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Article: In Silico

Magri, Meryam / Bouricha, El Mehdi / Hakmi, Mohammed / Jaoudi, Rachid El / Belyamani, Lahcen / Ibrahimi, Azeddine

2023 Volume 17, Page(s) 11779322231212755

Abstract: Pseudomonas ... ...

Abstract	Pseudomonas aeruginosa
Language	English
Publishing date	2023-11-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2423808-9
ISSN	1177-9322
ISSN	1177-9322
DOI	10.1177/11779322231212755
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Article ; Online: Potentially inappropriate medications and potential prescribing omissions in hospitalised older adults in New Zealand: A retrospective study.

Mohammed, Mohammed A / Chan, Amy Hai Yan / Chan, Stephanie / Ungureanu, Bianca / Seo, Hakmi / Ong, Patrick / Morrison, Caitlyn / Martini, Nataly

Australasian journal on ageing

2023 Volume 42, Issue 4, Page(s) 668–674

Abstract: Objective: Medication errors can have detrimental effects on patient outcomes, yet there are limited data on the prevalence of potentially inappropriate medications (PIMs) and potential prescribing omissions (PPOs) among older adult inpatients in New ... ...

Abstract	Objective: Medication errors can have detrimental effects on patient outcomes, yet there are limited data on the prevalence of potentially inappropriate medications (PIMs) and potential prescribing omissions (PPOs) among older adult inpatients in New Zealand (NZ). This study investigated exposure to PIMs and PPOs in older adults in a New Zealand hospital. Methods: Electronic medical records of 846 older adults (≥ 65 years) discharged from the Auckland District Health Board between June 2020 and May 2021 were retrospectively reviewed to extract data on sociodemographic, medication and diagnostic information. STOPP/START version 2 was used to evaluate PIMs and PPOs on admission and discharge. Results: The mean age was 77.47 ± 8.12 years, and 51% were female. On admission, 48% had ≥1 PIMs and 40% had ≥1 PPOs. On discharge, 45% had ≥1 PIMs and 40% had ≥1 PPOs. Increasing age (adjusted odds ratio [AOR] = 1.02, 95% CI [confidence interval] 1.01, 1.04), number of medicines (AOR = 1.23, CI 1.17, 1.29) and 28-day admission history (AOR = 1.58, CI 1.15, 2.18) were associated with higher odds of PIMs use on admission. At discharge, the number of medicines (AOR = 1.19, CI 1.13, 1.25) and history of readmission (AOR = 1.47, CI 1.08, 2.02) were associated with higher odds of PIMs. Female patients had higher odds of PPOs both on admission (AOR = 1.35, CI 1.02, 1.78) and discharge (AOR = 1.34, CI 1.01, 1.78). Māori, Asian and Pacific patients were more likely to have prescribing omissions compared to NZ Europeans. Conclusions: Prescribing omissions and inappropriate medications were common in older inpatients. There were differences observed between different ethnic groups, with NZ Europeans having fewer omissions than other ethnic groups. These findings highlight key opportunities for health-care providers to improve medication use in older adults in NZ.
MeSH term(s)	Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Inappropriate Prescribing ; New Zealand/epidemiology ; Potentially Inappropriate Medication List ; Retrospective Studies ; Hospitalization ; Inpatients
Language	English
Publishing date	2023-05-11
Publishing country	Australia
Document type	Journal Article
ZDB-ID	1457406-8
ISSN	1741-6612 ; 0726-4240 ; 1440-6381
ISSN (online)	1741-6612
ISSN	0726-4240 ; 1440-6381
DOI	10.1111/ajag.13210
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Article ; Online: Morel-Lavallée Lesion in a 35-year Female.

Sohail, Amir Humza / Liaquat, Muhammad Talha / Sohail, Mohammed Sachal / Khan, Muhammad Salman / Hakmi, Hazim

Journal of the College of Physicians and Surgeons--Pakistan : JCPSP

2021 Volume 31, Issue 3, Page(s) 342–345

Abstract: Morel-Lavallée lesion is a post-traumatic degloving cyst, usually filled with blood, lymph or necrotic tissue, which mostly develops in the area around greater trochanter. Early diagnosis and prompt treatment is essential to prevent further complications, ...

