168 results match your criteria biases scaffold

Genetic Variant XRCC1 rs1799782 (C194T) and Risk of Cancer Susceptibility in Indian Population: A Meta-analysis of Case-Control Studies.

Indian J Clin Biochem 2021 Apr 2;36(2):175-184. Epub 2020 Mar 2.

Department of Urology and Renal Transplantation, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India.

X-ray repair cross-complementing group 1 (XRCC1) plays a key role in the base excision repair pathway, as a scaffold protein that brings together proteins of the DNA repair complex. Several studies have reported contradictory results for exon 6 C>T (rs1799782) gene polymorphism and cancer risk in Indian population has provided inconsistent results. Therefore, we have performed this meta-analysis to evaluate the relationship between exon 6 C>T gene polymorphism and risk of cancer by published studies. Read More

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AUTOSTERE: Systematic Search for Scaffold Replacement Opportunities within Structural Databases.

J Chem Inf Model 2021 Apr 8;61(4):1778-1788. Epub 2021 Apr 8.

RxCelerate Limited, Dorothy Hodgkin Building, Babraham Research Campus, Babraham, Cambridge CB22 3FH, United Kingdom.

Medicinal chemists often bias toward working with scaffolds with which previously they have had direct experience and successes. In this way, it is often the case that scaffolds which have proven tractable within a research group are "reused" across multiple and sometimes unrelated drug targets. With this concept in mind, we designed a new computer algorithm AUTOSTERE which could systematically assess the opportunities to replace any part of any molecule within an entire database of known ligand structures with a target scaffold and automatically evaluate the potential designs in the context of the original ligand's protein environment. Read More

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One-shot object parsing in newborn chicks.

J Exp Psychol Gen 2021 Mar 22. Epub 2021 Mar 22.

Department of Informatics, Indiana University.

Controlled-rearing studies provide the unique opportunity to examine which psychological mechanisms are present at birth and which mechanisms emerge from experience. Here we show that one core component of visual perception-the ability to parse objects from backgrounds-is present when newborn animals see their first object. We reared newborn chicks in strictly controlled environments containing a single object on a single background, then tested the chicks' object parsing and recognition abilities. Read More

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Targeting tumor resistance mechanisms.

Fac Rev 2021 26;10. Epub 2021 Jan 26.

Laboratory of Molecular Cancer Biology, Molecular Physiology Research Unit (URPhyM), Namur Research Institute for Life Sciences (NARILIS), Faculty of Medicine, University of Namur, Namur, Belgium.

Cancer develops resistance to treatments through many mechanisms. Single-cell analyses reveal the intratumor heterogeneity and dynamic relationships between cancer cell subpopulations. These analyses also highlight that various mechanisms of resistance may coexist in a given tumor. Read More

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January 2021

Synthesis and biological evaluation of a ring analogs of the selective CB2 inverse agonist SMM-189.

Bioorg Med Chem 2021 Mar 25;33:116035. Epub 2021 Jan 25.

Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA. Electronic address:

Microglia are the principle cell type driving sustained neuroinflammation in neurodegenerative diseases such as Alzheimer's, Parkinson's, and Multiple Sclerosis. Interestingly, microglia locked into a chronic M1 pro-inflammatory phenotype significantly up-regulate the cannabinoid receptor 2 (CB2) expression. Our approach to exploiting CB2 as a therapeutic target in neuroinflammatory diseases focuses on the development of selective CB2 inverse agonists to shift microglia bias to a M2 pro-wound healing phenotype. Read More

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Semantic influences on episodic memory distortions.

J Exp Psychol Gen 2021 Jan 21. Epub 2021 Jan 21.

Department of Psychology.

Prior knowledge has long been known to shape new episodic memories. However, it is less clear how prior knowledge can scaffold the learning of a new class of information, and how this can bias memory for the episodes that contributed to its acquisition. We aimed to quantify distortions in episodic memories resulting from the use of prior category knowledge to facilitate learning new information. Read More

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January 2021

Computational fluid dynamics for enhanced tracheal bioreactor design and long-segment graft recellularization.

