cssi/SciSciGPT-SciSciNet huggingface dataset:
IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis

Next-Generation Sequencing has made available substantial amounts of large-scale Omics data, providing unprecedented opportunities to understand complex biological systems. Specifically, the value of RNA-Sequencing (RNA-Seq) data has been confirmed in inferring how gene regulatory systems will respond under various conditions (bulk data) or cell types (single-cell data). RNA-Seq can generate genome-scale gene expression profiles that can be further analyzed using correlation analysis, co-expression analysis, clustering, differential gene expression (DGE), among many other studies. While these analyses can provide invaluable information related to gene expression, integration and interpretation of the results can prove challenging. Here we present a tool called IRIS-EDA, which is a Shiny web server for expression data analysis. It provides a straightforward and user-friendly platform for performing numerous computational analyses on user-provided RNA-Seq or Single-cell RNA-Seq (scRNA-Seq) data. Specifically, three commonly used R packages (edgeR, DESeq2, and limma) are implemented in the DGE analysis with seven unique experimental design functionalities, including a user-specified design matrix option. Seven discovery-driven methods and tools (correlation analysis, heatmap, clustering, biclustering, Principal Component Analysis (PCA), Multidimensional Scaling (MDS), and t-distributed Stochastic Neighbor Embedding (t-SNE)) are provided for gene expression exploration which is useful for designing experimental hypotheses and determining key factors for comprehensive DGE analysis. Furthermore, this platform integrates seven visualization tools in a highly interactive manner, for improved interpretation of the analyses. It is noteworthy that, for the first time, IRIS-EDA provides a framework to expedite submission of data and results to NCBI's Gene Expression Omnibus following the FAIR (Findable, Accessible, Interoperable and Reusable) Data Principles. IRIS-EDA is freely available at http://bmbl.sdstate.edu/IRIS/.
Long-term risk governance: when do societies act before crisis?

Many environmental problems entail a temporal dilemma. Societies benefit from resource use now that will have cumulative negative impacts on future generations. All too often, societies only act to...
Power and Thermal Analysis of Commercial Mobile Platforms: Experiments and Case Studies

State-of-the-art mobile processors can deliver fast response time and high throughput to maximize the user experience. However, high performance comes at the expense of larger power density, which leads to higher skin temperatures. Since this can degrade the user experience, there is a strong need for power consumption and thermal analysis in mobile processors. In this paper, we first perform experiments on the Nexus 6P phone to study the power, performance and thermal behavior of modern smartphones. Using the insight from these experiments, we propose a control algorithm that throttles select applications without affecting other apps. We demonstrate our governor on the Exynos 5422 processor employed in the Odroid-XU3 board.
Learning to Generate Synthetic Data via Compositing

We present a task-specific approach to synthetic data generation. Our framework employs a trainable synthesizer network that is optimized to produce meaningful training samples by assessing the strengths and weaknesses of a ‘target’ classifier. The synthesizer and target networks are trained in an adversarial manner wherein each network is updated with a goal to outdo the other. Additionally, we ensure the synthesizer generates realistic data by pairing it with a discriminator trained on real-world images. Further, to make the target classifier invariant to blending artefacts, we introduce these artefacts to background regions of the training images so the target does not over-fit to them. We demonstrate the efficacy of our approach by applying it to different target networks including a classification network on AffNIST [46], and two object detection networks (SSD, Faster-RCNN) on different datasets. On the AffNIST benchmark, our approach is able to surpass the baseline results with just half the training examples. On the VOC person detection benchmark, we show improvements of up to 2.7% as a result of our data augmentation. Similarly on the GMU detection benchmark, we report a performance boost of 3.5% in mAP over the baseline method, outperforming the previous state of the art approaches by as much as 7.5% in individual categories.
HALLS: An Energy-Efficient Highly Adaptable Last Level STT-RAM Cache for Multicore Systems

Spin-Transfer Torque RAM (STT-RAM) is widely considered a promising alternative to SRAM in the memory hierarchy due to STT-RAM's non-volatility, low leakage power, high density, and fast read speed. The STT-RAM's small feature size is particularly desirable for the last-level cache (LLC), which typically consumes a large area of silicon die. However, long write latency and high write energy still remain challenges of implementing STT-RAMs in the CPU cache. An increasingly popular method for addressing this challenge involves trading off the non-volatility for reduced write speed and write energy by relaxing the STT-RAM's data retention time. However, in order to maximize energy saving potential, the cache configurations, including STT-RAM's retention time, must be dynamically adapted to executing applications’ variable memory needs. In this paper, we propose a highly adaptable last level STT-RAM cache (HALLS) that allows the LLC configurations and retention time to be adapted to applications’ runtime execution requirements. We also propose low-overhead runtime tuning algorithms to dynamically determine the best (lowest energy) cache configurations and retention times for executing applications. Compared to prior work, HALLS reduced the average energy consumption by 60.57 percent in a quad-core system, while introducing marginal latency overhead.
Using Shifts in Deployment and Operations to Test for Racial Bias in Police Stops

