cssi/SciSciGPT-SciSciNet huggingface dataset:
BEINGs: knowledge as interacting experts

Knowledge may be organized as a community of intfiacting modules Each module is granted a complex stiucture, to simulate a particular expert in some small domain An extended analogy is drawn to a group of cooperating human specialists Based on this, an internal constraint is imposed on the modules. Then structure must be standard over the entire community Some advantages of a uniform formalism are thereby preserved. An experimental community was implemented for the task domain of automatic programming. It has managed to synthesize a few inductive inference LISP programs, nonformally. from specific restricted dialogues with a human user.
End-to-End Resilience for HPC Applications

A plethora of resilience techniques have been investigated to protect application kernels. If, however, such techniques are combined and they interact across kernels, new vulnerability windows are created. This work contributes the idea of end-to-end resilience by protecting windows of vulnerability between kernels guarded by different resilience techniques. It introduces the live vulnerability factor (LVF), a new metric that quantifies any lack of end-to-end protection for a given data structure. The work further promotes end-to-end application protection across kernels via a pragma-based specification for diverse resilience schemes with minimal programming effort. This lifts the data protection burden from application programmers allowing them to focus solely on algorithms and performance while resilience is specified and subsequently embedded into the code through the compiler/library and supported by the runtime system. In experiments with case studies and benchmarks, end-to-end resilience has an overhead over kernel-specific resilience of less than \(3\%\) on average and increases protection against bit flips by a factor of three to four.
CD8β Depletion Does Not Prevent Control of Viral Replication or Protection from Challenge in Macaques Chronically Infected with a Live Attenuated Simian Immunodeficiency Virus.

ABSTRACT We evaluated the contribution of CD8αβ+ T cells to control of live-attenuated simian immunodeficiency virus (LASIV) replication during chronic infection and subsequent protection from pathogenic SIV challenge. Unlike previous reports with a CD8α-specific depleting monoclonal antibody (mAb), the CD8β-specific mAb CD8β255R1 selectively depleted CD8αβ+ T cells without also depleting non-CD8+ T cell populations that express CD8α, such as natural killer (NK) cells and γδ T cells. Following infusion with CD8β255R1, plasma viremia transiently increased coincident with declining peripheral CD8αβ+ T cells. Interestingly, plasma viremia returned to predepletion levels even when peripheral CD8αβ+ T cells did not. Although depletion of CD8αβ+ T cells in the lymph node (LN) was incomplete, frequencies of these cells were 3-fold lower (P = 0.006) in animals that received CD8β255R1 than in those that received control IgG. It is possible that these residual SIV-specific CD8αβ+ T cells may have contributed to suppression of viremia during chronic infection. We also determined whether infusion of CD8β255R1 in the LASIV-vaccinated animals increased their susceptibility to infection following intravenous challenge with pathogenic SIVmac239. We found that 7/8 animals infused with CD8β255R1, and 3/4 animals infused with the control IgG, were resistant to SIVmac239 infection. These results suggest that infusion with CD8β255R1 did not eliminate the protection afforded to LASIV vaccination. This provides a comprehensive description of the impact of CD8β255R1 infusion on the immunological composition in cynomolgus macaques, compared to an isotype-matched control IgG, while showing that the control of LASIV viremia and protection from challenge can occur even after CD8β255R1 administration. IMPORTANCE Studies of SIV-infected macaques that deplete CD8+ T cells in vivo with monoclonal antibodies have provided compelling evidence for their direct antiviral role. These studies utilized CD8α-specific mAbs that target both the major (CD8αβ+) and minor (CD8αα+) populations of CD8+ T cells but additionally deplete non-CD8+ T cell populations that express CD8α, such as NK cells and γδ T cells. In the current study, we administered the CD8β-specific depleting mAb CD8β255R1 to cynomolgus macaques chronically infected with a LASIV to selectively deplete CD8αβ+ T cells without removing CD8αα+ lymphocytes. We evaluated the impact on control of virus replication and protection from pathogenic SIVmac239 challenge. These results underscore the utility of CD8β255R1 for studying the direct contribution of CD8αβ+ T cells in various disease states.
Iron-Catalyzed C–N Bond Formation via the Beckmann Rearrangement

A simple, iron-based catalytic system allows for facile Beckmann rearrangement of various oximes. The mild conditions avoid the use of harsh or expensive acids, and the reactions do not require an ­inert atmosphere. Additionally, a range of amides can be accessed through this transformation.
Highly Selective Reduction of Acyclic β-Alkoxy Ketones to Protected syn-1,3-Diols

The conversion of 1-(2-methoxyethoxy)ethyl-protected β-hydroxy ketones to syn-1,3-ethylidene acetals is effected by Et3SiH and SnCl4. This reaction is proposed to proceed via a cyclic oxocarbenium ion intermediate and provides the products in yields that range from 69 to 94% and with diastereoselectivities that are >200:1.
Estimating Approximate Incentive Compatibility

