The solar dynamo begins near the surface.

The magnetic dynamo cycle of the Sun features a distinct pattern: a propagating region of sunspot emergence appears around 30° latitude and vanishes near the equator every 11 years (ref. 1). Moreover, longitudinal flows called torsional oscillations closely shadow sunspot migration, undoubtedly sharing a common cause2. Contrary to theories suggesting deep origins of these phenomena, helioseismology pinpoints low-latitude torsional oscillations to the outer 5-10% of the Sun, the near-surface shear layer3,4. Within this zone, inwardly increasing differential rotation coupled with a poloidal magnetic field strongly implicates the magneto-rotational instability5,6, prominent in accretion-disk theory and observed in laboratory experiments7. Together, these two facts prompt the general question: whether the solar dynamo is possibly a near-surface instability. Here we report strong affirmative evidence in stark contrast to traditional models8 focusing on the deeper tachocline. Simple analytic estimates show that the near-surface magneto-rotational instability better explains the spatiotemporal scales of the torsional oscillations and inferred subsurface magnetic field amplitudes9. State-of-the-art numerical simulations corroborate these estimates and reproduce hemispherical magnetic current helicity laws10. The dynamo resulting from a well-understood near-surface phenomenon improves prospects for accurate predictions of full magnetic cycles and space weather, affecting the electromagnetic infrastructure of Earth.

Allele-specific activation, enzyme kinetics, and inhibitor sensitivities of EGFR exon 19 deletion mutations in lung cancer.

Oncogenic mutations within the epidermal growth factor receptor (EGFR) are found in 15 to 30% of all non-small-cell lung carcinomas. The term exon 19 deletion (ex19del) is collectively used to refer to more than 20 distinct genomic alterations within exon 19 that comprise the most common EGFR mutation subtype in lung cancer. Despite this heterogeneity, clinical treatment decisions are made irrespective of which EGFR ex19del variant is present within the tumor, and there is a paucity of information regarding how individual ex19del variants influence protein structure and function. Herein, we identified allele-specific functional differences among ex19del variants attributable to recurring sequence and structure motifs. We built all-atom structural models of 60 ex19del variants identified in patients and combined molecular dynamics simulations with biochemical and biophysical experiments to analyze three ex19del mutations (E746_A750, E746_S752 > V, and L747_A750 > P). We demonstrate that sequence variation in ex19del alters oncogenic cell growth, dimerization propensity, enzyme kinetics, and tyrosine kinase inhibitor (TKI) sensitivity. We show that in contrast to E746_A750 and E746_S752 > V, the L747_A750 > P variant forms highly active ligand-independent dimers. Enzyme kinetic analysis and TKI inhibition experiments suggest that E746_S752 > V and L747_A750 > P display reduced TKI sensitivity due to decreased adenosine 5'-triphosphate Km. Through these analyses, we propose an expanded framework for interpreting ex19del variants and considerations for therapeutic intervention.

Demographic Correlates of Endometriosis Diagnosis Among United States Women Aged 15-50.

OBJECTIVE: To compare demographic characteristics of women with and without a diagnosis of endometriosis. DESIGN: Data were collected from the National Survey of Family Growth-a publicly available survey designed and administered by the Centers for Disease Control, which uses a nationally-representative sample of the United States population. Univariate data were reported as survey-weighted percentages and means and were analyzed using chi-square, t tests, and logistic regression. Analyses accounted for complex survey design. SETTING: United States. PARTICIPANTS: Interviews were conducted with 6141 female respondents, aged 15 to 50, between 2017 and 2019. INTERVENTIONS: Data were collected through in-person interviews. RESULTS: Nationally, 5.7% reported a diagnosis of endometriosis (95% CI 4.6-6.9%). Those with endometriosis were older, with a mean age of 39 (95% CI 38.1-39.9), compared to 31.7 (95% CI 31.2-32.2) among those without (p <.0005). Endometriosis diagnosis was significantly associated with race. Compared to non-Hispanic White women, Hispanic women had an adjusted odds ratio (aOR) of 0.37 (95% CI 0.21-0.65) for diagnosis of endometriosis, and non-Hispanic Black women had an aOR of 0.54 (95% CI 0.35-0.84). We also observed a difference in diagnosis by health insurance: compared to those with private insurance or Medi-Gap coverage, those with Medicare or military insurance had an aOR for endometriosis diagnosis of 2.49 (95% CI 1.36-4.55). Finally, compared to those with less than a high school education, those who had completed high school or greater had an aOR for endometriosis diagnosis of 2.84 (95% CI 1.15-6.99). CONCLUSION: These disparities in endometriosis diagnosis suggest that intersecting barriers may preclude certain groups from accessing timely endometriosis diagnosis and management. Further studies are warranted to explore these hypothesis-generating data and to identify and address specific barriers to equitable endometriosis diagnosis and management.

