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Article ; Online: Molecular classification of hepatocellular carcinoma: prognostic importance and clinical applications.

Raja, Aroosha / Haq, Farhan

Journal of cancer research and clinical oncology

2021 Volume 148, Issue 1, Page(s) 15–29

Abstract: Hepatocellular carcinoma (HCC) is a lethal human malignancy with a very low overall and long-term survival rate. Poor prognostic outcomes are predominantly associated with HCC due to a huge landscape of heterogeneity found in the deadliest disease. ... ...

Abstract	Hepatocellular carcinoma (HCC) is a lethal human malignancy with a very low overall and long-term survival rate. Poor prognostic outcomes are predominantly associated with HCC due to a huge landscape of heterogeneity found in the deadliest disease. However, molecular subtyping of HCC has significantly improved the knowledge of the underlying mechanisms that contribute towards the heterogeneity and progression of the disease. In this review, we have extensively summarized the current information available about molecular classification of HCC. This review can be of great significance for providing the insight information needed for development of novel, efficient and personalized therapeutic options for the treatment of HCC patients globally.
MeSH term(s)	Biomarkers, Tumor/genetics ; Carcinoma, Hepatocellular/classification ; Carcinoma, Hepatocellular/genetics ; Carcinoma, Hepatocellular/pathology ; DNA Copy Number Variations/genetics ; Humans ; Liver Neoplasms/classification ; Liver Neoplasms/genetics ; Liver Neoplasms/pathology ; Prognosis ; RNA, Circular/genetics ; RNA, Long Noncoding/genetics ; Tumor Microenvironment/genetics ; beta Catenin/genetics
Chemical Substances	Biomarkers, Tumor ; CTNNB1 protein, human ; RNA, Circular ; RNA, Long Noncoding ; beta Catenin
Language	English
Publishing date	2021-10-08
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	134792-5
ISSN	1432-1335 ; 0171-5216 ; 0084-5353 ; 0943-9382
ISSN (online)	1432-1335
ISSN	0171-5216 ; 0084-5353 ; 0943-9382
DOI	10.1007/s00432-021-03826-w
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Book ; Online: A Novel Hybrid Sampling Framework for Imbalanced Learning

Newaz, Asif / Haq, Farhan Shahriyar

2022

Abstract: Class imbalance is a frequently occurring scenario in classification tasks. Learning from imbalanced data poses a major challenge, which has instigated a lot of research in this area. Data preprocessing using sampling techniques is a standard approach to ...

Abstract	Class imbalance is a frequently occurring scenario in classification tasks. Learning from imbalanced data poses a major challenge, which has instigated a lot of research in this area. Data preprocessing using sampling techniques is a standard approach to deal with the imbalance present in the data. Since standard classification algorithms do not perform well on imbalanced data, the dataset needs to be adequately balanced before training. This can be accomplished by oversampling the minority class or undersampling the majority class. In this study, a novel hybrid sampling algorithm has been proposed. To overcome the limitations of the sampling techniques while ensuring the quality of the retained sampled dataset, a sophisticated framework has been developed to properly combine three different sampling techniques. Neighborhood Cleaning rule is first applied to reduce the imbalance. Random undersampling is then strategically coupled with the SMOTE algorithm to obtain an optimal balance in the dataset. This proposed hybrid methodology, termed "SMOTE-RUS-NC", has been compared with other state-of-the-art sampling techniques. The strategy is further incorporated into the ensemble learning framework to obtain a more robust classification algorithm, termed "SRN-BRF". Rigorous experimentation has been conducted on 26 imbalanced datasets with varying degrees of imbalance. In virtually all datasets, the proposed two algorithms outperformed existing sampling strategies, in many cases by a substantial margin. Especially in highly imbalanced datasets where popular sampling techniques failed utterly, they achieved unparalleled performance. The superior results obtained demonstrate the efficacy of the proposed models and their potential to be powerful sampling algorithms in imbalanced domain. Comment: Submitted to "Expert Systems with Applications"
Keywords	Computer Science - Machine Learning ; Computer Science - Artificial Intelligence
Subject code	006
Publishing date	2022-08-20
Publishing country	us
Document type	Book ; Online
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Article ; Online: Management of a giant lymphocele following varicose vein surgery: a case report.

