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Biology subjects

Hammad, H.

Publications and source records attributed to Hammad, H..

7 recordsLinked to original sources

ASD-FER: An Annotated Multi-Class Benchmark and Comparative Study for Facial Emotion Recognition in Children with Autism Spectrum Disorder

Autism Spectrum Disorder (ASD) affects social interaction and communication, and automatically recognizing emotions from the facial expressions of children with ASD remains challenging. A key barrier to facial emotion recognition (FER) in children with ASD is the absence of ASD-specific datasets with proper emotion-level annotations. To address this, we present ASD-FER, a benchmark of 2,779 facial images of children with ASD annotated across six emotion categories by three independent annotators using majority voting. We evaluate nine models -- CNN, SVM, AlexNet, ResNet34, ResNet50, MobileNetV2, and three backbone configurations of our proposed task-specific architecture, EQFormer: ViT, Swin-T, and a compact Hybrid CNN-Transformer (HybridT) -- under stratified 10-fold cross-validation and a held-out 90/10 evaluation. ResNet50 led conventional models at 84.89% mean cross-validation accuracy; among transformer-based models, ViT led with 88.27%, followed by Swin-T at 88.02% and HybridT at 86.58%. On the held-out set, ViT achieved the highest overall accuracy (91.01%), while Swin-T obtained the best balanced accuracy (74.47%) and macro-F1 (0.7078); HybridT remained competitive at 89.57% accuracy with a fraction of the parameters. To support explainability, Grad-CAM visualizations highlighted attention on emotion-relevant facial regions -- eyes, eyebrows, and mouth -- with Swin-T the most spatially focused and the HybridT the most parameter-efficient (2.66M). Class imbalance and cross-dataset generalization remain open challenges.

neuroscience↗

Rational Design Reveals Structural Plasticity of the CsgA β-Solenoid Enabling Programmable Autogenic Engineered Living Materials

Microbial functional amyloids play central roles in biofilm formation and serve as foundational building blocks for autogenic engineered living materials (ELM), yet the structural design space governing their assembly and stability remains poorly defined. In Escherichia coli, the {beta}-solenoid protein CsgA functions as a canonical extracellular matrix scaffold, but prior engineering efforts have primarily focused on terminal functionalization rather than modification of the {beta}-solenoid core itself. Here, inspired by the evolutionary diversification of CsgA-like proteins, which expands along the vertical fiber axis, we explore a second orthogonal axis of structural plasticity: the horizontal dimension of the {beta}-solenoid. We rationally designed a library of CsgA variants in which the length of individual {beta}-strands was systematically reduced or extended from the native seven residues to lengths spanning 3-21 residues, while preserving conserved gate residues and loop regions. Integration of AI-based structure prediction using AlphaFold2 with all-atom molecular dynamics simulations reveals that {beta}-solenoid stability arises from a balance among strand length, residue composition, and solvent interactions, thereby defining both lower and optimal bounds for nanofiber assembly. Experimental validation demonstrates that engineered Escherichia coli can secrete and assemble these CsgA variants into extracellular nanofibers through the native curli biogenesis machinery, while preserving the characteristic cross-{beta} architecture. Additionally, the CsgA {beta}-solenoid variant library translates molecular design into macroscopic ELM, with deletion variants showing an inverse relationship between stiffness and extensibility, from highly extensible 3aa to stiff, strong 5aa films. Insertion-based variants largely retain CsgA-like extensibility while enabling tunable stiffness and strength across strand lengths. Together, these findings uncover previously unrecognized structural plasticity in microbial {beta}-solenoid proteins and establish {beta}-strand length as a generalizable design parameter linking molecular architecture to nanofiber stability, with implications spanning microbial functional amyloids and the rational design of autogenic engineered living materials.

bioengineering↗

IL-1 instructs para-bronchial cuff fibroblasts to organize lung antibody secreting cell niches during continued antigen exposure

Secondary lymphoid organs (SLO) are prototypic sites of antibody production, yet mucosal sites also generate and maintain mucosal antibodies during continued inflammation. Using a murine model of house dust mite-induced airway inflammation, we show that prolonged allergen exposure induces tertiary lymphoid organs (TLO) within para-bronchial adventitial cuffs. Within these regions, IL-1 signaling instructs fibroblasts to form niches that recruit, retain, and sustain lung antibody-secreting cells (ASCs) through chemokine induction. These mucosal ASCs share immunoglobulin repertoires with TLO-derived germinal center B cells. Thus, continued allergen exposure reshapes the lung microenvironment by converting para-bronchial fibroblasts into IL-1-dependent supportive niches for non-IgE antibody production, revealing a fibroblast-mediated mechanism for local immune regulation in chronic inflammation. One sentence summaryContinued allergen exposure drives lung TLO to generate ASCs that home to IL1-instructed para-bronchial cuffs.

immunology↗

TCR transgenic clone selection guided by immune receptor analysis and single cell RNA expression of polyclonal responders

Since the precursor frequency of naive T cells is extremely low, investigating the early steps of antigen-specific T cell activation is challenging. To overcome this detection problem, adoptive transfer of a cohort of T cells purified from T cell receptor (TCR) transgenic donors has been extensively used but is not readily available for emerging pathogens. Constructing TCR transgenic mice from T cell hybridomas is a labor-intensive and sometimes erratic process, since the best clones are selected based on antigen-induced CD69 upregulation or IL-2 production in vitro, and TCR chains are PCR-cloned into expression vectors. Here, we exploited the rapid advances in single cell sequencing and TCR repertoire analysis to select the best clones without hybridoma selection, and generated CORSET8 mice (CORona Spike Epitope specific CD8 T cell), carrying a TCR specific for the Spike protein of SARS-CoV-2. Implementing newly created DALI software for TCR repertoire analysis in single cell analysis enabled the rapid selection of the ideal responder CD8 T cell clone, based on antigen reactivity, proliferation and immunophenotype in vivo. Identified TCR sequences were inserted as synthetic DNA into an expression vector and transgenic CORSET8 donor mice were created. After immunization with Spike/CpG-motifs, mRNA vaccination or SARS-CoV2 infection, CORSET8 T cells strongly proliferated and showed signs of T cell activation. Thus, a combination of TCR repertoire analysis and scRNA immunophenotyping allowed rapid selection of antigen-specific TCR sequences that can be used to generate TCR transgenic mice.

