drMD: Molecular Dynamics for Experimentalists.

Molecular dynamics (MD) simulations can be used by protein scientists to investigate a wide array of biologically relevant properties such as the effects of mutations on a protein's structure and activity, or probing intermolecular interactions with small molecule substrates or other macromolecules. Within the world of computational structural biology, several programs have become popular for running these simulations, but each of these programs requires a significant time investment from the researcher to run even simple simulations. Even after learning how to run and analyse simulations, many elements remain a "black box.

Installation of an organocatalyst into a protein scaffold creates an artificial Stetterase.

Using a protein scaffold covalently functionalised with a thiamine-inspired N-heterocyclic carbene (NHC), we created an artificial Stetterase (ArtiSt) which catalyses a stereoselective, intramolecular Stetter reaction. We demonstrate that ArtiSt functions under ambient conditions with low catalyst loading. Furthermore, activity can be increased >20 fold by altering the protein scaffold.

Environmental and molecular control of tissue-specific ionocyte differentiation in zebrafish.

Organisms cope with environmental fluctuations and maintain fitness in part via reversible phenotypic changes (acclimation). Aquatic animals are subject to dramatic seasonal fluctuations in water salinity, which affect osmolarity of their cells and consequently cellular function. Mechanosensory lateral line hair cells detect water motion for swimming behavior and are especially susceptible to salinity changes due to their direct contact with the environment.

Using Text Messaging Surveys in General Practice Research to Engage With People From Low-Income Groups: Multi-Methods Study.

Background: SMS text messages through mobile phones are a common means of interpersonal communication. SMS text message surveys are gaining traction in health care and research due to their feasibility and patient acceptability. However, challenges arise in implementing SMS text message surveys, especially when targeting marginalized populations, because of barriers to accessing phones and data as well as communication difficulties.

Applications of cell free protein synthesis in protein design.

In protein design, the ultimate test of success is that the designs function as desired. Here, we discuss the utility of cell free protein synthesis (CFPS) as a rapid, convenient and versatile method to screen for activity. We champion the use of CFPS in screening potential designs.

Activated dormant stem cells recover spermatogenesis in chemoradiotherapy-induced infertility.

Male infertility is a recognized side effect of chemoradiotherapy. Extant spermatogonial stem cells (SSCs) may act as originators for any subsequent recovery. However, which type of SSCs, the mechanism by which they survive and resist toxicity, and how they act to restart spermatogenesis remain largely unknown.

Regulators of rDNA array morphology in fission yeast.

Nucleolar morphology is a well-established indicator of ribosome biogenesis activity that has served as the foundation of many screens investigating ribosome production. Missing from this field of study is a broad-scale investigation of the regulation of ribosomal DNA morphology, despite the essential role of rRNA gene transcription in modulating ribosome output. We hypothesized that the morphology of rDNA arrays reflects ribosome biogenesis activity.

Changes in opioid prescribing during the COVID-19 pandemic in England: an interrupted time-series analysis in the OpenSAFELY-TTP cohort.

Background: The COVID-19 pandemic disrupted health-care delivery, including difficulty accessing in-person care, which could have increased the need for strong pharmacological pain relief. Due to the risks associated with overprescribing of opioids, especially to vulnerable populations, we aimed to quantify changes to measures during the COVID-19 pandemic, overall, and by key subgroups.

Methods: For this interrupted time-series analysis study conducted in England, with National Health Service England approval, we used routine clinical data from more than 20 million general practice adult patients in OpenSAFELY-TPP, which is a a secure software platform for analysis of electronic health records.

Computational design of Periplasmic binding protein biosensors guided by molecular dynamics.

Periplasmic binding proteins (PBPs) are bacterial proteins commonly used as scaffolds for substrate-detecting biosensors. In these biosensors, effector proteins (for example fluorescent proteins) are inserted into a PBP such that the effector protein's output changes upon PBP-substate binding. The insertion site is often determined by comparison of PBP apo/holo crystal structures, but random insertion libraries have shown that this can miss the best sites.

Warming drives dissolved organic carbon export from pristine alpine soils.

Despite decades of research, the influence of climate on the export of dissolved organic carbon (DOC) from soil remains poorly constrained, adding uncertainty to global carbon models. The limited temporal range of contemporary monitoring data, ongoing climate reorganisation and confounding anthropogenic activities muddy the waters further. Here, we reconstruct DOC leaching over the last ~14,000 years using alpine environmental archives (two speleothems and one lake sediment core) across 4° of latitude from Te Waipounamu/South Island of Aotearoa New Zealand.

Cell extrusion - a novel mechanism driving neural crest cell delamination.

Neural crest cells (NCC) comprise a heterogeneous population of cells with variable potency, that contribute to nearly every tissue and organ system throughout the body. Considered unique to vertebrates, NCC are transiently generated within the dorsolateral region of the neural plate or neural tube, during neurulation. Their delamination and migration are crucial events in embryo development as the differentiation of NCC is heavily influenced by their final resting locations.