Abortion policies at the bedside: incorporating an ethical framework in the analysis and development of abortion legislation.

About 6% of women in the world live in countries that ban all abortions, and 34% in countries that only allow abortion to preserve maternal life or health. In the USA, over the last decades-even before Dobbs v. Jackson Women's Health Organization overturned the federal right to abortion-various states have sought to restrict abortion access. Often times, this legislation has been advanced based on legislators' personal moral values. At the bedside, in contrast, provision of abortion care should adhere to the normative principles of medical ethics and reproductive justice, centreing patients and their individual reproductive intentions and desires. Abortion regulations, through their influence on patients and providers, may facilitate or impede such ethical care at the bedside. In this paper, we present a framework to model how abortion legislation should fit into the patient-provider relationship and to clarify the dynamics by which legislation may affect healthcare encounters. Our proposed framework serves as a tool to analyse the ethical impact of abortion regulations. We propose a model for assessing abortion policies based not on legislators' or advocates' individual moral claims, but on the shared, normative framework of clinical medical ethics. Through contrasting case studies, we demonstrate how a robust normative ethical framework can recentre patients and their reproductive needs. Our model is one way to account for-and safeguard-patients' diverse viewpoints and needs in the development of abortion policy, and it can serve to ground narratives for advocacy by healthcare workers and their professional organisations.

BCL::Conf: Improved Open-Source Knowledge-Based Conformation Sampling Using the Crystallography Open Database.

We previously described BCL::Conf, a knowledge-based conformation sampling algorithm utilizing a small molecule fragment rotamer library derived from the Cambridge Structural Database (CSD, license required), as a component of the BioChemical Library (BCL) cheminformatics toolkit. This paper describes substantial improvements made to the BCL::Conf algorithm and a transition to a rotamer library derived from molecules in the Crystallography Open Database (COD, no license required). We demonstrate the performance of the new BCL::Conf on native conformer recovery in the Platinum dataset of high-quality protein-ligand complexes. This set of 2859 structures has previously been used to assess the performance of over a dozen conformer generation algorithms, including the Conformator, Balloon, RDKit DG, ETKDG, Confab, Frog2, MultiConf-DOCK, CSD conformer generator, ConfGenX-OPSL3 force field, Omega, excalc, iCon, and MOE. These benchmarks suggest that the CSD conformer generator is at the state of the art of reported conformer generators. Our results indicate that the improved BCL::Conf significantly outperforms the CSD conformer generation algorithm at binding conformer recovery across a range of ensemble sizes and with similarly fast rates of conformer generation. BCL::Conf is now distributed with the COD-derived rotamer library and is free for academic use. The BCL can be downloaded at http://meilerlab.org/bclcommons for Windows, Linux, or Apple operating systems. BCL::Conf can now also be accessed via webserver at http://meilerlab.org/bclconf.

General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps.

The BioChemical Library (BCL) is an academic open-source cheminformatics toolkit comprising ligand-based virtual high-throughput screening (vHTS) tools such as quantitative structure-activity/property relationship (QSAR/QSPR) modeling, small molecule flexible alignment, small molecule conformer generation, and more. Here, we expand the capabilities of the BCL to include structure-based virtual screening. We introduce two new score functions, BCL-AffinityNet and BCL-DockANNScore, based on novel distance-dependent signed protein-ligand atomic property correlations. Both metrics are conventional feed-forward dropout neural networks trained on the new descriptors. We demonstrate that BCL-AffinityNet is one of the top performing score functions on the comparative assessment of score functions 2016 affinity prediction and affinity ranking tasks. We also demonstrate that BCL-AffinityNet performs well on the CSAR-NRC HiQ I and II test sets. Furthermore, we demonstrate that BCL-DockANNScore is competitive with multiple state-of-the-art methods on the docking power and screening power tasks. Finally, we show how our models can be decomposed into human-interpretable pharmacophore maps to aid in hit/lead optimization. Altogether, our results expand the utility of the BCL for structure-based scoring to aid small molecule discovery and design. BCL-AffinityNet, BCL-DockANNScore, and the pharmacophore mapping application, as well as the remainder of the BCL cheminformatics toolkit, are freely available with an academic license at the BCL Commons site hosted on http://meilerlab.org/.

