cssi/SciSciGPT-SciSciNet huggingface dataset:
Online learning with an almost perfect expert

We study multiclass online learning, where a forecaster predicts a sequence of elements drawn from a finite set using the advice of n experts. Our main contributions are to analyze the scenario where the best expert makes a bounded number b of mistakes and to show that, in the low-error regime where b = o ( log ⁡ n ) , the expected number of mistakes made by the optimal forecaster is at most log 4 n + o ( log ⁡ n ) . We also describe an adversary strategy showing that this bound is tight and that the worst case is attained for binary prediction.
Relationship-Specific Investment and Hold-Up Problems in Supply Chains: Theory and Experiments

Supply chains today routinely use third parties for many strategic activities, such as manufacturing, R&D, or software development. These activities often include relationship-specific investment on the part of the vendor, while final outcomes can be uncertain. Therefore, writing complete contracts for such arrangements is often not feasible, but incomplete contracts, especially when relationship-specific investment is required, may leave the supplier vulnerable to a version of the “hold-up problem,” which is known to result in sub-optimal levels of investment. We model the phenomenon as a sequential move game with asymmetric information. Absent behavioral considerations, the unique Perfect Bayesian Equilibrium implies zero investment. However, with social preferences, the hold-up problem may be mitigated. We propose a model that incorporates social preferences and random errors, and solve for the equilibrium. In addition, we look at reputation and find it to be effective for increasing investment. We conduct laboratory experiments with human subjects and find that a model with social preferences and random errors organizes our data well.
CTAP: Complementary Temporal Action Proposal Generation

Temporal action proposal generation is an important task, akin to object proposals, temporal action proposals are intended to capture “clips” or temporal intervals in videos that are likely to contain an action. Previous methods can be divided to two groups: sliding window ranking and actionness score grouping. Sliding windows uniformly cover all segments in videos, but the temporal boundaries are imprecise; grouping based method may have more precise boundaries but it may omit some proposals when the quality of actionness score is low. Based on the complementary characteristics of these two methods, we propose a novel Complementary Temporal Action Proposal (CTAP) generator. Specifically, we apply a Proposal-level Actionness Trustworthiness Estimator (PATE) on the sliding windows proposals to generate the probabilities indicating whether the actions can be correctly detected by actionness scores, the windows with high scores are collected. The collected sliding windows and actionness proposals are then processed by a temporal convolutional neural network for proposal ranking and boundary adjustment. CTAP outperforms state-of-the-art methods on average recall (AR) by a large margin on THUMOS-14 and ActivityNet 1.3 datasets. We further apply CTAP as a proposal generation method in an existing action detector, and show consistent significant improvements.
Local decodability of the Burrows-Wheeler transform

The Burrows-Wheeler Transform (BWT) is among the most influential discoveries in text compression and DNA storage. It is a reversible preprocessing step that rearranges an n-letter string into runs of identical characters (by exploiting context regularities), resulting in highly compressible strings, and is the basis of the bzip compression program. Alas, the decoding process of BWT is inherently sequential and requires Ω(n) time even to retrieve a single character. We study the succinct data structure problem of locally decoding short substrings of a given text under its compressed BWT, i.e., with small additive redundancy r over the Move-To-Front (bzip) compression. The celebrated BWT-based FM-index (FOCS ’00), as well as other related literature, yield a trade-off of r=O(n/√t) bits, when a single character is to be decoded in O(t) time. We give a near-quadratic improvement r=O(nlg(t)/t). As a by-product, we obtain an exponential (in t) improvement on the redundancy of the FM-index for counting pattern-matches on compressed text. In the interesting regime where the text compresses to o(n) (say, n/polylg(n)) bits, these results provide an exp(t) overall space reduction. For the local decoding problem of BWT, we also prove an Ω(n/t2) cell-probe lower bound for “symmetric” data structures. We achieve our main result by designing a compressed partial-sums (Rank) data structure over BWT. The key component is a locally-decodable Move-to-Front (MTF) code: with only O(1) extra bits per block of length nΩ(1), the decoding time of a single character can be decreased from Ω(n) to O(lgn). This result is of independent interest in algorithmic information theory.
Sequence-Based OOK for Orthogonal Multiplexing of Wake-Up Radio Signals and OFDM Waveforms

