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. RESULTS: We find that for functional annotation of proteins, as represented by Gene Ontology (GO) terms, direct fine-tuning of language models on a simple classification loss has an immediate positive impact on protein embedding quality. Fine-tuned embeddings show stronger performance as representations for K-nearest neighbor classifiers, reaching stronger performance for GO annotation than even directly comparable fine-tuned classifiers, while maintaining interpretability through protein similarity comparisons. They also maintain their quality in related tasks, such as rediscovering protein families with clustering. AVAILABILITY AND IMPLEMENTATION: github.com/mofradlab/go_metric.

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. The ability of ophthalmic surgeons to achieve satisfactory system registration in each model was assessed. Subsequently, navigational accuracy was recorded using defined anatomical landmarks as ground truth. Qualitative feedback on the system was also attained. RESULTS: Three independent surgeons participated in the study, one junior trainee, one fellow and one consultant. Across models, more senior participants were able to achieve a smaller system-generated registration error in a fewer number of attempts. When assessing navigational accuracy, submillimetre accuracy was achieved for the majority of points (16 landmarks per model, per participant). Qualitative surgeon feedback suggested acceptability of the technology, although interference from mobile phones near the operative field was noted. CONCLUSION: This study suggests the feasibility and accuracy of EM-IGS in a preclinical validation study for orbital surgery using patient specific 3D-printed skulls. This preclinical study provides the foundation for clinical studies to explore the safety and effectiveness of this technology.

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. Thus, the significance of improvements for these models remains unclear. RESULTS: The Gene Benchmarking database is the first effort to provide an easy-to-use and configurable hub for the learning and evaluation of gene annotation models. It provides easy access to pre-specified datasets and takes the non-trivial steps of preprocessing and filtering all data according to custom presets using a web interface. The GO bench web application can also be used to evaluate and display any trained model on leaderboards for annotation tasks. AVAILABILITY AND IMPLEMENTATION: The GO Benchmarking dataset is freely available at www.gobench.org. Code is hosted at github.com/mofradlab, with repositories for website code, core utilities and examples of usage (Supplementary Section S.7). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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. This bundle was composed of 90 fibres with a 14 µm diameter. This fibre bundle was first coated with polylactic acid (PLA) in order to produce a polymer-coated continuous stainless steel filament, with diameters tailored in the range from 0.5 to 0.9 mm. These filaments were then used to print composite parts using the material extrusion (MEX) technique. The SSF's volume fraction (Vf) was controlled in the printed composite structures in the range from 4 to 30 Vf%. This was facilitated by incorporating a novel polymer pressure vent into the printer nozzle, which allowed the removal of excess polymer. This thus enabled the control of the metal fibre content within the printed composites as the print layer height was varied in the range from 0.22 to 0.48 mm. It was demonstrated that a lower layer height yielded a more homogeneous distribution of steel fibres within the PLA polymer matrix. The PLA-SSF composites were assessed to evaluate their mechanical performance, volume fraction, morphology and porosity. Composite porosities in the range of 2-21% were obtained. Mechanical testing demonstrated that the stainless steel composites exhibited a twofold increase in interlaminar shear strength (ILSS) and a fourfold increase in its tensile strength compared with the PLA-only polymer prints. When comparing the 4 and 30 Vf% composites, the latter exhibited a significant increase in both the tensile strength and modulus. The ILSS values obtained for the steel composites were up to 28.5 MPa, which is significantly higher than the approximately 13.8 MPa reported for glass fibre-reinforced PLA composites.

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. Despite the fundamental role of the NPC in cell and nuclear biology, the detailed mechanisms underlying how the NPC works have remained largely unknown. The critical components of NPCs enabling their selective barrier function are the natively unfolded phenylalanine- and glycine-rich proteins called "FG-nucleoporins" (FG Nups). These intrinsically disordered proteins are tethered to the inner wall of the NPC, and together form a highly dynamic polymeric meshwork whose physicochemical conformation has been the subject of intense debate. We observed that specific sequence features (called largest positive like-charge regions, or lpLCRs), characterized by extended subsequences that only possess positively charged amino acids, significantly affect the conformation of FG Nups inside the NPC. Here we investigate how the presence of lpLCRs affects the interactions between FG Nups and their interactions with the cargo complex. We combine coarse-grained molecular dynamics simulations with time-resolved force distribution analysis to disordered proteins to explore the behavior of the system. Our results suggest that the number of charged residues in the lpLCR domain directly governs the average distance between Phe residues and the intensity of interaction between them. As a result, the number of charged residues within lpLCR determines the balance between the hydrophobic interaction and the electrostatic repulsion and governs how dense and disordered the hydrophobic network formed by FG Nups is. Moreover, changing the number of charged residues in an lpLCR domain can interfere with ultrafast and transient interactions between FG Nups and the cargo complex.