Modulation of the proteoglycan receptor PTPσ promotes recovery after spinal cord injury.

Contusive spinal cord injury leads to a variety of disabilities owing to limited neuronal regeneration and functional plasticity. It is well established that an upregulation of glial-derived chondroitin sulphate proteoglycans (CSPGs) within the glial scar and perineuronal net creates a barrier to axonal regrowth and sprouting. Protein tyrosine phosphatase σ (PTPσ), along with its sister phosphatase leukocyte common antigen-related (LAR) and the nogo receptors 1 and 3 (NgR), have recently been identified as receptors for the inhibitory glycosylated side chains of CSPGs. Here we find in rats that PTPσ has a critical role in converting growth cones into a dystrophic state by tightly stabilizing them within CSPG-rich substrates. We generated a membrane-permeable peptide mimetic of the PTPσ wedge domain that binds to PTPσ and relieves CSPG-mediated inhibition. Systemic delivery of this peptide over weeks restored substantial serotonergic innervation to the spinal cord below the level of injury and facilitated functional recovery of both locomotor and urinary systems. Our results add a new layer of understanding to the critical role of PTPσ in mediating the growth-inhibited state of neurons due to CSPGs within the injured adult spinal cord.

BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping.

Small molecule flexible alignment is a critical component of both ligand- and structure-based methods in computer-aided drug discovery. Despite its importance, the availability of high-quality flexible alignment software packages is limited. Here, we present BCL::MolAlign, a freely available property-based molecular alignment program. BCL::MolAlign accommodates ligand flexibility through a combination of pregenerated conformers and on-the-fly bond rotation. BCL::MolAlign converges on alignment poses by sampling the relative orientations of mutually matching atom pairs between molecules through Monte Carlo Metropolis sampling. Across six diverse ligand data sets, BCL::MolAlign flexible alignment outperforms MOE, ROCS, and FLEXS in recovering native ligand binding poses. Moreover, the BCL::MolAlign alignment score is more predictive of ligand activity than maximum common substructure similarity across 10 data sets. Finally, on a recently published benchmark set of 20 high quality congeneric ligand-protein complexes, BCL::MolAlign is able to recover a larger fraction of native binding poses than maximum common substructure-based alignment and RosettaLigand. BCL::MolAlign can be obtained as part of the Biology and Chemistry Library (BCL) software package freely with an academic license or can be accessed via Web server at http://meilerlab.org/index.php/servers/molalign .

Conductive-AFM Patterning of Organic Semiconductors.

Using a conductive atomic force microscope (c-AFM) redox-writing technique, it is shown that it is possible to locally, and reversibly, pattern conducting, and nonconducting features on the surface of a low molecular weight aniline-based organic (semi)-conductor thin film using a commercial c-AFM. It is shown that application of a voltage between the tip and sample causes localized redox reactions at the surface without damage.

Interpreting medicine: lessons from a Spanish-language clinic.

Caring for patients is an act of interpretation: we labor to understand the significance of a particular symptom and, when we have reached a diagnosis, we convert our medical jargon into plain language for the benefit of the patient. Caring for patients of limited English proficiency-a population that needs a very literal form of interpretation-underscores this lesson. Working with predominantly Spanish-speaking patients has shown me the importance of bearing witness to patients' struggles and has brought me to realize that good physicians must work to forge a common language with all their patients, not only with those who do not speak English.

Approximating Projections of Conformational Boltzmann Distributions with AlphaFold2 Predictions: Opportunities and Limitations.

Protein thermodynamics is intimately tied to biological function and can enable processes such as signal transduction, enzyme catalysis, and molecular recognition. The relative free energies of conformations that contribute to these functional equilibria evolved for the physiology of the organism. Despite the importance of these equilibria for understanding biological function and developing treatments for disease, computational and experimental methods capable of quantifying the energetic determinants of these equilibria are limited to systems of modest size. Recently, it has been demonstrated that the artificial intelligence system AlphaFold2 can be manipulated to produce structurally valid protein conformational ensembles. Here, we extend these studies and explore the extent to which AlphaFold2 contact distance distributions can approximate projections of the conformational Boltzmann distributions. For this purpose, we examine the joint probability distributions of inter-residue contact distances along functionally relevant collective variables of several protein systems. Our studies suggest that AlphaFold2 normalized contact distance distributions can correlate with conformation probabilities obtained with other methods but that they suffer from peak broadening. We also find that the AlphaFold2 contact distance distributions can be sensitive to point mutations. Overall, we anticipate that our findings will be valuable as the community seeks to model the thermodynamics of conformational changes in large biomolecular systems.