In this study, we propose an approach to constructing on-off keying (OOK) symbols for wake- up radios (WURs) by using sequences in the frequency domain. The proposed method enables orthogonal multiplexing of wake-up signals (WUSs) and orthogonal frequency division multiplexing (OFDM) waveforms. We optimize the sequences with a tractable algorithm by considering the reliability of WUSs in fading channels. The proposed algorithm relies on an alternating minimization technique, i.e. cyclic algorithm-new (CAN), which was originally proposed for obtaining a unimodular sequence with good aperiodic correlation properties. In this study, we extend CAN to generate OOK waveforms with Manchester coding. We demonstrate the performance of four optimized sequences and compare with state-of-the-art approaches. We show that the proposed scheme improves the wake-up radio receiver (WURx) performance by controlling the energy distribution in frequency domain while removing the interference-floor at the OFDM receiver.
Tumor-stroma interactions differentially alter drug sensitivity based on the origin of stromal cells

Abstract Due to tumor heterogeneity, most believe that effective treatments should be tailored to the features of an individual tumor or tumor subclass. It is still unclear, however, what information should be considered for optimal disease stratification, and most prior work focuses on tumor genomics. Here, we focus on the tumor microenvironment. Using a large‐scale coculture assay optimized to measure drug‐induced cell death, we identify tumor–stroma interactions that modulate drug sensitivity. Our data show that the chemo‐insensitivity typically associated with aggressive subtypes of breast cancer is not observed if these cells are grown in 2D or 3D monoculture, but is manifested when these cells are cocultured with stromal cells, such as fibroblasts. Furthermore, we find that fibroblasts influence drug responses in two distinct and divergent manners, associated with the tissue from which the fibroblasts were harvested. These divergent phenotypes occur regardless of the drug tested and result from modulation of apoptotic priming within tumor cells. Our study highlights unexpected diversity in tumor–stroma interactions, and we reveal new principles that dictate how fibroblasts alter tumor drug responses.
Following anticancer drug activity in cell lysates with DNA devices.

Abstract There is a great need to track the selectivity of anticancer drug activity and to understand the mechanisms of associated biological activity. Here we focus our studies on the specific NQO1 bioactivatable drug, s-lapachone, which is in several Phase I clinical trials to treat human non-small cell lung, pancreatic and breast cancers. Multi-electrode chips with electrochemically-active DNA monolayers are used to track anticancer drug activity in cellular lysates and correlate cell death activity with DNA damage. Cells were prepared from the triple-negative breast cancer (TNBC) cell line, MDA-MB-231 (231) to be proficient or deficient in expression of the NAD(P)H:quinone oxidoreductase 1 (NQO1) enzyme, which is overexpressed in most solid cancers and lacking in control healthy cells. Cells were lysed and added to chips, and the impact of β-lapachone (β-lap), an NQO1-dependent DNA-damaging drug, was tracked with DNA electrochemical signal changes arising from drug-induced DNA damage. Electrochemical DNA devices showed a 3.7-fold difference in the electrochemical responses in NQO1+ over NQO1− cell lysates, as well as 10–20-fold selectivity to catalase and dicoumarol controls that deactivate DNA damaging pathways. Concentration-dependence studies revealed that 1.4 µM β-lap correlated with the onset of cell death from viability assays and the midpoint of DNA damage on the chip, and 2.5 µM β-lap correlated with the midpoint of cell death and the saturation of DNA damage on the chip. Results indicate that these devices could inform therapeutic decisions for cancer treatment.
Friedman and Phelps on the Phillips Curve Viewed from a Half Century's Perspective

In the late 1960s the stable negatively sloped Phillips Curve (PC) was overturned by the Friedman-Phelps natural rate model. Their PC was vertical in the long run at the natural unemployment rate, and their short-run curve shifted up whenever unemployment was pushed below the natural rate. This paper criticizes the underlying assumption of the Friedman-Phelps approach that the labor market continuously clears and that changes in unemployment down or up occur only in response to “fooling” of workers, firms, or both. A preferable and resolutely Keynesian approach explains quantity rationing by inertia in price and wage setting. The positive correlation of inflation and unemployment in the 1970s and again in the 1990s is explained by joining the negatively sloped Phillips Curve with a positively sloped dynamic demand curve. For any given growth of nominal GDP, higher inflation caused by adverse supply shocks implies slower real GDP growth and higher unemployment. This “triangle” model based on inflation inertia, demand, and supply worked well to explain why inflation and unemployment were both positively and negatively correlated between the 1960s and 1990s, but in the past decade the slope of the short-run Phillips Curve has flattened as inflation exhibited a muted response to high unemployment in 2009-13 and low unemployment in 2016-2018. It remains to be seen whether a continuation of low unemployment will cause a modest and fixed extra amount of inflation, thus reviving the stable Phillips curve of the early 1960s, or whether inflation will continuously accelerate as Friedman and Phelps would have predicted.
Player Experience Extraction from Gameplay Video.

