Phosphoinositide acyl chain saturation drives CD8+ effector T cell signaling and function.

How lipidome changes support CD8+ effector T (Teff) cell differentiation is not well understood. Here we show that, although naive T cells are rich in polyunsaturated phosphoinositides (PIPn with 3-4 double bonds), Teff cells have unique PIPn marked by saturated fatty acyl chains (0-2 double bonds). PIPn are precursors for second messengers. Polyunsaturated phosphatidylinositol bisphosphate (PIP2) exclusively supported signaling immediately upon T cell antigen receptor activation. In late Teff cells, activity of phospholipase C-γ1, the enzyme that cleaves PIP2 into downstream mediators, waned, and saturated PIPn became essential for sustained signaling. Saturated PIP was more rapidly converted to PIP2 with subsequent recruitment of phospholipase C-γ1, and loss of saturated PIPn impaired Teff cell fitness and function, even in cells with abundant polyunsaturated PIPn. Glucose was the substrate for de novo PIPn synthesis, and was rapidly utilized for saturated PIP2 generation. Thus, separate PIPn pools with distinct acyl chain compositions and metabolic dependencies drive important signaling events to initiate and then sustain effector function during CD8+ T cell differentiation.

Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance.

Conventional immunization strategies will likely be insufficient for the development of a broadly neutralizing antibody (bnAb) vaccine for HIV or other difficult pathogens because of the immunological hurdles posed, including B cell immunodominance and germinal center (GC) quantity and quality. We found that two independent methods of slow delivery immunization of rhesus monkeys (RMs) resulted in more robust T follicular helper (TFH) cell responses and GC B cells with improved Env-binding, tracked by longitudinal fine needle aspirates. Improved GCs correlated with the development of >20-fold higher titers of autologous nAbs. Using a new RM genomic immunoglobulin locus reference, we identified differential IgV gene use between immunization modalities. Ab mapping demonstrated targeting of immunodominant non-neutralizing epitopes by conventional bolus-immunized animals, whereas slow delivery-immunized animals targeted a more diverse set of epitopes. Thus, alternative immunization strategies can enhance nAb development by altering GCs and modulating the immunodominance of non-neutralizing epitopes.

A dynamic kinetic model captures cell-free metabolism for improved butanol production.

Cell-free systems are useful tools for prototyping metabolic pathways and optimizing the production of various bioproducts. Mechanistically-based kinetic models are uniquely suited to analyze dynamic experimental data collected from cell-free systems and provide vital qualitative insight. However, to date, dynamic kinetic models have not been applied with rigorous biological constraints or trained on adequate experimental data to the degree that they would give high confidence in predictions and broadly demonstrate the potential for widespread use of such kinetic models. In this work, we construct a large-scale dynamic model of cell-free metabolism with the goal of understanding and optimizing butanol production in a cell-free system. Using a combination of parameterization methods, the resultant model captures experimental metabolite measurements across two experimental conditions for nine metabolites at timepoints between 0 and 24 h. We present analysis of the model predictions, provide recommendations for butanol optimization, and identify the aldehyde/alcohol dehydrogenase as the primary bottleneck in butanol production. Sensitivity analysis further reveals the extent to which various parameters are constrained, and our approach for probing valid parameter ranges can be applied to other modeling efforts.

Role of π-Radical Localization on Thermally Stable Cross-Links Between Polycyclic Aromatic Hydrocarbons.

The thermal stability of cross-links between polycyclic aromatic hydrocarbons (PAHs) is critical for understanding the formation of soot pollutants, graphite, and carbon blacks. Recently, a variety of different π-radicals have been directly imaged and suggested to enable thermally stable bonding; however, a systematic study of reactivity has been lacking. In this work, we use density functional theory to study the reactivity of PAH π-radicals. The Mulliken spin densities are initially used to categorize the different classes of localization, and the bond energy is computed to determine the degree of localization required for thermal stability. The results showed that the bond energies of PAHs are strongly correlated with the calculated spin densities, but bond energies do not exist with the bond lengths due to significant rearrangement and steric effects during bond formation. A threshold for π-radical localization is suggested that will be stable in combustion and pyrolysis environments of ρMα ≥ 0.5. Finally, the formation of multicenter bonds between localized and delocalized π-radicals was investigated using the nudge elastic band (NEB) scan, and it was found that only delocalized π-radicals provided local energy minima. These results show that the localization of π-radicals is critical for the formation of thermally stable single-center bonds between aromatic radicals.

