterial pressure (mmHg), reversal rate of HRS, mortality rate, blood plasma renin activity (ng/ml/h), plasma aldosterone concentration (pg/ml), urine sodium (mEq/l), and creatinine clearance (ml/min). RESULTS: Our analysis of nine clinical studies revealed that the noradrenaline group was associated with higher creatinine clearance (MD = 4.22 [0.40, 8.05]), (P = 0.03). There were no significant differences in serum creatinine levels (MD = 0.03 [-0.07, 0.13]), urinary sodium (MD = -1.02 [-5.15, 3.11]), urine output (MD = 32.75 [-93.94, 159.44]), mean arterial pressure (MD = 1.40 [-1.17, 3.96]), plasma renin activity (MD = 1.35 [-0.17, 2.87]), plasma aldosterone concentration (MD = 55.35 [-24.59, 135.29]), reversal rate of HRS (RR = 1.15 [0.96, 1.37]), or mortality rate (RR = 0.87 [0.74, 1.01]) between the two groups (p-values > 0.05). CONCLUSIONS: Noradrenaline is a safe alternative medical therapy for HRS.

DeepPLM_mCNN: An approach for enhancing ion channel and ion transporter recognition by multi-window CNN based on features from pre-trained language models.

Accurate classification of membrane proteins like ion channels and transporters is critical for elucidating cellular processes and drug development. We present DeepPLM_mCNN, a novel framework combining Pretrained Language Models (PLMs) and multi-window convolutional neural networks (mCNNs) for effective classification of membrane proteins into ion channels and ion transporters. Our approach extracts informative features from protein sequences by utilizing various PLMs, including TAPE, ProtT5_XL_U50, ESM-1b, ESM-2_480, and ESM-2_1280. These PLM-derived features are then input into a mCNN architecture to learn conserved motifs important for classification. When evaluated on ion transporters, our best performing model utilizing ProtT5 achieved 90% sensitivity, 95.8% specificity, and 95.4% overall accuracy. For ion channels, we obtained 88.3% sensitivity, 95.7% specificity, and 95.2% overall accuracy using ESM-1b features. Our proposed DeepPLM_mCNN framework demonstrates significant improvements over previous methods on unseen test data. This study illustrates the potential of combining PLMs and deep learning for accurate computational identification of membrane proteins from sequence data alone. Our findings have important implications for membrane protein research and drug development targeting ion channels and transporters. The data and source codes in this study are publicly available at the following link: https://github.com/s1129108/DeepPLM_mCNN.