The ability to extract the sequence of game events for a given player's play-through has traditionally required access to the game's engine or source code. This serves as a barrier to researchers, developers, and hobbyists who might otherwise benefit from these game logs. In this paper we present two approaches to derive game logs from game video via convolutional neural networks and transfer learning. We evaluate the approaches in a Super Mario Bros. clone, Mega Man and Skyrim. Our results demonstrate our approach outperforms random forest and other transfer baselines.
High-precision measurements of krypton and xenon isotopes with a new static-mode quadrupole ion trap mass spectrometer

Measuring the abundance and isotopic composition of noble gases in planetary atmospheres can answer fundamental questions in cosmochemistry and comparative planetology. However, noble gases are rare elements, a feature making their measurement challenging even on Earth. Furthermore, in space applications, power consumption, volume and mass constraints on spacecraft instrument accommodations require the development of compact innovative instruments able to meet the engineering requirements of the mission while still meeting the science requirements. Here we demonstrate the ability of the quadrupole ion trap mass spectrometer (QITMS) developed at the Jet Propulsion Laboratory (Caltech, Pasadena) to measure low quantities of heavy noble gases (Kr, Xe) in static operating mode and in the absence of a buffer gas such as helium. The sensitivity reaches 10^(13) cps Torr^(−1) (about 10^(11) cps Pa^(−1)) of gas (Kr or Xe). The instrument is able to measure gas in static mode for extended periods of time (up to 48 h) enabling the acquisition of thousands of isotope ratios per measurement. Errors on isotope ratios follow predictions of the counting statistics and the instrument provides reproducible results over several days of measurements. For example, 1.7 × 10^(−10) Torr (2.3 × 10^(−8) Pa) of Kr measured continuously for 7 hours yielded a 0.6‰ precision on the ^(86)Kr/^(84)Kr ratio. Measurements of terrestrial and extraterrestrial samples reproduce values from the literature. A compact instrument based upon the QITMS design would have a sensitivity high enough to reach the precision on isotope ratios (e.g. better than 1% for ^(129,131–136)Xe/^(130)Xe ratios) necessary for a scientific payload measuring noble gases collected in the Venus atmosphere.
Mining Directional Drug Interaction Effects on Myopathy Using the FAERS Database

Mining high-order drug-drug interaction (DDI) induced adverse drug effects from electronic health record databases is an emerging area, and very few studies have explored the relationships between high-order drug combinations. We investigate a novel pharmacovigilance problem for mining directional DDI effects on myopathy using the FDA Adverse Event Reporting System (FAERS) database. Our paper provides information on the risk of myopathy associated with adding new drugs on the already prescribed medication, and visualizes the identified directional DDI patterns as user-friendly graphical representation. We utilize the Apriori algorithm to extract frequent drug combinations from the FAERS database. We use odds ratio to estimate the risk of myopathy associated with directional DDI. We create a tree-structured graph to visualize the findings for easy interpretation. Our method confirmed myopathy association with previously reported HMG-CoA reductase inhibitors like rosuvastatin, fluvastatin, simvastatin, and atorvastatin. New, previously unidentified but mechanistically plausible associations with myopathy were also observed, such as the DDI between pamidronate and levofloxacin. Additional top findings are gadolinium-based imaging agents, which however are often used in myopathy diagnosis. Other DDIs with no obvious mechanism are also reported, such as that of sulfamethoxazole with trimethoprim and potassium chloride. This study shows the feasibility to estimate high-order directional DDIs in a fast and accurate manner. The results of the analysis could become a useful tool in the specialists’ hands through an easy-to-understand graphic visualization.
Packing Sparse Convolutional Neural Networks for Efficient Systolic Array Implementations: Column Combining Under Joint Optimization

