The Many Faces of Guilt: A Review Mapping Unique and Overlapping Expressions in OCD and Depression.

Background: Guilt, a complex emotional experience pervading many lives, takes on an intricate form when intertwined with psychiatric conditions. As a multifaceted concept, guilt represents a key diagnostic feature in depression and is an integral part of obsessive compulsive disorder (OCD).

Methods: This systematic review aimed to synthesize empirical research on the varied dimensions of guilt across these two mental illnesses, where guilt is emphasized as a pathognomonic factor.

Evaluation of Multiplex loop-mediated isothermal amplification assay for the detection of complex from clinically suspected cases of pulmonary tuberculosis.

Tuberculosis (TB) is the second leading cause of death from a single infectious agent worldwide. Bangladesh ranks 7th among the 30 high TB burdened countries in the world. Accurate detection of complex (MTBC) is challenging for developing countries as most of the resource poor settings are not suitable to perform molecular techniques.

lociPARSE: A Locality-aware Invariant Point Attention Model for Scoring RNA 3D Structures.

A scoring function that can reliably assess the accuracy of a 3D RNA structural model in the absence of experimental structure is not only important for model evaluation and selection but also useful for scoring-guided conformational sampling. However, high-fidelity RNA scoring has proven to be difficult using conventional knowledge-based statistical potentials and currently available machine learning-based approaches. Here, we present lociPARSE, a locality-aware invariant point attention architecture for scoring RNA 3D structures.

Single-sequence protein-RNA complex structure prediction by geometric attention-enabled pairing of biological language models.

Ground-breaking progress has been made in structure prediction of biomolecular assemblies, including the recent breakthrough of AlphaFold 3. However, it remains challenging for AlphaFold 3 and other state-of-the-art deep learning-based methods to accurately predict protein-RNA complex structures, in part due to the limited availability of evolutionary and structural information related to protein-RNA interactions that are used as inputs to the existing approaches. Here, we introduce ProRNA3D-single, a new deep-learning framework for protein-RNA complex structure prediction with only single-sequence input.

The landscape of RNA 3D structure modeling with transformer networks.

Transformers are a powerful subclass of neural networks catalyzing the development of a growing number of computational methods for RNA structure modeling. Here, we conduct an objective and empirical study of the predictive modeling accuracy of the emerging transformer-based methods for RNA structure prediction. Our study reveals multi-faceted complementarity between the methods and underscores some key aspects that affect the prediction accuracy.

EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks.

Protein language models (pLMs) trained on a large corpus of protein sequences have shown unprecedented scalability and broad generalizability in a wide range of predictive modeling tasks, but their power has not yet been harnessed for predicting protein-nucleic acid binding sites, critical for characterizing the interactions between proteins and nucleic acids. Here, we present EquiPNAS, a new pLM-informed E(3) equivariant deep graph neural network framework for improved protein-nucleic acid binding site prediction. By combining the strengths of pLM and symmetry-aware deep graph learning, EquiPNAS consistently outperforms the state-of-the-art methods for both protein-DNA and protein-RNA binding site prediction on multiple datasets across a diverse set of predictive modeling scenarios ranging from using experimental input to AlphaFold2 predictions.

lociPARSE: a locality-aware invariant point attention model for scoring RNA 3D structures.

A scoring function that can reliably assess the accuracy of a 3D RNA structural model in the absence of experimental structure is not only important for model evaluation and selection but also useful for scoring-guided conformational sampling. However, high-fidelity RNA scoring has proven to be difficult using conventional knowledge-based statistical potentials and currently-available machine learning-based approaches. Here we present lociPARSE, a locality-aware invariant point attention architecture for scoring RNA 3D structures.

EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks.

