cssi/SciSciGPT-SciSciNet huggingface dataset:
Evolving trade undercurrents at the regional level: tides of India’s preferential trading in the Indian Ocean and beyond

The Indian Ocean region has seen an exchange of goods and commodities since antiquity. Long before the emergence of modern nation states and the Westphalian concept of sovereignty, Indian territory saw a regular arrival of foreign merchants and commodities. At the same time, there is a long history of Indian merchants and commodities exploring the expanses of Southeast Asia, West Asia, Southeast Africa and beyond. The Indian Ocean region comprises a number of emerging and developing economies and is considered a dynamic region in terms of trade prospects. A number of preferential trade agreements are doing the round in this region which not only present a prospect to revive the age-old trade linkages within the Indian Ocean region but also foster a promising model of South-South cooperation. Being a large economy, India has an important role to play within the region. Not only that, platforms such as RCEP present India an opportunity to participate in rule-making in the realms of international economic law. Such engagements become even more significant when rule-making at the global trade institution WTO is experiencing a phase of stagnation and while the world is witnessing a wave of protectionism, isolationism, and very recently, a trade war between two giant economies.
Marx‐biased technical change and income distribution: A panel data analysis

This paper provides a further empirical evaluation of the Neoclassical theory of distribution as opposed to Marx‐biased technical change (MBTC) using a series of panel estimators. We argue that a panel data analysis is instrumental in increasing the efficiency and validity of the test. Our results generalize previous findings in providing support for MBTC and against the Neoclassical theory of income distribution.
Exceptional contours and band structure design in parity-time symmetric photonic crystals

We investigate the properties of 2D parity-time symmetric periodic systems whose periodicity is an integer multiple of the underlying Hermitian system’s periodicity. Such systems possess novel band structure engineering, and yield supercollimation.
Does computer vision matter for action

Computer vision produces representations of scene content. Much computer vision research is predicated on the assumption that these intermediate representations are useful for action. Recent work at the intersection of machine learning and robotics calls this assumption into question by training sensorimotor systems directly for the task at hand, from pixels to actions, with no explicit intermediate representations. Thus the central question of our work: Does computer vision matter for action? We probe this question and its offshoots via immersive simulation, which allows us to conduct controlled reproducible experiments at scale. We instrument immersive three-dimensional environments to simulate challenges such as urban driving, off-road trail traversal, and battle. Our main finding is that computer vision does matter. Models equipped with intermediate representations train faster, achieve higher task performance, and generalize better to previously unseen environments. A video that summarizes the work and illustrates the results can be found at this https URL
An Online Admission Control Mechanism for Electric Vehicles at Public Parking Infrastructures

We study an online reservation system that allows electric vehicles (EVs) to park and charge at parking facilities equipped with EV supply equipment (EVSEs). We consider the case where EVs arrive in an online fashion and the facility coordinator must immediately make an admission or rejection decision as well as assign a specific irrevocable parking spot to each admitted EV. By means of strategic user admittance and smart charging, the objective of the facility coordinator is to maximize total user utility minus the operational costs of the facilities. We discuss an online pricing mechanism based on primal-dual methods for combinatorial auctions that functions as both an admission controller and a distributor of the facilities’ limited charging resources. We analyze the online pricing mechanism’s performance compared to the optimal offline solution and provide numerical results that validate the mechanism’s performance for various test cases.
Rural Clients' Continuity Into Follow-Up Substance Use Disorder Treatment: Impacts of Travel Time, Incentives, and Alerts.

Purpose Treatment after discharge from detoxification or residential treatment is associated with improved outcomes. We examined the influence of travel time on continuity into follow-up treatment and whether financial incentives and weekly alerts have a modifying effect. Methods For a research intervention during October 2013 to December 2015, detoxification and residential substance use disorder treatment programs in Washington State were randomized into 4 groups: potential financial incentives for meeting performance goals, weekly alerts to providers, both interventions, and control. Travel time was used as both a main effect and interacted with other variables to explore its modifying impact on continuity of care in conjunction with incentives or alerts. Continuity was defined as follow-up care occurring within 14 days of discharge from detoxification or residential treatment programs. Travel time was estimated as driving time from clients' home ZIP Code to treatment agency ZIP Code. Findings Travel times to the original treatment agency were in some cases significant with longer travel times predicting lower likelihood of continuity. For detoxification clients, those with longer travel times (over 91 minutes from their residence) are more likely to have timely continuity. Conversely, residential clients with travel times of more than 1 hour are less likely to have timely continuity. Interventions such as alerts or incentives for performance had some mitigating effects on these results. Travel times to the closest agency for potential further treatment were not significant. Conclusions Among rural clients discharged from detoxification and residential treatment, travel time can be an important factor in predicting timely continuity.
Bounded Fluctuations and Translation Symmetry Breaking in One-Dimensional Particle Systems

