Javad Zahiri
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View article: A Quantitative Comparison Between Focal Loss and Binary Cross-Entropy Loss in Brain Tumor Auto-Segmentation Using U-Net
A Quantitative Comparison Between Focal Loss and Binary Cross-Entropy Loss in Brain Tumor Auto-Segmentation Using U-Net Open
Introduction: Brain tumors are among the most fatal cancers and cause the deaths of many people annually. Early diagnosis of a brain tumor can help save the patient’s life. Methods: We have collected a dataset consisting of 314 brain MRI i…
View article: Large-scale examination of early-age sex differences in neurotypical toddlers and those with autism spectrum disorder or other developmental conditions
Large-scale examination of early-age sex differences in neurotypical toddlers and those with autism spectrum disorder or other developmental conditions Open
Autism spectrum disorder (ASD) is clinically heterogeneous, with ongoing debates about phenotypic differences between boys and girls. Understanding these differences, particularly at the age of first symptom onset, is critical for advancin…
View article: Evaluation of optimal dam release to achieve agricultural economic-ecological development from stakeholders' perspectives in the Karkheh basin, Iran
Evaluation of optimal dam release to achieve agricultural economic-ecological development from stakeholders' perspectives in the Karkheh basin, Iran Open
Study region: The Karkheh Dam and its sub-basin are located in Khuzestan Province, Iran. The Karkheh Dam has a storage capacity of 7.5 × 10^9 cubic meters and is the largest dam in Iran by volume. Study focus: The increasing demand for agr…
View article: Liposomal Cancer Drug Database (LCDD): a comprehensive resource for liposome research in cancer therapy and diagnosis
Liposomal Cancer Drug Database (LCDD): a comprehensive resource for liposome research in cancer therapy and diagnosis Open
The Liposomal Cancer Drug Database (LCDD) is a comprehensive web-based resource that provides an extensive overview of liposome-based formulations used in cancer therapy and diagnostics. LCDD compiles data from about 4500 research articles…
View article: Beyond the Spectrum: Subtype-Specific Molecular Insights into Autism Spectrum Disorder Via Multimodal Data Integration
Beyond the Spectrum: Subtype-Specific Molecular Insights into Autism Spectrum Disorder Via Multimodal Data Integration Open
Some toddlers with autism spectrum disorder (ASD) have mild social symptoms and developmental improvement in skills, but for others, symptoms and abilities are moderately or even severely affected. Those with profound autism have the most …
View article: Beyond Algorithms: The Impact of Simplified CNN Models and Multifactorial Influences on Radiological Image Analysis
Beyond Algorithms: The Impact of Simplified CNN Models and Multifactorial Influences on Radiological Image Analysis Open
This paper demonstrates that simplified Convolutional Neural Network (CNN) models can outperform traditional complex architectures, such as VGG-16, in the analysis of radiological images, particularly in datasets with fewer samples. We int…
View article: Differences in regional brain structure in toddlers with autism are related to future language outcomes
Differences in regional brain structure in toddlers with autism are related to future language outcomes Open
Language and social symptoms improve with age in some autistic toddlers, but not in others, and such outcome differences are not clearly predictable from clinical scores alone. Here we aim to identify early-age brain alterations in autism …
View article: Multimodality Integration of Neural Social Activation and Social and Language Scores Reveals Three Replicable Profound and Milder Autism Subtypes With Divergent Clinical Outcomes
Multimodality Integration of Neural Social Activation and Social and Language Scores Reveals Three Replicable Profound and Milder Autism Subtypes With Divergent Clinical Outcomes Open
Social affective and communication symptoms stand at the center of autism, and usually become apparent within the first 1-3 years of life. Symptom severity differs widely across toddlers and clinical outcomes, ranging from near-neurotypica…
View article: Predictive three-biomarker panel in peripheral blood mononuclear cells for detecting hepatocellular carcinoma
Predictive three-biomarker panel in peripheral blood mononuclear cells for detecting hepatocellular carcinoma Open
Hepatocellular carcinoma (HCC) ranks among the most prevalent cancers and accounts for a significant proportion of cancer-associated deaths worldwide. This disease, marked by multifaceted etiology, often poses diagnostic challenges. Findin…
View article: 123FASTQ: an intuitive and efficient tool for preprocessing Illumina FASTQ reads
123FASTQ: an intuitive and efficient tool for preprocessing Illumina FASTQ reads Open
Next-generation sequencing (NGS) has revolutionized genetic research, but preprocessing raw sequencing reads remains a crucial step. Existing tools for quality control (QC) and trimming have limitations, leading to fragmented workflows. In…
View article: 123VCF: an intuitive and efficient tool for filtering VCF files
123VCF: an intuitive and efficient tool for filtering VCF files Open
Background The advent of Next-Generation Sequencing (NGS) has catalyzed a paradigm shift in medical genetics, enabling the identification of disease-associated variants. However, the vast quantum of data produced by NGS necessitates a robu…
View article: COMPARATIVE ASSESSMENT OF BIOBANK DATASETS FOR THE STUDY OF INFLAMMATORY BOWEL DISEASE