Calcium-triggered fusion of lipid membranes is enabled by amphiphilic nanoparticles.

Lipid membrane fusion is an essential process for a number of critical biological functions. The overall process is thermodynamically favorable but faces multiple kinetic barriers along the way. Inspired by nature's engineered proteins such as SNAP receptor [soluble N-ethylmale-imide-sensitive factor-attachment protein receptor (SNARE)] complexes or viral fusogenic proteins that actively promote the development of membrane proximity, nucleation of a stalk, and triggered expansion of the fusion pore, here we introduce a synthetic fusogen that can modulate membrane fusion and equivalently prime lipid membranes for calcium-triggered fusion. Our fusogen consists of a gold nanoparticle functionalized with an amphiphilic monolayer of alkanethiol ligands that had previously been shown to fuse with lipid bilayers. While previous efforts to develop synthetic fusogens have only replicated the initial steps of the fusion cascade, we use molecular simulations and complementary experimental techniques to demonstrate that these nanoparticles can induce the formation of a lipid stalk and also drive its expansion into a fusion pore upon the addition of excess calcium. These results have important implications in general understanding of stimuli-triggered fusion and the development of synthetic fusogens for biomedical applications.

Enhancing humoral immunity via sustained-release implantable microneedle patch vaccination.

Sustained exposure of lymphoid tissues to vaccine antigens promotes humoral immunity, but traditional bolus immunizations lead to rapid antigen clearance. We describe a technology to tailor vaccine kinetics in a needle-free platform translatable to human immunization. Solid pyramidal microneedle (MN) arrays were fabricated with silk fibroin protein tips encapsulating a stabilized HIV envelope trimer immunogen and adjuvant, supported on a dissolving polymer base. Upon brief skin application, vaccine-loaded silk tips are implanted in the epidermis/upper dermis where they release vaccine over a time period determined by the crystallinity of the silk matrix. Following MN immunization in mice, Env trimer was released over 2 wk in the skin, correlating with increased germinal center (GC) B cell responses, a ∼1,300-fold increase in serum IgG titers and a 16-fold increase in bone marrow (BM) plasma cells compared with bolus immunization. Thus, implantable MNs provide a practical means to substantially enhance humoral immunity to subunit vaccines.

π-Diradical Aromatic Soot Precursors in Flames.

Soot emitted from incomplete combustion of hydrocarbon fuels contributes to global warming and causes human disease. The mechanism by which soot nanoparticles form within hydrocarbon flames is still an unsolved problem in combustion science. Mechanisms proposed to date involving purely chemical growth are limited by slow reaction rates, whereas mechanisms relying on solely physical interactions between molecules are limited by weak intermolecular interactions that are unstable at flame temperatures. Here, we show evidence for a reactive π-diradical aromatic soot precursor imaged using non-contact atomic force microscopy. Localization of π-electrons on non-hexagonal rings was found to allow for Kekulé aromatic soot precursors to possess a triplet diradical ground state. Barrierless chain reactions are shown between these reactive sites, which provide thermally stable aromatic rim-linked hydrocarbons under flame conditions. Quantum molecular dynamics simulations demonstrate physical condensation of aromatics that survive for tens of picoseconds. Bound internal rotors then enable the reactive sites to find each other and become chemically cross-linked before dissociation. These species provide a rapid, thermally stable chain reaction toward soot nanoparticle formation and could provide molecular targets for limiting the emission of these toxic combustion products.

Effect of treatment center volume on outcomes in gastroenteropancreatic neuroendocrine tumor patients.