In practice, most mechanisms for selling, buying, matching, voting, and so on are not incentive compatible. We present techniques for estimating how far a mechanism is from incentive compatible. Given samples from the agents' type distribution, we show how to estimate the extent to which an agent can improve his utility by misreporting his type. We do so by first measuring the maximum utility an agent can gain by misreporting his type on average over the samples, assuming his true and reported types are from a finite subset---which our technique constructs---of the type space. The challenge is that by measuring utility gains over a finite subset of the type space, we might miss pairs of types t and t' where an agent with type t can greatly improve his utility by reporting the type t'. Our technique discretizes the type space by constructing a learning-theoretic cover in a higher-dimensional space. The key technical contribution is proving that the maximum utility gain over this finite subset nearly matches the maximum utility gain overall, despite the volatility of the utility functions we study. We apply our tools to the single-item and combinatorial first-price auctions, generalized second-price auction, discriminatory auction, uniform-price auction, and second-price auction with spiteful bidders. To our knowledge, these are the first guarantees for estimating approximate incentive compatibility from the mechanism designer's perspective.
D-amino acids as novel P2/P3 ligands for inhibitors of HIV-1 protease

Abstract Noncoded D-amino acids have been synthesized which effectively replace the P2/P3 ligands of the HIV-1 protease inhibitor LY289612. Several analogues are shown to have potent enzyme inhibitory and antiviral activities.
[H2bipy]2[(UO2)6Zn2(PO3OH)4(PO4)4].H2O: an open-framework uranyl zinc phosphate templated by diprotonated 4,4'-bipyridyl.

Under mild hydrothermal conditions, a new organically templated uranyl zinc phosphate, [H 2 bipy] 2 [(UO 2 ) 6 -Zn 2 (PO 3 OH) 4 (PO 4 ) 4 ]· H 2 O (UZnP-2), has been synthesized. Structural analysis reveals that UZnP-2 is constructed from UO 7 pentagonal bipyramids that are linked into edge-sharing dimers that are in turn joined together by ZnO 4 and PO 4 tetrahedra to form a three-dimensional network. Intersecting channels occur along the a, b, and c axes. These channels house the diprotonated 4,4'-bipyridyl cations and water molecules. Ion-exchange experiments demonstrate that replacement of the 4,4'-bipyridyl cations by alkali and alkaline-earth metal cations results in a rearrangement of the framework. Further characterization of UZnP-2 is provided by Raman and fluorescence spectroscopy. The latter method reveals strong emission from the uranyl moieties with characteristic fine structure.
Proton conductivity of glycosaminoglycans.

Proton conductivity is important in many natural phenomena including oxidative phosphorylation in mitochondria and archaea, uncoupling membrane potentials by the antibiotic Gramicidin, and proton actuated bioluminescence in dinoflagellate. In all of these phenomena, the conduction of protons occurs along chains of hydrogen bonds between water and hydrophilic residues. These chains of hydrogen bonds are also present in many hydrated biopolymers and macromolecule including collagen, keratin, chitosan, and various proteins such as reflectin. All of these materials are also proton conductors. Recently, our group has discovered that the jelly found in the Ampullae of Lorenzini- shark’s electro-sensing organs- is the highest naturally occurring proton conducting substance. The jelly has a complex composition, but we proposed that the conductivity is due to the glycosaminoglycan keratan sulfate (KS). Here we measure the proton conductivity of hydrated keratan sulfate purified from Bovine Cornea. PdHx contacts at 0.50 ± 0.11 mS cm -1, which is consistent to that of Ampullae of Lorenzini jelly at 2 ± 1 mS cm -1. Proton conductivity, albeit with lower values, is also shared by other glycosaminoglycans with similar chemical structures including dermatan sulfate, chondroitin sulfate A, heparan sulfate, and hyaluronic acid. This observation supports the relationship between proton conductivity and the chemical structure of biopolymers.
Loss of One Engrailed1 Allele Enhances Induced α-Synucleinopathy.

Background Parkinson's disease (PD) is a synucleinopathy that has multiple neuropathological characteristics, with nigrostriatal dopamine system degeneration being a core feature. Current models of PD pathology typically fail to recapitulate several attributes of the pathogenic process and neuropathology. We aimed to define the effects of combining a mouse model exhibiting multiple PD-like changes with intrastriatal injections of α-synuclein (α-syn) pre-formed fibril (PFFs) aggregates. We employed the heterozygous Engrailed 1 (En1+/-) mouse that features several pathophysiological hallmarks of clinical PD. Objective To test the hypothesis that the neuropathological changes in the En1+/- mice will promote formation of α-syn aggregates following intrastriatal injections of pathogenic human α-syn PFFs. Methods We unilaterally injected PFFs into the striata of 1-month-old En1+/- and control wild-type mice and euthanized animals at 3 months for post-mortem analysis. Results Using immunohistochemistry and unbiased stereology, we established that PFF-injected En1+/- mice exhibited a near-threefold increase in pS129-α-syn-positive neurons in the substantia nigra compared to PFF-injected wild-type mice. The PFF-injected En1+/- mice also displayed significant increases in pS129-α-syn-positive neurons in the amygdala and ventral tegmental area; regions of known PD pathology with projections to the striatum. Additionally, we observed amplified pS129-α-syn-positive aggregation in En1+/- mice in multiple cortical regions. Conclusions Following intrastriatal injection of PFFs, absence of an En1 allele leads to additional aggregation of pathological α-syn, potentially due to En1-loss mediated nigrostriatal impairment. We propose that further development of this double-hit model could result in a PD mouse model that predicts which experimental therapies will be effective in PD.
A Pooled Sequencing Approach Identifies a Candidate Meiotic Driver in Drosophila