Abstract	Morel-Lavallée lesion is a post-traumatic degloving cyst, usually filled with blood, lymph or necrotic tissue, which mostly develops in the area around greater trochanter. Early diagnosis and prompt treatment is essential to prevent further complications, such as compression of surrounding structures. X-rays have limited use and magnetic resonance imaging (MRI) is the modality of choice in diagnosing the lesion. We report a case of a 35-year female presenting with left thigh pain after a fall from motorcycle almost 21/2 years ago. Ultrasound and MRI confirmed the presence of Morel-Lavallée lesion involving the left pelvis and upper thigh. Given the chronicity of lesion and extensive tissue involvement, the patient underwent surgical excision of the lesion with favourable long-term outcomes. In this case report and literature review, we discuss the pathophysiology, clinical presentation, radiological findings and management options for Morel-Lavallée lesion. Key Words: Morel-Lavallée lesion, Post-traumatic cyst, Degloving Injury, Tangential cyst.
MeSH term(s)	Female ; Humans ; Magnetic Resonance Imaging ; Pelvis ; Radiography ; Soft Tissue Injuries/diagnostic imaging ; Soft Tissue Injuries/surgery ; Thigh
Language	English
Publishing date	2021-04-20
Publishing country	Pakistan
Document type	Case Reports ; Journal Article ; Review
ZDB-ID	2276646-7
ISSN	1681-7168 ; 1022-386X
ISSN (online)	1681-7168
ISSN	1022-386X
DOI	10.29271/jcpsp.2021.03.342
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Article: IDbSV: An Open-Access Repository for Monitoring SARS-CoV-2 Variations and Evolution.

Essabbar, Abdelmounim / Kartti, Souad / Alouane, Tarek / Hakmi, Mohammed / Belyamani, Lahcen / Ibrahimi, Azeddine

Frontiers in medicine

2021 Volume 8, Page(s) 765249

Abstract: Ending COVID-19 pandemic requires a collaborative understanding of SARS-CoV-2 and COVID-19 mechanisms. Yet, the evolving nature of coronaviruses results in a continuous emergence of new variants of the virus. Central to this is the need for a continuous ... ...

Abstract	Ending COVID-19 pandemic requires a collaborative understanding of SARS-CoV-2 and COVID-19 mechanisms. Yet, the evolving nature of coronaviruses results in a continuous emergence of new variants of the virus. Central to this is the need for a continuous monitoring system able to detect potentially harmful variants of the virus in real-time. In this manuscript, we present the International Database of SARS-CoV-2 Variations (IDbSV), the result of ongoing efforts in curating, analyzing, and sharing comprehensive interpretation of SARS-CoV-2's genetic variations and variants. Through user-friendly interactive data visualizations, we aim to provide a novel surveillance tool to the scientific and public health communities. The database is regularly updated with new records through a 4-step workflow (1-Quality control of curated sequences, 2-Call of variations, 3-Functional annotation, and 4-Metadata association). To the best of our knowledge, IDbSV provides access to the largest repository of SARS-CoV-2 variations and the largest analysis of SARS-CoV-2 genomes with over 60 thousand annotated variations curated from the 1,808,613 genomes alongside their functional annotations, first known appearance, and associated genetic lineages, enabling a robust interpretation tool for SARS-CoV-2 variations to help understanding SARS-CoV-2 dynamics across the world.
Language	English
Publishing date	2021-12-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2775999-4
ISSN	2296-858X
ISSN	2296-858X
DOI	10.3389/fmed.2021.765249
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Article ; Online: In-silico

Bouricha, El Mehdi / Hakmi, Mohammed / Akachar, Jihane / Zouaidia, Fouad / Ibrahimi, Azeddine

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 11, Page(s) 5203–5210

Abstract: Estrogen receptor α (ERα) plays a critical role in breast cancer (BC) development. The standard therapeutic strategies for ERα- positive (ERα+) BC consist of impairing ERα signalling pathway by either estrogen competitors blocking its interaction with ... ...

Abstract	Estrogen receptor α (ERα) plays a critical role in breast cancer (BC) development. The standard therapeutic strategies for ERα- positive (ERα+) BC consist of impairing ERα signalling pathway by either estrogen competitors blocking its interaction with the ligand binding domain (LBD) or agents inhibiting the production of estrogen. These strategies are limited by many factors that lead to constitutive activation of ERα and consequently, resistance to treatment. Targeting the DNA binding domain (DBD) of ERα instead of its LBD with small-molecule inhibitors could be an alternative to impair ERα's signalling pathway. For this purpose, we conducted a structure based virtual screening of DrugBank against the crystal structure of ERα-DBD (PDB ID: 1HCQ) using the Glide module in standard precision (SP) and extra precision (XP) mode of docking. Molecules with XP Gscore less than -8 kcal/mol were selected and visually inspected to keep only the reasonable docking poses. Subsequently, these molecules were clustered using structural interaction fingerprints analysis and the complexes of the top ranked molecules of each cluster based on XP Gscore were subjected to 200 ns molecular dynamics simulations followed by MM-GBSA binding free energy calculation for the last 100 ns of each complex. In this study, we identified three molecules from DrugBank namely DB03450, DB02593 and DB08001 showing significant stability and strong interaction with the key amino acids during MD simulation suggesting a potential inhibition of the target. These molecules could be used as promising lead compounds to impair the ERα signalisation in hormone therapy-resistant breast cancer.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Antineoplastic Agents/chemistry ; Binding Sites ; Breast Neoplasms/drug therapy ; DNA/metabolism ; Estrogen Receptor alpha/antagonists & inhibitors ; Estrogens ; Female ; Humans ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding
Chemical Substances	Antineoplastic Agents ; Estrogen Receptor alpha ; Estrogens ; Ligands ; DNA (9007-49-2)
Language	English
Publishing date	2021-01-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1869094
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Article ; Online: Computational modeling and druggability assessment of Aggregatibacter actinomycetemcomitans leukotoxin.