immunology↗

Influence of Diabetes Mellitus Type 2 on the angiogenic potential of Bone Marrow derived Mesenchymal Stem Cells

Mesenchymal stem cells (MSCs) are used as novel therapeutic tools in cell-based therapies including diabetic complications. However, diabetes may negatively affect the therapeutic potential of autologous MSCs. In order to enhance the utilization of diabetic MSCs, better characterization of their angiogenic capacity should be performed. The aim of this study was to investigate the effect of diabetes mellitus (DM) on the angiogenic potential of bone marrow derived MSCs. MSCs were isolated from DM subjects and were compared with MSCs isolated from non-DM subjects. The angiogenic potential of MSCs was assessed in which there was insignificant difference in the proliferation and expression of angiogenic factors between the two groups. Moreover, no statistically significant change was found in the viability and angiogenic activities of endothelial cells isolated from both groups. Results indicate that the hyperglycemic milieu had no significant impact on the angiogenic-related functional properties of MSCs and they are able to survive the harsh diabetic conditions.

cell biology↗

Ym1 protein crystals promote type 2 immunity

Spontaneous protein crystallization is a rare event, yet protein crystals are frequently found in eosinophil-rich inflammation. In humans, Charcot-Leyden crystals (CLCs) are made from galectin-10 (Gal10) protein, an abundant protein in eosinophils. Whereas mice do not encode Gal10 in their genome, they do form pseudo-CLCs, made from the chitinase-like proteins Ym1 and/or Ym2, encoded by Chil3 and Chil4 and made by myeloid and epithelial cells respectively. Here, we investigated the biological effects of pseudo-CLCs since their function is currently unknown. We produced recombinant Ym1 crystals which were shown to have identical crystal packing and structure by X-ray crystallography as in vivo native crystals derived from murine lung. When administered to the airways of mice, crystalline but not soluble Ym1 stimulated innate and adaptive immunity and acted as a type 2 immune adjuvant for eosinophilic inflammation via triggering of dendritic cells (DCs). Murine Ym1 protein crystals found at sites of eosinophilic inflammation reinforce type 2 immunity and could serve as a surrogate model for studying the biology of human CLCs.

immunology↗

Sterilizing Immunity against SARS-CoV-2 Infection in Mice by a Single-Shot and Modified Imidazoquinoline TLR7/8 Agonist-Adjuvanted Recombinant Spike Protein Vaccine

The search for vaccines that protect from severe morbidity and mortality as a result of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19) is a race against the clock and the virus. Several vaccine candidates are currently being tested in the clinic. Inactivated virus and recombinant protein vaccines can be safe options but may require adjuvants to induce robust immune responses efficiently. In this work we describe the use of a novel amphiphilic imidazoquinoline (IMDQ-PEG-CHOL) TLR7/8 adjuvant, consisting of an imidazoquinoline conjugated to the chain end of a cholesterol-poly(ethylene glycol) macromolecular amphiphile). This amphiphile is water soluble and exhibits massive translocation to lymph nodes upon local administration, likely through binding to albumin. IMDQ-PEG-CHOL is used to induce a protective immune response against SARS-CoV-2 after single vaccination with trimeric recombinant SARS-CoV-2 spike protein in the BALB/c mouse model. Inclusion of amphiphilic IMDQ-PEG-CHOL in the SARS-CoV-2 spike vaccine formulation resulted in enhanced immune cell recruitment and activation in the draining lymph node. IMDQ-PEG-CHOL has a better safety profile compared to native soluble IMDQ as the former induces a more localized immune response upon local injection, preventing systemic inflammation. Moreover, IMDQ-PEG-CHOL adjuvanted vaccine induced enhanced ELISA and in vitro microneutralization titers, and a more balanced IgG2a/IgG1 response. To correlate vaccine responses with control of virus replication in vivo, vaccinated mice were challenged with SARS-CoV-2 virus after being sensitized by intranasal adenovirus-mediated expression of the human angiotensin converting enzyme 2 (ACE2) gene. Animals vaccinated with trimeric recombinant spike protein vaccine without adjuvant had lung virus titers comparable to non-vaccinated control mice, whereas animals vaccinated with IMDQ-PEG-CHOL-adjuvanted vaccine controlled viral replication and infectious viruses could not be recovered from their lungs at day 4 post infection. In order to test whether IMDQ-PEG-CHOL could also be used to adjuvant vaccines currently licensed for use in humans, proof of concept was also provided by using the same IMDQ-PEG-CHOL to adjuvant human quadrivalent inactivated influenza virus split vaccine, which resulted in enhanced hemagglutination inhibition titers and a more balanced IgG2a/IgG1 antibody response. Enhanced influenza vaccine responses correlated with better virus control when mice were given a lethal influenza virus challenge. Our results underscore the potential use of IMDQ-PEG-CHOL as an adjuvant to achieve protection after single immunization with recombinant protein and inactivated vaccines against respiratory viruses, such as SARS-CoV-2 and influenza viruses.

microbiology↗