The impact of COVID-19 on medication reviews in English primary care. An OpenSAFELY-TPP analysis of 20 million adult electronic health records.

Aims: The COVID-19 pandemic caused significant disruption to routine activity in primary care. Medication reviews are an important primary care activity ensuring safety and appropriateness of prescribing. A disruption could have significant negative implications for patient care.

TIMED-Design: flexible and accessible protein sequence design with convolutional neural networks.

Sequence design is a crucial step in the process of designing or engineering proteins. Traditionally, physics-based methods have been used to solve for optimal sequences, with the main disadvantages being that they are computationally intensive for the end user. Deep learning-based methods offer an attractive alternative, outperforming physics-based methods at a significantly lower computational cost.

Environmental and molecular control of tissue-specific ionocyte differentiation in zebrafish.

Organisms adjust their physiology to cope with environmental fluctuations and maintain fitness. These adaptations occur via genetic changes over multiple generations or through acclimation, a set of reversible phenotypic changes that confer resilience to the individual. Aquatic organisms are subject to dramatic seasonal fluctuations in water salinity, which can affect the function of lateral line mechanosensory hair cells.

On-chip Raman spectroscopy of live single cells for the staging of oesophageal adenocarcinoma progression.

The absence of early diagnosis contributes to oesophageal cancer being the sixth most common cause of global cancer-associated deaths, with a 5-year survival rate of < 20%. Barrett's oesophagus is the main pre-cancerous condition to adenocarcinoma development, characterised by the morphological transition of oesophageal squamous epithelium to metaplastic columnar epithelium. Early tracking and treatment of oesophageal adenocarcinoma could dramatically improve with diagnosis and monitoring of patients with Barrett's Oesophagus.

Encoding a magic state with beyond break-even fidelity.

To run large-scale algorithms on a quantum computer, error-correcting codes must be able to perform a fundamental set of operations, called logic gates, while isolating the encoded information from noise. We can complete a universal set of logic gates by producing special resources called magic states. It is therefore important to produce high-fidelity magic states to conduct algorithms while introducing a minimal amount of noise to the computation.

A streamlined Emergency Department approach to moderate risk chest pain in patients with no pre-existing coronary artery disease: A pilot study.

Objective: Moderate risk patients with chest pain and no previously diagnosed coronary artery disease (CAD) who present to ED require further risk stratification. We hypothesise that management of these patients by ED physicians can decrease length of stay (LOS), without increasing patient harm.

Methods: A prospective pilot study with comparison to a pre-intervention control group was performed on patients presenting with chest pain to an ED in Perth, Australia between May and October 2021, following the introduction of a streamlined guideline consisting of ED led decision making and early follow up.

Correction: Batch-produced, GIS-informed range maps for birds based on provenanced, crowd-sourced data inform conservation assessments.

[This corrects the article DOI: 10.1371/journal.pone.

Urinary miRNAs Predict Metastasis in Patients With Clinically Localized Clear Cell Renal Cell Carcinoma Treated With Nephrectomy.

Purpose: Patients with clear cell renal cell carcinoma (ccRCC) might develop metastasis after surgery with curative intent. We aimed to characterize the expression levels of microRNAs in the urine (UmiRNAs) of patients before and after nephrectomy to determine the impact of UmiRNAs expression in the emergence of metastases.

Methods: We prospectively collected pre- and post-nephrectomy urine samples from 117 patients with clinically localized and locally advanced ccRCC.

Contemporary Patients Have Better Perioperative Outcomes Following Cytoreductive Nephrectomy: A Multi-institutional Analysis of 1272 Consecutive Patients.

Objective: To evaluate factors associated with perioperative outcomes in a multi-institutional cohort of patients treated with cytoreductive nephrectomy (CN).

Methods: Data were analyzed for metastatic renal cell carcinoma patients treated with CN at 6 tertiary academic centers from 2005 to 2019. Outcomes included: Clavien-Dindo complications, mortality, length of hospitalization, 30-day readmission rate, and time to systemic therapy.

Pharmacokinetic Analysis of Intravenous Push Cefepime in Burn Patients with Augmented Renal Clearance.

Patients with augmented renal clearance (ARC) are a subset of critically ill patients including burn patients that exhibit increased renal elimination of medications beyond that of similarly injured patients. Currently approved maximum regimens of medications primarily eliminated by the kidney, such as cefepime (>90% unchanged in the urine), may be inadequate (eg, compromising the bactericidal activity of cefepime) in patients with ARC. Due to recent resource limitations, centers have changed infusion practices of commonly prescribed medications to intravenous push (IVP), potentially exacerbating the problem of maintaining bactericidal cefepime concentrations.