BACKGROUND: Medical centers with varying levels of expertise treat gastroenteropancreatic neuroendocrine tumors (GEP-NETs), which are relatively rare tumors. This study assesses the impact of center volume on GEP-NET treatment outcomes. METHODS: We used the Surveillance, Epidemiology, and End Results (SEER) registry linked to Medicare claims data. The data includes patients diagnosed between 1995 and 2010 who had no health maintenance organization (HMO) coverage, participated in Medicare parts A and B, were older than 65 at diagnosis, had tumor differentiation information, and had no secondary cancer. We identified medical centers at which patients received GEP-NET treatment (surgery, chemotherapy, somatostatin analogues, or radiation therapy) using Medicare claims data. Center volume was divided into 3 tiers - low, medium, and high - based on the number of unique GEP-NET patients treated by a medical center over 2 years. We used Kaplan-Meier curves and Cox regression to assess the association between volume and disease-specific survival. RESULTS: We identified 899 GEP-NET patients, of whom 37, 45, and 18% received treatment at low, medium volume, and high-volume centers, respectively. Median disease-specific survival for patients at low and medium tiers were 1.4 years and 5.3 years, respectively, but was not reached for patients at high volume centers. Results showed that patients treated at high volume centers had better survival than those treated in low volume centers (HR: 0.63, 95% CI: 0.4-0.9), but showed no difference in outcomes between medium and high-volume centers. CONCLUSIONS: Our results suggest that for these increasingly common tumors, referral to a tertiary care center may be indicated. Physicians caring for GEP-NET patients should consider early referral to high volume centers.

Comparison of V̇o2peak and V̇o2max at Different Sampling Intervals in Collegiate Wrestlers.

ABSTRACT: Sell, KM, Ghigiarelli, JJ, Prendergast, JM, Ciani, GJ, Martin, J, and Gonzalez, AM. Comparison of V̇o2peak and V̇o2max at different sampling intervals in collegiate wrestlers. J Strength Cond Res 35(10): 2915-2917, 2021-The purpose of this study was to determine the difference in the highest oxygen uptake (V̇o2peak) achieved during a maximal effort graded exercise test (GXT) in 20 NCAA Division I male wrestlers using breath-by-breath (BbB) values to the maximal uptake averaged across different time- and breath-based oxygen consumption sampling intervals (V̇o2max). Given the need for aerobic fitness and anaerobic power in wrestling, the accurate determination of V̇o2max is imperative if it is to be used to identify current aerobic fitness and consequently guide sport-specific training programs to address weaknesses in this area. Each subject completed a cycle ergometer GXT during which BbB data were collected via indirect calorimetry and V̇o2peak determined as the highest value. V̇o2max was considered as the average value of 3-s, 5-s, 10-s, 20-s, and 30-s sampling, and 3-b, 7-b, and 11-b sampling during the GXT. Results show that the BbB V̇o2peak was significantly higher than the 5-s, 10-s, 20-s, 30-s, and 11-b (p < 0.05). The 3-b V̇o2max was significantly higher than the 20-s and 30-s V̇o2max values (p < 0.05). The underestimation of V̇o2peak for each time-based interval sampling approach compared with BbB V̇o2peak is consistent with previous research, but the comparison of BbB data to breath-based interval sampling has not been widely addressed in prior research. The use of a 7-b sampling interval for the determination of V̇o2max may be a promising approach to minimize the systematic errors associated with BbB or less frequent sampling intervals, but future research is needed to further support its application with elite athletic populations such as those in the current study.

From shape to meaning: Evidence for multiple fast feedforward hierarchies of concept processing in the human brain.

A number of fMRI studies have provided support for the existence of multiple concept representations in areas of the brain such as the anterior temporal lobe (ATL) and inferior parietal lobule (IPL). However, the interaction among different conceptual representations remains unclear. To better understand the dynamics of how the brain extracts meaning from sensory stimuli, we conducted a human high-density electroencephalography (EEG) study in which we first trained participants to associate pseudowords with various animal and tool concepts. After training, multivariate pattern classification of EEG signals in sensor and source space revealed the representation of both animal and tool concepts in the left ATL and tool concepts within the left IPL within 250 â€‹ms. Finally, we used Granger Causality analyses to show that orthography-selective sensors directly modulated activity in the parietal-tool selective cluster. Together, our results provide evidence for distinct but parallel "perceptual-to-conceptual" feedforward hierarchies in the brain.

Reactivity of Polycyclic Aromatic Hydrocarbon Soot Precursors: Kinetics and Equilibria.