Meiotic drive occurs when a selfish element increases its transmission frequency above the Mendelian ratio by hijacking the asymmetric divisions of female meiosis. Meiotic drive causes genomic conflict and potentially has a major impact on genome evolution, but only a few drive loci of large effect have been described. New methods to reliably detect meiotic drive are therefore needed, particularly for discovering moderate-strength drivers that are likely to be more prevalent in natural populations than strong drivers. Here, we report an efficient method that uses sequencing of large pools of backcross (BC1) progeny to test for deviations from Mendelian segregation genome-wide with single-nucleotide polymorphisms (SNPs) that distinguish the parental strains. We show that meiotic drive can be detected by a characteristic pattern of decay in distortion of SNP frequencies, caused by recombination unlinking the driver from distal loci. We further show that control crosses allow allele-frequency distortion caused by meiotic drive to be distinguished from distortion resulting from developmental effects. We used this approach to test whether chromosomes with extreme telomere-length differences segregate at Mendelian ratios, as telomeric regions are a potential hotspot for meiotic drive due to their roles in meiotic segregation and multiple observations of high rates of telomere sequence evolution. Using four different pairings of long and short telomere strains, we find no evidence that extreme telomere-length variation causes meiotic drive in Drosophila However, we identify one candidate meiotic driver in a centromere-linked region that shows an ∼8% increase in transmission frequency, corresponding to a ∼54:46 segregation ratio. Our results show that candidate meiotic drivers of moderate strength can be readily detected and localized in pools of BC1 progeny.
Application of β-lactams in the synthesis of substance P antagonists: Preparation of 2-azabicyclo[3.3.1]nonane ring systems

Abstract Intramolecular ureidomercuration of β-aminoacids synthesized from appropriate β-lactams provides an expeditious route to the synthesis of 2-aza-bicyclo[3.3.1]nonane ring systems. Synthesis of the locked-in chair conformer 2 of CP-99,994 is described.
Boiler: lossy compression of RNA-seq alignments using coverage vectors

We describe Boiler, a new software tool for compressing and querying large collections of RNA-seq alignments. Boiler discards most per-read data, keeping only a genomic coverage vector plus a few empirical distributions summarizing the alignments. Since most per-read data is discarded, storage footprint is often much smaller than that achieved by other compression tools. Despite this, the most relevant per-read data can be recovered; we show that Boiler compression has only a slight negative impact on results given by downstream tools for isoform assembly and quantification. Boiler also allows the user to pose fast and useful queries without decompressing the entire file. Boiler is free open source software available from github.com/jpritt/boiler.
Validating Antibodies for Quantitative Western Blot Measurements with Microwestern Array

Fluorescence-based western blots are quantitative in principal, but require determining linear range for each antibody. Here, we use microwestern array to rapidly evaluate suitable conditions for quantitative western blotting, with up to 192 antibody/dilution/replicate combinations on a single standard size gel with a seven-point, two-fold lysate dilution series (~100-fold range). Pilot experiments demonstrate a high proportion of investigated antibodies (17/24) are suitable for quantitative use; however this sample of antibodies is not yet comprehensive across companies, molecular weights, and other important antibody properties, so the ubiquity of this property cannot yet be determined. In some cases microwestern struggled with higher molecular weight membrane proteins, so the technique may not be uniformly applicable to all validation tasks. Linear range for all validated antibodies is at least 8-fold, and up to two orders of magnitude. Phospho-specific and total antibodies do not have discernable trend differences in linear range or limit of detection. Total antibodies generally required higher working concentrations, but more comprehensive antibody panels are required to better establish whether this trend is general or not. Importantly, we demonstrate that results from microwestern analyses scale to normal “macro” western for a subset of antibodies.
Reaction of triflyl-imidazole with aldoximes: facile synthesis of nitriles and formation of novel aldoxime-bis(N-triflyl)-imidazole adducts

Abstract The synthetic utility of N -triflylimidazole as an in situ reagent for facile, high yielding, synthesis of various aliphatic, aromatic, and heteroaromatic nitriles from the corresponding aldoximes has been demonstrated. With benzaldoximes, in the presence of certain substitutents (2-F; 2-OMe; 3-CF 3 ; 2-Me-5-F) a different course of reaction was observed, leading instead to novel 1:1 aldoxime-bis( N -triflyl)imidazole covalent adducts, in which the aldoxime oxygen atom is bonded to the imidazole C-2 ring carbon. For these aldoximes, conversion to nitrile could be effected by reaction with Tf 2 O in the absence of imidazole. The molecular structure of the adduct formed from 2-methyl-5-fluoro-benzaldoxime was confirmed by X-ray analysis. Plausible mechanisms for the formation of 1:1 covalent adducts have been considered. Various attempts to isolate such adducts via the reaction of an authentic sample of bis( N -triflyl)imidazolium trifate with aldoxime were unsuccessful. Remarkably, whereas isolated benzaldoxime adducts undergo deprotonation/methylation with NaH/MeI, an authentic sample of bis( N -triflyl)imidazolium triflate did not undergo H/Me exchange under these conditions. These transformations are discussed.
Synthetic Routes to 4H-7-Hydroxybenzo[b]tellurin-4-ones