We present general results for one-dimensional systems of point charges (signed point measures) on the line with a translation invariant distribution μ for which the variance of the total charge in an interval is uniformly bounded (instead of increasing with the interval length). When the charges are restricted to multiples of a common unit, and their average charge density does not vanish, then the boundedness of the variance implies translation-symmetry breaking—in the sense that there exists a function of the charge configuration that is nontrivially periodic under translations—and hence that μ is not “mixing.” Analogous results are formulated also for one dimensional lattice systems under some constraints on the values of the charges at the lattice sites and their averages. The general results apply to one-dimensional Coulomb systems, and to certain spin chains, putting on common grounds different instances of symmetry breaking encountered there.
Intercalation of Nickel into the New Ternary Phosphide Hf5NiP3

Hf5Ni1+xP3, synthesized by arc-melting HfP, Hf, and Ni in Hf:Ni:P ratios varying between 5:1:3 and 2:1:1, crystallizes in a filled Hf5CoP3 structure type, space group Pnma, lattice constants a = 17.021(3) A, b = 3.596(2) A, c = 10.146(2) A, V = 621.0(8) A3 for x = 0.130(8). Its structure consists of an extended framework of connected channels formed by hafnium. Each channel is filled with an infinite −Ni−P− zigzag chain, whereas two other P sites are located in trigonal prismatic voids of the Hf sublattice. In contrast to Hf5Co1+xP3-x, where additional Co atoms replace P atoms, additional Ni atoms in Hf5Ni1+xP3 can occupy a trigonal Hf6 prism, three-capped by P atoms. No Ni/P exchange has been observed. However, Hf5Ni1+xP3 is assumed to be metallic, corresponding to the calculated band structure as well as to the Pauli paramagnetism experimentally obtained.
Synthesis of 1,1-bis(1,2,4-triazol-1-yl)-based potential aromatase inhibitors†

Reactions of bis-(1,2,4-triazolyl) sulfoxide 2 with various carbonyl compounds 3 led to the formation of twelve corresponding 1,1 -bis-(1,2,4-triazolyl) compounds, with structures resembling closely some previously prepared aromatase inhibitors.
Asymmetric Total Synthesis of the Caribbean Fruit Fly Pheromone (+)-Epianastrephin

An asymmetric total synthesis of (+)-epianastrephin (1) from the chiral benzamide 2 (15 steps, 9.5% overall yield) is described. Birch reduction−alkylation of 2 with methyl iodide gave 3 in 91% yield as a single diastereomer. Cyclohexadiene 3 was converted to olefinic carboxylic acid 6b, and a tandem iodolactonization−radical reduction sequence provided lactone 8 with three contiguous stereogenic centers. Chiral HPLC comparison of diol 12b, the immediate precursor to (+)-epianastrephin (1), with 12b prepared from racemic epianastrephin demonstrated that 1 had been prepared with >98% ee.
7-Methyl trimethoprim analogues as inhibitors of the folate metabolizing enzymes

A series of 5-(1-phenylethyl)pyrimidines 2–10 (Table I) were designed and synthesized as potent and selective inhibitors of Pneumocystis carinii (P. carinii), Toxoplasma gondii (T. gondii) and Mycobacterium avium (M. avium) dihydrofolate reductases (DHFR). The structure of 2–10 incorporates a 7-methyl group to increase the potency of monocyclic trimethoprim (TMP). The target compounds were synthesized by an acid catalyzed condensation of ethyl cyanoacetate and appropriately substituted benzaldehydes followed by a Michael addition using methyl copper-lithium. The resulting adduct was cyclocondensed with guanidine to afford 2,6-diamino-4-hydroxy-5-(1-phenylethyl)pyrimidines 2–7. Both amino moieties of 2–4 were protected with pivaloyl groups and their 4-hydroxy group chlorinated with phosphorus oxychloride. The resulting intermediates were subjected to hydrogenation and deprotection to afford 8–10. Compound 7 was a good inhibitor of DHFR, however the other compounds were poor inhibitors of P. carinii, T. gondii and M. avium DHFR.
Catalyst controlled diastereoselective N-alkylations of α-amino esters

Abstract Asymmetric N-alkylation of α-amino esters in which a new stereogenic center is created at carbon is dictated by the catalyst and not the substrate.
An Improved Protocol for the Preparation of 2,6-DI(tert-Butyl)-4-methylphenyl (BHT) Alkanoates

Abstract Treatment of the acid chloride derivatives 2a-e with potassium 2,6-di(tert-butyl)-4-methyl phenoxide 1b afforded the corresponding BHT esters 3a-e in 83–95% yield.
Highly stereocontrolled and regiocontrolled syntheses of polyoxygenated [2.2.2]oxabicyclic synthons

Abstract Highly oxygenated cyclohexanes (known as cyclitols or carba-sugars) were synthesized regiospecifically and stereoselectively via a key inverse electron demand Diels–Alder cycloaddition of electron poor 2-pyrones with electron rich tert-butyldimethylsilyl vinyl ether. The resulting [2.2.2]oxabicyclic lactones proved to be versatile synthons; syn-dihydroxylations were achieved with very high stereocontrol, with up to five stereocenters being produced from commercially available or easily prepared planar starting materials.
A neutral, water-soluble olefin metathesis catalyst based on an N-heterocyclic carbene ligand

