cssi/SciSciGPT-SciSciNet huggingface dataset:
Robust local and string stability for a decentralized car following control strategy for connected automated vehicles

Abstract This paper presents a robust car-following control strategy under uncertainty for connected and automated vehicles (CAVs). The proposed control is designed as a decentralized linear feedback and feedforward controller with a focus on robust local and string stability under (i) time-varying uncertain vehicle dynamics and (ii) time-varying uncertain communication delay. The former uncertainty is incorporated into the general longitudinal vehicle dynamics (GLVD) equation that regulates the difference between the desired acceleration (prescribed by the control model) and the actual acceleration by compensating for nonlinear vehicle dynamics (e.g., due to aerodynamic drag force). The latter uncertainty is incorporated into acceleration information received from the vehicle immediately ahead. As a primary contribution, this study derives and proves (i) a sufficient and necessary condition for local stability and (ii) sufficient conditions for robust string stability in the frequency domain using the Laplacian transformation. Simulation experiments verify the correctness of the mathematical proofs and demonstrate that the proposed control is effective for ensuring stability against uncertainties.
PeakPass: Automating ChIP-Seq Blacklist Creation.

ChIP-Seq blacklists contain genomic regions that frequently produce artifacts and noise in ChIP-Seq experiments. To improve signal-to-noise ratio, ChIP-Seq pipelines often remove data points that map to blacklist regions. Existing blacklists have been compiled in a manual or semi-automated way. In this paper we describe PeakPass, an efficient method to generate blacklists, and present evidence that blacklists can increase ChIP-Seq data quality. PeakPass leverages machine learning and attempts to automate blacklist generation. PeakPass uses a random forest classifier in combination with genomic features such as sequence, annotated repeats, complexity, assembly gaps, and the ratio of multi-mapping to uniquely mapping reads to identify artifact regions. We have validated PeakPass on a large dataset and tested it for the purpose of upgrading a blacklist to a new reference genome version. We trained PeakPass on the ENCODE blacklist for the hg19 human reference genome, and created an updated blacklist for hg38. To assess the performance of this blacklist we tested 42 ChIP-Seq replicates from 24 experiments using the Relative Strand Correlation (RSC) metric as a quality measure. Using the blacklist generated by PeakPass resulted in a statistically significant increase in RSC over the existing ENCODE blacklist for hg38 – average RSC was increased by 50% over the ENCODE blacklist, while only filtering an average of 0.1% of called peaks.
TISMorph: A tool to quantify texture, irregularity and spreading of single cells

A number of recent studies have shown that cell shape and cytoskeletal texture can be used as sensitive readouts of the physiological state of the cell. However, utilization of this information requires the development of quantitative measures that can describe relevant aspects of cell shape. In this paper we develop a toolbox, TISMorph, that calculates a set of quantitative measures to address this need. Some of the measures introduced here have been used previously, while others are new and have desirable properties for shape and texture quantification of cells. These measures, broadly classifiable into the categories of textural, irregularity and spreading measures, are tested by using them to discriminate between osteosarcoma cell lines treated with different cytoskeletal drugs. We find that even though specific classification tasks often rely on a few measures, these are not the same between all classification tasks, thus requiring the use of the entire suite of measures for classification and discrimination. We provide detailed descriptions of the measures, as well as the TISMorph package to implement them. Quantitative morphological measures that capture different aspects of cell morphology will help enhance large-scale image-based quantitative analysis, which is emerging as a new field of biological data.
Hash Functions in the Dedicated-Key Setting: Design Choices and MPP Transforms.

In the dedicated-key setting, one starts with a compression function f : {0, 1}×{0, 1} → {0, 1} and builds a family of hash functions H : K×M→ {0, 1} indexed by a key space K. This is different from the more traditional design approach used to build hash functions such as MD5 or SHA-1, in which compression functions and hash functions do not have dedicated key inputs. We explore the benefits and drawbacks of building hash functions in the dedicated-key setting (as compared to the more traditional approach), highlighting several unique features of the former. Should one choose to build hash functions in the dedicated-key setting, we suggest utilizing multi-property-preserving (MPP) domain extension transforms. We analyze seven existing dedicated-key transforms with regard to the MPP goal and propose two simple new MPP transforms. ∗Dept. of Computer Science & Engineering 0404, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0404, USA. Email: mihir@cs.ucsd.edu. URL: http://www-cse.ucsd.edu/users/mihir. Supported in part by NSF grant CNS 0524765 and a gift from Intel Corporation. †Dept. of Computer Science & Engineering 0404, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0404, USA. Email: tristenp@cs.ucsd.edu. URL: http://www-cse.ucsd.edu/users/tristenp. Supported in part by above-mentioned grants of first author.
A simple and general synthesis of 4-oxo-4,5,6,7-tetrahydroindoles via a novel intramolecular 1,3-dipolar cycloaddition approach

Abstract A general synthesis of 4-keto-4,5,6,7-tetrahydroindoles 6–12 has been achieved in two steps using a new intramolecular 1,3-dipolar cycloaddition approach in moderate yields (45–60%). The potential of this methodology is demonstrated by the synthesis of a mitomycin skeleton ( 15 ) and a topoisomerase-1 inhibitor skeleton ( 17 ).
Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction.