Intramolecular acylation of Z-3-(3-hydroxyphenyltelluro)propenoic acids 9 with P2O5/CH3SO3H gave 4H-7-hydroxybenzo[b]tellurin-4-ones 10a−c in 42%, 25%, and 20% isolated yields, respectively. 4H-7-Hydroxybenzo[b]tellurin-4-ones 10a−d were also prepared by demethylation of 4H-7-methoxybenzo[b]tellurin-4-ones 11 with BBr3 in CH2Cl2 in 88%, 70%, 66%, and 78% isolated yields.
PHOTOLUMINESCENT PROPERTIES OF CADMIUM SELENIDE IN CONTACT WITH SOLUTIONS AND FILMS OF VASKA'S COMPLEX : EFFECTS OF OXYGEN AND CARBON MONOXIDE

The band-edge photoluminescence (PL) intensity of etched n-CdSe single crystals is reversibly enhanced in the presence of nitrogen-saturated toluene solutions of trans-IrCl(CO)(PPh3)2, Vaska's comp...
Stereoselective Reactions of δ2-Isoxazoline Exo-azaenolates. A Model for Construction of the C-Ring of Sesbanimide A

Abstract A Stereoselective aldol reaction between bis(tert-butyldimethylsilyloxy) acetone and an isoxazoline-derived azaenolate is a key step in the construction of a C-ring model of sesbanimide A.
Synthesis and self-assembly of supramolecular dendritic "Bow-Ties": effect of peripheral functionality on association constants.

Self-assembled polyester dendritic bow-ties with various peripheral groups were prepared, and their association constants were measured by 1H NMR in CDCl3. The two complementary dendrons were prepared by attachment of either a bis(adamantylurea) or a glycinylurea to the focal point of the dendron. The parent self-assembled system with benzylidene acetals on one periphery and isopropylidene acetals on the other had an association constant of 520 M-1. Upon deprotection of one dendron, the association constant is increased by more than an order of magnitude as the solubility of the hydroxyl-terminated dendron in CDCl3 is decreased. In contrast, attachment of tri(ethylene oxide) units to the periphery of one dendron lowers the association constant by almost an order of magnitude. The causes of these relatively large changes in complex strength are discussed in terms of solubility, steric effects, competitive hydrogen bonding, and the structure of the dendritic scaffold.
Artemisinin: A Case Study in the Evolution of Synthetic Strategy

Artemisinin represents one of the most important discoveries in the fight against malaria over the last 50 years. As the first endoperoxide-containing natural product, artemisinin has attracted chemists and biologists alike with its potent activity and rapid onset against malaria-causing Plasmodium species. Since its disclosure in 1979, artemisinin has been the subject of several elegant syntheses. Herein, the evolution of synthetic strategy is discussed in the context of artemisinin.
A Probabilistic Model of Compound Nouns

Compound nouns such as example noun compound are becoming more common in natural language and pose a number of difficult problems for NLP systems, notably increasing the complexity of parsing. In this paper we develop a probabilistic model for syntactically analysing such compounds. The model predicts compound noun structures based on knowledge of affinities between nouns, which can be acquired from a corpus. Problems inherent in this corpus-based approach are addressed: data sparseness is overcome by the use of semantically motivated word classes and sense ambiguity is explicitly handled in the model. An implementation based on this model is described in Lauer (1994) and correctly parses 77% of the test set.
Tuning the oxidation properties of vanadium(V) through ligand stoichiometry

Abstract Vanadium(V) (5 mol %) and hydroxamic acid ligand (45 mol %) were found to promote the selective tert -butyl hydroperoxide-mediated oxidation of allylic and propargylic alcohols to the corresponding aldehydes and ketones.
A Chemical Biology View of Bioactive Small Molecules and a Binder-Based Approach to Connect Biology to Precision Medicines.

A simplistic view of drug discovery is that it begins, most often using “model organisms”, with biological inferences of a disease that suggest the need to interfere with some activity, function or process. An enzyme should be inhibited or a pathogen should be killed. Chemical experimentation yields the desired inhibitor, and clinical investigations then test the underlying hypothesis in humans. If the stars align, an effective drug emerges. The high cost of testing and low rate of success of this paradigm has led the drug-discovery enterprise to search for new and more effective approaches. In this essay, I explore a concept that focuses on the discovery of compounds that bind targets rather than inhibit a biochemical activity. I present evidence that such ‘binders’ can affect protein activity in under-appreciated ways that have therapeutic potential. This approach is well aligned with a current trend in drug discovery – to exploit insights from human biology in order to select therapeutic targets with greater confidence and to understand the deficiencies of the targets that need correction. The targets emerging from this approach most frequently lack the “simple” activities that drive much of past drug discovery. Compounds are needed that engage these targets in new and challenging ways to elicit the novel activities suggested by human biology, especially enhancing functions of proteins and conferring new (neo) functions to proteins (Figure 1). Open in a separate window Figure 1 Topographically complex hot spots on proteins can be liganded with suitably shaped, often 3-D small molecules, which results in modulating functions in different ways. Binding alters the dynamic and structural features of proteins, resulting in: 1) novel interactions with other proteins and 2) changes in protein dynamics, stability, turnover rates, and tendency to be chemically modified by cellular enzymes. Each of these under-appreciated effects can have therapeutic consequences. In addition to the common use of binders to inhibit function, they can also restore or enhance function, or even create a new function. Achieving a framework of chemical biology that emulates nature and evolution, where nature evolves and optimizes not so much by losing functions, but by enhancing functions and inventing new ones, promises to unlock potential not only for eliminating disease states but also for enhancing and augmenting states of health and wellness.
High temperature redox reactions with uranium: Synthesis and characterization of Cs(UO2)Cl(SeO3), Rb2(UO2)3O2(SeO3)2, and RbNa5U2(SO4)7