A water-soluble ruthenium-based olefin metathesis catalyst supported by a poly(ethylene glycol) conjugated N-heterocyclic carbene ligand is reported. The catalyst displays greater activity in aqueous ring-opening metathesis polymerization (ROMP) reactions than previously reported water-soluble metathesis catalysts.
Syntheses, Structures, Physical Properties, and Theoretical Study of LaCu0.40Te2, NdCu0.37Te2, SmCu0.34Te2, GdCu0.33Te2, and DyCu0.32Te2

Five rare-earth copper tellurides have been synthesized by the reactions of the elements at 1073 K. The isostructural compounds LaCu0.40Te2 (a = 7.7063(13) A, b = 8.5882(14) A, c = 6.3115(10) A, T ...
Preparation of Sec-Alkyl Isouronium Salts

Abstract Eight examples of sec-alkyl isouronium salts were readily prepared from sec-alcohols, cynamide, and methanesulfonic acid (or CF3SO3H or HBF4).
Efficient phase diagram information and computational thermodynamics

Industries that process and use metals, from microelectronics to aerospace, can use phase equilibria data for designing and processing complex alloys (three or more components) and diffusion data for controlling the formation and dissolution of precipitate phases within a matrix or at an interface. The number of images or data tables that would be needed for the graphic representation of such data is prohibitively large for systems with a large number of components. Databases that store thermodynamic and diffusion data as analytical functions provide a compact, retrievable storage method. They also permit the extrapolation of properties from binary and ternary systems to higher-order systems based on a physical model. Special task software that allows the nonexpert to extract the required information has been developed for the casting of superalloys and the solidification of Pb-free solders. Examples of user-friendly data representation and data utilization in advanced applications are presented.
Low-Temperature Nanoparticle-Directed Solid-State Synthesis of Ternary and Quaternary Transition Metal Oxides

Ternary and quaternary transition metal oxides, which offer a wide variety of important physical properties, are traditionally synthesized using high-temperature reactions that often require several days of heating. A new nanoparticle-directed approach for the rapid low-temperature synthesis of nanocrystalline bulk-scale ternary and quaternary transition metal oxides has been developed. Readily available metal oxide nanoparticles can serve as a robust toolkit of highly reactive reagents, which can be mixed in solution in known ratios to form nanomodulated precursors and rapidly transformed, at relatively low temperatures, into more complex oxides. This approach is initially demonstrated for pyrochlore-type Y2Ti2O7 and Eu2Ti2O7 using XRD, DSC, and TEM to monitor the reaction. A nanocomposite of Y2O3 and TiO2 nanoparticles transforms into nanocrystalline Y2Ti2O7 within 2 h of heating to 700 °C, and Eu2Ti2O7 forms within 2 h of heating a nanocomposite of Eu2O3 and TiO2 nanoparticles to 800 °C. NiTiO3, CoTiO3...
Structure and Thermal Decomposition of Some 5-(Cyclohexyloxy)thianthreniumyl Perchlorates

Five sets of cis- and trans-substituted cyclohexanols were used for reaction with thianthrene cation radical perchlorate, namely, cis- and trans-cyclohexane-1,2-diol, cis- and trans-2-methyl-, 3-methyl-, and 4-methylcyclohexanol, and cis,cis- and trans,trans-3,5-dimethylcyclohexanol. Reaction in CH2Cl2 solution and precipitation with ether gave the corresponding crystalline 5-(cyclohexyloxy)thianthreniumyl perchlorate salts. The configuration of each salt in CDCl3 was shown by 1H and 13C NMR spectroscopy to correspond with the configuration of the cyclohexanol from which it was made. X-ray Ortep diagrams of four of the salts confirmed the structure deduced from NMR spectroscopy. In the NMR, inequivalence of the 1H and 13C signals from the thianthreniumyl 4- and 6-, 1- and 9-, 2- and 8-, and 3- and 7-positions was found when the 1‘-position of the cyclohexyl ring was stereogenic. In the four Ortep diagrams, the orientation of the S−O bond was psuedoaxial. Thermal decomposition of the salts made from the mo...
Trifluoromethyl-Containing Transition Metal Complexes

Publisher Summary This chapter examines the current status of the chemistry of trifluoromethyl—containing transition metal compounds where the term “transition metal” had been defined to include the metals of groups. The CF3 ligand is a desirable ligand for many applications in both organic and inorganic chemistry. In transitional metal organometallic chemistry, the substitution of a CF3 group for a CH3 group commonly dramatically improves the thermal, oxidative, and hydrolytic stability of the product. The first trifluoromethyl, containing derivative of a d block element was formed when Mn(CO)5(COCF3) was thermally decarbonylated to give Mn(CO)5(CF3). This chapter reviews some of the early results that were reported in the trifluoromethyl transition metal area. The survey is followed by a discussion of more recent studies, which is presented by group of the periodic table. This chapter focuses the X-ray crystallographic data that have been obtained, while it indicates some aspects of the importance of trifluoromethyl transition metal chemistry and its future.
Hydroamination of Alkynes Catalyzed by a Titanium Pyrrolyl Complex