Thermostable group II intron reverse transcriptases (TGIRTs) with high fidelity and processivity have been used for a variety of RNA sequencing (RNA-seq) applications, including comprehensive profiling of whole-cell, exosomal, and human plasma RNAs; quantitative tRNA-seq based on the ability of TGIRT enzymes to give full-length reads of tRNAs and other structured small ncRNAs; high-throughput mapping of post-transcriptional modifications; and RNA structure mapping. Here, we improved TGIRT-seq methods for comprehensive transcriptome profiling by rationally designing RNA-seq adapters that minimize adapter dimer formation. Additionally, we developed biochemical and computational methods for remediating 5′- and 3′-end biases, the latter based on a random forest regression model that provides insight into the contribution of different factors to these biases. These improvements, some of which may be applicable to other RNA-seq methods, increase the efficiency of TGIRT-seq library construction and improve coverage of very small RNAs, such as miRNAs. Our findings provide insight into the biochemical basis of 5′- and 3′-end biases in RNA-seq and suggest general approaches for remediating biases and decreasing adapter dimer formation.
Radiation chemistry of organic liquids: Saturated hydrocarbons

Publisher Summary This chapter examines the radiolysis of neat organic liquids. By virtue of having low dielectric constant and only C-C and C-H bonds, hydrocarbons represent an ideal medium to examine the fundamental mechanisms of radiolysis in non-polar media. The chapter focuses on paraffins, branched alkanes, and cycloalkanes. The ionizing radiation interacts with the solvent to produce excited solvent molecules and electron-hole pairs. Spurs containing one or several electron-hole pairs are generated in scattering events involving the primary and secondary electrons. A large fraction of the ejected electrons thermalize before they escape the Coulomb attraction of the positive charges. Few of these electrons can escape beyond the Onsager radius, while the majority recombines with the holes. Being non-polar, hydrocarbons are unable to solvate the electrons and localized electrons remain close to the conduction band. Thermal promotion of these electrons to the conduction band leads to overall high mobility. The chapter discusses high-mobility solvent holes in cyclic alkanes and reviews the recent advances in understanding the spur chemistry, starting from the laser and VUV studies of isolated ion pairs to modeling the multiple-pair spurs. The chapter also examines the studies on solvent and solute excited states in radiolysis of hydrocarbons.
STIMULUS: Noninvasive Dynamic Patterns of Neurostimulation Using Spatio-Temporal Interference

Objective: This paper obtains strategies that can achieve spatially precise noninvasive deep brain stimulation using electrical currents. Methods: We provide the Spatio-Temporal Interference-based stiMULation focUsing Strategy (STIMULUS) that generates rich patterns of spatiotemporally interfering currents to stimulate precisely and deep inside the brain. To calibrate and compare the accuracy of stimulation using different techniques, we utilize computational Hodgkin–Huxley-type models for neurons and a model of current dispersion in the head. Results: In this computational model, STIMULUS dramatically outperforms the recently proposed Temporal Interference (TI) stimulation strategy in spatial precision. Our results also suggest that STIMULUS can attain steerable and multisite stimulation, which can be important in giving feedback in brain–machine interfaces. Finally, by examining more mammalian neuron types, we also observe that not every neuron exhibits temporal-interference stimulation. Conclusions: Computer simulations suggest that the proposed STIMULUS strategy has potential to achieve noninvasive electrical deep brain stimulation with high spatial precision and, further, has the flexibility of generating rich stimulation patterns. The fact that some neuron types do not exhibit TI stimulation suggests that caution is needed in evaluating conclusions of application of TI stimulation on large mammalian brains. Significance: A technique to reliably, noninvasively, and precisely stimulate deep inside the human brain could revolutionize human neuroscience and clinical treatments. We obtain the first computational demonstration of the recently proposed TI stimulation. Advancing on that, we propose a novel strategy that can perform stimulation with high precision and flexibility.
Enantioselective Synthesis of γ-Aryl-γ-butyrolactones by Sequential Asymmetric Epoxidation, Ring Expansion, and Baeyer−Villiger Oxidation

This paper describes an enantioselective synthesis of γ-butyrolactones, using the N-tolyl-substituted oxazolidinone-containing ketone as catalyst and Oxone as oxidant via a sequential asymmetric epoxidation of benzylidenecyclopropanes, ring expansion, and Baeyer−Villiger oxidation. Up to 91% ee was obtained. Optically active cyclobutanones can also be obtained by suppressing the Baeyer−Villiger oxidation with use of more ketone catalyst and less Oxone.
Intestinal crypts recover rapidly from focal damage with coordinated motion of stem cells that is impaired by aging