COMPARATIVE ASSESSMENT OF BIOBANK DATASETS FOR THE STUDY OF INFLAMMATORY BOWEL DISEASE Open
Lack of available multiomics datasets has slowed progress in understanding the relationship between genomic variants, gene expression, and disease progress in inflammatory bowel disease (IBD). Biobanks provide an opportunity to produce pop…
View article: Reconstructing the cell–cell interaction network among mouse immune cells
Reconstructing the cell–cell interaction network among mouse immune cells Open
Intercellular interactions and cell–cell communication are critical to regulating cell functions, especially in normal immune cells and immunotherapies. Ligand–receptor pairs mediating these cell–cell interactions can be identified using d…
View article: Level of Attention to Motherese Speech as an Early Marker of Autism Spectrum Disorder
Level of Attention to Motherese Speech as an Early Marker of Autism Spectrum Disorder Open
Importance Caregivers have long captured the attention of their infants by speaking in motherese, a playful speech style characterized by heightened affect. Reduced attention to motherese in toddlers with autism spectrum disorder (ASD) may…
View article: Language, Social, and Face Regions Are Affected in Toddlers with Autism and Predictive of Language Outcome
Language, Social, and Face Regions Are Affected in Toddlers with Autism and Predictive of Language Outcome Open
Identifying prognostic early brain alterations is crucial for autism spectrum disorder (ASD). Leveraging structural MRI data from 166 ASD and 109 typical developing (TD) toddlers and controlling for brain size, we found that, compared to T…
View article: Language and Social Regions Are Affected in Toddlers with Autism and Predict Later Language Outcome
Language and Social Regions Are Affected in Toddlers with Autism and Predict Later Language Outcome Open
Autism spectrum disorder is a heterogeneous neurodevelopmental disorder. Early brain overgrowth yet reduced cerebellar size is well recognized for autism, but cortical regions involved show inconsistent patterns of alteration. No complete …
View article: Identifying Key Lysosome-Related Genes Associated with Drug-Resistant Breast Cancer Using Computational and Systems Biology Approach
Identifying Key Lysosome-Related Genes Associated with Drug-Resistant Breast Cancer Using Computational and Systems Biology Approach Open
Background: Drug resistance in breast cancer is an unsolved problem in treating patients. It has been recently discussed that lysosomes contribute to the invasion and angiogenesis of cancer cells. There is evidence that lysosomes can also …
View article: Editorial: Artificial Intelligence in Environmental Microbiology
Editorial: Artificial Intelligence in Environmental Microbiology Open
Perhaps twenty-first century is so called “Digital Era” since digitalization and artificial intelligence (AI) is finding its way into every aspect of human life. Nowadays, AI-based approaches are gaining a lot of traction as components of …
View article: Large scale validation of an early-age eye-tracking biomarker of an autism spectrum disorder subtype
Large scale validation of an early-age eye-tracking biomarker of an autism spectrum disorder subtype Open
Few clinically validated biomarkers of ASD exist which can rapidly, accurately, and objectively identify autism during the first years of life and be used to support optimized treatment outcomes and advances in precision medicine. As such,…
View article: Discovering Common Pathogenic Mechanisms of COVID-19 and Parkinson Disease: an Integrated Bioinformatics Analysis
Discovering Common Pathogenic Mechanisms of COVID-19 and Parkinson Disease: an Integrated Bioinformatics Analysis Open
Coronavirus disease 2019 (COVID-19) has emerged since December 2019 and was later characterized as a pandemic by WHO, imposing a major public health threat globally. Our study aimed to identify common signatures from different biological l…
View article: Additional file 5 of Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies
Additional file 5 of Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies Open
Additional file 5. Scripts and Commands: All codes and scripts used in this study are available at https://github.com/Naseri1374/phageome-in-liver-cirrhosis . All information about each group including filtered genes (with FDR above 0.01),…
View article: Additional file 4 of Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies
Additional file 4 of Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies Open
Additional file 4. Scripts and Commands: All codes and scripts used in this study are available at https://github.com/Naseri1374/phageome-in-liver-cirrhosis . All information about each group including filtered genes (with FDR above 0.01),…
View article: PSSMCOOL: a comprehensive R package for generating evolutionary-based descriptors of protein sequences from PSSM profiles
PSSMCOOL: a comprehensive R package for generating evolutionary-based descriptors of protein sequences from PSSM profiles Open
Position-specific scoring matrix (PSSM), also called profile, is broadly used for representing the evolutionary history of a given protein sequence. Several investigations reported that the PSSM-based feature descriptors can improve the pr…
View article: Additional file 2 of Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies
Additional file 2 of Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies Open
Additional file 2. Scripts and Commands: All codes and scripts used in this study are available at https://github.com/Naseri1374/phageome-in-liver-cirrhosis . All information about each group including filtered genes (with FDR above 0.01),…