Analysis of EGFR binding hotspots for design of new EGFR inhibitory biologics.

The epidermal growth factor (EGF) receptor (EGFR) is activated by the binding of one of seven EGF-like ligands to its ectodomain. Ligand binding results in EGFR dimerization and stabilization of the active receptor conformation subsequently leading to activation of downstream signaling. Aberrant activation of EGFR contributes to cancer progression through EGFR overexpression/amplification, modulation of its positive and negative regulators, and/or activating mutations within EGFR. EGFR targeted therapeutic antibodies prevent dimerization and interaction with endogenous ligands by binding the ectodomain of EGFR. However, these antibodies have had limited success in the clinic, partially due to EGFR ectodomain resistance mutations, and are only applicable to a subset of patients with EGFR-driven cancers. These limitations suggest that alternative EGFR targeted biologics need to be explored for EGFR-driven cancer therapy. To this end, we analyze the EGFR interfaces of known inhibitory biologics with determined structures in the context of endogenous ligands, using the Rosetta macromolecular modeling software to highlight the most important interactions on a per-residue basis. We use this analysis to identify the structural determinants of EGFR targeted biologics. We suggest that commonly observed binding motifs serve as the basis for rational design of new EGFR targeted biologics, such as peptides, antibodies, and nanobodies.

Iterative methods for Navier-Stokes inverse problems.

Even when the partial differential equation underlying a physical process can be evolved forward in time, the retrospective (backward in time) inverse problem often has its own challenges and applications. Direct adjoint looping (DAL) is the defacto approach for solving retrospective inverse problems, but it has not been applied to deterministic retrospective Navier-Stokes inverse problems in 2D or 3D. In this paper, we demonstrate that DAL is ill-suited for solving retrospective 2D Navier-Stokes inverse problems. Alongside DAL, we study two other iterative methods: simple backward integration (SBI) and the quasireversible method (QRM). As far as we know, our iterative SBI approach is novel, while iterative QRM has previously been used. Using these three iterative methods, we solve two retrospective inverse problems: 1D Korteweg-de Vries-Burgers (decaying nonlinear wave) and 2D Navier-Stokes (unstratified Kelvin-Helmholtz vortex). In both cases, SBI and QRM reproduce the target final states more accurately and in fewer iterations than DAL. We attribute this performance gap to additional terms present in SBI and QRM's respective backward integrations which are absent in DAL.

Computer-Aided Design and Biological Evaluation of Diazaspirocyclic D4R Antagonists.

Parkinson's disease (PD) is a neurodegenerative disorder characterized by the progressive loss of dopaminergic neurons in the substantia nigra, resulting in motor dysfunction. Current treatments are primarily centered around enhancing dopamine signaling or providing dopamine replacement therapy and face limitations such as reduced efficacy over time and adverse side effects. To address these challenges, we identified selective dopamine receptor subtype 4 (D4R) antagonists not previously reported as potential adjuvants for PD management. In this study, a library screening and artificial neural network quantitative structure-activity relationship (QSAR) modeling with experimentally driven library design resulted in a class of spirocyclic compounds to identify candidate D4R antagonists. However, developing selective D4R antagonists suitable for clinical translation remains a challenge.

Longitudinal impact of a residency-based postplacental levonorgestrel intrauterine device insertion program: Expulsion rates in years 1, 2, and 3.

OBJECTIVE: To evaluate expulsion rates in the first 3 years of an academic postplacental levonorgestrel intrauterine device (LNG-IUD) insertion program. STUDY DESIGN: Retrospective case series, January 2016 to December 2018. We measured LNG-IUD expulsion rates by 12 weeks postpartum. RESULTS: Of 235 LNG-IUD insertions, in years 1, 2, and 3, expulsion rates were 11/39 (28%), 9/94 (10%), and 15/102 (15%) (p = 0.03). After vaginal delivery, manual insertion was associated with a higher expulsion rate than ring-forceps (10/28 [36%] vs 17/105 [16%], p = 0.04). CONCLUSIONS: LNG-IUD expulsion rates decreased after program year 1, suggesting program maturity may be associated with a lower expulsion risk.

Opportunities in high-speed atomic force microscopy.