Abstract Cs(UO2)Cl(SeO3) (1), Rb2(UO2)3O2(SeO3)3 (2), and RbNa5U2(SO4)7 (3) single crystals were synthesized using CsCl, RbCl, and a CuCl/NaCl eutectic mixture as fluxes, respectively. Their lattice parameters and space groups are as follows: P21/n (a=6.548(1) A, b=11.052(2) A, c=10.666(2) A and β=93.897(3)°), P 1 ¯ (a=7.051(2) A, b=7.198(2) A, c=8.314(2) A, α=107.897(3)°, β=102.687(3)° and γ=100.564(3)°) and C2/c (a=17.862(4) A, b=6.931(1) A, c=20.133(4) A and β=109.737(6)°. The small anionic building units found in these compounds are SeO32− and SO42− tetrahedra, oxide, and chloride. The crystal structure of the first compound is composed of [(UO2)2Cl2(SeO3)2]2− chains separated by Cs+ cations. The structure of (2) is constructed from [(UO2)3O11]16− chains further connected through selenite units into layers stacked perpendicularly to the [0 1 0] direction, with Rb+ cations intercalating between them. The structure of compound (3) is made of uranyl sulfate layers formed by edge and vertex connections between dimeric [U2O16] and [SO4] polyhedra. These layers contain unusual sulfate–metal connectivity as well as large voids.
Cis-selective preparation of 2,2-difluorocyclopropyl ketones via non-metal hydride reduction of 2,2-difluorocyclopropenyl ketones

Abstract Diastereoselective reduction of gem -difluorocyclopropenyl ketones was accomplished by their Bronsted acid catalyzed reactions with the non-metal based hydride transfer reagent, Hantzsch ester (diethyl 1,4-dihydro-2,6-dimethyl-3,5-pyridinedicarboxylate) (HEH). The high yield reactions produced a significantly cis -enriched product mixture, from which the cis -isomer could be readily separated by column chromatography.
The yeast scavenger decapping enzyme DcpS and its application for in vitro RNA recapping

Eukaryotic mRNAs are modified at their 5' end early during transcription by the addition of N7-methylguanosine (m7G), which forms the "cap" on the first 5' nucleotide. Identification of the 5' nucleotide on mRNA is necessary for determination of the Transcription Start Site (TSS). We explored the effect of various reaction conditions on the activity of the yeast scavenger mRNA decapping enzyme DcpS and examined decapping of 30 chemically distinct cap structures varying the state of methylation, sugar, phosphate linkage, and base composition on 25mer RNA oligonucleotides. Contrary to the generally accepted belief that DcpS enzymes only decap short oligonucleotides, we found that the yeast scavenger decapping enzyme decaps RNA transcripts as long as 1400 nucleotides. Further, we validated the application of yDcpS for enriching capped RNA using a strategy of specifically tagging the 5' end of capped RNA by first decapping and then recapping it with an affinity-tagged guanosine nucleotide.
Reactions of isocyanates with methyl N-(cyanothioformyl)anthranilate

The triethylamine-catalyzed reactions of methyl N-(cyanothioformyl)anthranilate (1) with isocyanates result in cyclization involving the cyano group to form methyl 2-(4-imino-2-oxo-3-substituted-5-thioxoimi-dazolidin-1-yl)benzoates (4). Ring closure at the ester carbonyl to form 3-aryl-3,4-dihydro-4-oxoquinazo-line-2-carbonitriles (8) is observed when the S-methyl derivative of 1 is allowed to react with aromatic amines.
Oligomeric Thioglycosides with α-d-manno-(1‘→2) Linkages from a Glycal-1,2-episulfide

Under basic conditions, phenyl 1,2-dithio-α-d-mannopyranoside forms a glycal-1,2-episulfide, which undergoes controlled oligomerization to afford a family of thio-oligo-α-d-mannopyranosides in a single reaction. The episulfide can also be intercepted by added thiolates, which leads to other sorts of thioglycosides. These α-(1→2)-linked thio-mannopyranosides might have application as mimics of natural structures such as viral high-mannose glycoproteins or ManLAM.
Chromium catalyzed kinetic resolution of 2,2-disubstituted epoxides

Abstract Chiral (salen)Cr(III) complex 2 is an efficient catalyst for the kinetic resolution of 2,2-disubstituted epoxides. The scope and limitations of this methodology are described.
Transition-Metal Silyl Complexes and Chemistry in the Reactions of Silanes with Transition-Metal Complexes