Despite the continuous renewal and turnover of the small intestinal epithelium, the intestinal crypt maintains a 'soccer ball-like', alternating pattern of stem and Paneth cells at the base of the crypt. To study the robustness of the alternating pattern, we used intravital two-photon microscopy in mice with fluorescently-labeled Lgr5+ intestinal stem cells and precisely perturbed the mosaic pattern with femtosecond laser ablation. Ablation of one to three cells initiated rapid motion of crypt cells that restored the alternation in the pattern within about two hours with only the rearrangement of pre-existing cells, without any cell division. Crypt cells then performed a coordinated dilation of the crypt lumen, which resulted in peristalsis-like motion that forced damaged cells out of the crypt. Crypt cell motion was reduced with inhibition of the ROCK pathway and attenuated with old age, and both resulted in incomplete pattern recovery. This suggests that in addition to proliferation and self-renewal, motility of stem cells is critical for maintaining homeostasis. Reduction of this newly-identified behavior of stem cells could contribute to disease and age-related changes.
Conversion of hydrazones to alkyl chlorides under Swern oxidation conditions

The unsubstituted hydrazones derived from aromatic ketones and aldehydes were converted in high yield to the corresponding alkyl chlorides under Swern oxidation conditions. In this unusual oxidation/reduction sequence the substrate undergoes a net reduction under the well established Swern oxidation conditions. Unsubstituted hydrazones derived from cyclohexyl ketones returned elimination products.
Facile Preparation and Reactivity of Polymer-Supported N-(2-Iodyl-phenyl)-acylamide, an Efficient Oxidizing System

A simple three-step preparation of polymer-supported N-(2-iodyl-phenyl)-acylamide (NIPA resin) starting from 2-iodoaniline is described. The resin was obtained with good loading levels (0.7-0.8 mmol g(-1)) and has been successfully used for efficient oxidation of a diverse collection of alcohols. Thus, treating alcohols with 1.0 equiv of the resin in 1,2-dichloroethane under reflux for 30-60 min allowed rapid and in most cases complete conversion to the corresponding carbonyl compound.
Boron tribromide-catalyzed rearrangement of 7,7-diphenylhydromorphone to 6,7-diphenylmorphine: A novel conversion of ketones to allylic alcohols

A novel boron tribromide-catalyzed rearrangement of ketones to allylic alcohols was discovered in the 7-phenylmorphinan-6-one system. The reaction involved the stereospecific migration of an axial 7β-phenyl (or a hydrogen) to the C-6 carbonyl carbon, followed by the elimination of the H-8 proton leading to the generation of allylic alcohols. A possible mechanistic pathway for this rearrangement is discussed.
Comparative Genomics Approaches Accurately Predict Deleterious Variants in Plants

Recent advances in genome resequencing have led to increased interest in prediction of the functional consequences of genetic variants. Variants at phylogenetically conserved sites are of particular interest, because they are more likely than variants at phylogenetically variable sites to have deleterious effects on fitness and contribute to phenotypic variation. Numerous comparative genomic approaches have been developed to predict deleterious variants, but the approaches are nearly always assessed based on their ability to identify known disease-causing mutations in humans. Determining the accuracy of deleterious variant predictions in nonhuman species is important to understanding evolution, domestication, and potentially to improving crop quality and yield. To examine our ability to predict deleterious variants in plants we generated a curated database of 2,910 Arabidopsis thaliana mutants with known phenotypes. We evaluated seven approaches and found that while all performed well, their relative ranking differed from prior benchmarks in humans. We conclude that deleterious mutations can be reliably predicted in A. thaliana and likely other plant species, but that the relative performance of various approaches does not necessarily translate from one species to another.
A highly diastereoselective synthesis of 3-carbethoxy-2,5-disubstituted-3-pyrrolines by phosphine catalysis

Abstract Tributylphosphine was used as catalyst to facilitate a [3+2] cycloaddition between γ-substituted allenoates and N-sulfonylimines. The resulting adducts, 3-carbethoxy-2,5-disubstituted-3-pyrrolines, were formed in excellent yields with high diastereoselectivity. The reaction went to completion in several hours at room temperature, and the starting materials were easily prepared with one step from commercially available compounds via known procedures.
A fully-automated, robust, and versatile algorithm for long-term budding yeast segmentation and tracking