This paper describes a novel approach of packing sparse convolutional neural networks into a denser format for efficient implementations using systolic arrays. By combining multiple sparse columns of a convolutional filter matrix into a single dense column stored in the systolic array, the utilization efficiency of the systolic array can be substantially increased (e.g., 8x) due to the increased density of nonzero weights in the resulting packed filter matrix. In combining columns, for each row, all filter weights but the one with the largest magnitude are pruned. The remaining weights are retrained to preserve high accuracy. We study the effectiveness of this joint optimization for both high utilization efficiency and classification accuracy with ASIC and FPGA designs based on efficient bit-serial implementations of multiplier-accumulators. We demonstrate that in mitigating data privacy concerns the retraining can be accomplished with only fractions of the original dataset (e.g., 10% for CIFAR-10). We present analysis and empirical evidence on the superior performance of our column combining approach against prior arts under metrics such as energy efficiency (3x) and inference latency (12x).
Occupational Health and Sleep Issues in Underserved Populations

Sleep disorders and occupational hazards, injuries, and illnesses impact an individual's overall health. In the United States, substantial racial, ethnic, and socioeconomic disparities exist in sleep and occupational health. Primary care physicians working in underserved communities should be aware of this disparity and target these higher-risk populations for focused evaluation and intervention.
Markets for Information: An Introduction

We survey a recent and growing literature on markets for information. We offer a comprehensive view of information markets through an integrated model of consumers, information intermediaries, and ...
Time scales and temperatures of crystal storage in magma reservoirs: implications for magma reservoir dynamics

The thermal and therefore physical state of magma bodies within the crust controls the processes and time scales required to mobilize magmas before eruptions, which in turn are critical to hazard a...
Herding and flash events: Evidence from the 2010 Flash Crash

Abstract Using intraday data on individual stocks included in the S&P 500 index, we present evidence of herd formation over the duration and aftermath of the Flash Crash on May 6, 2010, while no evidence of herding is observed preceding the event. The findings establish a clear link between herding among market participants and flash events that can drive sudden price fluctuations and underscore the importance of monitoring herd activity, particularly in the case of automated markets.
The Nopp140 gene in Drosophila melanogaster displays length polymorphisms in its large repetitive second exon

Nopp140, often called the nucleolar and Cajal body phosphoprotein (NOLC1), is an evolutionarily conserved chaperone for the transcription and processing of rRNA during ribosome subunit assembly. Metazoan Nopp140 contains an amino terminal LisH dimerization domain and a highly conserved carboxyl domain. A large central domain consists of alternating basic and acidic motifs of low sequence complexity. Orthologous versions of Nopp140 contain variable numbers of repeating basic-acidic units. While vertebrate Nopp140 genes use multiple exons to encode the central domain, the Nopp140 gene in Drosophila uses exclusively exon 2 to encode the central domain. Here, we define three overlapping repeat sequence patterns (P, P', and P″) within the central domain of D. melanogaster Nopp140. These repeat patterns are poorly conserved in other Drosophila species. We also describe a length polymorphism in exon 2 that pertains specifically to the P' pattern in D. melanogaster. The pattern displays either two or three 96 base pair repeats, respectively, referred to as Nopp140-Short and Nopp140-Long. Fly lines homozygous for one or the other allele, or heterozygous for both alleles, show no discernible phenotypes. PCR characterization of the long and short alleles shows a poorly defined, artifactual bias toward amplifying the long allele over the short allele. The significance of this polymorphism will be in discerning the largely unknown properties of Nopp140's large central domain in rDNA transcription and ribosome biogenesis.
$P(\omega)/{\rm fin}$ and projections in the Calkin algebra

We investigate the set-theoretic properties of the lattice of projections in the Calkin algebra of a separable infinite-dimensional Hilbert space in relation to those of the Boolean algebra $P(\omega)/{\rm fin}$, which is isomorphic to the sublattice of diagonal projections. In particular, we prove some basic consistency results about the possible cofinalities of well-ordered sequences of projections and the possible cardinalities of sets of mutually orthogonal projections that are analogous to well-known results about $P(\omega)/{\rm fin}$.
Bayesian Item Response Theory Estimation

The problem of fundamental importance in item response theory is the accurate estimation of the parameters that characterize the items and the ability or the proficiency levels of examinees. While in general, likelihood-based approaches such as joint, conditional, and marginal maximum likelihood procedures provide reasonable estimates of the item parameters, more often than not these procedures yield estimates in the two- and three-parameter models that are inadmissible in the sense that the estimates of the ability and item parameters fall outside acceptable ranges. Bayesian approaches, by taking into account prior and collateral information, overcome the problems encountered by likelihood-based approaches. Keywords: item response theory; item response model; maximum likelihood estimates; Bayesian estimation; prior information; posterior density
Transient Dynamics of Epidemic Spreading and Its Mitigation on Large Networks