We rely on a policy experiment in the New York City Police Department (NYPD) to address the well-known problems of omitted variable bias and infra-marginality in traditional outcomes tests of racial bias in police stops. The NYPD designated specific areas as impact zones and deployed extra officers to these areas and encouraged them to conduct more intensive stop, question, and frisk activity. We find that the NYPD are more likely to frisk black and Hispanic suspects after an area becomes an impact zone compared to other areas of the city.
Application of the Keck Radical Coupling Reaction to the Preparation of Allylated C5 Furanosides and C6 Pyranosides

Abstract Allylated C5 furanosides and C6 pyranosides were prepared from known monosaccharide diol or polyol derivatives via a reaction sequence involving the initial selective formation of the primary iodide followed by application of the Keck allyl radical coupling reaction. Although the yields of the products in the coupling reaction were somewhat modest (usually 55-65%), the protocol was applicable to a variety of substrates, including sterically crowded cases, is experimentally simple and suitable for large scale preparations.
A one-pot conversion of ortho-alkynyl benzaldehydes into indolo[2,1-a]isoquinolines

Abstract The conversion of readily available 2-halobenzaldehydes into indolo[2,1-a]isoquinolines in two operations represents a very direct entry to this class of molecules.
Two Carbon Homologation of Carboxylic Acids Using Acrylamide as a Radical Trap

Abstract Photolysis of O-acyl derivatives of N-hydroxy-2-thiopyridone in the presence of acrylamide in dichloromethane furnished crystalline 2-(pyridine-2-thiyl)-carboxamides. Desulfurization of the latter by nickel boride afforded primary amides in excellent yields. © 1997 Elsevier Science Ltd.
Activity of the C. elegans egg-laying behavior circuit is controlled by competing activation and feedback inhibition

Like many behaviors, Caenorhabditis elegans egg laying alternates between inactive and active states. To understand how the underlying neural circuit turns the behavior on and off, we optically recorded circuit activity in behaving animals while manipulating circuit function using mutations, optogenetics, and drugs. In the active state, the circuit shows rhythmic activity phased with the body bends of locomotion. The serotonergic HSN command neurons initiate the active state, but accumulation of unlaid eggs also promotes the active state independent of the HSNs. The cholinergic VC motor neurons slow locomotion during egg-laying muscle contraction and egg release. The uv1 neuroendocrine cells mechanically sense passage of eggs through the vulva and release tyramine to inhibit egg laying, in part via the LGC-55 tyramine-gated Cl- channel on the HSNs. Our results identify discrete signals that entrain or detach the circuit from the locomotion central pattern generator to produce active and inactive states.
Directed Pd(0)-catalyzed hydrostannations of internal alkynes

Abstract Hydrostannations of primary propargylic alcohols with Bu 3 SnH catalyzed by Pd(PPh 3 ) 2 yield ( E ) allylic alcohols in which the Bu 3 Sn group is affixed to the carbon proximal to the CH 2 OH substituent, suggestive of an OH directing effect. Hydrostannations of the related propargylic acetates show no such effect.
Geometric Satake, categorical traces, and arithmetic of Shimura varieties

We survey some recent work on the geometric Satake of p-adic groups and its applications to some arithmetic problems of Shimura varieties. We reformulate a few constructions appeared in the previous works more conceptually.
What NMR has told us about solid acidity

Publisher Summary A wide variety of NMR methods are being applied to understand solid acids including zeolites and metal halides. Proton NMR is useful for characterizing Bronsted sites in zeolites. Many nuclei are suitable for the study of probe molecules adsorbed directly or formed in situ as either intermediates or products. Adsorbates on metal halide powders display a rich carbenium ion chemistry. The interpretation of NMR experiments on solid acids has been greatly improved by the integration of theoretical chemistry and experiment. NMR of solids is a diverse collection of methods, and the practice of applying it to chemisorption is changing dramatically as a result of advances in theoretical chemistry including reliable chemical shift calculations. The wide application of NMR to solid state chemistry grew out of the revival of magic angle spinning in the mid 1970's. In addition to sample rotation, a particular solid state NMR experiment is characterized by the pulse sequence used. As in solution NMR, a multitude of such sequences exist for solids; many exploit through-space dipolar couplings for either signal enhancement, spectral assignment, internuclear distance determination, or full correlation of the spectra of different nuclei. The most commonly applied solid state NMR experiments are concerned with the measurement of spectra in which intensities relate to the numbers of spins in different environments and the resonance frequencies are dominated by isotropic chemical shifts, much like NMR spectra of solutions.
Synthesis of 1-[3-methyl-2(3H)-benzazolon-5- or 6-yl]-4-{4-[cis-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl-methyl)-1,3-dioxolan-4-yl]methyleneoxyphenyl}piperazines †

Reactions of 3-methyl-6-[4-(4-hydroxyphenyl)-1-piperazinyl]-2(3H)-benzoxazolone, 3-methyl-6-[4-(4-hydroxy-phenyl)-1-piperazinyl]-2(3H)-benzothiazolone and 1,3-dimethyl-5-[4-(4-hydroxyphenyl)-1-piperazinyl]-2(3H)-benzimidazolone with cis-{[2-(2,4-dichlorophenyl) -2-(1H-imidazol-1-ylmethyl)]-1,3-dioxolan-4-yl}methyl meth-anesulfonate in the presence of sodium hydride furnish the title compounds.
Preparation of α-phosphono lactams via electrophilic phosphorus reagents: An application in the synthesis of lactam-based farnesyl transferase inhibitors