Protein language models (pLMs) trained on a large corpus of protein sequences have shown unprecedented scalability and broad generalizability in a wide range of predictive modeling tasks, but their power has not yet been harnessed for predicting protein-nucleic acid binding sites, critical for characterizing the interactions between proteins and nucleic acids. Here we present EquiPNAS, a new pLM-informed E(3) equivariant deep graph neural network framework for improved protein-nucleic acid binding site prediction. By combining the strengths of pLM and symmetry-aware deep graph learning, EquiPNAS consistently outperforms the state-of-the-art methods for both protein-DNA and protein-RNA binding site prediction on multiple datasets across a diverse set of predictive modeling scenarios ranging from using experimental input to AlphaFold2 predictions.

Advanced bioactive glue tethering Lubricin/PRG4 to promote integrated healing of avascular meniscus tears.

Meniscus injuries are extremely common with approximately one million patients undergoing surgical treatment annually in the U.S. alone, but no regenerative therapy exist.

Influence of foliar spray and post-harvest treatments on head yield, shelf-life, and physicochemical qualities of broccoli.

Rapid senescence is the key factor in the deterioration of post-harvest shelf-life in broccoli heads. This study evaluates the head yield and its related traits, and physicochemical attributes of broccoli under four foliar sprays of mineral nutrients (B, Zn, Mo, and B + Zn + Mo) with control. The interaction effects of shelf-life and physicochemical attributes of broccoli for these five pre-harvest and five post-harvest storage treatments (LDP bag, HDP vacuum pack, 2% eggshell powder solution, 2% ascorbic acid, and control) both at cold storage and room temperature were evaluated with three replications.

Drowsiness Detection Using Ocular Indices from EEG Signal.

Drowsiness is one of the main causes of road accidents and endangers the lives of road users. Recently, there has been considerable interest in utilizing features extracted from electroencephalography (EEG) signals to detect driver drowsiness. However, in most of the work performed in this area, the eyeblink or ocular artifacts present in EEG signals are considered noise and are removed during the preprocessing stage.

Figbird: a probabilistic method for filling gaps in genome assemblies.

Motivation: Advances in sequencing technologies have led to the sequencing of genomes of a multitude of organisms. However, draft genomes of many of these organisms contain a large number of gaps due to the repeats in genomes, low sequencing coverage and limitations in sequencing technologies. Although there exists several tools for filling gaps, many of these do not utilize all information relevant to gap filling.

24 loci MIRU-VNTR analysis and pattern of drug resistance in pre-extensively drug resistant pulmonary tuberculosis in Bangladesh.

Phylogenetic diversity and distinct phylogeographic distribution of Mycobacterium tuberculosis (MTB) contribute to regional differences in drug resistance. The emergence of pre-extensively drug resistant tuberculosis (Pre-XDR-TB) becomes obstacles to achieve End TB strategy in Bangladesh. This cross-sectional study was conducted to identify the strains of different lineages of MTB, their variations of distribution among Pre-XDR-TB cases and to observe the linkage of particular strains of MTB with drug resistance.

Quantum dots-labeled polymeric scaffolds for tracking of degradation and tissue formation.

The inevitable gap between and degradation rate of biomaterials has been a challenging factor in the optimal designing of scaffold's degradation to be balanced with new tissue formation. To enable non-/minimum-invasive tracking of scaffold degradation, chemical modifications have been applied to label polymers with fluorescent dyes. However, the previous approaches may have limited expandability due to complicated synthesis processes.

The use of connective tissue growth factor mimics for flexor tendon repair.

Intrasynovial flexor tendon lacerations of the hand are clinically problematic, typically requiring operative repair and extensive rehabilitation. The small-molecule connective tissue growth factor (CTGF) mimics, oxotremorine M (Oxo-M) and 4-PPBP maleate (4-PPBP), have been shown to improve tendon healing in small animal models by stimulating the expansion and differentiation of perivascular CD146+ cells. To enhance intrasynovial flexor tendon healing, small-molecule CTGF mimics were delivered to repaired canine flexor tendons via porous sutures.

Oxo-M and 4-PPBP Delivery Multi-Domain Peptide Hydrogel Toward Tendon Regeneration.

