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Showing "Biotools Labs" PubMed Articles 1–25 of 62

Randomly auditing research labs could be an affordable way to improve research quality: A simulation study.

The "publish or perish" incentive drives many researchers to increase the quantity of their papers at the cost of quality. Lowering quality increases the number of false positive errors which is a key cause of the reproducibility crisis. We adapted a previously published simulation of the research world where labs that produce many papers are more likely to have "child" labs that inherit their characteristics. This selection creates a competitive spiral that favours quantity over quality. To try to halt the...

Culled banana resistant starch-soy protein isolate conjugate based emulsion enriched with astaxanthin to enhance its stability.

The conjugates of biomacromolecules such as protein and polysaccharides have potential to stabilize the emulsion system and encapsulate valuable bioactive compounds for biofortification in food systems. In this study, native banana starch (NBS) was isolated from green culled banana and modified into resistant starch (type III) by lintnerization followed by autoclaving-cooling process, resulting in lintnerized-autoclaved banana starch (LABS). Soy protein isolate (SPI) was used for developing the polysacchari...


Measurements of the dose equivalent at different distances from the isocenter of the proton therapy center at iThemba LABS were previously performed with a tissue-equivalent proportional counter (TEPC). These measurements showed that the scattered radiation levels were one or two orders of magnitude higher in comparison to other passive scattering delivery systems. In order to reduce these radiation levels, additional shielding was installed shortly after the measurements were done. Therefore, the aim of th...

Cardiac Cath Labs: Their Origins and Their Future.

Life Cycle Assessment of Traction Lead-acid Batteries for Electric Bikes in China.

This research undertook a life cycle assessment (LCA) for lead-acid batteries (LABs) used in electric bikes, the fastest growing LABs in China. A cradle-to-grave LCA model was established to identify the key materials or processes that contribute most to environmental impacts within the life cycle of LABs, including material production, battery manufacture, transportation, use, and end-of-life. A large amount of primary data obtained from enterprisers and a Chinese LCA database were used in this research to...

AttrActin' Attention to Early Mouse Development.

A new study by Zenker et al. uses time-lapse imaging to discover how dynamic actin movements contribute to epithelialization of living mouse embryos. Together with work from other labs, this study presents exciting new ways to think about the emergence of cell fates during mammalian development.

Serum biomarkers of inflammation and adiposity in the LABS cohort: associations with metabolic disease and surgical outcomes.

The utility of serum biomarkers related to inflammation and adiposity as predictors of metabolic disease prevalence and outcomes after bariatric surgery are not well-defined.

Computer-based simulation: Effective tool or hindrance for undergraduate nursing students?

Undergraduate nursing programs continuously strive to improve student learning outcomes within the simulation lab experience. As a result, simulation labs are evaluating computer-based simulation programs to engage the millennial student learner.

Broom: Application for non-redundant storage of High Throughput Sequencing data.

The data generation capabilities of High Throughput Sequencing (HTS) instruments have exponentially increased over the last few years, while the cost of sequencing has dramatically decreased allowing this technology to become widely used in biomedical studies. For small labs and individual researchers, however, storage and transfer of large amounts of HTS data present a significant challenge. The recent trends in increased sequencing quality and genome coverage can be used to reconsider HTS data storage str...

Comparison of simultaneous static standing balance data on a pressure mat and force plate in typical children and in children with cerebral palsy.

Balance testing is an important component in treatment planning and outcome assessment for children with Cerebral Palsy (CP). Objective measurement for static standing balance is typically conducted in motion labs utilizing force plates; however, a plantar pressure mat may prove to be a viable alternative for this type of balance assessment.

An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics.

DNA fluorescence in situ hybridization (DNA FISH) has emerged as a powerful microscopy technique that allows a unique view into the composition and arrangement of the genetic material in its natural context-be it the cell nucleus in interphase, or chromosomes in metaphase spreads. The core principle of DNA FISH is the ability of fluorescently labeled DNA probes (either double- or single-stranded DNA fragments) to bind to their complementary sequences in situ in cells or tissues, revealing the location of th...

Mapping molecular HLA typing data to UNOS antigen equivalents.

Histocompatibility labs must convert molecular HLA typing data to antigen equivalencies for entry into the United Network for Organ Sharing (UNOS) UNet system. While an Organ Procurement and Transplantation Network (OPTN) policy document provides general guidelines for conversion, the process is complex because no antigen mapping table is available. We present a UNOS antigen equivalency table for all IPD-IMGT/HLA alleles at the A, B, C, DRB1, DRB3/4/5, DQA1, and DQB1 loci.

An insider's view on how Ki-67, the bright beacon of cell proliferation, became very popular.A tribute to Johannes Gerdes (1950 - 2016).

In July 2016 Johannes Gerdes passed away, 25 years after the Journal of Pathology published a groundbreaking paper on Ki-67. The manuscript has been quoted nearly 1400 times since then.Thomas Scholzen, Christiane Gerlach and Giorgio Cattoretti, former coworkers, collaborators and friends of Hannes present a reconstruction of the scientific ambience of the field in the world and in their labs, anecdoctes of the discovery and a very brief summary of published and unpublished research on Ki-67 as a tribute to ...

Interactive web-based identification and visualization of transcript shared sequences.

We have developed TraC (Transcript Consensus), a web-based tool for detecting and visualizing shared sequences among two or more mRNA transcripts such as splice variants. Results including exon-exon boundaries are returned in a highly intuitive, data-rich, interactive plot that permits users to explore the similarities and differences of multiple transcript sequences. The online tool ( is free to use. The source code is freely available for download (https://github....

