Publications by authors named "Malik L"

Elucidating the genetic contributions to Parkinson's disease (PD) etiology across diverse ancestries is a critical priority for the development of targeted therapies in a global context. We conducted the largest sequencing characterization of potentially disease-causing, protein-altering and splicing mutations in 710 cases and 11,827 controls from genetically predicted African or African admixed ancestries. We explored copy number variants (CNVs) and runs of homozygosity (ROHs) in prioritized early onset and familial cases.

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Recently, a novel African ancestry specific Parkinson's disease (PD) risk signal was identified at the gene encoding glucocerebrosidase (). This variant (rs3115534-G) is carried by ~50% of West African PD cases and imparts a dose-dependent increase in risk for disease. The risk variant has varied frequencies across African ancestry groups, but is almost absent in European and Asian ancestry populations.

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Processed electroencephalography (pEEG) is increasingly used to titrate the depth of anesthesia. Whether such intra-procedural pEEG monitoring can offer additional information on cerebral perfusion or acute focal or global cerebral ischemia is unknown. This scoping review aimed to provide a narrative analysis of the current literature reporting the potential role of pEEG in adults with acute cerebral ischemia.

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Structural variants (SVs) drive gene expression in the human brain and are causative of many neurological conditions. However, most existing genetic studies have been based on short-read sequencing methods, which capture fewer than half of the SVs present in any one individual. Long-read sequencing (LRS) enhances our ability to detect disease-associated and functionally relevant structural variants (SVs); however, its application in large-scale genomic studies has been limited by challenges in sample preparation and high costs.

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Proliferating trichilemmal tumor (PTT) is a rare, benign adnexal tumor of hair follicles that commonly mimics malignancy. Excellent outcomes can be achieved with early surgical excision. Delayed presentations-as in this giant shoulder PTT-are made possible, in part, by patient education and healthcare accessibility in low-resource settings.

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 Surgical procedures of curettage and surgical resection are used to treat giant cell tumor (GCT) of the distal radius, but it is still controversial whether one provides better functional outcomes than the other. The present study aims to determine and compare both procedures regarding complications, local recurrence, and mobility.  A complete search of the applicable literature was done and independently assessed by three authors.

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Objective: Variants in PRKN and PINK1 are the leading cause of early-onset autosomal recessive Parkinson's disease, yet many cases remain genetically unresolved. We previously identified a 7 megabases complex structural variant in a pair of monozygotic twins using Oxford Nanopore Technologies (ONT) long-read sequencing. This study aims to determine if ONT long-read sequencing can detect a second variant in other unresolved early-onset Parkinson's disease (EOPD) cases with 1 heterozygous PRKN or PINK1 variant.

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Article Synopsis
  • The ProFATE trial investigated the impact of temporary blood flow arrest during endovascular thrombectomy on vessel recanalization in patients with acute ischemic stroke.
  • Conducted across four UK centers, the study randomly assigned 134 adults to either a flow arrest or nonflow arrest group to assess the effectiveness of the procedure.
  • Results showed a slight increase in vessel recanalization in the flow arrest group (74.4%) compared to the nonflow arrest group (70.8%), suggesting a potential benefit of temporary blood flow arrest during treatment.
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Objective: To establish diagnostic performance of a single axial T2-weighted sequence for detection of brain tumours in children with non-localizing symptoms, compared to a standard MRI protocol.

Methods: Retrospective analysis of children undergoing MRI brain imaging for suspected brain tumours with non-localizing symptoms over a 3-year period. Axial T2-weighted images were blindly reviewed by 2 experienced paediatric neuroradiologists.

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Recently, an African ancestry-specific Parkinson disease (PD) risk signal was identified at the gene encoding glucocerebrosidase (GBA1). This variant ( rs3115534 -G) is carried by ~50% of West African PD cases and imparts a dose-dependent increase in risk for disease. The risk variant has varied frequencies across African ancestry groups but is almost absent in European and Asian ancestry populations.

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Article Synopsis
  • Copy Number Variations (CNVs) are crucial in understanding complex diseases and vary across different populations, necessitating large sample studies for accurate analysis.
  • The CNV-Finder pipeline utilizes deep learning, specifically Long Short-Term Memory (LSTM) networks, to streamline the identification of CNVs in specific genomic areas, making subsequent analyses like genome sequencing more efficient.
  • The tool has been validated with data from various cohorts, focusing on genes related to neurological diseases, and includes an interactive web application for researchers to visualize and refine their findings based on model predictions.
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Background: Plant growth and development can be greatly impacted by drought stress. Suitable plant growth promoting rhizobacteria (PGPR) or biochar (BC) application has been shown to alleviate drought stress for plants. However, their co-application has not been extensively explored in this regard.

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DFSP is a cutaneous soft tissue sarcoma. A 35 year old male patient presented with DFSP in the inguinal region which is a rare soft tissue sarcoma which usually presents in the torso, occurring very rarely in the inguinal region. Hence in case of any swelling in the inguinal region, DFSP should be in differential diagnosis.