The readily prepared pyrrolyl complex Ti(NMe2)2(dpma), where dpma is di(pyrrolyl-α-methyl)methylamine, is an effective precatalyst for the hydroamination of alkynes by primary amines. The catalysis is Markovnikov-selective and rapid with terminal alkynes.
An Enantioselective Synthetic Route to Atractyligenin Using the Oxazaborolidine-Catalyzed Reduction of β-Silyl- or β-Stannyl-Substituted α,β-Enones as a Key Step

In this paper, we describe a novel catalytic enantioselective synthetic route to the bicyclic tetraene ester 3, a key intermediate for the synthesis of the naturally occurring adenosine diphosphate transport inhibitor atractyligenin (2). The success of this route depended on the extension of the oxazaborolidine-catalyzed (CBS) reduction of an achiral β-stannyl-substituted α,β-enone (6c) to form a chiral allylic alcohol and further steps to effect simultaneous transfer of chirality, carbocycle formation, and quaternary stereocenter formation, which led to the triene acid 13. The conversion of 13 to 3 was carried out efficiently by a four-step sequence involving iodolactonization, double elimination, and esterification. The combined use of the CBS reduction of appropriate α,β-enones and Claisen rearrangement provides an important synthetic avenue to many types of natural products containing quaternary stereocenters embedded in cyclic networks.
A Novel Metal Iodide Promoted Three-Component Synthesis of Substituted Pyrrolidines

(Matrix Presented) A new one-pot procedure for the synthesis of substituted pyrrolidine derivatives with commercially available cyclopropyl ketones, aldehydes, and amines by a metal iodide promoted three-component reaction was developed.
Climate–fire–vegetation interactions and the rise of novel landscape patterns in subalpine ecosystems, Colorado

Interactions at multiple scales can shape how forest ecosystems respond to both climate change and disturbance. At landscape scales, feedbacks cause vegetation and wildfire regimes to alter one another, while forest patterns at local scales can result from feedbacks between plants and their abiotic environment. Consequently, disturbances and abiotic changes may give rise to forest patterns that further affect processes like wildfire. Examples may exist in the history of subalpine ribbon forests, which are alternating areas of forest and meadow where snow drifting and linear bands of trees depend upon each other. Just as ongoing climate changes may change snow levels and the dynamics in these forests, past climate changes and wildfires may have generated the conditions suitable for ribbon forests. To examine feedbacks in subalpine forests and the potential that climate changes and fires gave rise to ribbon forests, we obtained six fossil pollen records from a subalpine landscape in Colorado. Forests there may have responded to climate change and widespread wildfires ˜1,000 years ago when >80% of sites on the landscape burned within a century. The fires coincided with regional warming, but the extent of burning declined before the climate cooled, possibly driven by changes in fuel structure and composition. The pollen records indicate that large vegetation changes coincided with the widespread wildfires at five of the six sites. Pollen assemblages consistent with ribbon forests first became important at this time as sagebrush (Artemisia) and other meadow taxa increased and conifers, especially spruce (Picea) declined. The ribbon forests emerged as novel fuel breaks at the time when temperatures rose ˜0.5°C but the number of sites burned per century declined. Cooling during the Little Ice Age then expanded the openings and extent of ribbon forests, probably helping to reduce the frequency of fires across our sites to its minimum. Synthesis. The rise of ribbon forests in northern Colorado illustrates how climate and fire can interact to rapidly transform landscapes and disturbance regimes. The interactions can produce forest patterns with unexpected consequences such as reduced wildfire despite regional warming.
Multiobjective strain design: A framework for modular cell engineering

Diversity of cellular metabolism can be harnessed to produce a large space of molecules. However, development of optimal strains with high product titers, rates, and yields required for industrial production is laborious and expensive. To accelerate the strain engineering process, we have recently introduced a modular cell design concept that enables rapid generation of optimal production strains by systematically assembling a modular cell with an exchangeable production module(s) to produce target molecules efficiently. In this study, we formulated the modular cell design concept as a general multiobjective optimization problem with flexible design objectives derived from mass balance. We developed algorithms and an associated software package, named ModCell2, to implement the design. We demonstrated that ModCell2 can systematically identify genetic modifications to design modular cells that can couple with a variety of production modules and exhibit a minimal tradeoff among modularity, performance, and robustness. Analysis of the modular cell designs revealed both intuitive and complex metabolic architectures enabling modular production of these molecules. We envision ModCell2 provides a powerful tool to guide modular cell engineering and sheds light on modular design principles of biological systems.
Partitioning index and non-structural carbohydrate dynamics among contrasting cassava genotypes under early terminal water stress

