Benchmarking recent computational tools for DNA-binding protein identification.

Identification of DNA-binding proteins (DBPs) is a crucial task in genome annotation, as it aids in understanding gene regulation, DNA replication, transcriptional control, and various cellular processes. In this paper, we conduct an unbiased benchmarking of 11 state-of-the-art computational tools as well as traditional tools such as ScanProsite, BLAST, and HMMER for identifying DBPs. We highlight the data leakage issue in conventional datasets leading to inflated performance.

Evaluating the impact of surgery sequence on infection rates in hip or knee arthroplasty: does sequence matter?

Purpose: The potential influence of surgical sequence of elective hip-and-knee reconstructive surgery in relation to an infection-related procedure on postoperative infection rates is not clearly understood. Therefore, we aimed to examine the impact of surgical sequence on the incidence of postoperative infections within one-year and the longest available follow-up period in patients undergoing hip-and-knee reconstructive surgery.

Methods: A case-control study with propensity matching was utilized to examine elective surgeries conducted at Sunnybrook Holland Orthopaedic & Arthritic centre, Toronto, Canada between 2015 and 2018.

ELISA-based detection of fresh and frozen-thawed lamb meat: a promising analytical approach for meat authentication.

Fresh/chilled meat differs in quality from frozen-thawed meat, and consumers prefer fresh meat over frozen-thawed meat. Differentiating between the two types of meat is an important part of the meat quality control system. This study aimed to develop an ELISA based on cytoplasmic antioxidant enzyme superoxide dismutase (SOD) as a biomarker.

How much can ChatGPT really help computational biologists in programming?

ChatGPT, a recently developed product by openAI, is successfully leaving its mark as a multi-purpose natural language based chatbot. In this paper, we are more interested in analyzing its potential in the field of computational biology. A major share of work done by computational biologists these days involve coding up bioinformatics algorithms, analyzing data, creating pipelining scripts and even machine learning modeling and feature extraction.

Intraoperative scrub nurse turnover in orthopaedic surgery procedures: An opportunity for improved operating room efficiency.

Background: Scrub nurses play a crucial role in facilitating orthopaedic surgeries, and thus intraoperative scrub nurse turnover may disrupt the workflow of the surgical team and prolong duration of surgery (DOS). The purpose of this study was to quantify the impact of intraoperative scrub nurse turnover on operative time of orthopaedic surgeries lasting less than 3h in duration.

Methods: Prospectively collected databases from two institutions were retrospectively queried to identify all orthopaedic procedures of maximum mean duration of 180min from March 4th, 2018 to August 31st, 2022.

Riluzole-induced apoptosis in osteosarcoma is mediated through Yes-associated protein upon phosphorylation by c-Abl Kinase.

Our lab has previously demonstrated Riluzole to be an effective drug in inhibiting proliferation and inducing apoptosis in both human and mouse osteosarcoma. Yes-associated protein is a transcription co-activator, known to be involved in cell proliferation or apoptosis depending on its protein partner. In the present study we investigated the role of YAP in apoptosis in osteosarcoma, we hypothesized that YAP may be activated by Riluzole to induce apoptosis in osteosarcoma.

A convolution based computational approach towards DNA N6-methyladenine site identification and motif extraction in rice genome.

DNA N6-methylation (6mA) in Adenine nucleotide is a post replication modification responsible for many biological functions. Automated and accurate computational methods can help to identify 6mA sites in long genomes saving significant time and money. Our study develops a convolutional neural network (CNN) based tool i6mA-CNN capable of identifying 6mA sites in the rice genome.

Component-based face recognition using statistical pattern matching analysis.

The aim of this research is to develop a fusion concept to component-based face recognition algorithms for features analysis of binary facial components (BFCs), which are invariant to illumination, expression, pose variations and partial occlusion. To analyze the features, using statistical pattern matching concepts, which are the combination of Chi-square (CSQ), Hu moment invariants (HuMIs), absolute difference probability of white pixels (AbsDifPWPs) and geometric distance values (GDVs) have been proposed for face recognition. The individual grayscale face image is cropped by applying the Viola-Jones face detection algorithm from a face database having variations in illumination, appearance, pose and partial occlusion with complex backgrounds.

iPromoter-BnCNN: a novel branched CNN-based predictor for identifying and classifying sigma promoters.