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. Further analysis revealed that cells depleted of USP37 harbored increased levels of the replication stress and DNA damage markers γH2AX and 53BP1 in response to perturbed replication. Depletion of USP37 also reduced cellular proliferation and led to increased sensitivity to agents that induce replication stress. Underlying the increased sensitivity, we found that the checkpoint kinase 1 is destabilized in the absence of USP37, attenuating its function. We further demonstrated that USP37 deubiquitinates checkpoint kinase 1, promoting its stability. Together, our results establish that USP37 is required beyond S-phase entry to promote the efficiency and fidelity of replication. These data further define the role of USP37 in the regulation of cell proliferation and contribute to an evolving understanding of USP37 as a multifaceted regulator of genome stability.

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. Although most studies have been focused on analyzing the conformation and function of FG Nups from a biophysical standpoint, some recent studies have investigated the sequence-function relationship of FG Nups, with a few investigating amino acid sequences of a large number of FG Nups to understand common characteristics that might enable their function. Previously, we identified an evolutionarily conserved feature in FG Nup sequences, which are extended subsequences with low charge density, containing only positive charges, and located toward the N-terminus of FG Nups. We named these patterns longest positive like charge regions (lpLCRs). These patterns are specific to positively charged residues, and negatively charged residues do not demonstrate such a pattern. In this study, we compare FG Nups with other disordered proteins obtained from the DisProt and UniProt database in terms of presence of lpLCRs. Our results show that the lpLCRs are virtually exclusive to FG Nups and are not observed in other disordered proteins. Also, lpLCRs are what differentiate FG Nups from DisProt proteins in terms of charge distribution, meaning that excluding lpLCRs from the sequences of FG Nups make them similar to DisProt proteins in terms of charge distribution. We also previously showed the biophysical effect of lpLCRs in conformation of FG Nups. The results of this study are in line with our previous findings and imply that lpLCRs are virtually exclusive and functionally significant characteristics of FG Nups and nucleocytoplasmic transport.

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 2.5 ± 0.8% for healthy male users while converting the removed energy into 0.25 ± 0.02 watts of electrical power. By comparing two loading profiles, we demonstrate that the timing and magnitude of energy removal are vital for successful metabolic cost reduction.

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

Anthropogenic CO2 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 (AT) measurements can be used to directly determine the calcification rate, but they are time-consuming and require large sample volumes. Herein, we describe an automated and transportable flow-through system that can conduct continuous AT measurement using an ion sensitive field effect transistor (ISFET) - Ag/AgCl sensor and three different reference materials. The response time, stability, and uncertainty of our system were evaluated by comparing AT values of calibrated reference materials to those calculated by our system. Our system requires only small amounts of seawater (<10 mL) and a short time per sample (<5 min) to produce results with a relative uncertainty of less than 0.1% (approx. 2.2 µmol kg-1). This system is expected to facilitate easy and rapid in-situ measurement of AT. Continuous AT measurements would enable us to determine short-term calcification responses to changes in light or temperature and improve our understanding of the metabolic mechanisms of creatures such as corals.

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. This review focuses on the enhanced mechanical performance obtained through the printing of fibre-reinforced polymer composites, using the fused filament fabrication (FFF) 3D printing technique. The uses of both short and continuous fibre-reinforced polymer composites are reviewed. Finally, examples of some applications of FFF printed polymer composites using robotic processes are highlighted.

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. This viewpoint considers the impact of the role of the external clinical advisor by using extracts from an external clinical advisor's report to show how a power imbalance can be enacted in ACC decision making processes. Also considered are the way that the normal checks and balances in the system, particularly those provided by the Health & Disability Commissioner, are bypassed in most cases. Finally, a recommendation is made to potential external clinical advisors to precisely following the standards set by the Medical Council in all cases when writing reports for ACC.

