Revealing the Water Structure at Neutral and Charged Graphene/Water Interfaces through Quantum Simulations of Sum Frequency Generation Spectra.

The structure and dynamics of water at charged graphene interfaces fundamentally influence molecular responses to electric fields with implications for applications in energy storage, catalysis, and surface chemistry. Leveraging the realism of the MB-pol data-driven many-body potential and advanced path-integral quantum dynamics, we analyze the vibrational sum frequency generation (vSFG) spectrum of graphene/water interfaces under varying surface charges. Our quantum simulations reveal a distinctive dangling OH peak in the vSFG spectrum at neutral graphene, consistent with recent experimental findings yet markedly different from those of earlier studies.

Current Status of the MB-pol Data-Driven Many-Body Potential for Predictive Simulations of Water Across Different Phases.

Developing a molecular-level understanding of the properties of water is central to numerous scientific and technological applications. However, accurately modeling water through computer simulations has been a significant challenge due to the complex nature of the hydrogen-bonding network that water molecules form under different thermodynamic conditions. This complexity has led to over five decades of research and many modeling attempts.

Hypothiocyanous acid reductase is critical for host colonization and infection by Streptococcus pneumoniae.

The major human pathogen Streptococcus pneumoniae encounters the immune-derived oxidant hypothiocyanous acid (HOSCN) at sites of colonization and infection. We recently identified the pneumococcal hypothiocyanous acid reductase (Har), a member of the flavoprotein disulfide reductase enzyme family, and showed that it contributes to the HOSCN tolerance of S. pneumoniae in vitro.

Patient and clinician priorities for information on treatment outcomes for advanced ovarian cancer: a Delphi exercise.

Objective: Patients with advanced ovarian cancer face a range of treatment options, and there is unwarranted variation in treatment decision-making between UK providers. Decision support tools that produce data on treatment outcomes as a function of individual patient characteristics, would help both patients and clinicians to make informed, preference- and values-based choices. However, data on treatment outcomes to include in such tools are lacking.

Use of interactive mathematical simulations in Fundamentals of Biochemistry, a LibreText online educational resource, to promote understanding of dynamic reactions.

Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent properties such as memory, consciousness, and recognition of self and non-self. To understand how these interconnected reactions lead to cellular life characterized by activation, inhibition, regulation, homeostasis, and adaptation, computational analyses and simulations are essential, a fact recognized by the biological communities.

Molecular Insights into the Influence of Ions on the Water Structure. I. Alkali Metal Ions in Solution.

In this study, we explore the impact of alkali metal ions (Li, Na, K, Rb, and Cs) on the hydration structure of water using molecular dynamics simulations carried out with MB-nrg potential energy functions (PEFs). Our analyses include radial distribution functions, coordination numbers, dipole moments, and infrared spectra of water molecules, calculated as a function of solvation shells. The results collectively indicate a highly local influence of all of the alkali metal ions on the hydrogen-bond network established by the surrounding water molecules, with the smallest and most densely charged Li ion exerting the most pronounced effect.

Use of Interactive Simulations in Fundamentals of Biochemistry, a LibreText Online Educational Resource, to Promote Understanding of Dynamic Reactions.

Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent properties such as memory, consciousness, and recognition of self and non-self. To understand how these interconnected reactions lead to cellular life characterized by activation, inhibition, regulation, homeostasis, and adaptation, computational analyses and simulations are essential, a fact recognized by the biological communities.

MBX: A many-body energy and force calculator for data-driven many-body simulations.

Many-Body eXpansion (MBX) is a C++ library that implements many-body potential energy functions (PEFs) within the "many-body energy" (MB-nrg) formalism. MB-nrg PEFs integrate an underlying polarizable model with explicit machine-learned representations of many-body interactions to achieve chemical accuracy from the gas to the condensed phases. MBX can be employed either as a stand-alone package or as an energy/force engine that can be integrated with generic software for molecular dynamics and Monte Carlo simulations.

Non-Covalent Interactions Enforce Conformation in Switchable and Water-Soluble Diketopiperazine-Pyridine Foldamers.

To reach their potential as mimics of the dynamic molecules present in biological systems, foldamers must be designed to display stimulus-responsive behavior. Here we report such a foldamer architecture based on alternating pyridine-diketopiperazine linkers. Epimerization is conveniently prevented through a copper-catalyzed coupling protocol.

Uncovering the link between the restriction modification system and LuxS in meningitis isolates.

is capable of randomly switching their genomic DNA methylation pattern between six distinct bacterial subpopulations (A-F) via recombination of a type 1 restriction-modification locus, . These pneumococcal subpopulations exhibit phenotypic changes which favor carriage or invasive disease. In particular, the allele has been associated with increased nasopharyngeal carriage and the downregulation of the gene.