Conversion of N-alkyl lactams to the corresponding α-phosphono lactams has been investigated through procedures that involve formation of the lactam enolate and reaction with a phosphorus electrophile. With N-octylpyrrolidinone, the enolate could be trapped efficiently on oxygen by reaction with diethyl phosphorochloridate, and the resulting vinyl phosphate rearranges smoothly to the desired phosphonate upon treatment with additional LDA. Attempts to apply the same protocol to N-farnesyl lactams met with limited success. Studies with an isolated α-phosphono N-farnesyl lactam have shown that the farnesyl group is not stable to the excess of strong base required for rearrangement of a vinyl phosphate. However, a series of N-farnesyl lactams and imides was converted to the desired phosphonates through formation of the lactam enolate, reaction with diethyl phosphorochloridite, and subsequent oxidation of the phosphorus intermediate to the P(V) state.
Frequent sgRNA-barcode recombination in single-cell perturbation assays

Simultaneously detecting CRISPR-based perturbations and induced transcriptional changes in the same cell is a powerful approach to unraveling genome function. Several lentiviral approaches have been developed, some of which rely on the detection of distally located genetic barcodes as an indirect proxy of sgRNA identity. Since barcodes are often several kilobases from their corresponding sgRNAs, viral recombination-mediated swapping of barcodes and sgRNAs is feasible. Using a self-circularization-based sgRNA-barcode library preparation protocol, we estimate the recombination rate to be ~50% and we trace this phenomenon to the pooled viral packaging step. Recombination is random, and decreases the signal-to-noise ratio of the assay. Our results suggest that alternative approaches can increase the throughput and sensitivity of single-cell perturbation assays.
Stereoselective synthesis of functionalized pyroglutamates

Abstract Novel stereoselective synthesis of α-methylene-β-substituted pyroglutamates, and α-alkylidene-pyroglutamates has been achieved via substrate controlled asymmetric alkylation of l -threonine derived oxazole with Baylis–Hillman reaction based allyl bromides and acetates, respectively. The synthesized compounds were evaluated for their proteasome inhibition and cytotoxicity on multiple myeloma cells.
Alexander of Hales on the Ethics of Vigilantism

Very little has been published on the topic of vigilantism within recent applied ethics. Part of this dearth may be due to a perception that the issue lacks historical moorings, with little in the way of precedent in prior philosophical literature. However such a perception would be inaccurate; in fact there are interesting discussions of vigilantism in the history of philosophy. By way of illustration, this article examines an early treatment of the topic by the influential (though today oft-neglected) thirteenth-century Franciscan thinker, Alexander of Hales. Hales’ perspective reflects what would become a fairly general mediaeval consensus against the permissibility of vigilantism (or at least vigilantism involving deadly force). His discussion is interesting on its own account, but the main goal of this study is to help spur further historical inquiries – and perhaps by extension to prompt further interest in vigilantism within current applied ethics.
Intramolecular formal aza-[3 + 3] cycloaddition approach to indoloquinolizidine alkaloids. A stereoselective total synthesis of (+/-)-tangutorine.

A 19-step stereoselective total synthesis of (±)-tangutorine is described here. The total synthesis features an intramolecular aza-[3 + 3] formal cycloaddition strategy and also a Heck coupling for constructing the C2−C3 bond. This work provides a novel approach toward the indoloquinolizidine family of alkaloids.
Identifying progressive gene network perturbation from single-cell RNA-seq data

Identifying the gene regulatory networks that control development or disease is one of the most important problems in biology. Here, we introduce a computational approach, called PIPER (ProgressIve network PERturbation), to identify the perturbed genes that drive differences in the gene regulatory network across different points in a biological progression. PIPER employs algorithms tailor-made for single cell RNA sequencing (scRNA-seq) data to jointly identify gene networks for multiple progressive conditions. It then performs differential network analysis along the identified gene networks to identify master regulators. We demonstrate that PIPER outperforms state-of-the-art alternative methods on simulated data and is able to predict known key regulators of differentiation on real scRNA-Seq datasets.
High-contrast spectroscopy testbed for Segmented Telescopes: instrument overview and development progress

The High Contrast spectroscopy testbed for Segmented Telescopes (HCST) is being developed at Caltech. It aims at addressing the technology gap for future exoplanet imagers and providing the U.S. community with an academic facility to test components and techniques for high contrast imaging, focusing on segmented apertures proposed for future ground-based (TMT, ELT) and space-based telescopes (HabEx, LUVOIR). We present an overview of the design of the instrument and a detailed look at the testbed build and initial alignment. We offer insights into stumbling blocks encountered along the path and show that the testbed is now operational and open for business. We aim to use the testbed in the future for testing of high contrast imaging techniques and technologies with amongst with thing, a TMT-like pupil.
Galleria mellonella as an insect model for P. destructans, the cause of White-nose Syndrome in bats.