Motivation: Promoter is a short region of DNA which is responsible for initiating transcription of specific genes. Development of computational tools for automatic identification of promoters is in high demand. According to the difference of functions, promoters can be of different types.

Performance Characteristics of a Multiplex Flow Immunoassay for Detection of IgG-Class Antibodies to Measles, Mumps, Rubella, and Varicella-Zoster Viruses in Presumptively Immune Health Care Workers.

Immunity to measles, mumps, rubella, and varicella-zoster viruses (VZV; MMRV) is a common condition of employment for health care workers (HCWs) to ensure compliance with national standards and state laws. When documentation of complete vaccination or laboratory-confirmed infection is not available, Advisory Committee on Immunization Practices (ACIP) criteria are used to guide vaccination or anti-MMRV IgG testing. We assessed the performance of the BioPlex 2200 MMRV IgG multiplex flow immunoassay (MFI; Bio-Rad Laboratories, Hercules, CA) and matched immunofluorescence assays (IFAs; MBL Bion, Des Plaines, IL) in 220 HCWs categorized by ACIP criteria for presumptive immunity to MMRV.

Dragonfly Algorithm and Its Applications in Applied Science Survey.

One of the most recently developed heuristic optimization algorithms is dragonfly by Mirjalili. Dragonfly algorithm has shown its ability to optimizing different real-world problems. It has three variants.

Osteosarcoma growth suppression by riluzole delivery via iron oxide nanocage in nude mice.

Osteosarcomas are the most commonly occurring malignant bone cancer in young individuals. The survival rate of patients with metastatic osteosarcoma is low and has been stagnant for over two decades. We previously demonstrated that the glutamate release inhibitor, riluzole inhibits osteosarcoma cell growth.

BAP1 gene mutations in Egyptian patients with advanced sporadic malignant pleural mesothelioma (MPM): relation with clinical outcomes and survival.

Background: Malignant Pleural Mesothelioma (MPM) is a lethal cancer with few therapeutic options. Patients with MPM have a poor prognosis, with estimated 1 year median survival and currently no treatment is curative. The BRCA associated protein 1 (BAP1) has the highest prevalence of protein-altering mutations identified in MPM.

3-Methyl-1-{()-[1-(4-methyl-pyridin-2-yl)ethyl-idene]amino}-thio-urea: crystal structure and Hirshfeld surface analysis.

The title disubstituted thio-urea derivative, CHNS, features an almost planar imine ( configuration, CN) core flanked by thio-urea (CNS) and methyl-pyridyl (CN) residues (each plane has a r.m.s.

Surface modification of PdlLGA microspheres with gelatine methacrylate: Evaluation of adsorption, entrapment, and oxygen plasma treatment approaches.

Unlabelled: Injectable poly (dl-lactic-co-glycolic acid) (PdlLGA) microspheres are promising candidates as biodegradable controlled release carriers for drug and cell delivery applications; however, they have limited functional groups on the surface to enable dense grafting of tissue specific biocompatible molecules. In this study we have evaluated surface adsorption, entrapment and oxygen plasma treatment as three approaches to modify the surfaces of PdlLGA microspheres with gelatine methacrylate (gel-MA) as a biocompatible and photo cross-linkable macromolecule. Time of flight secondary ion mass spectroscopy (TOF SIMS) and X-ray photoelectron spectroscopy (XPS) were used to detect and quantify gel-MA on the surfaces.

Physicomechanical properties of sintered scaffolds formed from porous and protein-loaded poly(DL-lactic-co-glycolic acid) microspheres for potential use in bone tissue engineering.