Studies from the authors' group of early-transition-metal silyl complexes and pathways in the reactions of silanes with transition-metal complexes are reviewed. Cyclopentadienyl-free, group 4 alkyl silyl, group 5 alkylidene silyl, group 6 alkylidyne silyl, and groups 4 and 5 amide and imide silyl complexes have been prepared and characterized. In the reactions of silanes with alkylidene and amide complexes, the MCH− π bonds and d−p π bonds in MNR2 were found to attack Si in silanes. The mechanistic studies here help in understanding the formation of mixtures of TiN and Si3N4 from the reactions of Ti(NMe2)4 and SiH4 as microelectronic diffusion barrier materials.
Lewis acid mediated diastereoselective and enantioselective cyclopropanation of Michael acceptors with sulfur ylides

Abstract The reaction of N-enoyloxazolidinones with diphenylsulfonium isoproylide in the presence of Lewis acids is explored. The diastereoselectivity of the reaction of N-enoyloxazolidinones 1a and 1b with diphenylsulfonium isopropylide could be mediated by the addition of some Lewis acids. The reaction of N-enoyloxazolidinone 4 with diphenylsulfonium isoproylide was also explored with chiral Lewis acids. When this reaction was run with bis(oxazoline) ligand 6 and a number of Lewis acids, product was obtained in as high as 95% ee. A loss of stereoselectivity was observed with less than stoichiometric amounts of Lewis acid.
Shifts in outcrossing rates and changes to floral traits are associated with the evolution of herbicide resistance in the common morning glory.

Human-mediated selection can strongly influence the evolutionary response of natural organisms within ecological timescales. But what traits allow for, or even facilitate, adaptation to the strong selection humans impose on natural systems? Using a combination of laboratory and greenhouse studies of 32 natural populations of the common agricultural weed, Ipomoea purpurea, we show that herbicide-resistant populations self-fertilise more than susceptible populations. We likewise show that anther–stigma distance, a floral trait associated with self-fertilisation in this species, exhibits a nonlinear relationship with resistance such that the most and least resistant populations exhibit lower anther–stigma separation compared to populations with moderate levels of resistance. Overall, our results extend the general finding that plant mating can be impacted by human-mediated agents of selection to that of the extreme selection of the agricultural system. This work highlights the influence of human-mediated selection on rapid responses of natural populations that can lead to unexpected long-term evolutionary consequences.
Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community

Urban streams are susceptible to stormwater and sewage inputs that can impact their ecological health and water quality. Microbial communities in streams play important functional roles, and their composition and metabolic potential can help assess ecological state and water quality. Although these environments are highly heterogenous, little is known about the influence of isolated perturbations, such as those resulting from rain events on urban stream microbiota. Here, we examined the microbial community composition and diversity in an urban stream during dry and wet weather conditions with both 16S rRNA gene sequencing across multiple years and shotgun metagenomics to more deeply analyze a single storm flow event. Metagenomics was used to assess population-level dynamics as well as shifts in the microbial community taxonomic profile and functional potential before and after a substantial rainfall. The results demonstrated general trends present in the stream under storm flow versus base flow conditions and also highlighted the influence of increased effluent flow following rain in shifting the stream microbial community from abundant freshwater taxa to those more associated with urban/anthropogenic settings. Shifts in the taxonomic composition were also linked to changes in functional gene content, particularly for transmembrane transport and organic substance biosynthesis. We also observed an increase in relative abundance of genes encoding degradation of organic pollutants and antibiotic resistance after rain. Overall, this study highlighted some differences in the microbial community of an urban stream under storm flow conditions and showed the impact of a storm flow event on the microbiome from an environmental and public health perspective.IMPORTANCE Urban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and storm flow events represent one such source of complex physical, chemical, and biological perturbations. Microorganisms are important components of these streams from both ecological and public health perspectives. Analysis of the effect of perturbations on the stream microbial community can help improve current knowledge on the impact such chronic disturbances can have on these water resources. This study examines microbial community dynamics during rain-induced storm flow conditions in an urban stream of the Chicago Area Waterway System. Additionally, using shotgun metagenomics we identified significant shifts in the microbial community composition and functional gene content following a high-rainfall event, with potential environment and public health implications. Previous work in this area has focused on specific genes/organisms or has not assessed immediate storm flow impact.
A Theoretical Study of ClONO2 + Cl- → Cl2 + NO3- on Ice

The title reaction, of interest in connection with the central heterogeneous reaction HCl + ClONO2 → Cl2 + HNO3 for polar stratospheric ozone depletion, is studied quantum chemically at the Hartree−Fock level via a Cl-·ClONO2 complex anion embedded in a model ice lattice Cl-·ClONO2·(H2O)8·W29 comprising both quantum chemical and classical polarizable water molecules (W). The calculated reaction mechanism involves the nucleophilic attack of Cl- on the electrophilic Clδ+ in ClONO2, assisted by changes in hydrogen bonding involving both the desolvation of Cl- and the increased solvation of the nitrate group. The calculated reaction barrier at 0 K, including the zero-point energy correction, is 5.7 kcal/mol. This result is compared with previous results for the HCl + ClONO2 → Cl2 + HNO3 reaction (Bianco, R.; Hynes, J. T. J. Phys. Chem. A 1999, 103, 3797), and implications for stratospheric heterogeneous chemistry are discussed.
Submodular maximization with matroid and packing constraints in parallel