Pseudogymnoascus destructans is the fungal pathogen responsible for White-nose Syndrome (WNS), a disease that has killed millions of bats in North America over the last decade. A major obstacle to research on P. destructans has been the lack of a tractable infection model for monitoring virulence. Here, we establish a high-throughput model of infection using larvae of Galleria mellonella, an invertebrate used to study host-pathogen interactions for a wide range of microbial species. We demonstrate that P. destructans can kill G. mellonella larvae in an inoculum-dependent manner when infected larvae are housed at 13°C or 18°C. Larval killing is an active process, as heat-killed P. destructans spores caused significantly decreased levels of larval death compared to live spores. We also show that fungal spores that were germinated prior to inoculation were able to kill larvae 3–4 times faster than non-germinated spores. Lastly, we identified chemical inhibitors of P. destructans and used G. mellonella to evaluate these inhibitors for their ability to reduce virulence. We demonstrate that amphotericin B can effectively block larval killing by P. destructans and thereby establish that this infection model can be used to screen biocontrol agents against this fungal pathogen.
Life history effects on the molecular clock of autosomes and sex chromosomes

One of the foundational results in molecular evolution is that the rate at which neutral substitutions accumulate on a lineage equals the rate at which mutations arise. Traits that affect rates of mutation therefore also affect the phylogenetic “molecular clock.” We consider the effects of sex-specific generation times and mutation rates in species with two sexes. In particular, we focus on the effects that the age of onset of male puberty and rates of spermatogenesis have likely had in hominids (great apes), considering a model that approximates features of the mutational process in mammals, birds, and some other vertebrates. As we show, this model can account for a number of seemingly disparate observations: notably, the puzzlingly low X-to-autosome ratios of substitution rates in humans and chimpanzees and differences in rates of autosomal substitutions among hominine lineages (i.e., humans, chimpanzees, and gorillas). The model further suggests how to translate pedigree-based estimates of human mutation rates into split times among extant hominoids (apes), given sex-specific life histories. In so doing, it largely bridges the gap reported between estimates of split times based on fossil and molecular evidence, in particular suggesting that the human–chimpanzee split may have occurred as recently as 6.6 Mya. The model also implies that the “generation time effect” should be stronger in short-lived species, explaining why the generation time has a major influence on yearly substitution rates in mammals but only a subtle one in human pedigrees.
Preparation of β-Amido Ketones and Aldehydes via Amidoalkylation of Enamines, Enol Silyl Ethers, and Vinyl Ethers

Novel syntheses of β-amidoalkyl ketones and aldehydes via amidoalkylations of enamines, silyl enol ethers, and vinyl ethers with N-(1-benzotriazol-1-ylalkyl)amides are described.
The Wacker Reaction and Related Alkene Oxidation Reactions

The objective of this review is to survey the current state of the Wacker and related alkene oxidation reactions focusing on the reactions of higher alkenes and emphasizing the mechanistic pictures that have evolved, the current understanding regarding issues of selectivity, recent applications of the chemistry in synthesis, and the use of other transition metal catalysts to effect related oxidation reactions. The Wacker oxidation reaction has been extensively studied over the years. There are a number of excellent reviews published on various aspects of the reaction (1), with a series of reviews by Tsuji deserving particular note for their special insight into the development of this reaction (2-4).
Widespread intronic polyadenylation diversifies immune cell transcriptomes

Alternative cleavage and polyadenylation (ApA) is known to alter untranslated region (3'UTR) length but can also recognize intronic polyadenylation (IpA) signals to generate transcripts that lose part or all of the coding region. We analyzed 46 3'-seq and RNA-seq profiles from normal human tissues, primary immune cells, and multiple myeloma (MM) samples and created an atlas of 4927 high-confidence IpA events represented in these cell types. IpA isoforms are widely expressed in immune cells, differentially used during B-cell development or in different cellular environments, and can generate truncated proteins lacking C-terminal functional domains. This can mimic ectodomain shedding through loss of transmembrane domains or alter the binding specificity of proteins with DNA-binding or protein-protein interaction domains. MM cells display a striking loss of IpA isoforms expressed in plasma cells, associated with shorter progression-free survival and impacting key genes in MM biology and response to lenalidomide.
Antibiotic resistance is lower in Staphylococcus aureus isolated from antibiotic-free raw meat as compared to conventional raw meat

The frequent use of antibiotics contributes to antibiotic resistance in bacteria, resulting in an increase in infections that are difficult to treat. Livestock are commonly administered antibiotics in their feed, but there is current interest in raising animals that are only administered antibiotics during active infections. Staphylococcus aureus (SA) is a common pathogen of both humans and livestock raised for human consumption. SA has achieved high levels of antibiotic resistance, but the origins and locations of resistance selection are poorly understood. We determined the prevalence of SA and MRSA in conventional and antibiotic-free (AF) meat products, and also measured rates of antibiotic resistance in these isolates. We isolated SA from raw conventional turkey, chicken, beef, and pork samples and also from AF chicken and turkey samples. We found that SA contamination was common, with an overall prevalence of 22.6% (range of 2.8–30.8%) in conventional meats and 13.0% (range of 12.5–13.2%) in AF poultry meats. MRSA was isolated from 15.7% of conventional raw meats (range of 2.8–20.4%) but not from AF-free meats. The degree of antibiotic resistance in conventional poultry products was significantly higher vs AF poultry products for a number of different antibiotics, and while multi-drug resistant strains were relatively common in conventional meats none were detected in AF meats. The use of antibiotics in livestock contributes to high levels of antibiotic resistance in SA found in meat products. Our results support the use of AF conditions for livestock in order to prevent antibiotic resistance development in SA.
A regioselective synthesis of 3-benzazepinones via intramolecular hydroamidation of acetylenes