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Teledentistry has emerged as a promising approach to improving access to dental care, particularly for underserved populations. This systematic review aims to evaluate the effectiveness of teledentistry interventions in enhancing access to dental care. A comprehensive search across multiple databases was conducted to identify studies evaluating teledentistry interventions.

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Background: The efficacy and safety of endovascular thrombectomy (EVT) beyond 6 hours from stroke onset for patients with large vessel occlusion (LVO) selected without CT perfusion(CTP) or MR imaging(MRI) is undetermined. We conducted a systematic review and meta-analysis of the current literature comparing outcomes for late presenting patients with LVO treated by best medical management (BMM) with those selected for EVT based only on non-contrast CT(NCCT)/CT angiography(CTA) (without CTP or MRI).

Methods: PRISMA guidelines were employed.

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Size-controlled monodisperse droplets are indispensable in food, cosmetics, and healthcare industries. Although emulsion formation from bulk phases is well-explored, a robust method to continuously reform existing emulsions is unavailable. Remarkably, we introduce a continuous flow acousto-microfluidics technique which enables simultaneous trapping-coalescence-splitting of droplets to reform an existing polydisperse emulsion into size-controlled droplets with improved monodispersity.

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Background: Mutations within the genes and are the leading cause of early onset autosomal recessive Parkinson's disease (PD). However, the genetic cause of most early-onset PD (EOPD) cases still remains unresolved. Long-read sequencing has successfully identified many pathogenic structural variants that cause disease, but this technology has not been widely applied to PD.

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Article Synopsis
  • Parkinson's disease (PD) is influenced by genetics, but much of its heritability is still unclear due to previous focus on single nucleotide variants, while more complex genetic variations have been less studied.
  • A specific CT-rich region in the SNCA gene may connect to PD risk, but its detailed role has not been explored until now.
  • The study utilized advanced sequencing techniques on a large participant group, confirming existing associations and identifying new ones, while suggesting that the CT-rich region's disease association may not be solely driven by SNCA gene expression.
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Electrochemical sensing is emerging as a method of choice for the sensing and monitoring of contaminants in water. Various sensing platforms have been designed for sensing heavy metal ions and organic pollutants in water bodies. Herein, we report a new electrochemical platform that can be used for the detection of both heavy metal ions and nitro-based organic contaminants in water bodies.

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Article Synopsis
  • The study aimed to analyze how often and in what ways healthcare providers use choice frames when discussing care options with surrogate decision-makers in the ICU.
  • Researchers conducted a content analysis of 101 recorded meetings between clinicians and surrogates, identifying key decision episodes related to patient care, including mechanical ventilation and goals of care.
  • Findings revealed that clinicians predominantly used default framing, where a default option is set unless an alternative is chosen, and often presented polar questions, leading to a preference for discussing both potential losses and gains in decisions.
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A biallelic (AAGGG) expansion in the poly(A) tail of an AluSx3 transposable element within the gene RFC1 is a frequent cause of cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS), and more recently, has been reported as a rare cause of Parkinson's disease (PD) in the Finnish population. Here, we investigate the prevalence of RFC1 (AAGGG) expansions in PD patients of non-Finnish European ancestry in 1609 individuals from the Parkinson's Progression Markers Initiative study. We identified four PD patients carrying the biallelic RFC1 (AAGGG) expansion and did not identify any carriers in controls.

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DNA methylation most commonly occurs as 5-methylcytosine (5-mC) in the human genome and has been associated with human diseases. Recent developments in single-molecule sequencing technologies (Oxford Nanopore Technologies (ONT) and Pacific Biosciences) have enabled readouts of long, native DNA molecules, including cytosine methylation. ONT recently upgraded their Nanopore sequencing chemistry and kits from R9 to the R10 version, which yielded increased accuracy and sequencing throughput.

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Cervical cancer is caused by human papillomavirus (HPV) infection, has few approved targeted therapeutics, and is the most common cause of cancer death in low-resource countries. We characterized 19 cervical and four head and neck cancer cell lines using long-read DNA and RNA sequencing and identified the HPV types, HPV integration sites, chromosomal alterations, and cancer driver mutations. Structural variation analysis revealed telomeric deletions associated with DNA inversions resulting from breakage-fusion-bridge (BFB) cycles.

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Background: Half of patients who achieve successful recanalization following endovascular thrombectomy (EVT) for acute ischemic stroke experience poor functional outcome. We aim to investigate whether the use of adjunctive intra-arterial antithrombotic therapy (AAT) during EVT is safe and efficacious compared with standard therapy (ST) of EVT with or without prior intravenous thrombolysis.

Methods: Electronic databases were searched (PubMed/MEDLINE, Embase, Cochrane Library) from 2010 until October 2023.

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Introduction: Knee osteoarthritis (KOA) is a progressive joint disease commonly treated with intra-articular injections, including platelet-rich plasma (PRP), hyaluronic acid (HA), or corticosteroids (CS). This updated meta-analysis aims to enhance the statistical power of the results and provide comprehensive clinical evidence that reflects the most current research. By doing so, the authors aim to suggest a reliable estimate for the development of guidelines, addressing the pressing need for effective and minimally invasive treatment options.

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