Gynecological malignancies and obesity.

The global pandemic of obesity has had a significant impact on gynecological malignancies, most notably endometrial cancer. It has resulted in worldwide increases in the incidence of endometrial cancer and a change in patient demographics, resulting in more diagnoses than ever before being made in pre-menopausal women, who are often keen to pursue fertility-sparing treatments. Obesity increases the risk of gynecological cancers by creating a pro-carcinogenic environment of unopposed estrogen, hyperinsulinemia, and chronic inflammation.

Interventions for weight reduction in obesity to improve survival in women with endometrial cancer.

Background: This is an updated version of the original Cochrane Review published in Issue 2, 2018. Diagnoses of endometrial cancer are increasing secondary to the rising prevalence of obesity. Obesity plays an important role in promoting the development of endometrial cancer, by inducing a state of unopposed oestrogen excess, insulin resistance and inflammation.

Quantitative SWATH-based proteomic profiling of urine for the identification of endometrial cancer biomarkers in symptomatic women.

Background: A non-invasive endometrial cancer detection tool that can accurately triage symptomatic women for definitive testing would improve patient care. Urine is an attractive biofluid for cancer detection due to its simplicity and ease of collection. The aim of this study was to identify urine-based proteomic signatures that can discriminate endometrial cancer patients from symptomatic controls.

Serum HE4 predicts progestin treatment response in endometrial cancer and atypical hyperplasia: A prognostic study.

Objective: To investigate serum human epididymis-4 (HE4) as a predictive biomarker of intrauterine progestin response in endometrial cancer and atypical endometrial hyperplasia (AEH).

Design: Prospective prognostic factor study.

Setting: Consecutive sample of women attending a tertiary gynaecological oncology centre in northwest England.

Impact of Type 2 Diabetes Mellitus on Endometrial Cancer Survival: A Prospective Database Analysis.

Purpose: Type 2 diabetes mellitus (T2DM) is an established risk factor for endometrial cancer but its impact on endometrial cancer survival outcomes is unclear. The aim of this study was to investigate whether pre-existing T2DM impacts survival outcomes in endometrial cancer.

Patients And Methods: Women diagnosed with endometrial cancer were recruited to a single centre prospective cohort study.

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface.

Strains Isolated From a Single Pediatric Patient Display Distinct Phenotypes.

is the leading cause of bacterial paediatric meningitis after the neonatal period worldwide, but the bacterial factors and pathophysiology that drive pneumococcal meningitis are not fully understood. In this work, we have identified differences in raffinose utilization by isolates of identical serotype and sequence type from the blood and cerebrospinal fluid (CSF) of a single pediatric patient with meningitis. The blood isolate displayed defective raffinose metabolism, reduced transcription of the raffinose utilization pathway genes, and an inability to grow when raffinose was the sole carbon source.

The Role of in the Middle Ear Isolate 947.

The LuxS protein, encoded by , is required for the production of autoinducer 2 (AI-2) in . The AI-2 molecule serves as a quorum sensing signal, and thus regulates cellular processes such as carbohydrate utilisation and biofilm formation, as well as impacting virulence. The role of in biology and lifestyle has been predominantly assessed in the laboratory strain D39.

Protein Catalyzed Capture (PCC) Agents for Antigen Targeting.

The protein catalyzed capture agent (PCC) method is a powerful combinatorial screening strategy for discovering synthetic macrocyclic peptide ligands, called PCCs, to designated protein epitopes. The foundational concept of the PCC method is the use of in situ click chemistry to survey large combinatorial libraries of peptides for ligands to designated biological targets. State-of-the-art PCC screens integrate synthetic libraries of constrained macrocyclic peptides with epitope-specific targeting strategies to identify high-affinity (<100 nM) binders de novo.

Protein-Catalyzed Capture Agents.

Protein-catalyzed capture agents (PCCs) are synthetic and modular peptide-based affinity agents that are developed through the use of single-generation in situ click chemistry screens against large peptide libraries. In such screens, the target protein, or a synthetic epitope fragment of that protein, provides a template for selectively promoting the noncopper catalyzed azide-alkyne dipolar cycloaddition click reaction between either a library peptide and a known ligand or a library peptide and the synthetic epitope. The development of epitope-targeted PCCs was motivated by the desire to fully generalize pioneering work from the Sharpless and Finn groups in which in situ click screens were used to develop potent, divalent enzymatic inhibitors.

Visual attention, biological motion perception, and healthy ageing.

Biological motion perception is the ability of the visual system to perceive complex human movement patterns. The previous studies have shown a direct link between attentional abilities and performance on biological motion tasks, both of which have been shown to deteriorate with age. However, it is not known whether there is a direct link between age-related deficits in biological motion processing and attention.