The thermodynamics and kinetics of cross-linking reactions between PAHs of various reactive edge types that are observed in soot precursors are explored using density functional theory. The forward rate constants confirm that reactions involving aryl σ-radicals are faster than others, but rate constants for reactions between aryl σ-radicals and localized π-radicals can be as large or even larger than for two aryl σ-radicals. However, rates for all cross-linking reactions between small PAHs are likely too slow to explain soot formation. The equilibrium constants show that reactions involving σ and π-radical PAHs are the most favorable at flame temperatures. Equilibrium constants for larger PAHs show that the ability to form bonded-and-stacked structures results in enhanced equilibrium constants for the reaction of two large localized π-radicals compared to those for other edge types. This suggests that combined physical and chemical interactions between larger π-radical PAHs could be important in flame environments.

Topology of Disordered 3D Graphene Networks.

Disordered carbons comprise graphene fragments assembled into three-dimensional networks. It has long been debated whether these networks contain positive curvature, as seen in fullerenes, negative curvature, as proposed for the schwarzite structures, or zero curvature, as in ribbons. We present a mesh-based approach to analyze the topology of a set of nanoporous and glassy carbon models that accurately reproduce experimental properties. Although all three topological elements are present, negatively curved structures dominate. At the atomic level, analysis of local environments shows that sp- and sp^{3}-bonded atoms are associated with line defects and screw dislocations that resolve topological complexities such as termination of free edges and stacking of low curvature regions into ribbons. These results provide insight into the synthesis of porous carbon materials, glassy carbon and the graphitizability of carbon materials.

Validity of the DSM-5 anxious distress specifier for major depressive disorder.

BACKGROUND: DSM-5 introduced the anxious distress specifier in recognition of the clinical significance of anxiety in depressed patients. Recent studies that supported the validity of the specifier did not use measures that were designed to assess the criteria of the specifier but instead approximated the DSM-5 criteria from scales that were part of an existing data base. In the present report from the Rhode Island Methods to Improve Diagnostic Assessment and Services (MIDAS) project, we examined the validity of the specifier diagnosed with a semistructured interview. METHODS: Two hundred sixty patients with a principal diagnosis of major depressive disorder were evaluated with semistructured diagnostic interviews. The patients were rated on clinician rating scales of depression, anxiety and irritability, and completed self-report measures. RESULTS: Approximately three-quarters of the depressed patients met the criteria for the anxious distress specifier. Patients with anxious distress had a higher frequency of anxiety disorders, particularly panic disorder and generalized anxiety disorder, as well as higher scores on measures of anxiety, depression, and anger. The patients meeting the anxious distress subtype reported higher rates of drug use disorders, poorer functioning during the week before the evaluation, and poorer coping ability compared to the patients who did not meet the anxious distress specifier. Moreover, anxious distress was associated with poorer functioning and coping after controlling for the presence of an anxiety disorder. CONCLUSIONS: The results of the present study indicate that anxious distress is common in depressed patients and support the validity of the DSM-5 anxious distress specifier.

An Ontology and Semantic Web Service for Quantum Chemistry Calculations.

The purpose of this article is to present an ontology, termed OntoCompChem, for quantum chemistry calculations as performed by the Gaussian quantum chemistry software, as well as a semantic web service named MolHub. The OntoCompChem ontology has been developed based on the semantics of concepts specified in the CompChem convention of Chemical Markup Language (CML) and by extending the Gainesville Core (GNVC) ontology. MolHub is developed in order to establish semantic interoperability between different tools used in quantum chemistry and thermochemistry calculations, and as such is integrated into the J-Park Simulator (JPS)-a multidomain interactive simulation platform and expert system. It uses the OntoCompChem ontology and implements a formal language based on propositional logic as a part of its query engine, which verifies satisfiability through reasoning. This paper also presents a NASA polynomial use-case scenario to demonstrate semantic interoperability between Gaussian and a tool for thermodynamic data calculations within MolHub.

Nanostructure of Gasification Charcoal (Biochar).