Bibi, Noshi / Ehtesham-Ul-Haq / Zahoor, Arsh / Haroon-Ur-Rashid / Eitezaaz, Farhan / Azeem, Ali

Journal of medical case reports

2023 Volume 17, Issue 1, Page(s) 265

Abstract: Background: A lymphocele or lymphocyst is formed when lymphatic fluid accumulates in a space, following disruption of lymphatic channels. Here, we report a case of a giant lymphocele in a middle-aged female, who underwent Trendelenburg operation ( ... ...

Abstract	Background: A lymphocele or lymphocyst is formed when lymphatic fluid accumulates in a space, following disruption of lymphatic channels. Here, we report a case of a giant lymphocele in a middle-aged female, who underwent Trendelenburg operation (saphenofemoral junction ligation) for varicose veins of her right lower limb. Case presentation: A 48-year-old Pakistani Punjabi female presented to the plastic surgery outpatient department with a history of painful, progressive swelling of the right groin and medial aspect of the right thigh for 4 months. After investigation, it was diagnosed as a giant lymphocele. A pedicled gracilis muscle flap was used to reconstruct and obliterate the cavity. There was no recurrence of the swelling. Conclusion: Lymphocele is a common complication after extensive vascular surgeries. In the unfortunate case of its development, prompt intervention must be done to prevent its growth and ensuing complications.
MeSH term(s)	Middle Aged ; Humans ; Female ; Lymphocele/etiology ; Lymphocele/surgery ; Thigh ; Varicose Veins/surgery ; Varicose Veins/complications ; Femoral Vein ; Edema ; Vascular Surgical Procedures/adverse effects
Language	English
Publishing date	2023-06-27
Publishing country	England
Document type	Case Reports ; Journal Article
ZDB-ID	2269805-X
ISSN	1752-1947 ; 1752-1947
ISSN (online)	1752-1947
ISSN	1752-1947
DOI	10.1186/s13256-023-04016-7
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Article ; Online: Similar immune responses to alpha1-oleate and Bacillus Calmette-Guérin treatment in patients with bladder cancer.

Ahmadi, Shahram / Ambite, Ines / Brisuda, Antonín / Háček, Jaromír / Haq, Farhan / Sabari, Samudra / Vanarsa, Kamala / Mohan, Chandra / Babjuk, Marek / Svanborg, Catharina

Cancer medicine

2024 Volume 13, Issue 7, Page(s) e7091

Abstract: Background: The molecular content of urine is defined by filtration in the kidneys and by local release from tissues lining the urinary tract. Pathological processes and different therapies change the molecular composition of urine and a variety of ... ...

Abstract	Background: The molecular content of urine is defined by filtration in the kidneys and by local release from tissues lining the urinary tract. Pathological processes and different therapies change the molecular composition of urine and a variety of markers have been analyzed in patients with bladder cancer. The response to BCG immunotherapy and chemotherapy has been extensively studied and elevated urine concentrations of IL-1RA, IFN-α, IFN-γ TNF-α, and IL-17 have been associated with improved outcome. Methods: In this study, the host response to intravesical alpha 1-oleate treatment was characterized in patients with non-muscle invasive bladder cancer by proteomic and transcriptomic analysis. Results: Proteomic profiling detected a significant increase in multiple cytokines in the treatment group compared to placebo. The innate immune response was strongly activated, including IL-1RA and pro-inflammatory cytokines in the IL-1 family (IL-1α, IL-1β, IL-33), chemokines (MIP-1α, IL-8), and interferons (IFN-α2, IFN-γ). Adaptive immune mediators included IL-12, Granzyme B, CD40, PD-L1, and IL-17D, suggesting broad effects of alpha 1-oleate treatment on the tumor tissues. Conclusions: The cytokine response profile in alpha 1-oleate treated patients was similar to that reported in BCG treated patients, suggesting a significant overlap. A reduction in protein levels at the end of treatment coincided with inhibition of cancer-related gene expression in tissue biopsies, consistent with a positive treatment effect. Thus, in addition to killing tumor cells and inducing cell detachment, alpha 1-oleate is shown to activate a broad immune response with a protective potential.
MeSH term(s)	Humans ; BCG Vaccine/therapeutic use ; Interleukin 1 Receptor Antagonist Protein/therapeutic use ; Oleic Acid ; Proteomics ; Cytokines ; Urinary Bladder Neoplasms/pathology ; Interferon-alpha/pharmacology ; Interferon-alpha/therapeutic use ; Immunity
Chemical Substances	BCG Vaccine ; Interleukin 1 Receptor Antagonist Protein ; Oleic Acid (2UMI9U37CP) ; Cytokines ; Interferon-alpha
Language	English
Publishing date	2024-03-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	2659751-2
ISSN	2045-7634 ; 2045-7634
ISSN (online)	2045-7634
ISSN	2045-7634
DOI	10.1002/cam4.7091
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Article ; Online: Disparities in pediatric clinical trials for acne vulgaris: A cross-sectional study.