We consider the problem of maximizing the multilinear extension of a submodular function subject a single matroid constraint or multiple packing constraints with a small number of adaptive rounds of evaluation queries. We obtain the first algorithms with low adaptivity for submodular maximization with a matroid constraint. Our algorithms achieve a 1−1/e−є approximation for monotone functions and a 1/e−є approximation for non-monotone functions, which nearly matches the best guarantees known in the fully adaptive setting. The number of rounds of adaptivity is O(log2n/є3), which is an exponential speedup over the existing algorithms. We obtain the first parallel algorithm for non-monotone submodular maximization subject to packing constraints. Our algorithm achieves a 1/e−є approximation using O(log(n/є) log(1/є) log(n+m)/ є2) parallel rounds, which is again an exponential speedup in parallel time over the existing algorithms. For monotone functions, we obtain a 1−1/e−є approximation in O(log(n/є)logm/є2) parallel rounds. The number of parallel rounds of our algorithm matches that of the state of the art algorithm for solving packing LPs with a linear objective (Mahoney et al., 2016). Our results apply more generally to the problem of maximizing a diminishing returns submodular (DR-submodular) function.
Exchange Rate Reconnect

It is surprisingly difficult to find economic variables that strongly co-move with exchange rates, a phenomenon codified in a large literature on “exchange rate disconnect.” We demonstrate that a v...
Locally solvable subgroups of PLo(I) are countable

We show every locally solvable subgroup of PLo(I) is countable. A corollary is that an uncountable wreath product of copies of ℤ with itself does not embed into PLo(I).
MORF: A Framework for Predictive Modeling and Replication At Scale With Privacy-Restricted MOOC Data

Big data repositories from online learning platforms such as Massive Open Online Courses (MOOCs) represent an unprecedented opportunity to advance research on education at scale and impact a global population of learners. To date, such research has been hindered by poor reproducibility and a lack of replication, largely due to three types of barriers: experimental, inferential, and data. We present a novel system for large-scale computational research, the MOOC Replication Framework (MORF), to jointly address these barriers. We discuss MORF’s architecture, an open- source platform-as-a-service (PaaS) which includes a simple, flexible software API providing for multiple modes of research (predictive modeling or production rule analysis) integrated with a high-performance computing environment. All experiments conducted on MORF use executable Docker containers which ensure complete reproducibility while allowing for the use of any software or language which can be installed in the linux-based Docker container. Each experimental artifact is assigned a DOI and made publicly available. MORF has the potential to accelerate and democratize research on its massive data repository, which currently includes over 200 MOOCs, as demonstrated by initial research conducted on the platform. We also highlight ways in which MORF represents a solution template to a more general class of problems faced by computational researchers in other domains.
CNN-Based cascaded multi-task learning of high-level prior and density estimation for crowd counting

Estimating crowd count in densely crowded scenes is an extremely challenging task due to non-uniform scale variations. In this paper, we propose a novel end-to-end cascaded network of CNNs to jointly learn crowd count classification and density map estimation. Classifying crowd count into various groups is tantamount to coarsely estimating the total count in the image thereby incorporating a high-level prior into the density estimation network. This enables the layers in the network to learn globally relevant discriminative features which aid in estimating highly refined density maps with lower count error. The joint training is performed in an end-to-end fashion. Extensive experiments on highly challenging publicly available datasets show that the proposed method achieves lower count error and better quality density maps as compared to the recent state-of-the-art methods.
ChronoNet: A Deep Recurrent Neural Network for Abnormal EEG Identification

Brain-related disorders such as epilepsy can be diagnosed by analyzing electroencephalograms (EEG). However, manual analysis of EEG data requires highly trained clinicians, and is a procedure that is known to have relatively low inter-rater agreement (IRA). Moreover, the volume of the data and the rate at which new data becomes available make manual interpretation a time-consuming, resource-hungry, and expensive process. In contrast, automated analysis of EEG data offers the potential to improve the quality of patient care by shortening the time to diagnosis and reducing manual error. In this paper, we focus on one of the first steps in interpreting an EEG session - identifying whether the brain activity is abnormal or normal. To address this specific task, we propose a novel recurrent neural network (RNN) architecture termed ChronoNet which is inspired by recent developments from the field of image classification and designed to work efficiently with EEG data. ChronoNet is formed by stacking multiple 1D convolution layers followed by deep gated recurrent unit (GRU) layers where each 1D convolution layer uses multiple filters of exponentially varying lengths and the stacked GRU layers are densely connected in a feed-forward manner. We used the recently released TUH Abnormal EEG Corpus dataset for evaluating the performance of ChronoNet. Unlike previous studies using this dataset, ChronoNet directly takes time-series EEG as input and learns meaningful representations of brain activity patterns. ChronoNet outperforms previously reported results on this dataset thereby setting a new benchmark.
Limitations on dispersion relations for Generalized Parton Distributions