An injectable poly(DL-lactic-co-glycolic acid) (PLGA) system comprising both porous and protein-loaded microspheres capable of forming porous scaffolds at body temperature was developed for tissue regeneration purposes. Porous and non-porous (lysozyme loaded) PLGA microspheres were formulated to represent 'low molecular weight' 22-34 kDa, 'intermediate molecular weight' (IMW) 53 kDa and 'high molecular weight' 84-109 kDa PLGA microspheres. The respective average size of the microspheres was directly related to the polymer molecular weight.

Surgical delivery of drug releasing poly(lactic-co-glycolic acid)/poly(ethylene glycol) paste with in vivo effects against glioblastoma.

Introduction: The median survival of patients with glioblastoma multiforme (astrocytoma grade 4) remains less than 18 months despite radical surgery, radiotherapy and systemic chemotherapy. Surgical implantation of chemotherapy eluting wafers into the resection cavity has been shown to improve length of survival but the current licensed therapy has several drawbacks. This paper investigates in vivo efficacy of a novel drug eluting paste in glioblastoma.

Injectable and porous PLGA microspheres that form highly porous scaffolds at body temperature.

Injectable scaffolds are of interest in the field of regenerative medicine because of their minimally invasive mode of delivery. For tissue repair applications, it is essential that such scaffolds have the mechanical properties, porosity and pore diameter to support the formation of new tissue. In the current study, porous poly(dl-lactic acid-co-glycolic acid) (PLGA) microspheres were fabricated with an average size of 84±24μm for use as injectable cell carriers.

Investigation of localized delivery of diclofenac sodium from poly(D,L-lactic acid-co-glycolic acid)/poly(ethylene glycol) scaffolds using an in vitro osteoblast inflammation model.

Nonunion fractures and large bone defects are significant targets for osteochondral tissue engineering strategies. A major hurdle in the use of these therapies is the foreign body response of the host. Herein, we report the development of a bone tissue engineering scaffold with the ability to release anti-inflammatory drugs, in the hope of evading this response.

A biodegradable antibiotic-impregnated scaffold to prevent osteomyelitis in a contaminated in vivo bone defect model.

Open fractures are at risk of serious infection and, if infected, require several surgical interventions and courses of systemic antibiotics. We investigated a new injectable formulation that simultaneously hardens in vivo to form a porous scaffold for bone repair and delivers antibiotics at high concentrations to the local site of infection. Duration of antimicrobial activity against Staphylococcus aureus was determined using the serial plate transfer test.

The osteogenic response of mesenchymal stem cells to an injectable PLGA bone regeneration system.

The enrichment of substrates/surfaces with selected functional groups, methyl (-CH3), allyl amine (-NH2), allyl alcohol (-OH) and acrylic acid (-COOH), can be used to trigger mesenchymal stem (MSC) cell differentiation into specified lineages, minimising the need for exogenous biological supplementation. We present the successful translation of this research phenomenon to an injectable two phase injectable PLGA system, utilising plasma techniques, for the repair of bone defects. Modified microspheres were characterised using water contact angel (WCA), X-ray Photon Spectroscopy (XPS) and scanning electron microscopy (SEM).

Development of a porous poly(DL-lactic acid-co-glycolic acid)-based scaffold for mastoid air-cell regeneration.

Objectives/hypothesis: To develop a porous, biodegradable scaffold for mastoid air-cell regeneration.

Study Design: In vitro development of a temperature-sensitive poly(DL-lactic acid-co-glycolic acid)/poly(ethylene glycol) (PLGA/PEG) scaffold tailored for this application.

Methods: Human mastoid bone microstructure and porosity were investigated using micro-computed tomography.

PLGA/PEG-hydrogel composite scaffolds with controllable mechanical properties.

Biodegradable polymer scaffolds have great potential for regenerative medicine applications such as the repair of musculoskeletal tissues. Here, we describe the development of scaffolds that blend hydrogel components with thermoplastic materials, combining the unique properties of both components to create mouldable formulations. This study focuses on the structural and mechanical properties of the composite scaffolds, produced by combining temperature-sensitive poly(DL-lactic acid-co-glycolic acid) (PLGA)/poly(ethylene glycol) (PEG) particles with a hydrogel component [Pluronic F127, fibrin or hyaluronic acid (HyA)].