Ion Funnels for the Masses: Experiments and Simulations with a Simplified Ion Funnel

A modified ion funnel is described. Counterintuitively, increased spacing between electrodes results in enhanced “focusing” of the ions through the funnel. Consequently, the internal diameter (i.d.) of the funnel need not decrease to the conductance limit (as in previous designs). A simple dc-only lens, which also serves as the conductance limit, combined with the natural flow of gas is used to extract the ions from the funnel. Ions with mass to charge ratios varying between 75 and 3000 m/z are passed through the funnel with no apparent discrimination. The funnel can be operated under mild conditions that preserve weakly bound noncovalent complexes. After testing several designs, a thin closely spaced dc lens was found to be the best solution for extracting ions. A simple method for simulating ion trajectories at nonzero pressures based on ion mobility and explicit diffusion is described. This theoretical approach was used to design and calculate ion trajectories for the modified funnel presented here. Finally, the increased spacing between electrodes in the current funnel significantly relaxes machining constraints, reduces cost, and enhances ease of use versus previous funnel designs

Conditionally Combining Robot Skills using Large Language Models

This paper combines two contributions. First, we introduce an extension of the Meta-World benchmark, which we call "Language-World," which allows a large language model to operate in a simulated robotic environment using semi-structured natural language queries and scripted skills described using natural language. By using the same set of tasks as Meta-World, Language-World results can be easily compared to Meta-World results, allowing for a point of comparison between recent methods using Large Language Models (LLMs) and those using Deep Reinforcement Learning. Second, we introduce a method we call Plan Conditioned Behavioral Cloning (PCBC), that allows finetuning the behavior of high-level plans using end-to-end demonstrations. Using Language-World, we show that PCBC is able to achieve strong performance in a variety of few-shot regimes, often achieving task generalization with as little as a single demonstration. We have made Language-World available as open-source software at https://github.com/krzentner/language-world/

Spatial Structuring and Life History Connectivity of Antarctic Silverfish Along the Southern Continental Shelf of the Weddell Sea

A multi-disciplinary approach was employed to examine a physical-biological population hypothesis for a critical forage species, the Antarctic silverfish Pleuragramma antarctica. Caccavo et al. (2018; Sci Rep 8:17856) had shown strong gene flow along the westward Antarctic Slope Current, in addition to spatially recurring length modes that provided evidence for episodic connectivity. In this paper, otolith nucleus chemistry from a subset of fish collected in the southern Weddell Sea as part of a hydrographic survey of the Filchner Trough system was used to test between connectivity scenarios. Nucleus chemistry, which reflects environmental exposure during early life, showed significant spatial structuring despite homogeneity in microsatellite allele frequencies. Mg:Ca and Sr:Ca differentiated length modes, and Mg:Ca showed significant contrasts between Atka Bay, Halley Bay, and Filchner Trough. Physical-biological mechanisms may help reconcile structuring shown by otolith chemistry, length, and abundance data with prior evidence of gene flow. Such mechanisms include self-recruitment shaped by circulation associated with the Filchner Trough, fluctuations in mixing between immigrant and locally recruited fish, and feeding opportunities between inflowing Modified Warm Deep Water and outflowing Ice Shelf Water. The results illustrate how comparisons between multi-disciplinary techniques based on integrated sampling designs that incorporate hydrography can enhance understanding of population structure and connectivity around the Southern Ocean

From Cellular Characteristics to Disease Diagnosis: Uncovering Phenotypes with Supercells

Cell heterogeneity and the inherent complexity due to the interplay of multiple molecular processes within the cell pose difficult challenges for current single-cell biology. We introduce an approach that identifies a disease phenotype from multiparameter single-cell measurements, which is based on the concept of ‘‘supercell statistics’’, a single-cell-based averaging procedure followed by a machine learning classification scheme. We are able to assess the optimal tradeoff between the number of single cells averaged and the number of measurements needed to capture phenotypic differences between healthy and diseased patients, as well as between different diseases that are difficult to diagnose otherwise. We apply our approach to two kinds of single-cell datasets, addressing the diagnosis of a premature aging disorder using images of cell nuclei, as well as the phenotypes of two non-infectious uveitides (the ocular manifestations of Behc¸et’s disease and sarcoidosis) based on multicolor flow cytometry. In the former case, one nuclear shape measurement taken over a group of 30 cells is sufficient to classify samples as healthy or diseased, in agreement with usual laboratory practice. In the latter, our method is able to identify a minimal set of 5 markers that accurately predict Behc¸et’s disease and sarcoidosis. This is the first time that a quantitative phenotypic distinction between these two diseases has been achieved. To obtain this clear phenotypic signature, about one hundred CD8+ T cells need to be measured. Although the molecular markers identified have been reported to be important players in autoimmune disorders, this is the first report pointing out that CD8+ T cells can be used to distinguish two systemic inflammatory diseases. Beyond these specific cases, the approach proposed here is applicable to datasets generated by other kinds of state-of-the-art and forthcoming single-cell technologies, such as multidimensional mass cytometry, single-cell gene expression, and single-cell full genome sequencing techniques.Fil: Candia, Julian Marcelo. University of Maryland; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; ArgentinaFil: Maunu, Ryan. University of Maryland; Estados UnidosFil: Driscoll, Meghan. University of Maryland; Estados UnidosFil: Biancotto, Angélique. National Institutes of Health; Estados UnidosFil: Dagur, Pradeep. National Institutes of Health; Estados UnidosFil: McCoy Jr., J Philip. National Institutes of Health; Estados UnidosFil: Nida Sen, H.. National Institutes of Health; Estados UnidosFil: Wei, Lai. National Institutes of Health; Estados UnidosFil: Maritan, Amos. Università di Padova; ItaliaFil: Cao, Kan. University of Maryland; Estados UnidosFil: Nussenblatt, Robert B. National Institutes of Health; Estados UnidosFil: Banavar, Jayanth R.. University of Maryland; Estados UnidosFil: Losert, Wolfgang. University of Maryland; Estados Unido