Sci Rep 2021 Jan 13;11(1):1187. Epub 2021 Jan 13.

Department of Mechanical and Industrial Engineering, University of Toronto, 5 King's College Road, Toronto, ON, M5S 3G8, Canada.

Successful re-epithelialization of de-epithelialized tracheal scaffolds remains a challenge for tracheal graft success. Currently, the lack of understanding of the bioreactor hydrodynamic environment, and its relation to cell seeding outcomes, serve as major obstacles to obtaining viable tracheal grafts. In this work, we used computational fluid dynamics to (a) re-design the fluid delivery system of a trachea bioreactor to promote a spatially uniform hydrodynamic environment, and (b) improve the perfusion cell seeding protocol to promote homogeneous cell deposition. Read More

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January 2021

Synthetic Scaffold/Dental Pulp Stem Cell (DPSC) Tissue Engineering Constructs for Bone Defect Treatment: An Animal Studies Literature Review.

Int J Mol Sci 2020 Dec 21;21(24). Epub 2020 Dec 21.

Department of Innovative Technologies in Medicine & Dentistry, University of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy.

Background: Recently a greater interest in tissue engineering for the treatment of large bone defect has been reported. The aim of the present systematic review and meta-analysis was to investigate the effectiveness of dental pulp stem cells and synthetic block complexes for bone defect treatment in preclinical in vivo articles.

Methods: The electronic database and manual search was conducted on Pubmed, Scopus, and EMBASE. Read More

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December 2020

Semantic Segmentation of Intralobular and Extralobular Tissue from Liver Scaffold H&E Images.

Sensors (Basel) 2020 Dec 10;20(24). Epub 2020 Dec 10.

Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic.

Decellularized tissue is an important source for biological tissue engineering. Evaluation of the quality of decellularized tissue is performed using scanned images of hematoxylin-eosin stained (H&E) tissue sections and is usually dependent on the observer. The first step in creating a tool for the assessment of the quality of the liver scaffold without observer bias is the automatic segmentation of the whole slide image into three classes: the background, intralobular area, and extralobular area. Read More

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December 2020

Clinical and Radiological Outcomes After Autologous Matrix-Induced Chondrogenesis Versus Microfracture of the Knee: A Systematic Review and Meta-analysis With a Minimum 2-Year Follow-up.

Orthop J Sports Med 2020 Nov 4;8(11):2325967120959280. Epub 2020 Nov 4.

Department of Orthopedic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.

Background: Microfracture (MFx) is the most common procedure for treating chondral lesions in the knee; however, initial improvements decline after 2 years. Autologous matrix-induced chondrogenesis (AMIC) may overcome this shortcoming by combining MFx with collagen scaffolds. However, the outcomes of AMIC and MFx in the knee have not been compared. Read More

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November 2020

Innate connectivity patterns drive the development of the visual word form area.

Sci Rep 2020 10 22;10(1):18039. Epub 2020 Oct 22.

Department of Psychology, The Ohio State University, Columbus, OH, USA.

What determines the functional organization of cortex? One hypothesis is that innate connectivity patterns, either structural or functional connectivity, set up a scaffold upon which functional specialization can later take place. We tested this hypothesis by asking whether the visual word form area (VWFA), an experience-driven region, was already functionally connected to proto language networks in neonates scanned within one week of birth. Using the data from the Human Connectone Project (HCP) and the Developing Human Connectome Project (dHCP), we calculated intrinsic functional connectivity during resting-state functional magnetic resonance imaging (fMRI), and found that neonates showed similar functional connectivity patterns to adults. Read More

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October 2020

From descent with modification to the origins of novelty.

Zoology (Jena) 2020 12 29;143:125836. Epub 2020 Aug 29.

Department of Biology, Indiana University, Bloomington, IN, 47405, United States.

Descent with modification is the foundational framework of all of evolution. Yet evolutionary novelties are defined as lacking affinities to structures that already existed in the ancestral state, i.e. Read More

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December 2020

Synthesis and structural insights into the binding mode of the albomycin δ1 core and its analogues in complex with their target aminoacyl-tRNA synthetase.