Abstract Cassava (Manihot esculenta Crantz.) is a storage root crop of importance in tropical regions where periodic dry season and drought affect performance. Cassava genotypes that differ in performance in ecosystems with various water regimes were subjected to water stress during storage-root initiation and early development. Plants were grown in 50 kg pots in a screen house environment under well-watered and water stress conditions for a 120-day period. Water stress had a significant effect on most traits analyzed. However, relative water content, partitioning index and non-structural carbohydrates were unaffected. Tolerant genotypes had a higher partitioning index than susceptible genotypes during water stress, associated with a larger number of storage roots initiated and larger storage root biomass, while they were shorter and had less fibrous root biomass. Tolerant lines were indistinguishable from susceptible lines in above ground biomass under stress. These findings suggest that early evaluation of storage root number, partitioning index, and associated traits at an early stage of cassava storage-root development could be an effective approach by which cassava genotypes are screened for favorable drought tolerance response.
Pd-Catalyzed Carbonylative Lactamization: A Novel Synthetic Approach to FR900482

An asymmetric synthesis of the benzazocine core of FR900482 has been achieved in 15 steps from 3,5-dinitro-p-toluic acid. Key features of the synthesis include an enantioselective N-methylephedrine-mediated zinc acetylide addition to a highly enolizable arylacetaldehyde and a novel Pd-catalyzed carbonylative lactamization to form an eight-membered ring. [reaction--see text]
Total synthesis of asimicin via highly stereoselective [3 + 2] annulation reactions of substituted allylsilanes.

A highly stereoselective total synthesis of (+)-asimicin (1) is reported. The synthesis features two chelate-controlled [3 + 2] annulation reactionsone of which (e.g., 2 + 3) constitutes a key, convergent fragment assembly stepthat establish all of the stereochemistry of the bis-tetrahydrofuran unit of the natural product.
Neural Decipherment via Minimum-Cost Flow: from Ugaritic to Linear B

In this paper we propose a novel neural approach for automatic decipherment of lost languages. To compensate for the lack of strong supervision signal, our model design is informed by patterns in language change documented in historical linguistics. The model utilizes an expressive sequence-to-sequence model to capture character-level correspondences between cognates. To effectively train the model in unsupervised manner, we innovate the training procedure by formalizing it as a minimum-cost flow problem. When applied to decipherment of Ugaritic, we achieve 5% absolute improvement over state-of-the-art results. We also report first automatic results in deciphering Linear B, a syllabic language related to ancient Greek, where our model correctly translates 67.3% of cognates.
Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes.

BACKGROUND De novo transcriptome assemblies are required prior to analyzing RNA sequencing data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or "pipelines," on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short-read data collected as part of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research. RESULTS New transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics. Assemblies from the Dinoflagellata showed a higher number of contigs and unique k-mers than transcriptomes from other phyla, while assemblies from Ciliophora had a lower percentage of open reading frames compared to other phyla. CONCLUSIONS Given current bioinformatics approaches, there is no single "best" reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.
Supervised Machine Learning Based Multi-Task Artificial Intelligence Classification of Retinopathies

Artificial intelligence (AI) classification holds promise as a novel and affordable screening tool for clinical management of ocular diseases. Rural and underserved areas, which suffer from lack of access to experienced ophthalmologists may particularly benefit from this technology. Quantitative optical coherence tomography angiography (OCTA) imaging provides excellent capability to identify subtle vascular distortions, which are useful for classifying retinovascular diseases. However, application of AI for differentiation and classification of multiple eye diseases is not yet established. In this study, we demonstrate supervised machine learning based multi-task OCTA classification. We sought (1) to differentiate normal from diseased ocular conditions, (2) to differentiate different ocular disease conditions from each other, and (3) to stage the severity of each ocular condition. Quantitative OCTA features, including blood vessel tortuosity (BVT), blood vascular caliber (BVC), vessel perimeter index (VPI), blood vessel density (BVD), foveal avascular zone (FAZ) area (FAZ-A), and FAZ contour irregularity (FAZ-CI) were fully automatically extracted from the OCTA images. A stepwise backward elimination approach was employed to identify sensitive OCTA features and optimal-feature-combinations for the multi-task classification. For proof-of-concept demonstration, diabetic retinopathy (DR) and sickle cell retinopathy (SCR) were used to validate the supervised machine leaning classifier. The presented AI classification methodology is applicable and can be readily extended to other ocular diseases, holding promise to enable a mass-screening platform for clinical deployment and telemedicine.
Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

Knowledge of cell type composition in disease relevant tissues is an important step towards the identification of cellular targets of disease. We present MuSiC, a method that utilizes cell-type specific gene expression from single-cell RNA sequencing (RNA-seq) data to characterize cell type compositions from bulk RNA-seq data in complex tissues. By appropriate weighting of genes showing cross-subject and cross-cell consistency, MuSiC enables the transfer of cell type-specific gene expression information from one dataset to another. When applied to pancreatic islet and whole kidney expression data in human, mouse, and rats, MuSiC outperformed existing methods, especially for tissues with closely related cell types. MuSiC enables the characterization of cellular heterogeneity of complex tissues for understanding of disease mechanisms. As bulk tissue data are more easily accessible than single-cell RNA-seq, MuSiC allows the utilization of the vast amounts of disease relevant bulk tissue RNA-seq data for elucidating cell type contributions in disease. Bulk tissue RNA-seq data reveals transcriptomic profiles but masks the contributions of different cell types. Here, the authors develop a new method for estimating cell type proportions from bulk tissue RNA-seq data guided by multi-subject single-cell expression reference.
Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution.