Live cell time-lapse microscopy, a widely-used technique to study gene expression and protein dynamics in single cells, relies on segmentation and tracking of individual cells for data generation. The potential of the data that can be extracted from this technique is limited by the inability to accurately segment a large number of cells from such microscopy images and track them over long periods of time. Existing segmentation and tracking algorithms either require additional dyes or markers specific to segmentation or they are highly specific to one imaging condition and cell morphology and/or necessitate manual correction. Here we introduce a fully automated, fast and robust segmentation and tracking algorithm for budding yeast that overcomes these limitations. Full automatization is achieved through a novel automated seeding method, which first generates coarse seeds, then automatically fine-tunes cell boundaries using these seeds and automatically corrects segmentation mistakes. Our algorithm can accurately segment and track individual yeast cells without any specific dye or biomarker. Moreover, we show how existing channels devoted to a biological process of interest can be used to improve the segmentation. The algorithm is versatile in that it accurately segments not only cycling cells with smooth elliptical shapes, but also cells with arbitrary morphologies (e.g. sporulating and pheromone treated cells). In addition, the algorithm is independent of the specific imaging method (bright-field/phase) and objective used (40X/63X/100X). We validate our algorithm's performance on 9 cases each entailing a different imaging condition, objective magnification and/or cell morphology. Taken together, our algorithm presents a powerful segmentation and tracking tool that can be adapted to numerous budding yeast single-cell studies.
Synthesis and testing of new end-functionalized oligomers for molecular electronics

Abstract Several new classes of oligomers have been synthesized with functionalities designed to aid in the understanding of molecular device behavior, specifically when molecules are interfaced between proximal electronic probes. The compounds synthesized are series of azobenzenes, bipyridines and oligo(phenylene vinylene)s that bear acetyl-protected thiols for ultimate attachment to metallic surfaces. Some initial electrochemical and solid-state test results are also reported.
An improved chiral auxiliary for the allene ether version of the Nazarov cyclization.

α-2-Deoxy-d-glucose derived ether 14 is a superior reagent for the allene ether version of the Nazarov cyclization. Enantiomeric excesses of products derived from trisubstituted morpholino enamides varied between 85% and 93% ee.
Aqueous phase catalytic hydroformylation reactions of alkenes

Abstract The present article provides an overview of the recent developments in the area of aqueous phase hydroformylation of alkenes. The commercial application of aqueous phase hydroformylation reaction is restricted to the lower carbon chain alkenes due to the solubility and mass transfer limitations of the higher carbon chain alkenes in aqueous phase. The approaches which have been developed to improve the solubility of higher carbon chain length alkenes for aqueous phase hydroformylation reaction are emphasized in this article.
Human hippocampal replay during rest prioritizes weakly learned information and predicts memory performance

The hippocampus replays experiences during quiet rest periods, and this replay benefits subsequent memory. A critical open question is how memories are prioritized for this replay. We used functional magnetic resonance imaging (fMRI) pattern analysis to track item-level replay in the hippocampus during an awake rest period after participants studied 15 objects and completed a memory test. Objects that were remembered less well were replayed more during the subsequent rest period, suggesting a prioritization process in which weaker memories-memories most vulnerable to forgetting-are selected for replay. In a second session 12 hours later, more replay of an object during a rest period predicted better subsequent memory for that object. Replay predicted memory improvement across sessions only for participants who slept during that interval. Our results provide evidence that replay in the human hippocampus prioritizes weakly learned information, predicts subsequent memory performance, and relates to memory improvement across a delay with sleep.
The trauma severity model: an ensemble machine learning approach to risk prediction

Statistical theory indicates that a flexible model can attain a lower generalization error than an inflexible model, provided that the setting is appropriate. This is highly relevant for mortality risk prediction with trauma patients, as researchers have focused exclusively on the use of generalized linear models for trauma risk prediction, and generalized linear models may be too inflexible to capture the potentially complex relationships in trauma data. To improve trauma risk prediction, we propose a machine learning model, the Trauma Severity Model (TSM). In order to validate TSM's performance, this study compares TSM to three established risk prediction models: the Bayesian Logistic Injury Severity Score, the Harborview Assessment for Risk of Mortality, and the Trauma Mortality Prediction Model. Our results indicate that TSM has superior predictive performance on National Trauma Data Bank data and on Nationwide Readmission Database data.
Synthesis and chemistry of α-iodoperfluoroacid esters

The title compounds have been synthesized by irradiation of acetonitrile solutions of perfluoroacid esters and diesters containing tetrabutylammonium iodide. They are versatile synthetic intermediates from which ketenes, Reformatsky adducts, α,β-unsaturated esters and α-hydroesters can be prepared.
DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis

RNA degradation affects RNA-seq quality when profiling transcriptional activities in cells. Here, we show that transcript degradation is both gene- and sample-specific and is a common and significant factor that may bias the results in RNA-seq analysis. Most existing global normalization approaches are ineffective to correct for degradation bias. We propose a novel pipeline named DegNorm to adjust the read counts for transcript degradation heterogeneity on a gene-by-gene basis while simultaneously controlling for the sequencing depth. The robust and effective performance of this method is demonstrated in an extensive set of simulated and real RNA-seq data.
Active Protein Neddylation or Ubiquitylation Is Dispensable for Stress Granule Dynamics

