Bacterial community dynamics as a result of growth-yield trade-off and multispecies metabolic interactions toward understanding the gut biofilm niche.

Bacterial communities are ubiquitous, found in natural ecosystems, such as soil, and within living organisms, like the human microbiome. The dynamics of these communities in diverse environments depend on factors such as spatial features of the microbial niche, biochemical kinetics, and interactions among bacteria. Moreover, in many systems, bacterial communities are influenced by multiple physical mechanisms, such as mass transport and detachment forces.

Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities.

The gut microbiome plays a major role in human health; however, little is known about the structural arrangement of microbes and factors governing their distribution. In this work, we present an in silico agent-based model (ABM) to conceptually simulate the dynamics of gut mucosal bacterial communities. We explored how various types of metabolic interactions, including competition, neutralism, commensalism, and mutualism, affect community structure, through nutrient consumption and metabolite exchange.

Fine-tuning protein embeddings for functional similarity evaluation.

Motivation: Proteins with unknown function are frequently compared to better characterized relatives, either using sequence similarity, or recently through similarity in a learned embedding space. Through comparison, protein sequence embeddings allow for interpretable and accurate annotation of proteins, as well as for downstream tasks such as clustering for unsupervised discovery of protein families. However, it is unclear whether embeddings can be deliberately designed to improve their use in these downstream tasks.

Image-guided orbital surgery: a preclinical validation study using a high-resolution physical model.

Objective: Preclinical validation study to assess the feasibility and accuracy of electromagnetic image-guided systems (EM-IGS) in orbital surgery using high-fidelity physical orbital anatomy simulators.

Methods: EM-IGS platform, clinical software, navigation instruments and reference system (StealthStation S8, Medtronic) were evaluated in a mock operating theatre at the Royal Victoria Eye and Ear Hospital, a tertiary academic hospital in Dublin, Ireland. Five high-resolution 3D-printed model skulls were created using CT scans of five anonymised patients with an orbital tumour that previously had a successful orbital biopsy or excision.

Fabrication and Performance of Continuous 316 Stainless Steel Fibre-Reinforced 3D-Printed PLA Composites.

This study investigates the feasibility of 3D printing continuous stainless steel fibre-reinforced polymer composites. The printing study was carried out using 316L stainless steel fibre (SSF) bundles with an approximate diameter of 0.15 mm.

Protecting school communities from COVID-19 and other infectious disease outbreaks: the urgent need for healthy schools in Aotearoa New Zealand.

Nil.

GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations.

Motivation: Gene annotation is the problem of mapping proteins to their functions represented as Gene Ontology (GO) terms, typically inferred based on the primary sequences. Gene annotation is a multi-label multi-class classification problem, which has generated growing interest for its uses in the characterization of millions of proteins with unknown functions. However, there is no standard GO dataset used for benchmarking the newly developed new machine learning models within the bioinformatics community.

The deubiquitinating enzyme USP37 enhances CHK1 activity to promote the cellular response to replication stress.

The deubiquitinating enzyme USP37 is known to contribute to timely onset of S phase and progression of mitosis. However, it is not clear if USP37 is required beyond S-phase entry despite expression and activity of USP37 peaking within S phase. We have utilized flow cytometry and microscopy to analyze populations of replicating cells labeled with thymidine analogs and monitored mitotic entry in synchronized cells to determine that USP37-depleted cells exhibited altered S-phase kinetics.

Nucleoporins' exclusive amino acid sequence features regulate their transient interaction with and selectivity of cargo complexes in the nuclear pore.

Nucleocytoplasmic traffic of nucleic acids and proteins across the nuclear envelop via the nuclear pore complexes (NPCs) is vital for eukaryotic cells. NPCs screen transported macromolecules based on their morphology and surface chemistry. This selective nature of the NPC-mediated traffic is essential for regulating the fundamental functions of the nucleus, such as gene regulation, protein synthesis, and mechanotransduction.

FG nucleoporins feature unique patterns that distinguish them from other IDPs.

FG nucleoporins (FG Nups) are intrinsically disordered proteins and are the putative regulators of nucleocytoplasmic transport. They allow fast, yet selective, transport of molecules through the nuclear pore complex, but the underlying mechanism of nucleocytoplasmic transport is not yet fully discovered. As a result, FG Nups have been the subject of extensive research in the past two decades.

Removing energy with an exoskeleton reduces the metabolic cost of walking.

Evolutionary pressures have led humans to walk in a highly efficient manner that conserves energy, making it difficult for exoskeletons to reduce the metabolic cost of walking. Despite the challenge, some exoskeletons have managed to lessen the metabolic expenditure of walking, either by adding or storing and returning energy. We show that the use of an exoskeleton that strategically removes kinetic energy during the swing period of the gait cycle reduces the metabolic cost of walking by 2.

Development of an automated transportable continuous system to measure the total alkalinity of seawater.

Anthropogenic CO emissions are contributing to global warming and ocean acidification. Rapid and accurate measurements of seawater carbonate chemistry are critical to understand current changes in the ocean and to predict future effects of such changes on marine organisms and ecosystems. Total alkalinity (A) measurements can be used to directly determine the calcification rate, but they are time-consuming and require large sample volumes.

3D Printing of Fibre-Reinforced Thermoplastic Composites Using Fused Filament Fabrication-A Review.