In this work, we investigate the molecular composition and nanostructure of gasification charcoal (biochar) by comparing it with heat-treated fullerene arc-soot. Using ultrahigh resolution Fourier transform ion-cyclotron resonance and laser desorption ionization time-of-flight mass spectrometry, Raman spectroscopy, and high resolution transmission electron microscopy we analyzed charcoal of low tar content obtained from gasification. Mass spectrometry revealed no magic number fullerenes such as C60 or C70 in the charcoal. The positive molecular ion m/ z 701, previously considered a graphitic part of the nanostructure, was found to be a breakdown product of pyrolysis and not part of the nanostructure. A higher mass distribution of ions similar to that found in thermally treated fullerene soot indicates that they share a nanostructure. Recent insights into the formation of all carbon fullerenes reveal that conditions in charcoal formation are not optimal for the formation of fullerenes, but instead, curved carbon structures coalesce into fulleroid-like structures. Microscopy and spectroscopy support such a stacked, fulleroid-like nanostructure, which was explored using reactive molecular dynamics simulations.

Optical band gap of cross-linked, curved, and radical polyaromatic hydrocarbons.

In this work, the optical band gaps of polycyclic aromatic hydrocarbons (PAHs) crosslinked via an aliphatic bond, curved via pentagon integration and with radical character were computed using density functional theory. A variety of different functionals were benchmarked against optical band gaps (OBGs) measured by ultraviolet-visible spectroscopy with HSE06 being most accurate with a percentage error of 6% for a moderate basis set. Pericondensed aromatics with different symmetries were calculated with this improved functional providing new scaling relationships for the OBG versus size. Further calculations showed crosslinks cause a small decrease in the OBG of the monomers which saturates after 3-4 crosslinks. Curvature in PAHs was shown to increase the optical band gap due to the resulting change in hybridisation of the system, but this increase saturated at larger sizes. The increase in OBG between a flat PAH and a strained curved one was shown to be equivalent to a difference of several rings in size for pericondensed aromatic systems. The effect of σ-radicals on the optical band gap was also shown to be negligible, however, π-radicals were found to decrease the band gap by ∼0.5 eV. These findings have applications in understanding the molecular species involved in soot formation.

Sphere Encapsulated Monte Carlo: Obtaining Minimum Energy Configurations of Large Aromatic Systems.

We introduce a simple global optimization approach that is able to find minimum energy configurations of clusters containing aromatic molecules. The translational and rotational perturbations required in Monte Carlo-based methods often lead to unrealistic configurations within which two or more molecular rings intersect, causing many of the computational steps to be rejected and the optimization process to be inefficient. Here we develop a modification of the basin-hopping global optimization procedure tailored to tackle problems with intersecting molecular rings. Termed the Sphere Encapsulated Monte Carlo (SEMC) method, this method introduces sphere-based rearrangement and minimization steps at each iteration, and its performance is shown through the exploration of potential energy landscapes of polycyclic aromatic hydrocarbon (PAH) clusters, systems of interest in combustion and astrophysics research. The SEMC method provides clusters that are accurate to 5% mean difference of the minimum energy at a 10-fold speed up compared to previous work using advanced molecular dynamics simulations. Importantly, the SEMC method captures key structural characteristics and molecular size partitioning trends as measured by the molecular radial distances and coordination numbers. The advantages of the SEMC method are further highlighted in its application to previously unstudied heterogeneous PAH clusters.

A crash in visual processing: Interference between feedforward and feedback of successive targets limits detection and categorization.

The human visual system can detect objects in streams of rapidly presented images at presentation rates of 70 Hz and beyond. Yet, target detection is often impaired when multiple targets are presented in quick temporal succession. Here, we provide evidence for the hypothesis that such impairments can arise from interference between "top-down" feedback signals and the initial "bottom-up" feedforward processing of the second target. Although it is has been recently shown that feedback signals are important for visual detection, this "crash" in neural processing affected both the detection and categorization of both targets. Moreover, experimentally reducing such interference between the feedforward and feedback portions of the two targets substantially improved participants' performance. The results indicate a key role of top-down re-entrant feedback signals and show how their interference with a successive target's feedforward process determine human behavior. These results are not just relevant for our understanding of how, when, and where capacity limits in the brain's processing abilities can arise, but also have ramifications spanning topics from consciousness to learning and attention.