Hakmi, Mohammed / Bouricha, El Mehdi / El Harti, Jaouad / Amzazi, Said / Belyamani, Lahcen / Khanfri, Jamal Eddine / Ibrahimi, Azeddine

Computer methods and programs in biomedicine

2022 Volume 222, Page(s) 106952

Abstract: The leukotoxin (LtxA) of Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans) is a protein exotoxin belonging to the repeat-in-toxin family (RTX). Numerous studies have demonstrated that LtxA may play a critical role in the pathogenicity of A. ...

Abstract	The leukotoxin (LtxA) of Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans) is a protein exotoxin belonging to the repeat-in-toxin family (RTX). Numerous studies have demonstrated that LtxA may play a critical role in the pathogenicity of A. actinomycetemcomitans since hyper-leukotoxic strains have been associated with severe disease. Accordingly, considerable effort has been made to elucidate the mechanisms by which LtxA interacts with host cells and induce their death. However, these attempts have been hampered by the unavailability of a tertiary structure of the toxin, which limits the understanding of its molecular properties and mechanisms. In this paper, we used homology and template free modeling algorithms to build the complete tertiary model of LtxA at atomic level in its calcium-bound Holo-state. The resulting model was refined by energy minimization, validated by Molprobity and ProSA tools, and subsequently subjected to a cumulative 600ns of all-atom classical molecular dynamics simulation to evaluate its structural aspects. The druggability of the proposed model was assessed using Fpocket and FTMap tools, resulting in the identification of four putative cavities and fifteen binding hotspots that could be targeted by rational drug design tools to find new ligands to inhibit LtxA activity.
MeSH term(s)	Aggregatibacter actinomycetemcomitans/chemistry ; Aggregatibacter actinomycetemcomitans/metabolism ; Computer Simulation ; Exotoxins/chemistry ; Exotoxins/metabolism ; Exotoxins/pharmacology
Chemical Substances	Exotoxins ; leukotoxin
Language	English
Publishing date	2022-06-13
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	632564-6
ISSN	1872-7565 ; 0169-2607
ISSN (online)	1872-7565
ISSN	0169-2607
DOI	10.1016/j.cmpb.2022.106952
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Article: In silico

Bouricha, El Mehdi / Hakmi, Mohammed / Akachar, Jihane / Belyamani, Lahcen / Ibrahimi, Azeddine

3 Biotech

2020 Volume 10, Issue 11, Page(s) 483

Abstract: SARS-CoV-2, which causes severe pneumonia epidemics, probably originated from Chinese horseshoe bats, but the intermediate and host range is still unknown. ACE2 is the entry receptor for SARS-CoV-2. The binding capacity of SARS-CoV-2 spike protein to ... ...

Abstract	SARS-CoV-2, which causes severe pneumonia epidemics, probably originated from Chinese horseshoe bats, but the intermediate and host range is still unknown. ACE2 is the entry receptor for SARS-CoV-2. The binding capacity of SARS-CoV-2 spike protein to ACE2 is the critical determinant of viral host range and cross-species infection. Here, we used an
Keywords	covid19
Language	English
Publishing date	2020-10-21
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2600522-0
ISSN	2190-5738 ; 2190-572X
ISSN (online)	2190-5738
ISSN	2190-572X
DOI	10.1007/s13205-020-02471-3
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Article: Repurposing of known anti-virals as potential inhibitors for SARS-CoV-2 main protease using molecular docking analysis.

Hakmi, Mohammed / Bouricha, El Mehdi / Kandoussi, Ilham / Harti, Jaouad El / Ibrahimi, Azeddine

Bioinformation

2020 Volume 16, Issue 4, Page(s) 301–306

Abstract: The new SARS-CoV-2 coronavirus is the causative agent of the COVID-19 pandemic outbreak that affected more than 190 countries worldwide with more than 292,000 confirmed cases and over 12,700 deaths. There is at the moment no vaccine or effective ... ...

Abstract	The new SARS-CoV-2 coronavirus is the causative agent of the COVID-19 pandemic outbreak that affected more than 190 countries worldwide with more than 292,000 confirmed cases and over 12,700 deaths. There is at the moment no vaccine or effective treatment for this disease which constitutes a serious global health problem. It is of interest to use a structure based virtual screening approach for the identification of potential inhibitors of the main protease of SARS-CoV-2 (M
Keywords	covid19
Language	English
Publishing date	2020-04-30
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	2203786-X
ISSN	0973-2063
ISSN	0973-2063
DOI	10.6026/97320630016301
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Article: In Silico Analyses of All STAT3 Missense Variants Leading to Explore Divergent AD-HIES Clinical Phenotypes.