In this paper, we aim to understand the transient dynamics of a susceptible-infected (SI) epidemic spreading process on a large network. The SI model has been largely overlooked in the literature, while it is naturally a better fit for modeling the malware propagation in early times when patches/vaccines are not available, or over a wider range of timescales when massive patching is practically infeasible. Nonetheless, its analysis is simply non-trivial, as its important dynamics are all transient and the usual stability/steady-state analysis no longer applies. To this end, we develop a theoretical framework that allows us to obtain an accurate closed-form approximate solution to the original SI dynamics on any arbitrary network, which captures the temporal dynamics over all time and is tighter than the existing approximation, and also to provide a new interpretation via reliability theory. As its applications, we further develop vaccination policies with or without knowledge of already-infected nodes, to mitigate the future epidemic spreading to the extent possible, and demonstrate their effectiveness through numerical simulations.
Learning the Structure of a Nonstationary Vector Autoregression

We adapt graphical causal structure learning methods to apply to nonstationary time series data, specifically to processes that exhibit stochastic trends. We modify the likelihood component of the BIC score used by score-based search algorithms, such that it remains a consistent selection criterion for integrated or cointegrated processes. We use this modified score in conjunction with the SVAR-GFCI algorithm, which allows us to recover qualitative structural information about the underlying data-generating process even in the presence of latent (unmeasured) factors. We demonstrate our approach on both simulated and real macroeconomic data.
The Return to Protectionism

After decades of supporting free trade, in 2018 the United States raised import tariffs and major trade partners retaliated. We analyze the short-run impact of this return to protectionism on the U.S. economy. Import and retaliatory tariffs caused large declines in imports and exports. Prices of imports targeted by tariffs did not fall, implying complete pass-through of tariffs to duty-inclusive prices. The resulting losses to U.S. consumers and firms that buy imports was $51 billion, or 0.27% of GDP. We embed the estimated trade elasticities in a general-equilibrium model of the U.S. economy. After accounting for tariff revenue and gains to domestic producers, the aggregate real income loss was $7.2 billion, or 0.04% of GDP. Import tariffs favored sectors concentrated in politically competitive counties, and the model implies that tradeable-sector workers in heavily Republican counties were the most negatively affected due to the retaliatory tariffs. JEL Code: F1.
Computational Methods in Environmental and Resource Economics

Computational methods are required to solve problems without closed-form solutions in environmental and resource economics. Efficiency, stability, and accuracy are key elements for computational me...
Granger predictability of oil prices after the Great Recession

Abstract Real oil prices surged from 2009 through 2014, comparable to the 1970s oil shock period. Standard explanations based on monopoly markup fall short since inflation remained low after 2009. This paper contributes strong evidence of Granger (1969) predictability of nominal factors to oil prices, using one adjustment to monetary aggregates. This adjustment is the subtraction from the monetary aggregates of the 2008–2009 Federal Reserve borrowing of reserves from other Central Banks (Swaps), made after US reserves turned negative. This adjustment is key in that Granger predictability from standard monetary aggregates is found only with the Swaps subtracted.
Relative particle dispersion in two-dimensional and quasi-geostrophic turbulence

Abstract In this paper, phenomenological developments are used to explore relative particle dispersion (RPD) in two-dimensional (2D) and quasi-geostrophic (QG) fully-developed turbulence (FDT). The role played by the 2D and QG FDT cascade physics underlying this process is given special attention. Prevalence of spatial intermittency effects in 2D FDT enstrophy cascade, however small, is shown to lead to a structural change in the RPD growth law, more specifically the development of power-law scaling of RPD; this corroborates the difficulty in observing Lin’s (1972) exponential scaling law in laboratory experiments (Jullien (2003)). QG effects are found to lead to an enhanced RPD in the baroclinic regime of the energy cascade, which seems to be traceable to a negative eddy-viscosity characterizing the latter regime. They are also found to lead to particle clumping in the baroclinic regime of the enstrophy cascade (this aspect appears to be associated with the tendency of divorticity sheets to occur near the vortex nulls where particle clumping is known, as per numerical simulations and laboratory experiments, to be favored to occur). These results are developed from the established scaling relations for 2D and QG FDT and are validated further via alternative dimensional/scaling developments for 2D and QG FDT similar to the one given for 3D FDT by Batchelor and Townsend (1956). The feasibility of spatial intermittency effects is underscored via the nonlinear scaling dependence of RPD on the enstrophy (or energy) dissipation rate.
Counterfactual off-policy evaluation with gumbel-max structural causal models