Abstract Synthesis of 3-benzazepinones by palladium-catalyzed intramolecular addition of amides to alkynes is achieved. Phenyl acetylenes substituted in the ortho -position with tethered amide functionality were prepared in a few steps from readily available starting materials. It was found that 5% Pd(OAc) 2 (PPh 3 ) 2 and KOH most effectively promoted cyclization. When the tethered group is an acetamide and an alkyl substituent is on the acetylene unit, regioselective 3-benzazepinone synthesis could be achieved in good yields.
Synthesis and binding studies of 2-O- and 11-O-substituted N-alkylnoraporphines.

Abstract We synthesized several novel 2- O - or 11- O -substituted N -alkylnoraporphines and assessed their affinities at dopamine D 1 and D 2 , and serotonin 5-HT 1A receptors in rat forebrain tissue. Tested compounds displayed moderate to high affinities to D 2 receptors but low affinities to D 1 and 5HT 1A receptors. The findings accord with previous evidence of a lipophilic cavity on the surface of the D 2 receptor to accommodate N -alkyl moieties of aporphines. The most D 2 -potent ( K i = 97 nM) and selective novel agent (>100-fold vs. D 1 and 5-HT 1A sites) was R (−)-2-(2-hydroxyethoxy)-11-hydroxy- N - n -propylnoraporphine (compound 11 ).
Oxidative rearrangements of arylalkenes with [hydroxy(tosyloxy)iodo]benzene in 95% methanol: a general, regiospecific synthesis of α-aryl ketones

The treatment of arylalkenes with [hydroxy(tosyloxy)iodo]benzene in 95% methanol affords the corresponding α-aryl ketones. This oxidative rearrangement is general for acyclic and cyclic arylalkenes and permits regioselective syntheses of isomeric α-phenyl ketone pairs.
Electronic Tuning of Fischer Carbene Complexes in the Preparation of Bicyclo[3.1.1]heptanones as Taxane A-ring Synthons

Abstract A synthetic route to taxol and other Taxus diterpenes is described which employs as a key step the reaction between a Fischer carbene complex and a 1,6 enyne to construct 1-substituted-7,7-dimethyl-2-methylenebicyclo[3.1.1]heptan-6-ones. It was found that the reaction between complex 2 and 7-methyl-3-methylene-6-octen-1-yne (dienyne 30) yielded a mixture of bicyclo[3.1.1]heptanone 35 and cyclobutenone 36, the latter possibly arising from the migration of the chromium fragment from an electron-rich alkene to a less electron-rich alkene in the vinyl carbene complex intermediate (i.e. 40–42). On this basis, it was expected that bicycloheptanone yields would increase with increasing electron deficiency in the intermediate 40 since this should lead to more competitive CO insertion. This was observed with a series of electronically modified carbene complexes (45 and 48a–d). The more electron deficient complexes gave good yields of bicycloheptanones, thus providing an efficient means for preparing taxane A-ring synthons.
The molecular structure of plant sporopollenin

Sporopollenin is a ubiquitous and extremely chemically inert biopolymer that constitutes the outer wall of all land-plant spores and pollen grains1. Sporopollenin protects the vulnerable plant gametes against a wide range of environmental assaults, and is considered a prerequisite for the migration of early plants onto land2. Despite its importance, the chemical structure of plant sporopollenin has remained elusive1. Using a newly developed thioacidolysis degradative method together with state-of-the-art solid-state NMR techniques, we determined the detailed molecular structure of pine sporopollenin. We show that pine sporopollenin is primarily composed of aliphatic-polyketide-derived polyvinyl alcohol units and 7-O-p-coumaroylated C16 aliphatic units, crosslinked through a distinctive dioxane moiety featuring an acetal. Naringenin was also identified as a minor component of pine sporopollenin. This discovery answers the long-standing question about the chemical make-up of plant sporopollenin, laying the foundation for future investigations of sporopollenin biosynthesis and for the design of new biomimetic polymers with desirable inert properties. A distinct feature of pollen gains is their resistant outer wall, called the exine, which is mainly composed of sporopollenin, the toughest biopolymer known to date despite an unknown detailed structure. Now, a structural model of pine sporopollenin is revealed by the application of new degradation chemistry and solid-state NMR spectroscopy.
Deprotection of silyl ethers using ZnBr2 and H2O in CH2Cl2

Abstract TES- and TBS-protected alcohols undergo deprotection upon treatment with excess ZnBr2 and water in CH2Cl2 at 44–50°C. TIPS-protected alcohols also undergo deprotection but at slower rates. TBDPS-protected alcohols and silyl-protected phenols are unreactive under these conditions, allowing for selective deprotection of differentially-protected bis-silyl ethers.
John Ellipsoid and the Center of Mass of a Convex Body