Three-dimensional (3D) printing has been successfully applied for the fabrication of polymer components ranging from prototypes to final products. An issue, however, is that the resulting 3D printed parts exhibit inferior mechanical performance to parts fabricated using conventional polymer processing technologies, such as compression moulding. The addition of fibres and other materials into the polymer matrix to form a composite can yield a significant enhancement in the structural strength of printed polymer parts.

A balanced opinion? Considering the role of the external clinical advisor in ACC processes.

The role of the external clinical advisor is critical to the adjudication of complex claims in the processes of the Accident Compensation Corporation (ACC). This is particularly true of claims for treatment injury that occur during birth, which are often very complicated. In most cases external clinical advisors are non-treating doctors, whose opinion strongly guides the hand of ACC.

Chk1-mediated phosphorylation of Cdh1 promotes the SCF-dependent degradation of Cdh1 during S-phase and efficient cell-cycle progression.

APC/C is a ubiquitin ligase with roles in numerous diverse processes, including control of cellular proliferation and multiple aspects of the DNA damage response. Precise regulation of APC/C activity is central to efficient cell-cycle progression and cellular homeostasis. Here, we have identified Cdh1 as a direct substrate of the replication stress checkpoint effector kinase Chk1 and demonstrate that Chk1-mediated phosphorylation of Cdh1 contributes to its recognition by the SCF ubiquitin ligase, promotes efficient S-phase entry, and is important for cellular proliferation during otherwise unperturbed cell cycles.

Analysing Sr isotopes in low-Sr samples such as single insects with inductively coupled plasma tandem mass spectrometry using N O as a reaction gas for in-line Rb separation.

Rationale: Strontium isotopes are valuable markers of provenance in a range of disciplines. Limited amounts of Sr in low-mass samples such as insects mean that conventional Sr isotope analysis precludes their use for geographic origins in many ecological studies or in applications such as biosecurity. Here we test the viability of using inductively coupled plasma tandem mass spectrometry (ICP-MS/MS) with N O as a reaction gas for accurately determining Sr isotopes in insects with Sr < 100 ng.

Simultaneous quantum yield measurements of carbon uptake and oxygen evolution in microalgal cultures.

The photosynthetic quantum yield (Φ), defined as carbon fixed or oxygen evolved per unit of light absorbed, is a fundamental but rarely determined biophysical parameter. A method to estimate Φ for both net carbon uptake and net oxygen evolution simultaneously can provide important insights into energy and mass fluxes. Here we present details for a novel system that allows quantification of carbon fluxes using pH oscillation and simultaneous oxygen fluxes by integration with a membrane inlet mass spectrometer.

Characterization of meta-Cresol Purple for spectrophotometric pH measurements in saline and hypersaline media at sub-zero temperatures.

Accurate pH measurements in polar waters and sea ice brines require pH indicator dyes characterized at near-zero and below-zero temperatures and high salinities. We present experimentally determined physical and chemical characteristics of purified meta-Cresol Purple (mCP) pH indicator dye suitable for pH measurements in seawater and conservative seawater-derived brines at salinities (S) between 35 and 100 and temperatures (T) between their freezing point and 298.15 K (25 °C).

Nanoengineering neural stem cells on biomimetic substrates using magnetofection technology.

Tissue engineering studies are witnessing a major paradigm shift to cell culture on biomimetic materials that replicate native tissue features from which the cells are derived. Few studies have been performed in this regard for neural cells, particularly in nanomedicine. For example, platforms such as magnetic nanoparticles (MNPs) have proven efficient as multifunctional tools for cell tracking and genetic engineering of neural transplant populations.

Characterization of an ion sensitive field effect transistor and chloride ion selective electrodes for pH measurements in seawater.

Characterization of several potentiometric cells without a liquid junction has been carried out in universal buffer, aqueous HCl, and artificial seawater media. The electrodes studied include Ion Sensitive Field Effect Transistor (ISFET) pH electrodes, and Chloride-Ion Selective Electrodes (Cl-ISE) directly exposed to the solution. These electrodes were compared directly to the conventional hydrogen electrode and silver-silver chloride electrode in order to report the degree to which they obey ideal Nernstian laws.

Elevated CO2 enhances otolith growth in young fish.

A large fraction of the carbon dioxide added to the atmosphere by human activity enters the sea, causing ocean acidification. We show that otoliths (aragonite ear bones) of young fish grown under high CO2 (low pH) conditions are larger than normal, contrary to expectation. We hypothesize that CO2 moves freely through the epithelium around the otoliths in young fish, accelerating otolith growth while the local pH is controlled.

Tracer monitored titrations: measurement of total alkalinity.

We introduce a new titration methodology, tracer monitored titration (TMT), in which analyses are free of volumetric and gravimetric measurements and insensitive to pump precision and reproducibility. Spectrophotometric monitoring of titrant dilution, rather than volume increment, lays the burden of analytical performance solely on the spectrophotometer. In the method described here, the titrant is a standardized mixture of acid-base indicator and strong acid.

Performance of forensic and non-forensic adult psychiatric inpatients on the Test of Memory Malingering.

This study compared performance on the Test of Memory Malingering (TOMM [Tombaugh, T. N. (1996).

Heme oxygenase in experimental intracerebral hemorrhage: the benefit of tin-mesoporphyrin.

The prognosis of intracerebral hemorrhage (ICH) is unfavorable. Beyond immediate mass effect and tissue destruction, ICHs cause additional neuronal loss in a "perifocal reactive zone." Heme in ICH induces heme oxygenase-1 (HO-1), and the action of this enzyme on heme yields ferrous iron, biliverdin, and carbon monoxide.