LMPTMSite: A Platform for PTM Site Prediction in Proteins Leveraging Transformer-Based Protein Language Models.

Protein post-translational modifications (PTMs) introduce new functionalities and play a critical role in the regulation of protein functions. Characterizing these modifications, especially PTM sites, is essential for unraveling complex biological systems. However, traditional experimental approaches, such as mass spectrometry, are time-consuming and expensive.

LMCrot: an enhanced protein crotonylation site predictor by leveraging an interpretable window-level embedding from a transformer-based protein language model.

Motivation: Recent advancements in natural language processing have highlighted the effectiveness of global contextualized representations from protein language models (pLMs) in numerous downstream tasks. Nonetheless, strategies to encode the site-of-interest leveraging pLMs for per-residue prediction tasks, such as crotonylation (Kcr) prediction, remain largely uncharted.

Results: Herein, we adopt a range of approaches for utilizing pLMs by experimenting with different input sequence types (full-length protein sequence versus window sequence), assessing the implications of utilizing per-residue embedding of the site-of-interest as well as embeddings of window residues centered around it.

Integrating Embeddings from Multiple Protein Language Models to Improve Protein -GlcNAc Site Prediction.

-linked β--acetylglucosamine (-GlcNAc) is a distinct monosaccharide modification of serine (S) or threonine (T) residues of nucleocytoplasmic and mitochondrial proteins. -GlcNAc modification (i.e.

LMPhosSite: A Deep Learning-Based Approach for General Protein Phosphorylation Site Prediction Using Embeddings from the Local Window Sequence and Pretrained Protein Language Model.

Phosphorylation is one of the most important post-translational modifications and plays a pivotal role in various cellular processes. Although there exist several computational tools to predict phosphorylation sites, existing tools have not yet harnessed the knowledge distilled by pretrained protein language models. Herein, we present a novel deep learning-based approach called LMPhosSite for the general phosphorylation site prediction that integrates embeddings from the local window sequence and the contextualized embedding obtained using global (overall) protein sequence from a pretrained protein language model to improve the prediction performance.

A Review of the Neutrophil Extracellular Traps (NETs) from Cow, Sheep and Goat Models.

This review provides insight into the importance of understanding NETosis in cows, sheep, and goats in light of the importance to their health, welfare and use as animal models. Neutrophils are essential to innate immunity, pathogen infection, and inflammatory diseases. The relevance of NETosis as a conserved innate immune response mechanism and the translational implications for public health are presented.

RF-NR: Random Forest Based Approach for Improved Classification of Nuclear Receptors.

The Nuclear Receptor (NR) superfamily plays an important role in key biological, developmental, and physiological processes. Developing a method for the classification of NR proteins is an important step towards understanding the structure and functions of the newly discovered NR protein. The recent studies on NR classification are either unable to achieve optimum accuracy or are not designed for all the known NR subfamilies.

CNN-BLPred: a Convolutional neural network based predictor for β-Lactamases (BL) and their classes.

Background: The β-Lactamase (BL) enzyme family is an important class of enzymes that plays a key role in bacterial resistance to antibiotics. As the newly identified number of BL enzymes is increasing daily, it is imperative to develop a computational tool to classify the newly identified BL enzymes into one of its classes. There are two types of classification of BL enzymes: Molecular Classification and Functional Classification.

Minimally invasive plate osteosynthesis on anterior pelvic ring injury and anterior column acetabular fracture.

Introduction: In performing surgery for fractures of the pelvis and acetabulum, various surgical approaches have been introduced with their own advantages and drawbacks. The extensile nature of ilioinguinal approach gives excellent exposure but was related to wound healing problems. Modified stoppa has a higher difficulty and poses a risk for neurovascular injury.

The Outcome of Complex Pelvic Fracture after Internal Fixation Surgery.

Complex pelvic fracture, which has a very high mortality and even higher morbidity, needs internal fixation surgery as an integral part for its management. It was necessary to conduct a study regarding outcome of complex pelvic fractures after internal fixation surgery. Twenty-six patients with complex pelvic fractures that had been treated with internal fixation surgery during 2011-2014 were enrolled.