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

APC/CCdh1 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/CCdh1 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 SCFßTRCP ubiquitin ligase, promotes efficient S-phase entry, and is important for cellular proliferation during otherwise unperturbed cell cycles. We also find that prolonged Chk1 activity in late S/G2 inhibits Cdh1 accumulation. In addition to promoting control of APC/CCdh1 activity by facilitating Cdh1 destruction, we find that Chk1 also antagonizes activity of the ligase by perturbing the interaction between Cdh1 and the APC/C. Overall, these data suggest that the rise and fall of Chk1 activity contributes to the regulation of APC/CCdh1 activity that enhances the replication process.

Analysing Sr isotopes in low-Sr samples such as single insects with inductively coupled plasma tandem mass spectrometry using N2 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 N2 O as a reaction gas for accurately determining Sr isotopes in insects with Sr < 100 ng. METHODS: Strontium isotopes were determined in solution mode using ICP-MS/MS with 0.14 L/min N2 O as a reaction gas to convert Sr+ into SrO+ for in-line separation of 87 Sr from 87 Rb. The Sr isotope reference standards NIST SRM 987, NIST SRM 1570a and NIST SRM 1547 were used to assess accuracy and reproducibility. Ten insect species collected from the wild as a proof-of-principle application were analysed for Sr concentration and Sr isotopes. RESULTS: Using ICP-MS/MS we show for the first time that internal mass bias correction of 87 Sr16 O/86 Sr16 O based on 88 Sr16 O/86 Sr16 O works to give for NIST SRM 987 a 87 Sr/86 Sr ratio of 0.7101 ± 0.012 (RSD = 0.17%) and for NIST SRM 1570a a 87 Sr/86 Sr ratio of 0.7100 ± 0.009 (RSD = 0.12%), which are within error of the accepted values. The first 87 Sr/86 Sr ratio of NIST SRM 1547 is 0.7596 ± 0.0014. Strontium analyses were run on 0.8 mL of 0.25-0.5 ppb Sr, which equates to 2-4 ng of Sr. Strontium isotope analysis with a precision of >99.8% can be achieved with in-line separation of 87 Sr from 87 Rb at least up to solutions with 25 ppb Rb. CONCLUSIONS: A minimum of 5 mg of insect tissue is required for Sr isotope analysis. This new ICP-MS/MS method enables Sr isotope analysis in single insects, allowing population-scale studies to be feasible and making possible applications with time-critical uses such as biosecurity.

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. The pHOS system was validated using Phaeodactylum tricornutum cultured with continuous illumination of 110 µmole quanta m-2 s-1 at 25°C. Furthermore, simultaneous measurements of carbon and oxygen flux using the pHOS-MIMS and photon flux based on spectral absorption were carried out to explore the kinetics of Φ in P. tricornutum during its acclimation from low to high light (110 to 750 µmole quanta m-2 s-1). Comparing results at 0 and 24 hours, we observed strong decreases in cellular chlorophyll a (0.58 to 0.21 pg cell-1), Fv/Fm (0.71 to 0.59) and maximum ΦCO2 (0.019 to 0.004) and ΦO2 (0.028 to 0.007), confirming the transition toward high light acclimation. The Φ time-series indicated a non-synchronized acclimation response between carbon uptake and oxygen evolution, which has been previously inferred based on transcriptomic changes for a similar experimental design with the same diatom that lacked physiological data. The integrated pHOS-MIMS system can provide simultaneous carbon and oxygen measurements accurately, and at the time-resolution required to resolve high-resolution carbon and oxygen physiological dynamics.

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). Within this temperature and salinity range, using purified mCP and a novel thermostated spectrophotometric device, the pH on the total scale (pHT) can be calculated from direct measurements of the absorbance ratio R of the dye in natural samples as[Formula: see text] Based on the mCP characterization in these extended conditions, the temperature and salinity dependence of the molar absorptivity ratios and - [Formula: see text] of purified mCP is described by the following functions: e 1 = -0.004363 + 3.598 × 10-5 T, e 3/e 2 = -0.016224 + 2.42851 × 10-4 T + 5.05663 × 10-5(S - 35), and - [Formula: see text] = -319.8369 + 0.688159 S -0.00018374 S 2 + (10508.724 - 32.9599 S + 0.059082S 2) T-1 + (55.54253 - 0.101639 S) ln T -0.08112151T. This work takes the characterisation of mCP beyond the currently available ranges of 278.15 K ≤ T ≤ 308.15 K and 20 ≤ S ≤ 40 in natural seawater, thereby allowing high quality pHT measurements in polar systems.