Ding, Jeffrey / Haq, Ahmed Farhan / Joseph, Marissa / Khosa, Faisal

Journal of the American Academy of Dermatology

2021 Volume 87, Issue 2, Page(s) 464–466

MeSH term(s)	Acne Vulgaris/drug therapy ; Child ; Cross-Sectional Studies ; Humans
Language	English
Publishing date	2021-10-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	603641-7
ISSN	1097-6787 ; 0190-9622
ISSN (online)	1097-6787
ISSN	0190-9622
DOI	10.1016/j.jaad.2021.10.013
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Article ; Online: Management of a giant lymphocele following varicose vein surgery

Noshi Bibi / Ehtesham-Ul-Haq / Arsh Zahoor / Haroon-Ur-Rashid / Farhan Eitezaaz / Ali Azeem

Journal of Medical Case Reports, Vol 17, Iss 1, Pp 1-

a case report

2023 Volume 5

Abstract: Abstract Background A lymphocele or lymphocyst is formed when lymphatic fluid accumulates in a space, following disruption of lymphatic channels. Here, we report a case of a giant lymphocele in a middle-aged female, who underwent Trendelenburg operation ( ...

Abstract	Abstract Background A lymphocele or lymphocyst is formed when lymphatic fluid accumulates in a space, following disruption of lymphatic channels. Here, we report a case of a giant lymphocele in a middle-aged female, who underwent Trendelenburg operation (saphenofemoral junction ligation) for varicose veins of her right lower limb. Case presentation A 48-year-old Pakistani Punjabi female presented to the plastic surgery outpatient department with a history of painful, progressive swelling of the right groin and medial aspect of the right thigh for 4 months. After investigation, it was diagnosed as a giant lymphocele. A pedicled gracilis muscle flap was used to reconstruct and obliterate the cavity. There was no recurrence of the swelling. Conclusion Lymphocele is a common complication after extensive vascular surgeries. In the unfortunate case of its development, prompt intervention must be done to prevent its growth and ensuing complications.
Keywords	Lymphocele ; Varicose vein ; Surgical flaps ; Gracilis muscle ; Sclerotherapy ; Medicine ; R
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: Genomic relevance of FGF14 and associated genes on the prognosis of pancreatic cancer.

Raja, Aroosha / Malik, Muhammad Faraz Arshad / Haq, Farhan

PloS one

2021 Volume 16, Issue 6, Page(s) e0252344

Abstract: Background: Fibroblast (FGFs) and insulin (IGF) growth factor pathways are among 10 most recurrently altered genomic pathways in pancreatic ductal adenocarcinoma (PDAC). However, the prognostic and therapeutic relevance of FGF and IGF pathways in PDAC ... ...