Bioorg Med Chem 2020 09 13;28(17):115645. Epub 2020 Jul 13.

Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000 Leuven, Belgium. Electronic address:

Despite of proven efficacy and well tolerability, albomycin is not used clinically due to scarcity of material. Several attempts have been made to increase the production of albomycin by chemical or biochemical methods. In the current study, we have synthesized the active moiety of albomycin δ1 and investigated its binding mode to its molecular target seryl-trna synthetase (SerRS). Read More

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September 2020

Vascular endothelial growth factor for in vivo bone formation: A systematic review.

J Orthop Translat 2020 Sep 7;24:46-57. Epub 2020 Jun 7.

Musculoskeletal Research Laboratory, Department of Orthopaedic Surgery & Traumatology, The Chinese University of Hong Kong, Hong Kong SAR, PR China.

Background: To achieve optimal bone formation one of the most influential parameters has been mentioned to be adequate blood supply. Vascular endothelial growth factor (VEGF) is hereby of particular interest in bone regeneration, because of its primary ability to induce neovascularization and chemokine affection for endothelial cells (EC), and is considered to be the main regulator of vascular formation. However, the growth factor has yet to be implemented in a clinical setting in orthopaedic intervention surgery. Read More

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September 2020

Optical coherence tomography features of neovascularization in proliferative diabetic retinopathy: a systematic review.

Int J Retina Vitreous 2020 29;6:26. Epub 2020 Jun 29.

Department of Ophthalmology, Centro Hospitalar Universitário de Lisboa Norte, EPE-Hospital de Santa Maria, Avenida Professor Egas Moniz, 1649-035 Lisbon, Portugal.

Background: Diabetic retinopathy (DR) is a leading cause of blindness due to diabetic macular edema (DME) or complications of proliferative diabetic retinopathy (PDR). Optical coherence tomography (OCT) is a noninvasive imaging technique well established for DME but less used to assess neovascularization in PDR. Developments in OCT imaging and the introduction of OCT angiography (OCTA) have shown significant potential in PDR. Read More

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Engineered Prevascularization for Oral Tissue Grafting: A Systematic Review.

Tissue Eng Part B Rev 2020 08 7;26(4):383-398. Epub 2020 Aug 7.

Univ. Bordeaux, INSERM, Laboratoire Bioingénierie Tissulaire (BioTis), U1026, CHU Bordeaux, 33000, Bordeaux, France.

Extensive dental and periodontal defects are frequent and with a limited regenerative potential. Tissue engineering could be a promising tool to obtain personalized oral grafts. However, current research shows a lack of engineered oral tissues. Read More

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Adhesive Sponge Based on Supramolecular Dimer Interactions as Scaffolds for Neural Stem Cells.

Biomacromolecules 2020 08 9;21(8):3394-3410. Epub 2020 Jul 9.

Institute of Chemistry, University of Campinas (UNICAMP), Campinas, SP 13083-970, Brazil.

Improving cell-material interactions of nonadhesive scaffolds is crucial for the success of biomaterials in tissue engineering. Due to their high surface area and open pore structure, sponges are widely reported as absorbent materials for biomedical engineering. The biocompatibility and biodegradability of polysaccharide sponges, coupled with the chemical functionalities of supramolecular dimers, make them promising combinations for the development of adhesive scaffolds. Read More

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Ferrocene on Insulator: Silane Coupling to a SiO Surface and Influence on Electrical Transport at a Buried Interface with an Organic Semiconductor Layer.

Langmuir 2020 Jun 21;36(21):5809-5819. Epub 2020 May 21.

Graduate School of Material Science, University of Hyogo, 3-2-1, Kouto, Kamigori, Ako, Hyogo 678-1297, Japan.