We have recently identified novel small molecules, Oxo-M and 4-PPBP, which specifically stimulate endogenous tendon stem/progenitor cells (TSCs), leading to potential regenerative healing of fully transected tendons. Here, we investigated an injectable, multidomain peptide (MDP) hydrogel providing controlled delivery of the small molecules for regenerative tendon healing. We investigated the release kinetics of Oxo-M and 4-PPBP from MDP hydrogels and the effect of MDP-released small molecules on tenogenic differentiation of TSCs and tendon healing.

The recent advances in scaffolds for integrated periodontal regeneration.

The periodontium is an integrated, functional unit of multiple tissues surrounding and supporting the tooth, including but not limited to cementum (CM), periodontal ligament (PDL) and alveolar bone (AB). Periodontal tissues can be destructed by chronic periodontal disease, which can lead to tooth loss. In support of the treatment for periodontally diseased tooth, various biomaterials have been applied starting as a contact inhibition membrane in the guided tissue regeneration (GTR) that is the current gold standard in dental clinic.

High-Strength Fiber-Reinforced Composite Hydrogel Scaffolds as Biosynthetic Tendon Graft Material.

The development of suitable synthetic scaffolds for use as human tendon grafts to repair tendon ruptures remains a significant engineering challenge. Previous synthetic tendon grafts have demonstrated suboptimal tissue ingrowth and synovitis due to wear particles from fiber-to-fiber abrasion. In this study, we present a novel fiber-reinforced hydrogel (FRH) that mimics the hierarchical structure of the native human tendon for synthetic tendon graft material.

Sulphur fertilization enhanced yield, its uptake, use efficiency and economic returns of L.

Sulphur plays a vital role in the formation and biosynthesis of protein, chlorophyll, and few amino acids. To investigate the effect of sulphur fertilizer on leaf biomass yield, critical sulphur concentration, sulphur requirement and uptake by L., a pot experiment was carried out following completely randomized design with six levels of sulphur viz.

Circulating strains of Mycobacterium tuberculosis: 24 loci MIRU-VNTR analysis in Bangladesh.

Bangladesh is among the high burden countries for tuberculosis (TB) and multidrug resistant TB (MDR-TB). As the genetic diversity and distinct phylogeographic distribution of Mycobacterium tuberculosis are responsible for regional differences in drug resistance, this cross sectional study was conducted to identify the circulating M. tuberculosis strains belonging to different lineages among pulmonary tuberculosis and, to investigate the contribution of distinct M.

Bioadhesives for musculoskeletal tissue regeneration.

Natural or synthetic materials designed to adhere to biological components, bioadhesives, have received significant attention in clinics and surgeries. As a result, there are several commercially available, FDA-approved bioadhesives used for skin wound closure, hemostasis, and sealing tissue gaps or cracks in soft tissues. Recently, the application of bioadhesives has been expanded to various areas including musculoskeletal tissue engineering and regenerative medicine.

Effect of local anesthetics on viability and differentiation of various adult stem/progenitor cells.

Background: Local anesthetics (LAs) are widely used to control pain during various clinical treatments. One of the side effects of LAs, cytotoxicity, has been investigated in various cells including stem/progenitor cells. However, our understanding of the effects of LAs on the differentiation capacity of stem/progenitor cells still remains limited.

Explant models for meniscus metabolism, injury, repair, and healing.

Knee meniscus is a wedge-shaped fibrocartilaginous tissue, playing important roles in maintaining joint stability and function. Injuries to the meniscus, particularly with the avascular inner third zone, hardly heal and frequently progress into structural breakdown, followed by the initiation of osteoarthritis. As the importance of meniscus in joint function and diseases is being recognized, the field of meniscus research is growing.

In situ tissue engineering of the tendon-to-bone interface by endogenous stem/progenitor cells.

The long-term success of surgical repair of rotator cuff tears is largely dependent on restoration of a functional tendon-to-bone interface. We implemented micro-precise spatiotemporal delivery of growth factors in three-dimensional printed scaffolds for integrative regeneration of a fibrocartilaginous tendon-to-bone interface. Sustained and spatially controlled release of tenogenic, chondrogenic and osteogenic growth factors was achieved using microsphere-based delivery carriers embedded in thin membrane-like scaffolds.