Stress granule (SG) formation is frequently accompanied by ubiquitin proteasome system (UPS) impairment and ubiquitylated protein accumulation. SGs, ubiquitin, and UPS components co-localize, but the relationship between the ubiquitin pathway and SGs has not been systematically characterized. We utilize pharmacological inhibition of either the ubiquitin- or NEDD8-activating enzyme (UAE or NAE) to probe whether active ubiquitylation or neddylation modulate SG dynamics. We show that UAE inhibition results in rapid loss of global protein ubiquitylation using ubiquitin-specific proteomics. Critically, inhibiting neither UAE nor NAE significantly affected SG formation or disassembly, indicating that active protein ubiquitylation or neddylation is dispensable for SG dynamics. Using antibodies with varying preference for free ubiquitin or polyubiquitin and fluorescently tagged ubiquitin variants in combination with UAE inhibition, we show that SGs co-localize primarily with unconjugated ubiquitin rather than polyubiquitylated proteins. These findings clarify the role of ubiquitin in SG biology and suggest that free ubiquitin may alter SG protein interactions.
Exploring the spatially explicit predictions of the Maximum Entropy Theory of Ecology

Aim The maximum entropy theory of ecology (METE) is a unified theory of biodiversity that attempts to simultaneously predict patterns of species abundance, size and spatial structure. The spatial predictions of this theory have repeatedly performed well at predicting diversity patterns across scales. However, the theoretical development and evaluation of METE has focused on predicting patterns that ignore intersite spatial correlations. As a result the theory has not been evaluated using one of the core components of spatial structure. We develop and test a semi-recursive version of the spatially explicit predictions of METE for the distance–decay relationship of community similarity and compare its performance with the classic random placement model of completely random species distributions. This provides a better understanding and stronger test of the spatial community predictions of METE. Location New World tropical and temperate plant communities. Methods We analytically derived and simulated the spatially explicit expectations of METE for the Sorensen index of community similarity. We then compared the distance–decay of community similarity of 16 mapped plant communities with METE and the random placement model. Results The version of METE we examined was successful at capturing the general functional form of the observed distance–decay relationships, a negative power function relationship between community similarity and distance. However, the semi-recursive approach consistently predicted lower intercepts and higher slopes than observed in the empirical distance–decay relationships and yielded worse predictions than the random placement model. Main conclusions Our results suggest that while the current spatial models of METE accurately predict the spatial scaling of species occupancy, and therefore core ecological patterns like the species–area relationship, its semi-recursive form does not accurately characterize spatially explicit patterns of correlation. More generally, this suggests that tests of spatial theories based only on the species–area relationship may appear to support the underlying theory despite significant deviations in important aspects of spatial structure.
miniMDS: 3D structural inference from high-resolution Hi-C data.

Motivation Recent experiments have provided Hi-C data at resolution as high as 1 kbp. However, 3D structural inference from high-resolution Hi-C datasets is often computationally unfeasible using existing methods. Results We have developed miniMDS, an approximation of multidimensional scaling (MDS) that partitions a Hi-C dataset, performs high-resolution MDS separately on each partition, and then reassembles the partitions using low-resolution MDS. miniMDS is faster, more accurate, and uses less memory than existing methods for inferring the human genome at high resolution (10 kbp). Availability and implementation A Python implementation of miniMDS is available on GitHub: https://github.com/seqcode/miniMDS . Contact mahony@psu.edu. Supplementary information Supplementary data are available at Bioinformatics online.
A role for the Smc3 hinge domain in the maintenance of sister chromatid cohesion.

A screen of cohesin subunit Smc3 reveals that its hinge is a nexus controlling the maintenance of sister chromatid cohesion and condensation.
Retrometabolic approaches for drug design and targeting.

Retrometabolic drug design approaches incorporate targeting and metabolic considerations into the drug design process and represent a novel, systematic methodology for the design of safe, localized compounds. Two major design concepts aimed to increase the therapeutic index (the activity/toxicity ratio) of drugs were developed. Chemical delivery systems (CDS) are primarily used to allow targeting of the active biological molecules to specific target sites or organs based on predictable enzymatic activation. Brain-targeted delivery of different agents like estradiol or AZT was successfully achieved, and recent progresses include delivery of peptides using a complex strategy designated as molecular packaging. Sequential site- and stereospecific enzymatic activation of oxime/alkoxime precursors of beta-adrenergic antagonists allows their eye targeted delivery. Soft drug approaches are used to design new drugs by building in the molecule, in addition to the activity, the most desired way in which the molecule is to be deactivated and detoxified subsequent to exerting its biological effects. Many examples are available to illustrate soft drug design, e.g., soft anticholinergics, soft b-blockers, soft antiinflammatory steroids. Special computer programs were developed that starting from a lead compound generate complete libraries of possible soft analogs and then help ranking these candidates based on molecular size/shape, electronic properties, predicted solubility/partition properties, and atomic charge distributions. Recent developments in the field are presented in a supplement to this issue.
Progress in tritium NMR: 1990-2005

Tritium NMR is a powerful spectroscopic technique whose understanding and applications have markedly expanded in the past few years. The growth of this area from 1990 to 2005 is reviewed.
Synthesis of bis-2,7-substituted 1,2,3,6,7,8-hexahydroisoindolo[5,6-f]isoindole-1,3,6,8-tetraones