It is natural to ask whether the center of mass of a convex body $$K\subset {\mathbb {R}}^n$$ lies in its John ellipsoid $$B_K$$ , i.e., in the maximal volume ellipsoid contained in K. This question is relevant to the efficiency of many algorithms for convex bodies. In this paper, we obtain an unexpected negative result. There exists a convex body $$K\subset {\mathbb {R}}^n$$ such that its center of mass does not lie in the John ellipsoid $$B_K$$ inflated $$\bigl (1-C\sqrt{\frac{\log (n)}{n}}\bigr )n$$ times about the center of $$B_K$$ . Moreover, there exists a polytope $$P \subset {\mathbb {R}}^n$$ with $$O(n^2)$$ facets whose center of mass is not contained in the John ellipsoid $$B_P$$ inflated $$O\bigl (\frac{n}{\log (n)}\bigr )$$ times about the center of $$B_P$$ .
Online Ensemble Multi-kernel Learning Adaptive to Non-stationary and Adversarial Environments

Kernel-based methods exhibit well-documented performance in various nonlinear learning tasks. Most of them rely on a preselected kernel, whose prudent choice presumes task-specific prior information. To cope with this limitation, multi-kernel learning has gained popularity thanks to its flexibility in choosing kernels from a prescribed kernel dictionary. Leveraging the random feature approximation and its recent orthogonality-promoting variant, the present contribution develops an online multi-kernel learning scheme to infer the intended nonlinear function `on the fly.' To further boost performance in non-stationary environments, an adaptive multi-kernel learning scheme (termed AdaRaker) is developed with affordable computation and memory complexity. Performance is analyzed in terms of both static and dynamic regret. To our best knowledge, AdaRaker is the first algorithm that can optimally track nonlinear functions in non-stationary settings with theoretical guarantees. Numerical tests on real datasets are carried out to showcase the effectiveness of the proposed algorithms.
Nearly Minimax One-Sided Mixture-Based Sequential Tests

Abstract We focus on one-sided, mixture-based stopping rules for the problem of sequential testing a simple null hypothesis against a composite alternative. For the latter, we consider two cases—either a discrete alternative or a continuous alternative that can be embedded into an exponential family. For each case, we find a mixture-based stopping rule that is nearly minimax in the sense of minimizing the maximal Kullback–Leibler information. The proof of this result is based on finding an almost Bayes rule for an appropriate sequential decision problem and on high-order asymptotic approximations for the performance characteristics of arbitrary mixture-based stopping times. We also evaluate the asymptotic performance loss of certain intuitive mixture rules and verify the accuracy of our asymptotic approximations with simulation experiments.
Approximating pointwise products of Laplacian eigenfunctions

Abstract We consider Laplacian eigenfunctions on a d-dimensional bounded domain M (or a d-dimensional compact manifold M) with Dirichlet conditions. These operators give rise to a sequence of eigenfunctions ( e l ) l ∈ N . We study the subspace of all pointwise products A n = span { e i ( x ) e j ( x ) : 1 ≤ i , j ≤ n } ⊆ L 2 ( M ) . Clearly, that vector space has dimension dim ( A n ) = n ( n + 1 ) / 2 . We prove that products e i e j of eigenfunctions are simple in a certain sense: for any e > 0 , there exists a low-dimensional vector space B n that almost contains all products. More precisely, denoting the orthogonal projection Π B n : L 2 ( M ) → B n , we have ∀ 1 ≤ i , j ≤ n ‖ e i e j − Π B n ( e i e j ) ‖ L 2 ≤ e and the size of the space dim ( B n ) is relatively small: for every δ > 0 , dim ( B n ) ≲ M , δ e − δ n 1 + δ . We obtain the same sort of bounds for products of arbitrary length, as well for approximation in H − 1 norm. Pointwise products of eigenfunctions are low-rank. This has implications, among other things, for the validity of fast algorithms in electronic structure computations.
Distributional Semantics Approach to Detect Intent in Twitter Conversations on Sexual Assaults

The recent surge in women reporting sexual assault and harassment (e.g., #metoo campaign) has highlighted a longstanding societal crisis. This injustice is partly due to a culture of discrediting women who report such crimes and also, rape myths (e.g., 'women lie about rape'). Social web can facilitate the further proliferation of deceptive beliefs and culture of rape myths through intentional messaging by malicious actors. This multidisciplinary study investigates Twitter posts related to sexual assaults and rape myths for characterizing the types of malicious intent, which leads to the beliefs on discrediting women and rape myths. Specifically, we first propose a novel malicious intent typology for social media using the guidance of social construction theory from policy literature that includes Accusational, Validational, or Sensational intent categories. We then present and evaluate a malicious intent classification model for a Twitter post using semantic features of the intent senses learned with the help of convolutional neural networks. Lastly, we analyze a Twitter dataset of four months using the intent classification model to study narrative contexts in which malicious intents are expressed and discuss their implications for gender violence policy design.
Nonlinear saturation of kinetic ballooning modes by zonal fields in toroidal plasmas