Summary Ribosome profiling (Ribo-seq) is a powerful technique for measuring protein translation; however, sampling errors and biological biases are prevalent and poorly understood. Addressing these issues, we present Scikit-ribo (https://github.com/schatzlab/scikit-ribo), an open-source analysis package for accurate genome-wide A-site prediction and translation efficiency (TE) estimation from Ribo-seq and RNA sequencing data. Scikit-ribo accurately identifies A-site locations and reproduces codon elongation rates using several digestion protocols ( r = 0.99). Next, we show that the commonly used reads per kilobase of transcript per million mapped reads-derived TE estimation is prone to biases, especially for low-abundance genes. Scikit-ribo introduces a codon-level generalized linear model with ridge penalty that correctly estimates TE, while accommodating variable codon elongation rates and mRNA secondary structure. This corrects the TE errors for over 2,000 genes in S. cerevisiae , which we validate using mass spectrometry of protein abundances ( r = 0.81), and allows us to determine the Kozak-like sequence directly from Ribo-seq. We conclude with an analysis of coverage requirements needed for robust codon-level analysis and quantify the artifacts that can occur from cycloheximide treatment.
Experimental Thermochemistry of the SiCl and SiBr Radicals; Enthalpies of Formation of Species in the Si−Cl and Si−Br Systems

Gaseous reaction equilibria involving the radical species SiCl and SiBr were studied by mass spectrometric monitoring of the molecular beam issuing from a heated effusion cell source, and the resul...
Substituent effects in the reaction of allyl trichloroacetimidates with N-halosuccinimides: Cyclization vs aza-Claisen rearrangement

Abstract We report a novel substituent effect in the reaction of allylic trichloroacetimidates with N-halosuccinimides. Reaction of E allylic tricloroacetimidates bearing phosphonate or cyano substituents with NBS in CHCl3 results in a [3.3] sigmatropic rearrangement. In contrast, the Z allylic phosphonate or phenyl substituted allylic trichloroacetimidate undergo halocyclization.
Impact of regulatory variation across human iPSCs and differentiated cells

Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. We investigated the use of iPSCs and iPSC-derived cells to study the impact of genetic variation on gene regulation across different cell types and as models for studies of complex disease. To do so, we established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. We characterized regulatory variation across individuals and cell types by measuring gene expression levels, chromatin accessibility, and DNA methylation. Our analysis focused on a comparison of inter-individual regulatory variation across cell types. While most cell-type-specific regulatory quantitative trait loci (QTLs) lie in chromatin that is open only in the affected cell types, we found that 20% of cell-type-specific regulatory QTLs are in shared open chromatin. This observation motivated us to develop a deep neural network to predict open chromatin regions from DNA sequence alone. Using this approach, we were able to use the sequences of segregating haplotypes to predict the effects of common SNPs on cell-type-specific chromatin accessibility.
An Effective Model of the Retinoic Acid Induced HL-60 Differentiation Program

In this study, we present an effective model All-Trans Retinoic Acid (ATRA)-induced differentiation of HL-60 cells. The model describes reinforcing feedback between an ATRA-inducible signalsome complex involving many proteins including Vav1, a guanine nucleotide exchange factor, and the activation of the mitogen activated protein kinase (MAPK) cascade. We decomposed the effective model into three modules; a signal initiation module that sensed and transformed an ATRA signal into program activation signals; a signal integration module that controlled the expression of upstream transcription factors; and a phenotype module which encoded the expression of functional differentiation markers from the ATRA-inducible transcription factors. We identified an ensemble of effective model parameters using measurements taken from ATRA-induced HL-60 cells. Using these parameters, model analysis predicted that MAPK activation was bistable as a function of ATRA exposure. Conformational experiments supported ATRA-induced bistability. Additionally, the model captured intermediate and phenotypic gene expression data. Knockout analysis suggested Gfi-1 and PPARg were critical to the ATRAinduced differentiation program. These findings, combined with other literature evidence, suggested that reinforcing feedback is central to hyperactive signaling in a diversity of cell fate programs.
CORRECTIONS TO THE NUCLEAR AXIAL VECTOR COUPLING IN A NUCLEAR MEDIUM

There is experimental evidence of an increase in the temporal component of the weak axial vector current in nuclei. Most of this increase is accounted for by meson exchange currents. We consider further corrections from pions and the sigma mean-field. These corrections, however, are found to reduce the coupling, which is already insufficiently large.
Synthesis and biological evaluation of bryostatin analogues: the role of the A-ring

The first biologically active member and a key intermediate of a new family of simplified bryostatin analogues are synthesized through an optimized esterification–macrotransacetalization strategy. This family incorporates both an ester linkage between C5 and C9 in addition to a C9 t-butyl substituent to mimic the bryostatin A-ring. Importantly, a free C7 alcohol is revealed late in the synthesis, allowing access to numerous C7 derivatized analogues.
Assessing depression improvement with the remission evaluation and mood inventory tool (REMIT).