A series of bis-2,7-substituted 1,2,3,6,7,8-hexabydroisoindolo[5,6-f]isoindole-1,3,6,8-tetraones (naphthalene diimides) has been synthesized. The key intermediate required for synthesis of the naphthalene diimides, 2,3,6,7-naphthalenetetracarboxylic dianhydride (2) was prepared starting from allene and maleic anhydride. The bis-anhydride 2 was converted to the naphthalene diimides using conventional methodology by the reaction with amines in organic solvents
Combining Citizen Science and Deep Learning to Amplify Expertise in Neuroimaging

Big Data promises to advance science through data-driven discovery. However, many standard lab protocols rely on manual examination, which is not feasible for large-scale datasets. Meanwhile, automated approaches lack the accuracy of expert examination. We propose to (1) start with expertly labeled data, (2) amplify labels through web applications that engage citizen scientists, and (3) train machine learning on amplified labels, to emulate the experts. Demonstrating this, we developed a system to quality control brain magnetic resonance images. Expert-labeled data were amplified by citizen scientists through a simple web interface. A deep learning algorithm was then trained to predict data quality, based on citizen scientist labels. Deep learning performed as well as specialized algorithms for quality control (AUC = 0.99). Combining citizen science and deep learning can generalize and scale expert decision making; this is particularly important in disciplines where specialized, automated tools do not yet exist.
KMn3O2(Ge2O7): An S = 2 Magnetic Insulator Featuring Pillared Kagome Lattice

KMn3O2(Ge2O7) (I) and K0.35Rb0.65Mn3O2 (Ge2O7) (II) are prepared by high-temperature flux-growth methods from mixtures of KO2, Mn2O3, and GeO2 in the molar ratio of 2:3:4, and an excess of KCl or RbCl (silica tube, 800 °C, 3 d, 60% yield for (II)).
Predicting aquatic development and mortality rates of Aedes aegypti

Mosquito-borne pathogens continue to be a significant burden within human populations, with Aedes aegypti continuing to spread dengue, chikungunya, and Zika virus throughout the world. Using data from a previously conducted study, a linear regression model was constructed to predict the aquatic development rates based on the average temperature, temperature fluctuation range, and larval density. Additional experiments were conducted with different parameters of average temperature and larval density to validate the model. Using a paired t-test, the model predictions were compared to experimental data and showed that the prediction models were not significantly different for average pupation rate, adult emergence rate, and juvenile mortality rate. The models developed will be useful for modeling and estimating the upper limit of the number of Aedes aegypti in the environment under different temperature, diurnal temperature variations, and larval densities.
Predator odor increases avoidance and glutamatergic synaptic transmission in the prelimbic cortex via corticotropin-releasing factor receptor 1 signaling.

Acute exposure to a salient stressor, such as in post-traumatic stress disorder, can have lasting impacts upon an individual and society. To study stress in rodents, some naturalistic methods have included acute exposure to a predator odor, such as the synthetic fox odor 2,4,5, trimethyl-3-thiazoline (TMT). These experiments explore the stress-related behaviors and cortical activity induced by TMT exposure in adult male C57BL/6J mice and the influence of the stress neuropeptide corticotropin-releasing factor (CRF) on these responses. Compared to H2O and a novel odorant, vanilla, mice exposed to TMT in the home cage showed increased avoidance and defensive burying indicative of evident stress responses. Consistent with stress-induced activation of the medial prefrontal cortex (mPFC), we found that the prelimbic (PL) and infralimbic (IL) subregions of the mPFC had elevated c-Fos immunolabeling after TMT and vanilla compared to H2O. Slice physiology recordings were performed in layers 2/3 and 5 of the PL and IL, following TMT, vanilla, or H2O exposure. In TMT mice, but not vanilla or H2O mice, PL layers 2/3 showed heightened spontaneous excitatory post-synaptic currents and synaptic drive, suggesting TMT enhanced excitatory transmission. Synaptic drive in PL was increased in both TMT and H2O mice following bath application of 300 nM CRF, but only H2O mice increased excitatory currents with 100 nM CRF, suggesting dose-effect curve shifts in TMT mice. Further, systemic pretreatment with the CRF-R1 antagonist CP154526 and bath application with the CRF-R1 antagonist NBI27914 reduced excitatory transmission in TMT mice, but not H2O mice. CP154526 also reduced stress-reactive behaviors induced by TMT. Taken together, these findings suggest that exposure to TMT leads to CRF-R1 driven changes in behavior and changes in synaptic function in layer 2/3 neurons in the PL, which are consistent with previous findings that CRF-R1 in the mPFC plays an important role in predator odor-related behaviors.
Direct synthesis of esters and amides from unprotected hydroxyaromatic and -aliphatic carboxylic acids.