1- Department of Physics and AstronomyTufts University - Medford, MA 02155, USA2- Department of PhysicsUniversity of Virginia - Charlottesville, VA 22901, USA.Deeply Virtual Compton Scattering and electroproduction of mesons involve ampli-tudes that are analytic in energy. Analyticity enables Dispersion Relations (DR’s)for such amplitudes, relating real and imaginary parts. Lately it has been suggestedthat DR’s be applied to the integrated Generalized Parton Distributions that embodythe spin-dependent soft, but factorizable part of the scattering. However, at non-zeromomentum transfer, DRs require integration over unphysical regions of the variables.We show that the relevant unphysical region of the non-forward DRs is considerable,vitiating eﬀorts to avoid the actual measurement of the real parts more directly.
Universum Prescription: Regularization using Unlabeled Data

This paper shows that simply prescribing "none of the above" labels to unlabeled data has a beneficial regularization effect to supervised learning. We call it universum prescription by the fact that the prescribed labels cannot be one of the supervised labels. In spite of its simplicity, universum prescription obtained competitive results in training deep convolutional networks for CIFAR-10, CIFAR-100, STL-10 and ImageNet datasets. A qualitative justification of these approaches using Rademacher complexity is presented. The effect of a regularization parameter — probability of sampling from unlabeled data — is also studied empirically.
Simply Exponential Approximation of the Permanent of Positive Semidefinite Matrices

We design a deterministic polynomial time cn approximation algorithm for the permanent of positive semidefinite matrices where c = e+1 &#x22CD; 4:84. We write a natural convex relaxation and show that its optimum solution gives a cn approximation of the permanent. We further show that this factor is asymptotically tight by constructing a family of positive semidefinite matrices. We also show that our result implies an approximate version of the permanent-ontop conjecture, which was recently refuted in its original form; we show that the permanent is within a cn factor of the top eigenvalue of the Schur power matrix.
Low-Coherence Frames From Group Fourier Matrices

Many problems in areas such as compressive sensing and coding theory seek to design a set of equal-norm vectors with large angular separation. This idea is essentially equivalent to constructing a frame with low coherence. The elements of such frames can in turn be used to build high-performance spherical codes, quantum measurement operators, and compressive sensing measurement matrices, to name a few applications. In this paper, we allude to the group-frame construction first described by Slepian and further explored in the works of Vale and Waldron. We present a method for selecting representations of a finite group to construct a group frame that achieves low coherence. Our technique produces a tight frame with a small number of distinct inner product values between the frame elements, in a sense approximating a Grassmannian frame. We identify special cases in which our construction yields some previously known frames with optimal coherence meeting the Welch lower bound, and other cases in which the entries of our frame vectors come from small alphabets. In particular, we apply our technique to the problem choosing a subset of rows of an Hadamard matrix so that the resulting columns form a low-coherence frame. Finally, we give an explicit calculation of the average coherence of our frames, and find regimes in which they satisfy the strong coherence property described by Mixon, Bajwa, and Calderbank.
Answering Spatial Multiple-Set Intersection Queries Using 2-3 Cuckoo Hash-Filters

We show how to answer spatial multiple-set intersection queries in O(n(log w)/w + kt) expected time, where n is the total size of the t ≤ wc sets involved in the query, w is the number of bits in a memory word, k is the output size, and c ≥ 1 is any fixed constant.
Sterrett Procedure for the Generalized Group Testing Problem

Group testing is a useful method that has broad applications in medicine, engineering, and even in airport security control. Consider a finite population of N items, where item i has a probability pi to be defective. The goal is to identify all items by means of group testing. This is the generalized group testing problem. The optimum procedure, with respect to the expected total number of tests, is unknown even in case when all pi are equal. (Hwang 1975) proved that an ordered partition (with respect to pi) is the optimal for the Dorfman procedure (procedure D), and obtained an optimum solution (i.e., found an optimal partition) by dynamic programming. In this paper, we investigate the Sterrett procedure (procedure S). We provide close form expression for the expected total number of tests, which allows us to find the optimum arrangement of the items in the particular group. We also show that an ordered partition is not optimal for the procedure S or even for a slightly modified Dorfman procedure (procedure D′). This discovery implies that finding an optimal procedure S appears to be a hard computational problem. However, by using an optimal ordered partition for all procedures, we show that procedure D′ is uniformly better than procedure D, and based on numerical comparisons, procedure S is uniformly and significantly better than procedures D and D′.
Stacked Wasserstein Autoencoder

Abstract Approximating distributions over complicated manifolds, such as natural images, are conceptually attractive. The deep latent variable model, trained using variational autoencoders and generative adversarial networks, is now a key technique for representation learning. However, it is difficult to unify these two models for exact latent-variable inference and parallelize both reconstruction and sampling, partly due to the regularization under the latent variables, to match a simple explicit prior distribution. These approaches are prone to be oversimplified, and can only characterize a few modes of the true distribution. Based on the recently proposed Wasserstein autoencoder (WAE) with a new regularization as an optimal transport. The paper proposes a stacked Wasserstein autoencoder (SWAE) to learn a deep latent variable model. SWAE is a hierarchical model, which relaxes the optimal transport constraints at two stages. At the first stage, the SWAE flexibly learns a representation distribution, i.e., the encoded prior; and at the second stage, the encoded representation distribution is approximated with a latent variable model under the regularization encouraging the latent distribution to match the explicit prior. This model allows us to generate natural textual outputs as well as perform manipulations in the latent space to induce changes in the output space. Both quantitative and qualitative results demonstrate the superior performance of SWAE compared with the state-of-the-art approaches in terms of faithful reconstruction and generation quality.