The atomic force microscope (AFM) has become integrated into standard characterisation procedures in many different areas of research. Nonetheless, typical imaging rates of commercial microscopes are still very slow, much to the frustration of the user. Developments in instrumentation for "high-speed AFM" (HSAFM) have been ongoing since the 1990s, and now nanometer resolution imaging at video rate is readily achievable. Despite thorough investigation of samples of a biological nature, use of HSAFM instruments to image samples of interest to materials scientists, or to carry out AFM lithography, has been minimal. This review gives a summary of different approaches to and advances in the development of high-speed AFMs, highlights important discoveries made with new instruments, and briefly discusses new possibilities for HSAFM in materials science.

Orientability of the minor director of homeotropically aligned smectic-a elastomers in external mechanical fields.

We present studies on bulk smectic-A copolymer networks with end-on attached homeotropically oriented mesogens that show spontaneous optical biaxiality at room temperature. Orthoscopic and conoscopic investigations under uniaxial extension in the layer planes give first evidence of the orientability of the minor director in mechanical fields yielding biaxial monodomains with 3-d orientational long-range order of all three principle axes. This is an important step towards the synthesis of permanently oriented biaxial monodomain elastomers for which highly interesting mechanical and optical properties are expected.

Approximating conformational Boltzmann distributions with AlphaFold2 predictions.

Protein dynamics are intimately tied to biological function and can enable processes such as signal transduction, enzyme catalysis, and molecular recognition. The relative free energies of conformations that contribute to these functional equilibria are evolved for the physiology of the organism. Despite the importance of these equilibria for understanding biological function and developing treatments for disease, the computational and experimental methods capable of quantifying them are limited to systems of modest size. Here, we demonstrate that AlphaFold2 contact distance distributions can approximate conformational Boltzmann distributions, which we evaluate through examination of the joint probability distributions of inter-residue contact distances along functionally relevant collective variables of several protein systems. Further, we show that contact distance probability distributions generated by AlphaFold2 are sensitive to points mutations thus AF2 can predict the structural effects of mutations in some systems. We anticipate that our approach will be a valuable tool to model the thermodynamics of conformational changes in large biomolecular systems.

Contraception and Abortion Care for People Living With HIV: A Clinical Guide for Reproductive Health Practitioners.

People capable of pregnancy are disproportionately affected by HIV. Family planning needs and services are often unmet in this population, and clinical care guidelines regarding contraceptive options and abortion care are not well elucidated. Individuals living with HIV often face unique barriers in accessing contraception and abortion services due to internalized stigma, medically complex care (eg, drug-drug interactions, adverse effects of antiretroviral therapy), and distrust of health care providers. There is also a lack of clarity among reproductive health, primary, and infectious disease care providers on best-practice contraceptive counseling and contraceptive care for individuals living with HIV, given limited opportunities to enhance expertise in reproductive infectious disease. In this review, we summarize existing and updated evidence and clinical considerations regarding contraceptive counseling and abortion care in this population.

Macrocyclic Octapeptide Binding and Inferences on Protein Substrate Binding to Histone Deacetylase 6.

Histone deacetylases (HDACs) are essential for the regulation of myriad biological processes, and their aberrant function is implicated in cancer, neurodegeneration, and other diseases. The cytosolic isozyme HDAC6 is unique among the greater family of deacetylases in that it contains two catalytic domains, CD1 and CD2. HDAC6 CD2 is responsible for tubulin deacetylase and tau deacetylase activities, inhibition of which is a key goal as new therapeutic approaches are explored. Of particular interest as HDAC inhibitors are naturally occurring cyclic tetrapeptides such as Trapoxin A or HC Toxin, or the cyclic depsipeptides Largazole and Romidepsin. Even more intriguing are larger, computationally designed macrocyclic peptide inhibitors. Here, we report the 2.0 Å resolution crystal structure of HDAC6 CD2 complexed with macrocyclic octapeptide 1. Comparison with the previously reported structure of the complex with macrocyclic octapeptide 2 reveals that a potent thiolate-zinc interaction made by the unnatural amino acid (S)-2-amino-7-sulfanylheptanoic acid contributes to nanomolar inhibitory potency for each inhibitor. Apart from this zinc-binding residue, octapeptides adopt strikingly different overall conformations and make few direct hydrogen bonds with the protein. Intermolecular interactions are dominated by water-mediated hydrogen bonds; in essence, water molecules appear to cushion the enzyme-octapeptide interface. In view of the broad specificity observed for protein substrates of HDAC6 CD2, we suggest that the binding of macrocyclic octapeptides may mimic certain features of the binding of macromolecular protein substrates.