Total hip replacement: A meta-analysis to evaluate survival of cemented, cementless and hybrid implants.

Aim: To determine whether cemented, cementless, or hybrid implant was superior to the other in terms of survival rate.

Methods: Systematic searches across MEDLINE, CINAHL, and Cochrane that compared cemented, cementless and hybrid total hip replacement (THR) were performed. Two independent reviewers evaluated the risk ratios of revision due to any cause, aseptic loosening, infection, and dislocation rate of each implants with a pre-determined form.

Mesenchymal stem cell implantation in atrophic nonunion of the long bones: A translational study.

Objectives: To explore the therapeutic potential of combining bone marrow-derived mesenchymal stem cells (BM-MSCs) and hydroxyapatite (HA) granules to treat nonunion of the long bone.

Methods: Ten patients with an atrophic nonunion of a long bone fracture were selectively divided into two groups. Five subjects in the treatment group were treated with the combination of 15 million autologous BM-MSCs, 5g/cm(3) (HA) granules and internal fixation.

RF-Hydroxysite: a random forest based predictor for hydroxylation sites.

Protein hydroxylation is an emerging posttranslational modification involved in both normal cellular processes and a growing number of pathological states, including several cancers. Protein hydroxylation is mediated by members of the hydroxylase family of enzymes, which catalyze the conversion of an alkyne group at select lysine or proline residues on their target substrates to a hydroxyl. Traditionally, hydroxylation has been identified using expensive and time-consuming experimental methods, such as tandem mass spectrometry.

RF-Phos: A Novel General Phosphorylation Site Prediction Tool Based on Random Forest.

Protein phosphorylation is one of the most widespread regulatory mechanisms in eukaryotes. Over the past decade, phosphorylation site prediction has emerged as an important problem in the field of bioinformatics. Here, we report a new method, termed Random Forest-based Phosphosite predictor 2.

Existence of mesenchymal stem cellsin sites of atrophic nonunion.

Objectives: Nonunion is one of the most troublesome complications to treat in orthopaedics. Former authors believed that atrophic nonunion occurred as a result of lack of mesenchymal stem cells (MSCs). We evaluated the number and viability of MSCs in site of atrophic nonunion compared with those in iliac crest.

Effect of Staphylococcus aureus and Staphylococcus epidermidis debris and supernatant on bone marrow stromal cells growth.

Aim: the goal of this study is to observe the effect of SA and SE debris and supernatant on BMSCs growth.

Methods: SA and SE were isolated and cultured from lesion materials of spondylitis patients which were determined by gram staining and biochemical tests. BMSCs were cultured and incubated for 11 days to be further sub-cultured and tripsinized for cell counting before seeded.

Outcome of cloverleaf locking plate fixation for femoral neck fractures in young adults.

Abstract: Femoral neck fractures in young adults remain a major problem in orthopaedics. Although treatments using cannulated screws and sliding hip screws are widely accepted, they pose significant clinical challenges. In the present study, we evaluated the outcome of treatment using cloverleaf locking plate fixation (augmented with the addition of addition of nonvascularised autologous bone grafts for neglected fracture).

Minimal Invasive Plate Osteosynthesis (MIPO) Technique Using Anterolateral Approach for Treating Closed Proximal Humerus Fracture.

Abstract: Proximal humerus fracture is the second most common fracture of the upper extremity and presents several unique problems such as anatomical complexity, high risk of avascular necrosis, minimal bone stock for purchase, significant morbidity, and lack of a universally accepted treatment. Recent treatments for proximal humerus fractures include use of minimally invasive plate osteosynthysis (MIPO). The aim of this cross-sectional study was to evaluate the outcomes of our less invasive technique using a modified anterolateral approach for treatment of proximal humerus fractures.

Effects of implantation of bone marrow mesenchymal stem cells, disc distraction and combined therapy on reversing degeneration of the intervertebral disc.

Although success has been achieved with implantation of bone marrow mesenchymal stem cells (bMSCs) in degenerative discs, its full potential may not be achieved if the harsh environment of the degenerative disc remains. Axial distraction has been shown to increase hydration and nutrition. Combining both therapies may have a synergistic effect in reversing degenerative disc disease.