A facile method for the activation of hydroxy-substituted carboxylic acids using benzotriazole chemistry without prior protection of the hydroxy substituents is presented. The N-acylbenzotriazole intermediates 2a−g, 6a−d, and 9a−c have been used for high-yielding synthesis of both aliphatic (3a−l) and aromatic (7a−h, 10a−f) hydroxy carboxamides. High yields of aromatic hydroxy esters 12a−h and 13a−i were obtained using either neat alcohols in neutral microwave conditions or nucleophilic alkoxides and the intermediate N-(arylacyl)benzotriazoles. Moderate yields were obtained in the case of aliphatic hydroxy esters 11a,b and thiolesters 11e−g from the intermediates 2a−c.
Oxidation of hydroxyl-substituted organotrifluoroborates

Potassium- and tetra-n-butylammonium organotrifluoroborates containing hydroxyl groups have been prepared and oxidized using several common oxidants. Aryl-, alkenyl-, and alkyltrifluoroborates containing both primary and secondary hydroxyl groups were oxidized in moderate to excellent yields with complete retention of the trifluoroborate moiety. The utility of these oxidized products was demonstrated in a Suzuki−Miyaura cross-coupling reaction.
Deprotection of Homoallyl (hAllyl) Derivatives of Phenols, Alcohols, Acids, and Amines

The homoallyl moiety, hAllyl, is presented as a general protecting group for several functionalities. It can be chemoselectively removed via a sequential, one-pot cross-metathesis/elimination sequence.
Ruthenium-Catalyzed Ionic Hydrogenation of Aziridinium Cations

Hydride transfer from CpRu(dppm)H (dppm = bis(diphenylphosphino)methane) to asymmetrically substituted aziridinium cations occurs at the less substituted carbon when the substituents are alkyl, but at the more substituted carbon when the substituent is phenyl. Some of the phenyl-substituted aziridinium cations react with the amine resulting from H- transfer; the reaction of the same phenyl-substituted cation with Cp*Ru(dppf)H (dppf = 1,1‘-bis(diphenylphosphino)ferrocene) shows evidence of electron transfer. CpRu(dppm)H can catalyze the hydrogenation of the same aziridinium cations to ammonium cations; this reaction occurs with the same regioselectivity as the stoichiometric H- transfer reactions.
RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa

Species delimitations is problematic in many cases due to the difficulty of evaluating predictions from species hypotheses. In many cases delimitations rely on subjective interpretations of morphological and/or DNA data. Species with inadequate genetic resources needed to answer questions regarding evolutionary relatedness and genetic uniqueness are particularly problematic. In this study, we demonstrate the utility of restriction site associated DNA sequencing (RAD-seq) to objectively resolve unambiguous phylogenetic relationships in a recalcitrant group of deep-sea corals with divergences >80 million years. We infer robust species boundaries in the genus Paragorgia by testing alternative delimitation hypotheses using a Bayes Factors delimitation method. We present substantial evidence rejecting the current morphological species delimitation model for the genus and infer the presence of cryptic species associated with environmental variables. We argue that the suitability limits of RAD-seq for phylogenetic inferences cannot be assessed in terms of absolute time, but are contingent on taxon-specific factors. We show that classical taxonomy can greatly benefit from integrative approaches that provide objective tests to species delimitation hypotheses. Our results lead the way for addressing further questions in marine biogeography, community ecology, population dynamics, conservation, and evolution.
A very mild and selective method for O-benzoylation of hydroxamic acids

Abstract Selective O-benzoylation of hydroxamic acids is achieved by the treatment of BPO and DABCO. Aliphatic alcohols are not reactive under these conditions. Various radical or oxidation sensitive functional groups are compatible with this protocol, and no anhydrous reagents or solvents are required for the high yields of the benzoylations.
Synthesis of the Spatane Nucleus (cis-anti-cis-tricyclo[5.3.0.02,6]decane) using the Pauson−Khand Reaction with a Remarkable Reversal in Regioselectivity

The Pauson−Khand reaction of cyclobutenes 3−5 with a variety of acetylenes yielded cis-anti cis-tricyclo[5.3.0.02,6]decanes 9−17. The unwanted regioisomers 9a and 10a were the sole products using acetylene, but there was a remarkable reversal in orientation of the cyclobutene component yielding the desired regioisomer 13b upon using (trimethylsilyl)acetylene. The importance of the allylic methyl group in the cyclobutenes in directing the regiochemical outcome was substantiated by the lack of selectivity in Pauson−Khand reactions of desmethylcyclobutene 5 with acetylene and (trimethylsilyl)acetylene. The relative unimportance of electronic control of regiochemistry was concluded from the consistent ratio of Pauson−Khand reaction products from norbornenone 22 with various acetylenes. A hypothesis rationalizing the regiochemical outcome was based on steric interactions of the allylic methyl group from the cyclobutene component with either the smaller acetylene substituent or the CO ligands on the cobalt. Thi...
ENVIREM: an expanded set of bioclimatic and topographic variables increases flexibility and improves performance of ecological niche modeling