Abstract	Background: Fibroblast (FGFs) and insulin (IGF) growth factor pathways are among 10 most recurrently altered genomic pathways in pancreatic ductal adenocarcinoma (PDAC). However, the prognostic and therapeutic relevance of FGF and IGF pathways in PDAC is largely unknown. Methods: We investigated the relationship between fibroblast and insulin pathway gene expression and clinicopathological features in three independent transcriptomic cohorts of 532 PDAC patients. Furthermore, we have examined the coexpressed genes specific to the prognostic marker identified from these cohorts. Statistical tests including Fisher-exact\Chi-square, Kaplan-Meier, Pearson Correlation and cox regression analyses were performed. Additionally, pathway analysis of gene-specific co-expressed genes was also performed. Results: The dysregulation of six genes including FGF9, FGF14, FGFR1, FGFR4, IGF2BP2 and IGF2BP3 were significantly associated with different clinical characteristics (including grade, stage, recurrence and nodes) in PDAC cohorts. 11 genes (including FGF9, FGF13, FGF14, FGF17, FGFR1, FGFRL1, FGFBP3, IGFBP3, IGF2BP2, IGF2BP3 and IGFBPL1) showed association with overall survival in different PDAC cohorts. Interestingly, overexpression of FGF14 was found associated with better overall survival (OS) in all three cohorts. Of note, multivariate analysis also revealed FGF14 as an independent prognostic marker for better OS in all three cohorts. Furthermore, FMN2 and PGR were among the top genes that correlated with FGF14 in all 3 cohorts. Of note, overexpression of FMN2 and PGR was found significantly associated with good overall survival in PDAC patients, suggesting FMN2 and PGR can also act as potential markers for the prediction of prognosis in PDAC patients. Conclusion: FGF14 may define a distinct subset of PDAC patients with better prognosis. Moreover, FGF14-based sub-classification of PDAC suggests that FMN2 and PGR can be employed as good prognostic markers in PDAC and this classification may lead to new therapeutic approaches.
MeSH term(s)	Female ; Fibroblast Growth Factors/genetics ; Genomics ; Humans ; Male ; Middle Aged ; Pancreatic Neoplasms/diagnosis ; Pancreatic Neoplasms/genetics ; Prognosis ; Recurrence
Chemical Substances	fibroblast growth factor 14 ; Fibroblast Growth Factors (62031-54-3)
Language	English
Publishing date	2021-06-01
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0252344
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Article ; Online: Survival prediction of heart failure patients using machine learning techniques

Asif Newaz / Nadim Ahmed / Farhan Shahriyar Haq

Informatics in Medicine Unlocked, Vol 26, Iss , Pp 100772- (2021)

2021

Abstract: The goal of this research is to develop a reliable decision-support system for the survival prediction of heart failure patients by utilizing their clinical records and laboratory test results. Forecasting heart-failure related events in clinical ... ...

Abstract	The goal of this research is to develop a reliable decision-support system for the survival prediction of heart failure patients by utilizing their clinical records and laboratory test results. Forecasting heart-failure related events in clinical practice tend to be quite inaccurate and highly variable. Identifying the key drivers of heart failure is also clinically very important. In this regard, we develop a model to accurately identify the patients who are at risk utilizing machine learning techniques. This can help clinicians make informed decisions regarding the intensity of treatment required for a patient. For this study, we have utilized a heart failure dataset originally collected from the Faisalabad Institute of Cardiology and the Allied Hospital in Faisalabad, Pakistan. Sampling strategy is incorporated into the ensemble learning framework to develop a more robust Random Forest Classifier that can effectively deal with the imbalanced nature of the data and provide a more generalizable result with higher accuracy. Two different feature selection techniques - Chi-square test and Recursive Feature Elimination are utilized to identify the features that are most significant in terms of survival prediction of heart failure patients. Using our proposed approach, a maximum G-mean score of 76.83% with a sensitivity score of 80.21% was achieved, which is significantly higher than what has been reported by other researchers. Thus, our proposed framework has the potential to be an effective tool to identify the patients who are at risk and guide clinicians accordingly to take pertinent measures.
Keywords	Machine learning ; Random forest ; Recursive feature elimination ; Heart failure ; Ejection fraction ; Imbalanced classification ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	006
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomic relevance of FGF14 and associated genes on the prognosis of pancreatic cancer.