National Mosaic Embryo Transfer Practices: A Survey.

The growing use of preimplantation genetic testing (PGT) with in-vitro fertilization has provided clinicians with more information about the genetics of embryos. Embryos, however, sometimes result with a mixed composition of both aneuploid and euploid cells, called "mosaic embryos." The interpretation of these results has varied, leading some clinicians to transfer mosaic embryos and some opt not to. In addition, labs providing PGT for aneuploidy have differing thresholds for determining an embryo aneuploid...

Level of Alcohol Use Associated with HIV Care Continuum Targets in a National U.S. Sample of Persons Living with HIV Receiving Healthcare.

We evaluated associations between levels of alcohol use and HIV care continuum components using national Veterans Aging Cohort Study data for all patients with HIV and AUDIT-C screening (2/1/2008-9/30/2014). Poisson regression models evaluated associations between alcohol use levels (non-drinking, low-, medium-, high-, and very high-level drinking) and: (1) engagement with care (documented CD4 cells/µl or viral load copies/ml labs), (2) ART treatment (≥ 1 prescription), and (3) viral suppression (HIV R...

Lactococcus lactis KR-050L extract suppresses house dust mite induced-atopic skin inflammation through inhibition of keratinocyte and mast cell activation.

Atopic dermatitis (AD) is a chronic inflammatory skin disease, with a steadily increasing prevalence. Lactic acid bacteria (LAB) have been widely used in the food industry and are an attractive option for preventing and treating allergic skin diseases. We previously isolated new LABs including Lactococcus lactis KR-050L from Gajuknamu kimchi, and showed the anti-inflammatory effects of extract of Lactococcus lactis KR-050L culture broth (LLK). In this study, we investigated the effects of LLK on AD.

An economical and efficient method for postmortem DNA sampling in mass fatalities.

In mass fatality events, the need to identify large numbers of deceased persons using DNA can be a significant drain on already overburdened forensic practitioners, both in the field setting and the laboratory. The laboratory may be required to extract DNA from a variety of postmortem sample types, family or direct reference samples related to the missing, and perform matching of these results in a short period of time. While most forensic institutions are well equipped to handle both family and direct refe...

1,2-Diarylethylamine- and Ketamine-Based New Psychoactive Substances.

While phencyclidine (PCP) and ketamine remain the most well-studied and widely known dissociative drugs, a number of other agents have appeared since the late 1950s and early 1960s, when the pharmacological potential of this class was first realized. For example, hundreds of compounds have been pursued as part of legitimate research efforts to explore these agents. Some of these found their way out of the research labs and onto illicit markets of the 1960s and following decades as PCP analogs. Other "illici...

Multi-Scale Structural Design and Biomechanics of the Pistol Shrimp Snapper Claw.

The Arthropoda, the largest phylum of the Animal Kingdom, have successfully evolved to survive various ecological constraints under a wide range of environmental conditions. Central to this survival are the structural designs developed in their exoskeletons and their raptorial appendages for protection and hunting. One such example, the pistol shrimp, is a shallow-water crustacean that is well-known for its aggressive hunting behavior, using its snapper claw to trigger the nucleation of cavitation bubbles t...

Reproducibility of data-driven Parkinson's disease subtypes for clinical research.

PD subtype classification systems attempt to address heterogeneity in PD, a widely recognized feature of the disease with implications in prognosis and therapeutic development. There is no consensus on a valid PD subtype classification system, and its use in clinical research is sparse. Reproducibility has not been systematically assessed as a step for the validation of a PD subtype classification system. We aimed at assessing reproducibility of previously published data-driven PD subtypes classification sy...

FEBio finite element models of the human lumbar spine.

Finite element analysis has proven to be a viable method for assessing many structure-function relationships in the human lumbar spine. Several validated models of the spine have been published, but they typically rely on commercial packages and are difficult to share between labs. The goal of this study is to present the development of the first open-access models of the human lumbar spine in FEBio. This modeling framework currently targets three deficient areas in the field of lumbar spine modeling: 1) op...

Juvenile Myoclonic Epilepsy Presenting with Neurocognitive Impairment: A Case Report.

Juvenile myoclonic epilepsy (JME) is a genetically and clinically diverse disorder which is characterized by myoclonic jerks, usually after awakening from sleep. It affects both genders equally and manifests during the second decade of life. The various precipitating factors include stress, light, sleep deprivation, and alcohol. A history of morning clumsiness supported by typical electroencephalography (EEG) findings, together with a normal clinical examination all point towards a diagnosis of JME. We pres...

Molecular Design Towards Controlling Charge Transport.

Organic electronics generally deals with bulk, statistically averaged electrical properties of organic materials. Single molecular electronic devices can then be viewed as linkers to these bulk properties. However, controlling charge transport in single molecular systems still remains a formidable task which has prevented proliferation of these systems from research labs to household electronics. This concept article provides a general overview of the recent advances made by our group in the field. We will ...

C-NMR dereplication of Garcinia extracts: Predicted chemical shifts as reliable databases.

Usually isolated from Garcinia (Clusiaceae) or Hypericum (Hypericaceae) species, some Polycyclic Polyprenylated AcylPhloroglucinols (PPAPs) have been recently reported as potential research tools for immunotherapy. Aiming at exploring the chemodiversity of PPAPs amongst Garcinia genus, a dereplication process suitable for such natural compounds has been developed. Although less sensitive than mass spectrometry, NMR spectroscopy is perfectly reproducible and allows stereoisomers distinction, justifying the d...

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