We introduce an off-policy evaluation procedure for highlighting episodes where applying a reinforcement learned (RL) policy is likely to have produced a substantially different outcome than the observed policy. In particular, we introduce a class of structural causal models (SCMs) for generating counterfactual trajectories in finite partially observable Markov Decision Processes (POMDPs). We see this as a useful procedure for off-policy "debugging" in high-risk settings (e.g., healthcare); by decomposing the expected difference in reward between the RL and observed policy into specific episodes, we can identify episodes where the counterfactual difference in reward is most dramatic. This in turn can be used to facilitate review of specific episodes by domain experts. We demonstrate the utility of this procedure with a synthetic environment of sepsis management.
Event Trend Aggregation Under Rich Event Matching Semantics

Streaming applications from cluster monitoring to algorithmic trading deploy Kleene queries to detect and aggregate event trends. Rich event matching semantics determine how to compose events into trends. The expressive power of state-of-the-art streaming systems remains limited since they do not support many of these semantics. Worse yet, they suffer from long delays and high memory costs because they maintain aggregates at a fine granularity. To overcome these limitations, our Coarse-Grained Event Trend Aggregation (Cogra) approach supports a rich variety of event matching semantics within one system. Better yet, Cogra incrementally maintains aggregates at the coarsest granularity possible for each of these semantics. In this way, Cogra minimizes the number of aggregates -- reducing both time and space complexity. Our experiments demonstrate that Cogra achieves up to six orders of magnitude speed-up and up to seven orders of magnitude memory reduction compared to state-of-the-art approaches.
Quantifying pollen-vegetation relationships to reconstruct ancient forests using 19th-century forest composition and pollen data

Abstract Mitigation of climate change and adaptation to its effects relies partly on how effectively land-atmosphere interactions can be quantified. Quantifying composition of past forest ecosystems can help understand processes governing forest dynamics in a changing world. Fossil pollen data provide information about past forest composition, but rigorous interpretation requires development of pollen-vegetation models (PVMs) that account for interspecific differences in pollen production and dispersal. Widespread and intensified land-use over the 19th and 20th centuries may have altered pollen-vegetation relationships. Here we use STEPPS, a Bayesian hierarchical spatial PVM, to estimate key process parameters and associated uncertainties in the pollen-vegetation relationship. We apply alternate dispersal kernels, and calibrate STEPPS using a newly developed Euro-American settlement-era calibration data set constructed from Public Land Survey data and fossil pollen samples matched to the settlement-era using expert elicitation. Models based on the inverse power-law dispersal kernel outperformed those based on the Gaussian dispersal kernel, indicating that pollen dispersal kernels are fat tailed. Pine and birch have the highest pollen productivities. Pollen productivity and dispersal estimates are generally consistent with previous understanding from modern data sets, although source area estimates are larger. Tests of model predictions demonstrate the ability of STEPPS to predict regional compositional patterns.
Cyclic Thioanhydrides: Linchpins for Multicomponent Coupling Reactions Based on the Reaction of Thioacids with Electron-Deficient Sulfonamides and Azides

Reaction of cyclic thioanhydrides with amines affords amides functionalized with thioacids, which can be trapped in situ with electron-deficient azides or, preferably, 2,4-dinitrobenzenesulfonamides. In this manner the cyclic thioanhydride serves as a linchpin in a three-component coupling sequence. The use of thiomaleic anhydride and a bifunctional nucleophile extends the process to heterocycle synthesis, while a cyclic thioanhydride prepared from aspartic acid directly provides N-functionalized asparagine derivatives.
Synthesis of a molecular tripod to anchor molecular coordination compounds to semiconductor nanoparticles

A 1,3,5,7-tetraphenyladamantane derivative having three arms terminating with carboxylic acids and a fourth substituted with a 9,10-phenanthrolinyl ligand was prepared as a new kind of molecular linkage to study dynamics of electron injection at the interface of TiO2 nanoparticles.
Probabilistic Analysis of Linear Programming Decoding

We initiate the probabilistic analysis of linear programming (LP) decoding of low-density parity-check (LDPC) codes. Specifically, we show that for a random LDPC code ensemble, the linear programming decoder of Feldman succeeds in correcting a constant fraction of errors with high probability. The fraction of correctable errors guaranteed by our analysis surpasses previous nonasymptotic results for LDPC codes, and in particular, exceeds the best previous finite-length result on LP decoding by a factor greater than ten. This improvement stems in part from our analysis of probabilistic bit-flipping channels, as opposed to adversarial channels. At the core of our analysis is a novel combinatorial characterization of LP decoding success, based on the notion of a flow on the Tanner graph of the code. An interesting by-product of our analysis is to establish the existence of ldquoprobabilistic expansionrdquo in random bipartite graphs, in which one requires only that almost every (as opposed to every) set of a certain size expands, for sets much larger than in the classical worst case setting.
Threshold and Proactive Pseudo-Random Permutations.