The Application of Transformational Leadership Theory to Parenting: Questionnaire Development and Implications for Adolescent Self-Regulatory Efficacy and Life Satisfaction

We draw upon transformational leadership theory to develop an instrument to measure transformational parenting for use with adolescents. First, potential items were generated that were developmentally appropriate and evidence for content validity was provided through the use of focus groups with parents and adolescents. We subsequently provide evidence for several aspects of construct validity of measures derived from the Transformational Parenting Questionnaire (TPQ). Data were collected from 857 adolescents (Mage = 14.70 years), who rated the behaviors of their mothers and fathers. The results provided support for a second-order measurement model of transformational parenting. In addition, positive relationships between mothers’ and fathers’ transformational parenting behaviors, adolescents’ self-regulatory efficacy for physical activity and healthy eating, and life satisfaction were found. The results of this research support the application of transformational leadership theory to parenting behaviors, as well as the construct validity of measures derived from the TPQ. (AUTHORS' ABSTRACT

Cytochromec−Crown Ether Complexes as Supramolecular Catalysts: Cold-Active Synzymes for Asymmetric Sulfoxide Oxidation in Methanol

A series of supramolecular complexes of various cytochrome c proteins with 18-crown-6 derivatives behave as cold-active synzymes in the H_2O_2 oxidation of racemic sulfoxides. This interesting behavior contrasts with native functionality, where the employed proteins act as electron transfer carriers. ESI-MS, UV, CD, and Raman spectroscopic characterizations reveal that four or five 18-crown-6 molecules strongly bind to the surface of the cytochrome c and also that nonnatural low-spin hexacoordinate heme structures are induced in methanol. Significantly, crown ether complexation can convert catalytically inactive biological forms to catalytically active artificial forms. Horse heart, pigeon breast, and yeast cytochromes c all stereoselectively oxidize (S)-isomers of methyl tolyl sulfoxide and related sulfoxides upon crown ether complexation. These supramolecular catalysts show the highest efficiency and enantiomer selectivity at −40 °C in the H_2O_2-dependent sulfoxide oxidation, while oxidative decomposition of the heme moieties predominantly occurs at room temperature. The oxidation reactivity of the employed sulfoxides is apparently related to steric constraints and electrochemical oxidation potentials of their S O bonds. Among the cytochrome c complexes, yeast cytochrome c demonstrates the lowest catalytic activity and degradation reactivity. It has a significantly different protein sequence, suggesting that crown ether complexation effectively activates heme coordination but may additionally alter the native backbone structure. The proper combination of cytochrome c proteins, 18-crown-6 receptors, and external circumstances can be used to successfully generate “protein-based supramolecular catalysts” exhibiting nonbiological reactivities

Decoding the Fucose Migration Product during Mass-Spectrometric analysis of Blood Group Epitopes

Fucose is a signaling carbohydrate that is attached at the end of glycan processing. It is involved in a range of processes, such as the selectin-dependent leukocyte adhesion or pathogen-receptor interactions. Mass-spectrometric techniques, which are commonly used to determine the structure of glycans, frequently show fucose-containing chimeric fragments that obfuscate the analysis. The rearrangement leading to these fragments—often referred to as fucose migration—has been known for more than 25 years, but the chemical identity of the rearrangement product remains unclear. In this work, we combine ion-mobility spectrometry, radical-directed dissociation mass spectrometry, cryogenic IR spectroscopy of ions, and density-functional theory calculations to deduce the product of the rearrangement in the model trisaccharides Lewis x and blood group H2. The structural search yields the fucose moiety attached to the galactose with an α(1→6) glycosidic bond as the most likely product

Spontaneous Isomerization of Long-Lived Proteins Provides a Molecular Mechanism for the Lysosomal Failure Observed in Alzheimer's Disease.

Proteinaceous aggregation is a well-known observable in Alzheimer's disease (AD), but failure and storage of lysosomal bodies within neurons is equally ubiquitous and actually precedes bulk accumulation of extracellular amyloid plaque. In fact, AD shares many similarities with certain lysosomal storage disorders though establishing a biochemical connection has proven difficult. Herein, we demonstrate that isomerization and epimerization, which are spontaneous chemical modifications that occur in long-lived proteins, prevent digestion by the proteases in the lysosome (namely, the cathepsins). For example, isomerization of aspartic acid into l-isoAsp prevents digestion of the N-terminal portion of Aβ by cathepsin L, one of the most aggressive lysosomal proteases. Similar results were obtained after examination of various target peptides with a full series of cathepsins, including endo-, amino-, and carboxy-peptidases. In all cases peptide fragments too long for transporter recognition or release from the lysosome persisted after treatment, providing a mechanism for eventual lysosomal storage and bridging the gap between AD and lysosomal storage disorders. Additional experiments with microglial cells confirmed that isomerization disrupts proteolysis in active lysosomes. These results are easily rationalized in terms of protease active sites, which are engineered to precisely orient the peptide backbone and cannot accommodate the backbone shift caused by isoaspartic acid or side chain dislocation resulting from epimerization. Although Aβ is known to be isomerized and epimerized in plaques present in AD brains, we further establish that the rates of modification for aspartic acid in positions 1 and 7 are fast and could accrue prior to plaque formation. Spontaneous chemistry can therefore provide modified substrates capable of inducing gradual lysosomal failure, which may play an important role in the cascade of events leading to the disrupted proteostasis, amyloid formation, and tauopathies associated with AD