Kinetic ballooning modes (KBMs) are widely believed to play a critical role in disruptive dynamics as well as turbulent transport in magnetic fusion and space plasmas. While the nonlinear evolution of the ballooning modes has been proposed as a mechanism for “detonation” in various scenarios such as the edge localized modes in tokamaks, the role of the kinetic effects in such nonlinear dynamics remains largely unexplored. In this work, global gyrokinetic simulation results of KBM nonlinear behavior are presented. Instead of the finite-time singularity predicted by ideal magnetohydrodynamic theory, the kinetic instability is shown to develop into an intermediate nonlinear regime of exponential growth, followed by a nonlinear saturation regulated by spontaneously generated zonal fields. In the intermediate nonlinear regime, rapid growth of localized current sheets, which can induce magnetic reconnection, is observed.
Schur complement‐based domain decomposition preconditioners with low‐rank corrections

This paper introduces a robust preconditioner for general sparse symmetric matrices, that is based on low-rank approximations of the Schur complement in a Domain Decomposition (DD) framework. In this "Schur Low Rank" (SLR) preconditioning approach, the coefficient matrix is first decoupled by DD, and then a low-rank correction is exploited to compute an approximate inverse of the Schur complement associated with the interface points. The method avoids explicit formation of the Schur complement matrix. We show the feasibility of this strategy for a model problem, and conduct a detailed spectral analysis for the relationship between the low-rank correction and the quality of the preconditioning. Numerical experiments on general matrices illustrate the robustness and efficiency of the proposed approach.
Multi-year optimization of malaria intervention: a mathematical model

Malaria is a mosquito-borne, lethal disease that affects millions and kills hundreds of thousands of people each year, mostly children. There is an increasing need for models of malaria control. In this paper, a model is developed for allocating malaria interventions across geographic regions and time, subject to budget constraints, with the aim of minimizing the number of person-days of malaria infection. The model considers a range of several conditions: climatic characteristics, treatment efficacy, distribution costs, and treatment coverage. An expanded susceptible-infected-recovered compartment model for the disease dynamics is coupled with an integer linear programming model for selecting the disease interventions. The model produces an intervention plan for all regions, identifying which combination of interventions, with which level of coverage, to use in each region and year in a 5-year planning horizon. Simulations using the model yield high-level, qualitative insights on optimal intervention policies: The optimal intervention policy is different when considering a 5-year time horizon than when considering only a single year, due to the effects that interventions have on the disease transmission dynamics. The vaccine intervention is rarely selected, except if its assumed cost is significantly lower than that predicted in the literature. Increasing the available budget causes the number of person-days of malaria infection to decrease linearly up to a point, after which the benefit of increased budget starts to taper. The optimal policy is highly dependent on assumptions about mosquito density, selecting different interventions for wet climates with high density than for dry climates with low density, and the interventions are found to be less effective at controlling malaria in the wet climates when attainable intervention coverage is 60 % or lower. However, when intervention coverage of 80 % is attainable, then malaria prevalence drops quickly in all geographic regions, even when factoring in the greater expense of the higher coverage against a constant budget. The model provides a qualitative decision-making tool to weigh alternatives and guide malaria eradication efforts. A one-size-fits-all campaign is found not to be cost-effective; it is better to consider geographic variations and changes in malaria transmission over time when determining intervention strategies.
Weakly-Supervised Video Object Grounding from Text by Loss Weighting and Object Interaction

We study weakly-supervised video object grounding: given a video segment and a corresponding descriptive sentence, the goal is to localize objects that are mentioned from the sentence in the video. During training, no object bounding boxes are available, but the set of possible objects to be grounded is known beforehand. Existing approaches in the image domain use Multiple Instance Learning (MIL) to ground objects by enforcing matches between visual and semantic features. A naive extension of this approach to the video domain is to treat the entire segment as a bag of spatial object proposals. However, an object existing sparsely across multiple frames might not be detected completely since successfully spotting it from one single frame would trigger a satisfactory match. To this end, we propagate the weak supervisory signal from the segment level to frames that likely contain the target object. For frames that are unlikely to contain the target objects, we use an alternative penalty loss. We also leverage the interactions among objects as a textual guide for the grounding. We evaluate our model on the newly-collected benchmark YouCook2-BoundingBox and show improvements over competitive baselines.
Spatially Adaptive Colocalization Analysis in Dual-Color Fluorescence Microscopy

Colocalization analysis aims to study complex spatial associations between bio-molecules via optical imaging techniques. However, existing colocalization analysis workflows only assess an average degree of colocalization within a certain region of interest and ignore the unique and valuable spatial information offered by microscopy. In the current work, we introduce a new framework for colocalization analysis that allows us to quantify colocalization levels at each individual location and automatically identify pixels or regions where colocalization occurs. The framework, referred to as spatially adaptive colocalization analysis (SACA), integrates a pixel-wise local kernel model for colocalization quantification and a multi-scale adaptive propagation-separation strategy for utilizing spatial information to detect colocalization in a spatially adaptive fashion. Applications to simulated and real biological datasets demonstrate the practical merits of SACA in what we hope to be an easily applicable and robust colocalization analysis method. In addition, the theoretical properties of SACA are investigated to provide rigorous statistical justification.
Covert communications on renewal packet channels