Species distribution modeling is a valuable tool with many applications across ecology and evolutionary biology. The selection of biologically meaningful environmental variables that determine relative habitat suitability is a crucial aspect of the modeling pipeline. The 19 bioclimatic variables from WorldClim are frequently employed, primarily because they are easily accessible and available globally for past, present and future climate scenarios. Yet, the availability of relatively few other comparable environmental datasets potentially limits our ability to select appropriate variables that will most successfully characterize a species’ distribution. We identified a set of 16 climatic and two topographic variables in the literature, which we call the ENVIREM dataset, many of which are likely to have direct relevance to ecological or physiological processes determining species distributions. We generated this set of variables at the same resolutions as WorldClim, for the present, mid-Holocene, and Last Glacial Maximum (LGM). For 20 North American vertebrate species, we then assessed whether including the ENVIREM variables led to improved species distribution models compared to models using only the existing WorldClim variables. We found that including the ENVIREM dataset in the pool of variables to select from led to substantial improvements in niche modeling performance in 13 out of 20 species. We also show that, when comparing models constructed with different environmental variables, differences in projected distributions were often greater in the LGM than in the present. These variables are worth consideration in species distribution modeling applications, especially as many of the variables have direct links to processes important for species ecology. We provide these variables for download at multiple resolutions and for several time periods at envirem.github.io. Furthermore, we have written the ‘envirem’ R package to facilitate the generation of these variables from other input datasets.
Combinatorial tissue engineering partially restores function after spinal cord injury.

Hydrogel scaffolds provide a beneficial microenvironment in transected rat spinal cord. A combinatorial biomaterials-based strategy provided a microenvironment that facilitated regeneration while reducing foreign body reaction to the three-dimensional spinal cord construct. We used poly lactic-co-glycolic acid microspheres to provide sustained release of rapamycin from Schwann cell (SC)-loaded, positively charged oligo-polyethylene glycol fumarate scaffolds. The biological activity and dose-release characteristics of rapamycin from microspheres alone and from microspheres embedded in the scaffold were determined in vitro. Three dose formulations of rapamycin were compared with controls in 53 rats. We observed a dose-dependent reduction in the fibrotic reaction to the scaffold and improved functional recovery over 6 weeks. Recovery was replicated in a second cohort of 28 animals that included retransection injury. Immunohistochemical and stereological analysis demonstrated that blood vessel number, surface area, vessel diameter, basement membrane collagen, and microvessel phenotype within the regenerated tissue was dependent on the presence of SCs and rapamycin. TRITC-dextran injection demonstrated enhanced perfusion into scaffold channels. Rapamycin also increased the number of descending regenerated axons, as assessed by Fast Blue retrograde axonal tracing. These results demonstrate that normalization of the neovasculature was associated with enhanced axonal regeneration and improved function after spinal cord transection.
Pliable polaritons: Wannier exciton-plasmon coupling in metal-semiconductor structures

Plasmonic structures are known to support the modes with subwavelength volumes in which the field matter interactions are greatly enhanced. Coupling between the molecular excitations and plasmons leading to formation of plexcitons has been investigated for a number of organic molecules. However, plasmon-exciton coupling in metal semiconductor structures have not experienced the same degree of attention. In this work we show that the very strong coupling regime in which the Rabi energy exceeds the exciton binding energy is attainable in semiconductor cladded plasmonic nanoparticles and leads to formation of Wannier Exciton Plasmon Polariton (WEPP) that is bound to the metal nanoparticle and characterized by dramatically smaller (by factor of few) excitonic radius and correspondingly higher ionization energy. This higher ionization energy exceeding approaching 100meV for the CdS/Ag structures may make room temperature Bose Einstein condensation and polariton lasing in plasmonic/semiconductor structures possible
Linear Stability Analysis of Transient Electrodeposition in Charged Porous Media: Suppression of Dendritic Growth by Surface Conduction

We study the linear stability of transient electrodeposition in a charged random porous medium, whose pore surface charges can be of any sign, flanked by a pair of planar metal electrodes. Discretization of the linear stability problem results in a generalized eigenvalue problem for the dispersion relation that is solved numerically, which agrees well with the analytical approximation obtained from a boundary layer analysis valid at high wavenumbers. Under galvanostatic conditions in which an overlimiting current is applied, in the classical case of zero surface charges, the electric field at the cathode diverges at Sand's time due to electrolyte depletion. The same phenomenon happens for positive charges but earlier than Sand's time. However, negative charges allow the system to sustain an overlimiting current via surface conduction past Sand's time, keeping the electric field bounded. Therefore, at Sand's time, negative charges greatly reduce surface instabilities and suppress dendritic growth, while zero and positive charges magnify them. We compare theoretical predictions for overall surface stabilization with published experimental data for copper electrodeposition in cellulose nitrate membranes and demonstrate good agreement between theory and experiment. We also apply the stability analysis to how crystal grain size varies with duty cycle during pulse electroplating.