We construct a reasonably efficient threshold and proactive pseudo-random permutation (PRP). Our protocol needs only O(1) communication rounds. It tolerates up to (n − 1)/2 of n dishonest servers in the semi-honest environment. Many protocols that use PRPs (e.g., a CBC block cipher mode) can now be translated into the distributed setting. Our main technique for constructing invertible threshold PRPs is a distributed Luby-Rackoff construction where both the secret keys and the input are shared among the servers. We also present protocols for obliviously computing pseudo-random functions by Naor-Reingold [37] and Dodis-Yampolskiy [24] with shared input and keys.
Novel heterocycles. Synthesis of 2,3-dihydro-6-methyl-2-phenyl-4H,6H-pyrano[3,2-c][2,1]benzothiazin-4-one 5,5-dioxide and related compounds

The reaction of 2-chloro-4-(methylsulfonyl)benzoyl chloride (5) with 1-methyl-1H-2,1-benzothiazin-4-(3H)-one 2,2-dioxide (4) gave the O-benzoyl compound, 1-methyl-2,2-dioxido-1H-2,1-benzothiazin-4-yl 2-chloro-4-(methylsulfonyl)benzoate (6), which rearranged to give the C-benzoyl isomer, [2-chloro-4-(methylsulfonyl)phenyl] (4-hydroxy-1-mefhyl-2,2-dioxido-1H-2,1-benzothiazin-3-yl)methanone (7). The O-cinnamoyl compound 13 that resulted from the addition of 2,4-dichlorocinnamoyl chloride (11) to compound 4 rearranged to give the C-cinnamoyl compound, 3-(2,4-dichlorophenyl)-1-(4-hydroxy-1-methyl-2,2-dioxido-1H-2,1-benzothiazin-3yl)-2-propen-1-one (15). On the other hand, 1-methyl-2,2-dioxido-1H-2,1-benzothiazin-4-yl 3-phenyl-2-propenoate (19) (from cinnamoyl chloride (17) and compound 4) rearranged to give 2,3-dihydro-6-methyl-2-phenyl-4H,6H-pyrano[3,2-c][2,1]benzothiazin-4-one 5,5-dioxide (21), an example of a hitherto unknown ring system. Additional examples of this novel heterocycle were prepared from 1-methyl-7-(trifluoromethyl)-1H-pyrido[2,3-c][1,2]thiazin-4(3H)-one 2,2-dioxide (23) and 1-methyl-1H-thieno[3,2-c][1,2]thiazin-4(3H)-one 2,2-dioxide (8).
A regioselective synthesis of 8,9-dichloro-2,3,4,5-tetrahydro-1H-2-benzazepine (LY134046), a potent phenylethanolamine N-methyltransferase inhibitor

Abstract A regioselective synthesis of 2,3,4,5-tetrahydro-1 H -2-benzazepines substituted on the aryl and/or azepine rings is presented and used for the preparation of the title compound in overall yield of 22% from intermediate 1 .
Chiral cycloalkylidene α,β-unsaturated iminium approach to stereoselective formal [3+3] cycloaddition reaction in spiroheterocycle synthesis

Abstract An approach to stereoselective formal [3+3] cycloaddition reaction using chiral cycloalkylidene α,β-unsaturated iminiums is described here leading to preparations of spiroheterocycles in modest stereoselectivity. The reversibility of 6π-electron electrocyclic ring closure did not always lead to the thermodynamically more favored product. These observations led to other useful mechanistic understanding of electrocyclic ring closure of 1-oxatrienes.
An Improved Preparation of 4,7-Phenanthrolino-5,6:5′,6′-pyrazine

Abstract An overall three step preparation of the bis-diimine bridging ligand 4,7-phenanthrolino-5,6:5′,6′-pyrazine (ppz, 1) from 2-methoxy-1,4-phenylenediamine hydrosulfate 4 is reported.
Adsorption of Guest Molecules in Zeolitic Materials: Computational Aspects