Abstract Objective The Remission Evaluation and Mood Inventory Tool (REMIT) was developed as a brief complementary measure to provide a more robust assessment of depression improvement than tracking DSM-V symptom improvement alone. This study provides further validation of the REMIT tool and examines its utility in predicting depression improvement. Methods The sample comprised 294 primary care patients enrolled in a telecare trial of pain plus depression and/or anxiety. Assessments collected included: REMIT, PHQ-9 and measures assessing anxiety, pain, sleep, fatigue, somatization, health-related quality of life and disability. Data was analyzed to assess the REMIT's validity, its minimally important difference (MID), and its utility in predicting 6-month depression improvement. Results Convergent and construct validity of REMIT was supported by moderate correlations with mental health measures and weaker correlation with physical health measures. MID of approximately 2 points for REMIT was estimated by two metrics: 0.5 standard deviation and 1 standard error of measurement. Both baseline and 3-month change in REMIT scores predicted depression improvement at 6 months. Indeed, REMIT was as good or better predictor than the PHQ-9. Conclusion The REMIT measure is a brief 5-item tool that augments core DSM-V symptom-oriented metrics in assessing and predicting recovery from major depression.
A dynamic boundary guarding problem with translating targets

We introduce a problem in which a service vehicle seeks to defend a deadline (boundary) from dynamically arriving mobile targets. The environment is a rectangle and the deadline is one of its edges. Targets arrive continuously over time on the edge opposite the deadline, and move towards the deadline at a fixed speed. The goal for the vehicle is to maximize the fraction of targets that are captured before reaching the deadline. We consider two cases; when the service vehicle is faster than the targets, and; when the service vehicle is slower than the targets. In the first case we develop a novel vehicle policy based on computing longest paths in a directed acyclic graph. We give a lower bound on the capture fraction of the policy and show that the policy is optimal when the distance between the target arrival edge and deadline becomes very large. We present numerical results which suggest near optimal performance away from this limiting regime. In the second case, when the targets are slower than the vehicle, we propose a policy based on servicing fractions of the translational minimum Hamiltonian path. In the limit of low target speed and high arrival rate, the capture fraction of this policy is within a small constant factor of the optimal.
Convergence Stability for Ricci Flow

The principle of convergence stability for geometric flows is the combination of the continuous dependence of the flow on initial conditions, with the stability of fixed points. It implies that if the flow from an initial state $$g_0$$ exists for all time and converges to a stable fixed point, then the flows of solutions that start near $$g_0$$ also converge to fixed points. We show this in the case of the Ricci flow, carefully proving the continuous dependence on initial conditions. Symmetry assumptions on initial geometries are often made to simplify geometric flow equations. As an application of our results, we extend known convergence results to open sets of these initial data, which contain geometries with no symmetries.
Parallel Attention Mechanisms in Neural Machine Translation

Recent papers in neural machine translation have proposed the strict use of attention mechanisms over previous standards such as recurrent and convolutional neural networks (RNNs and CNNs). We propose that by running traditionally? stacked encoding branches from encoder-decoder attention-focused architectures in parallel, that even more sequential operations can be removed from the model and thereby decrease training time. In particular, we modify the recently published attention-based architecture called Transformer by Google, by replacing sequential attention modules with parallel ones, reducing the amount of training time and substantially improving BLEU scores at the same time. Experiments over the English to German and English to French translation tasks show that our model establishes a new state of the art.
Recovery from Link Failures in Networks with Arbitrary Topology via Diversity Coding

Link failures in wide area networks are common. To recover from such failures, a number of methods such as SONET rings, protection cycles, and source rerouting have been investigated. Two important considerations in such approaches are the recovery time and the needed spare capacity to complete the recovery. Usually, these techniques attempt to achieve a recovery time less than 50 ms. In this paper we introduce an approach that provides link failure recovery in a hitless manner, or without any appreciable delay. This is achieved by means of a method called diversity coding. We present an algorithm for the design of an overlay network to achieve recovery from single link failures in arbitrary networks via diversity coding. This algorithm is designed to minimize spare capacity for recovery. We compare the recovery time and spare capacity performance of this algorithm against conventional techniques in terms of recovery time, spare capacity, and a joint metric called Quality of Recovery (QoR). QoR incorporates both the spare capacity percentages and worst case recovery times. Based on these results, we conclude that the proposed technique provides much shorter recovery times while achieving similar extra capacity, or better QoR performance overall.
A hybrid observer for a distributed linear system with a changing neighbor graph