A silane coupling-based procedure for decoration of an insulator surface containing abundant hydroxy groups by constructing redox-active self-assembled monolayers (SAMs) is described. A newly synthesized ferrocene (Fc) derivative containing a triethoxysilyl group designated was immobilized on SiO/Si by a simple operation that involved immersing the substrate in a toluene solution of the Fc silane coupling reagent and then rinsing the resulting substrate. X-ray photoelectron spectroscopy (XPS) measurements confirmed that the Fc group was immobilized on SiO/Si in the Fe(II) state. Read More

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Synthetic Studies of Neoclerodane Diterpenes from : Design, Synthesis, and Evaluation of Analogues with Improved Potency and G-protein Activation Bias at the μ-Opioid Receptor.

ACS Chem Neurosci 2020 06 26;11(12):1781-1790. Epub 2020 May 26.

Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States.

Previous structure-activity relationship (SAR) studies identified the first centrally acting, non-nitrogenous μ-opioid receptor (MOR) agonist, kurkinorin (), derived from salvinorin A. In an effort to further probe the physiological effects induced upon activation of MORs with this nonmorphine scaffold, a variety of analogues were synthesized and evaluated for their ability to activate G-proteins and recruit β-arrestin-2 upon MOR activation. Through these studies, compounds that are potent agonists at MORs and either biased toward β-arrestin-2 recruitment or biased toward G-protein activation have been identified. Read More

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Does the Etiology of Pulp Necrosis Affect Regenerative Endodontic Treatment Outcomes? A Systematic Review and Meta-analyses.

J Evid Based Dent Pract 2020 Mar 29;20(1):101400. Epub 2020 Jan 29.

Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy; IRCCS Orthopedic Institute Galeazzi, Milan, Italy. Electronic address:

Objective: To evaluate if there is a connection between the causes of pulp necrosis (eg, caries, trauma, dental anomaly) and the success of regenerative endodontic treatment.

Methods: Electronic databases (PubMed, Scopus, Web of Science, Cochrane Central Register of Controlled Trials, Embase) were searched for studies on regenerative endodontic treatment, which used both clinical and radiographic evaluation of root maturation after at least 6 months of follow-up. The search terms "necrotic pulp", "regenerative endodontic treatment", "revascularization", and "revitalization" were combined using Boolean operators. Read More

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Deep conservation of prion-like composition in the eukaryotic prion-former Pub1/Tia1 family and its relatives.

PeerJ 2020 17;8:e9023. Epub 2020 Apr 17.

Department of Biology, McGill University, Montreal, QC, Canada.

Pub1 protein is an important RNA-binding protein functional in stress granule assembly in budding yeast and, as its co-ortholog Tia1, in humans. It is unique among proteins in evidencing prion-like aggregation in both its yeast and human forms. Previously, we noted that Pub1/Tia1 was the only protein linked to human disease that has prion-like character and and has demonstrated such aggregation in both species. Read More

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The Impact of Bioceramic Scaffolds on Bone Regeneration in Preclinical Studies: A Systematic Review.

Materials (Basel) 2020 Mar 25;13(7). Epub 2020 Mar 25.

Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Via Commenda 10, 20122 Milan, Italy.

Bioceramic scaffolds are appealing for alveolar bone regeneration, because they are emerging as promising alternatives to autogenous and heterogenous bone grafts. The aim of this systematic review is to answer to the focal question: in critical-sized bone defects in experimental animal models, does the use of a bioceramic scaffolds improve new bone formation, compared with leaving the empty defect without grafting materials or using autogenous bone or deproteinized bovine-derived bone substitutes? Electronic databases were searched using specific search terms. A hand search was also undertaken. Read More

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Predicting or Pretending: Artificial Intelligence for Protein-Ligand Interactions Lack of Sufficiently Large and Unbiased Datasets.

Front Pharmacol 2020 25;11:69. Epub 2020 Feb 25.

National Institute of Biological Sciences, Beijing, China.

Predicting protein-ligand interactions using artificial intelligence (AI) models has attracted great interest in recent years. However, data-driven AI models unequivocally suffer from a lack of sufficiently large and unbiased datasets. Here, we systematically investigated the data biases on the PDBbind and DUD-E datasets. Read More

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February 2020

Current evidence of tissue engineering for dentine regeneration in animal models: a systematic review.