Aroosha Raja / Muhammad Faraz Arshad Malik / Farhan Haq

PLoS ONE, Vol 16, Iss 6, p e

2021 Volume 0252344

Abstract: Background Fibroblast (FGFs) and insulin (IGF) growth factor pathways are among 10 most recurrently altered genomic pathways in pancreatic ductal adenocarcinoma (PDAC). However, the prognostic and therapeutic relevance of FGF and IGF pathways in PDAC is ... ...

Abstract	Background Fibroblast (FGFs) and insulin (IGF) growth factor pathways are among 10 most recurrently altered genomic pathways in pancreatic ductal adenocarcinoma (PDAC). However, the prognostic and therapeutic relevance of FGF and IGF pathways in PDAC is largely unknown. Methods We investigated the relationship between fibroblast and insulin pathway gene expression and clinicopathological features in three independent transcriptomic cohorts of 532 PDAC patients. Furthermore, we have examined the coexpressed genes specific to the prognostic marker identified from these cohorts. Statistical tests including Fisher-exact\Chi-square, Kaplan-Meier, Pearson Correlation and cox regression analyses were performed. Additionally, pathway analysis of gene-specific co-expressed genes was also performed. Results The dysregulation of six genes including FGF9, FGF14, FGFR1, FGFR4, IGF2BP2 and IGF2BP3 were significantly associated with different clinical characteristics (including grade, stage, recurrence and nodes) in PDAC cohorts. 11 genes (including FGF9, FGF13, FGF14, FGF17, FGFR1, FGFRL1, FGFBP3, IGFBP3, IGF2BP2, IGF2BP3 and IGFBPL1) showed association with overall survival in different PDAC cohorts. Interestingly, overexpression of FGF14 was found associated with better overall survival (OS) in all three cohorts. Of note, multivariate analysis also revealed FGF14 as an independent prognostic marker for better OS in all three cohorts. Furthermore, FMN2 and PGR were among the top genes that correlated with FGF14 in all 3 cohorts. Of note, overexpression of FMN2 and PGR was found significantly associated with good overall survival in PDAC patients, suggesting FMN2 and PGR can also act as potential markers for the prediction of prognosis in PDAC patients. Conclusion FGF14 may define a distinct subset of PDAC patients with better prognosis. Moreover, FGF14-based sub-classification of PDAC suggests that FMN2 and PGR can be employed as good prognostic markers in PDAC and this classification may lead to new therapeutic approaches.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Fractionation and Characterization of Metallic Elements in Soils in Land Use Systems.

Haq, Farid Ul / Faridullah, Faridullah / Irshad, Muhammad / Bacha, Aziz Ur Rahim / Hafeez, Farhan / Ullah, Zahid / Iqbal, Akhtar / Arifeen, Awais / Nabi, Iqra / Alrefaei, Abdulwahed Fahad / Almutairi, Mikhlid H

Toxics

2024 Volume 12, Issue 2

Abstract: Land use has a great impact on soil dynamics. The soils of various land use systems in Central Karakoram have been under immense pressure in the recent past due to certain anthropogenic activities such as land use practices and land use cover changes. ... ...

Abstract	Land use has a great impact on soil dynamics. The soils of various land use systems in Central Karakoram have been under immense pressure in the recent past due to certain anthropogenic activities such as land use practices and land use cover changes. These influences have an impact on the spatial distribution of metallic elements (MEs) in the soils of various land uses. Herein, we investigated the occurrence of the MEs, copper (Cu), zinc (Zn), and nickel (Ni), in soils of various land uses such as the permafrost, pasture, forest, and agricultural lands of the Central Karakorum region. The MEs were extracted in exchangeable, adsorbed, organically bound, carbonated, precipitated, and residual forms. The concentrations of MEs showed a significant dependence on the extraction method used, and the extraction trend followed the order of EDTA > HNO
Language	English
Publishing date	2024-01-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2733883-6
ISSN	2305-6304 ; 2305-6304
ISSN (online)	2305-6304
ISSN	2305-6304
DOI	10.3390/toxics12020110
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