A hybrid observer is described for estimating the state of an m > 0 channel, n-dimensional, continuous-time, linear system of the form x = Ax, y i = C ix , i ∊ {1, 2,…, m}. The system's state x is simultaneously estimated by m agents assuming each agent i senses yi and receives appropriately defined data from each of its current neighbors. Neighbor relations are characterized by a time-varying directed graph N(t) whose vertices correspond to agents and whose arcs depict neighbor relations. Agent i updates its estimate x i of x at “event times” t i , t 2 ,… using a local continuous-time linear observer and a local parameter estimator which for each j ≥ 1, iterates q times during the time interval [tj −1 , tj) to obtain an estimate of x(tj). Subject to the assumptions that none of the C i are zero, the neighbor graph N(t) is strongly connected for all time, and the system whose state is to be estimated is jointly observable, it is shown that for any number λ > 0 it is possible to choose q and the local observer gains so that each estimate x i converges to x as fast as e−λt converges to zero.
Counterfactual Fairness in Text Classification through Robustness

In this paper, we study counterfactual fairness in text classification, which asks the question: How would the prediction change if the sensitive attribute referenced in the example were different? Toxicity classifiers demonstrate a counterfactual fairness issue by predicting that "Some people are gay" is toxic while "Some people are straight" is nontoxic. We offer a metric, counterfactual token fairness (CTF), for measuring this particular form of fairness in text classifiers, and describe its relationship with group fairness. Further, we offer three approaches, blindness, counterfactual augmentation, and counterfactual logit pairing (CLP), for optimizing counterfactual token fairness during training, bridging the robustness and fairness literature. Empirically, we find that blindness and CLP address counterfactual token fairness. The methods do not harm classifier performance, and have varying tradeoffs with group fairness. These approaches, both for measurement and optimization, provide a new path forward for addressing fairness concerns in text classification.
Microscopically based calculations of the free energy barrier and dynamic length scale in supercooled liquids: the comparative role of configurational entropy and elasticity.

We compute the temperature-dependent barrier for α-relaxations in several liquids, without adjustable parameters, using experimentally determined elastic, structural, and calorimetric data. We employ the random first order transition (RFOT) theory, in which relaxation occurs via activated reconfigurations between distinct, aperiodic minima of the free energy. Two different approximations for the mismatch penalty between the distinct aperiodic states are compared, one due to Xia and Wolynes (Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 2990), which scales universally with temperature as for hard spheres, and one due to Rabochiy and Lubchenko (J. Chem. Phys. 2013, 138, 12A534), which employs measured elastic and structural data for individual substances. The agreement between the predictions and experiment is satisfactory, given the uncertainty in the measured experimental inputs. The explicitly computed barriers are used to calculate the glass transition temperature for each substance—a kinetic quantity—from ...
Basis-neutral Hilbert-space analyzers.

Interferometry is one of the central organizing principles of optics. Key to interferometry is the concept of optical delay, which facilitates spectral analysis in terms of time-harmonics. In contrast, when analyzing a beam in a Hilbert space spanned by spatial modes – a critical task for spatial-mode multiplexing and quantum communication – basis-specific principles are invoked that are altogether distinct from that of ‘delay’. Here, we extend the traditional concept of temporal delay to the spatial domain, thereby enabling the analysis of a beam in an arbitrary spatial-mode basis – exemplified using Hermite-Gaussian and radial Laguerre-Gaussian modes. Such generalized delays correspond to optical implementations of fractional transforms; for example, the fractional Hankel transform is the generalized delay associated with the space of Laguerre-Gaussian modes, and an interferometer incorporating such a ‘delay’ obtains modal weights in the associated Hilbert space. By implementing an inherently stable, reconfigurable spatial-light-modulator-based polarization-interferometer, we have constructed a ‘Hilbert-space analyzer’ capable of projecting optical beams onto any modal basis.
Information Theoretic Limits of Data Shuffling for Distributed Learning

Data shuffling is one of the fundamental building blocks for distributed learning algorithms, that increases the statistical gain for each step of the learning process. In each iteration, different shuffled data points are assigned by a central node to a distributed set of workers to perform local computation, which leads to communication bottlenecks. The focus of this paper is on formalizing and understanding the fundamental information-theoretic tradeoff between storage (per worker) and the worst-case communication overhead for the data shuffling problem. We completely characterize the information theoretic tradeoff for K = 2, and K = 3 workers, for any value of storage capacity, and show that increasing the storage across workers can reduce the communication overhead by leveraging coding. We propose a novel and systematic data delivery and storage update strategy for each data shuffle iteration, which preserves the structural properties of the storage across the workers, and aids in minimizing the communication overhead in subsequent data shuffling iterations.