In recent years, the information theory of covert communications, where the very presence of the communication is undetectable to a watchful adversary Willie, has been of great interest. Our recent work introduced the information-theoretic limits for communication by covert users Alice and Bob, over packet channels where the packet timings of legitimate users Jack and Steve are governed by a Poisson point process. Here we consider the extension to timing channels characterized by more general renewal processes of rate λ. We consider two scenarios. In the first scenario, the source of the packets on the channel cannot be authenticated by Willie, and therefore Alice can insert packets into the channel. We show that if the total number of transmitted packets by Jack is N, Alice can covertly insert O(√N)packets and, if she transmits more, she will be detected by Willie. In the second scenario, packets are authenticated by Willie but we assume that Alice and Bob share a secret key; hence, Alice alters the timings of the packets according to a pre-shared codebook with Bob to send information to him over a G/M/1 queue with service rate µ > λ. We show that Alice can covertly and reliably transmit O(N) bits to Bob when the total number of packets sent from Jack to Steve is N.
Asynchronous Distributed Optimization with Heterogeneous Regularizations and Normalizations

As multi-agent networks grow in size and scale, they become increasingly difficult to synchronize, though agents must work together even when generating and sharing different information at different times. Targeting such cases, this paper presents an asynchronous optimization framework in which the time between successive communications and computations is unknown and unspecified for each agent. Agents' updates are carried out in blocks, with each agent updating only a small subset of all decision variables. To provide robustness to asynchrony, each agent uses an independently chosen Tikhonov regularization. Convergence is measured with respect to a weighted block-maximum norm in which convergence of agents' blocks can be measured in different p-norms and weighted differently to heterogeneously normalize problems. Asymptotic convergence is shown and convergence rates are derived explicitly in terms of a problem's parameters, with only mild restrictions imposed upon them. Simulation results are provided to verify the theoretical developments made.
A positive Grassmannian analogue of the permutohedron

The classical permutohedron Perm is the convex hull of the points (w(1),...,w(n)) in R^n where w ranges over all permutations in the symmetric group. This polytope has many beautiful properties -- for example it provides a way to visualize the weak Bruhat order: if we orient the permutohedron so that the longest permutation w_0 is at the "top" and the identity e is at the "bottom," then the one-skeleton of Perm is the Hasse diagram of the weak Bruhat order. Equivalently, the paths from e to w_0 along the edges of Perm are in bijection with the reduced decompositions of w_0. Moreover, the two-dimensional faces of the permutohedron correspond to braid and commuting moves, which by the Tits Lemma, connect any two reduced expressions of w_0. In this note we introduce some polytopes Br(k,n) (which we call bridge polytopes) which provide a positive Grassmannian analogue of the permutohedron. In this setting, BCFW bridge decompositions of reduced plabic graphs play the role of reduced decompositions. We define Br(k,n) and explain how paths along its edges encode BCFW bridge decompositions of the longest element pi(k,n) in the circular Bruhat order. We also show that two-dimensional faces of Br(k,n) correspond to certain local moves for plabic graphs, which by a result of Postnikov [Pos06], connect any two reduced plabic graphs associated to pi(k,n). All of these results can be generalized to the positive parts of Schubert cells. A useful tool in our proofs is the fact that our polytopes are isomorphic to certain Bruhat interval polytopes. Conversely, our results on bridge polytopes allow us to deduce some corollaries about the structure of Bruhat interval polytopes.
Online Non-Additive Path Learning under Full and Partial Information

We study the problem of online path learning with non-additive gains, which is a central problem appearing in several applications, including ensemble structured prediction. We present new online algorithms for path learning with non-additive count-based gains for the three settings of full information, semi-bandit and full bandit with very favorable regret guarantees. A key component of our algorithms is the definition and computation of an intermediate context-dependent automaton that enables us to use existing algorithms designed for additive gains. We further apply our methods to the important application of ensemble structured prediction. Finally, beyond count-based gains, we give an efficient implementation of the EXP3 algorithm for the full bandit setting with an arbitrary (non-additive) gain.
Optimal binary constant weight codes and affine linear groups over finite fields

The affine linear group of degree one, $$\text {AGL}(1,\mathbb {F}_q)$$ , over the finite field $$\mathbb {F}_q$$ , acts sharply two-transitively on $$\mathbb {F}_q$$ . Given $$S<\text {AGL}(1,\mathbb {F}_q)$$ and an integer k, $$1\le k\le q$$ , does there exist a k-element subset $$B\subset \mathbb {F}_q$$ whose set-wise stabilizer is S? Our main result is the derivation of two formulas which provide an answer to this question. This result allows us to determine all possible parameters of binary constant weight codes that are constructed from the action of $$\text {AGL}(1,\mathbb {F}_q)$$ on $$\mathbb {F}_q$$ to meet the Johnson bound. Consequently, for many parameters, we are able to determine the values of the function $$A_2(n,d,w)$$ , which is the maximum number of codewords in a binary constant weight code of length n, weight w and minimum distance $$\ge d$$ .
PFA and guessing models

This paper explores the consistency strength of The Proper Forcing Axiom (PFA) and the theory (T) which involves a variation of the Viale–Weiβ guessing hull principle. We show that (T) is consistent relative to a supercompact cardinal. The main result of the paper is Theorem 0.2, which implies that the theory “ADR + ⊝ is regular” is consistent relative to (T) and to PFA. This improves significantly the previous known best lower-bound for consistency strength for (T) and PFA, which is roughly “ADR + DC”.