Regen Med 2020 02 9;15(2):1345-1360. Epub 2020 Mar 9.

Graduate Program in Dentistry, Ibirapuera University, São Paulo, SP, 04661-100, Brazil.

The aim of this study is to verify the type of scaffold effect on tissue engineering for dentine regeneration in animal models. Strategic searches were conducted through MEDLINE/PubMed, Web of Science and Scopus databases. The studies were included with the following eligibility criteria: studies evaluating dentine regeneration, and being an study. Read More

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February 2020

Observation of the Unbiased Conformers of Putative DNA-Scaffold Ribosugars.

ACS Cent Sci 2020 Feb 18;6(2):293-303. Epub 2020 Feb 18.

Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain.

The constitution, configuration, and flexibility of the core sugars of DNA molecules alter their function in diverse roles. Conformational itineraries of the ribofuranosides (s) have long been known to finely determine rates of processing, yet we also know that, strikingly, semifunctional DNAs containing pyranosides (s) or other configurations can be created, suggesting sufficient but incompletely understood plasticity. The multiple conformers involved in such processes are necessarily influenced by context and environment: solvent, hosts, ligands. Read More

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February 2020

Bone Marrow-Derived Cell Therapies to Heal Long-Bone Nonunions: A Systematic Review and Meta-Analysis-Which Is the Best Available Treatment?

Stem Cells Int 2019 27;2019:3715964. Epub 2019 Dec 27.

Cell and Tissue Engineering Laboratory, IRCCS Istituto Ortopedico Galeazzi, Milan 20161, Italy.

Nonunions represent one of the major indications for clinical settings with stem cell-based therapies. The objective of this research was to systematically assess the current evidence for the efficacy of bone marrow-derived cell-based approaches associated or not with bone scaffolds for the treatment of nonunions. We searched MEDLINE (PubMed) and CENTRAL up to July 2019 for clinical studies focused on the use of cell-based therapies and bone marrow derivatives to treat bone nonunions. Read More

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December 2019

Expression of autophagy-related factor p62 for lung cancer diagnosis and prognosis: A systematic review and meta-analysis.

Math Biosci Eng 2019 07;16(6):6805-6821

Department of Respiration, Ningbo Medical Center Lihuili Eastern Hospital, Taipei Medical University Ningbo Medical Center, Ningbo, Zhejiang 315000, China.

p62/SQSTM1 is the scaffold protein implicated in selective autophagy, which is induced by cellular stress. Research has shown that p62 is highly expressed in cancer. Moreover, p62 can easily promote tumor metastasis. Read More

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The genome of Populus alba x Populus tremula var. glandulosa clone 84K.

DNA Res 2019 Oct;26(5):423-431

Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China.

Poplar 84K (Populus alba x P. tremula var. glandulosa) is a fast-growing poplar hybrid. Read More

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October 2019

Scaffold-Based Analytics: Enabling Hit-to-Lead Decisions by Visualizing Chemical Series Linked across Large Datasets.

J Chem Inf Model 2019 11 29;59(11):4880-4892. Epub 2019 Oct 29.

National Center for Advancing Translational Science , 9800 Medical Center Drive , Rockville , Maryland 20850 , United States.

We present a method for visualizing and navigating large screening datasets while also taking into account their activities and properties. Our approach is to annotate the data with all possible scaffolds contained within each molecule. We have developed a Spotfire visualization, coupled to a fuzzy clustering approach based on the scaffold decomposition of the screening deck, used to drive the hit triage process. Read More

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November 2019

Periodontal regenerative medicine using mesenchymal stem cells and biomaterials: A systematic review of pre-clinical studies.

Dent Mater J 2019 Dec 11;38(6):867-883. Epub 2019 Sep 11.

Inserm, UMR 1229, RMeS, Regenerative Medicine and Skeleton, University of Nantes.

The aim of the systematic review was to analyze the use of mesenchymal stem cells (MSC) and biomaterial for periodontal regeneration from preclinical animal models and human. Electronic databases were searched and additional hand-search in leading journals was performed. The research strategy was achieved according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Read More

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December 2019