Mansouri, Mariam / El Haddoumi, Ghyzlane / Bendani, Houda / Boumajdi, Nasma / Hakmi, Mohammed / Abbou, Hanane / Bouricha, El Mehdi / Elgharbaoui, Boutaina / Kartti, Souad / El Jaoudi, Rachid / Belyamani, Lahcen / Kandoussi, Ilham / Ibrahimi, Azeddine / El Hafidi, Naima

Evolutionary bioinformatics online

2023 Volume 19, Page(s) 11769343231169374

Abstract: Autosomal dominant hyper-IgE syndrome (AD-HIES) is linked to dominant negative mutations of the STAT3 protein whose molecular basis for dysfunction is unclear and presenting with a variety of clinical manifestations with only supportive treatment. To ... ...

Abstract	Autosomal dominant hyper-IgE syndrome (AD-HIES) is linked to dominant negative mutations of the STAT3 protein whose molecular basis for dysfunction is unclear and presenting with a variety of clinical manifestations with only supportive treatment. To establish the relationship between the impact of STAT3 mutations in different domains and the severity of the clinical manifestations, 105 STAT3 mutations were analyzed for their impact on protein stability, flexibility, function, and binding affinity using in Silico approaches. Our results showed that 73% of the studied mutations have an impact on the physicochemical properties of the protein, altering the stability, flexibility and function to varying degrees. In particular, mutations affecting the DNA binding domain (DBD) and the Src Homology 2 (SH2) have a significant impact on the protein structure and disrupt its interaction either with DNA or other STAT3 to form a heterodomain complex, leading to severe clinical phenotypes. Collectively, this study suggests that there is a close relationship between the domain involving the mutation, the degree of variation in the properties of the protein and the degree of loss of function ranging from partial loss to complete loss, explaining the variability of clinical manifestations between mild and severe.
Language	English
Publishing date	2023-04-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2227610-5
ISSN	1176-9343
ISSN	1176-9343
DOI	10.1177/11769343231169374
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Article ; Online: Colon and Rectal Surgery Fellowship Applicant and Matching Trends in the United States: An Analysis of National Resident Matching Program Data.

Sohail, Amir H / Ye, Ivan B / Martinez, Kevin A / Campos, Marco A / Sohail, Sachal / Williams, Caroline E / Khan, Muhammad Salman / Bhatti, Umar / Hakmi, Hazim / Akhtar, Aisha / Quazi, Mohammed A / Sheikh, Abu Baker / Goyal, Aman / Khan, Aimal

The American surgeon

2023 Volume 90, Issue 5, Page(s) 985–990

Abstract: Background: Colon and Rectal Surgery fellowships are training programs that aim to train surgeons in the management of small bowel, colon, rectal, and anal pathologies.: Objective: We investigated trends in Colon and Rectal Surgery fellowship match ... ...

Abstract	Background: Colon and Rectal Surgery fellowships are training programs that aim to train surgeons in the management of small bowel, colon, rectal, and anal pathologies. Objective: We investigated trends in Colon and Rectal Surgery fellowship match to help applicants anticipate future fellowship application cycles. Design: This was a retrospective cohort study of applicants in the Colon and Rectal Surgery match from 2009 to 2023. Proportion of positions filled, match rates, and rank-order lists were collected. The impact of US-MD, non-US-MD, and DO status on match rate was assessed. We used the Mann Kendall trend test to obtain tau statistic and Results: Fellowship programs increased from 43 to 67, positions increased from 78 to 110, and number of applicants rose from 113 to 135. Nearly all positions were filled from 2009 to 2023 (range: 96.3%-100%). The overall match rate fluctuated between 67.3% and 80.7%. The match rate over the past 5 years was 72.0%. The match rate for US-MDs was 80.0%, while non-US-MDs had a 56.2% match rate. The percentage matching at each rank were first choice 28.0%, second choice 10.4%, third choice 6.9%, and fourth choice or lower 23.5%. Conclusion: Despite an increase in Colon and Rectal Surgery fellowship positions, the overall match rate has not changed significantly over the years, mainly as a result of increased applicants.
MeSH term(s)	Humans ; United States ; Internship and Residency ; Fellowships and Scholarships ; Retrospective Studies ; Education, Medical, Graduate ; Colon
Language	English
Publishing date	2023-12-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	202465-2
ISSN	1555-9823 ; 0003-1348
ISSN (online)	1555-9823
ISSN	0003-1348
DOI	10.1177/00031348231220574
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