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. However, as far as we are aware, all current studies have been conducted using neural cells propagated on non-neuromimetic substrates that fail to represent the mechano-elastic properties of brain and spinal cord microenvironments. Accordingly, it can be predicted that such data is of less translational and physiological relevance than that derived from cells grown in neuromimetic environments. Therefore, we have performed the first test of magnetofection technology (enhancing MNP delivery using applied magnetic fields with significant potential for therapeutic application) and its utility in genetically engineering neural stem cells (NSCs; a population of high clinical relevance) propagated in biomimetic hydrogels. We demonstrate magnetic field application safely enhances MNP mediated transfection of NSCs grown as 3D spheroid structures in collagen which more closely replicates the intrinsic mechanical and structural properties of neural tissue than routinely used hard substrates. Further, as it is well known that MNP uptake is mediated by endocytosis we also investigated NSC membrane activity grown on both soft and hard substrates. Using high resolution scanning electron microscopy we were able to prove that NSCs display lower levels of membrane activity on soft substrates compared to hard, a finding which could have particular impact on MNP mediated engineering strategies of cells propagated in physiologically relevant systems.

An ethnobotanical survey of medicinal plants used in the East Sepik province of Papua New Guinea.

BACKGROUND: Rapid modernization in the East Sepik (ES) Province of Papua New Guinea (PNG) is resulting in a decrease in individuals knowledgeable in medicinal plant use. Here we report a synthesis and comparison of traditional medicinal plant use from four ethnically distinct locations in the ES Province and furthermore compare them to two other previous reports of traditional plant use from different provinces of PNG. METHODS: This manuscript is based on an annotated combination of four Traditional Medicines (TM) survey reports generated by University of Papua New Guinea (UPNG) trainees. The surveys utilized a questionnaire titled "Information sheet on traditional herbal preparations and medicinal plants of PNG", administered in the context of the TM survey project which is supported by WHO, US NIH and PNG governmental health care initiatives and funding. Regional and transregional comparison of medicinal plant utilization was facilitated by using existing plant databases: the UPNG TM Database and the PNG Plant Database (PNG Plants) using Bayesian statistical analysis. RESULTS: Medicinal plant use between four distinct dialect study areas in the ES Province of PNG showed that only a small fraction of plants had shared use in each area, however usually utilizing different plant parts, being prepared differently and to treat different medical conditions. Several instances of previously unreported medicinal plants could be located. Medicinally under- and over-utilized plants were found both in the regional reports and in a transregional analysis, thus showing that these medicinal utilization frequencies differ between provinces. CONCLUSIONS: Documentation of consistent plant use argues for efficacy and is particularly important since established and effective herbal medicinal interventions are sorely needed in the rural areas of PNG, and unfortunately clinical validation for the same is often lacking. Despite the existence of a large corpus of medical annotation of plants for PNG, previously unknown medical uses of plants can be uncovered. Furthermore, comparisons of medicinal plant utilization is possible if databases are reformatted for consistencies that allow comparisons. A concerted effort in building easily comparable databases could dramatically facilitate ethnopharmacological analysis of the existing plant diversity.

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. These data provide a foundation for operating the ISFET|Cl-ISE pair in seawater as a pH sensor. In order to obtain the highest quality pH measurements from this sensor, its response to changes in pH and salinity must be properly characterized. Our results indicate near-ideal Nernstian response for both electrodes over a wide range of pH (2-12) and Cl(-) molality (0.01-1). We conclude that the error due to sub-Nernstian response of the cell ISFET|seawater|Cl-ISE over the range of seawater pH and salinity is negligible (<0.0001 pH). The cross sensitivity of the Cl-ISE to Br(-) does not seem to be a significant source of error (<0.003 pH) in seawater media in the salinity range 20-35.