Recent progress in the computation of thermodynamic properties of guest molecules in zeolites, using classical molecular simulation techniques, is reviewed. It is shown that grand canonical Monte Carlo simulations, using statistical biaising for studying large anisotropic molecules, together with an appropriate guest−guest force field, may provide a reasonably accurate prediction of single component and binary mixture adsorption data for systems such as normal and branched alkanes, benzene, alkyl benzene isomers and halocarbon molecules in a variety of aluminosilicate hosts. The Monte Carlo algorithms used to obtain reliable thermodynamics data (adsorption isotherms and heats) are discussed as well as the newly developed semiempirical force fields, which allow a better transferability of the potential parameters from one guest/host system to another.
Hypervalent Iodine Oxidation of Trimethylsilyl Ketene Acetals: A Convenient Route to α-Methoxylation of Esters and Lactones

Abstract Hypervalent iodine oxidation of trimethylsilyl ketene acetals of esters and lactones using iodosobenzene in methanol affords the corresponding α-methoxylated carbonyl compounds in good yields. #On leave of absence from Kurukshetra University, Kurukshetra, 136119, India.
A Study of the Complexation of Bis(m-Phenylene) Crown Ethers and Secondary Ammonium Ions

Two macrocycles, bis(m-phenylene)-26-crown-8 (1) and bis(m-phenylene)-32-crown-10 (2), were combined with several linear components, dibenzyl- (3·PF6), di-n-butyl- (4·PF6), and diphenethyl- (5·PF6) ammonium hexafluorophosphate salts. The smaller macrocycle 1 was shown not to complex effectively with any of the ammonium salts in solution by 1H NMR, but 1:1 complexes were shown to exist in the “gas phase” as [1:3], [1:4], and [1:5] by high-resolution fast atom bombardment mass spectrometry (HRFABMS) and electrospray ionization mass spectrometry (ESIMS). The X-ray crystal structure of macrocycle 1 is reported. The larger macrocycle 2 did form 1:2 complexes with the ammonium salts in solution, which were observed as well in the solid and gas phases. X-ray crystal structures of the pseudorotaxanes [2:(3)2]·2PF6 and [2:(5)2]·2PF6 were determined and are discussed. The pseudorotaxanes are stabilized by hydrogen bonding between the ammonium hydrogens of the linear salt unit and the oxygens of the crown ether macr...
[2,3] Sigmatropic Rearrangement of Propargylic Sulfinates by a Pale Ag1-USY Zeolite and Silver Salts

The applied catalyst (zeolite Ag-USY) can be recycled several times and therefore this reaction becomes “greener”.
γ- and δ-Hydroxynitriles: diastereoselective electrophile-dependent alkylations

Abstract Deprotonating γ- and δ-hydroxynitriles with i-PrMgCl allows highly diastereoselective alkylations controlled by the asymmetry of the remote carbinol stereocenter. Mechanistic experiments are consistent with γ-hydroxynitriles alkylating via a chelated magnesiated nitrile whereas δ-hydroxynitriles favor alkylation from acyclic magnesiated nitriles. Collectively these alkylations; are the first electrophile-dependent alkylations of acyclic nitriles, exhibit a unique influence on the nature of the Grignard used for the deprotonation, and address the challenge of installing quaternary centers in conformationally mobile, acyclic nitriles.
Deformation Microscopy for Dynamic Intracellular and Intranuclear Mapping of Mechanics with High Spatiotemporal Resolution.

Summary Structural heterogeneity is a hallmark of living cells that drives local mechanical properties and dynamic cellular responses. However, the robust quantification of intracellular mechanics is lacking from conventional methods. Here, we describe the development of deformation microscopy, which leverages conventional imaging and an automated hyperelastic warping algorithm to investigate strain history, deformation dynamics, and changes in structural heterogeneity within the interior of cells and cell nuclei. Using deformation microscopy, we found that partial or complete disruption of LINC complexes in cardiomyocytes in vitro and lamin A/C deficiency in myocytes in vivo abrogate dominant tensile loading in the nuclear interior. We also found that cells cultured on stiff substrates or in hyperosmotic conditions displayed abnormal strain burden and asymmetries at interchromatin regions, which are associated with active transcription. Deformation microscopy represents a foundational approach toward intracellular elastography, with the potential utility to provide mechanistic and quantitative insights in diverse mechanobiological applications.
Levels of growth factors from platelet-rich fibrin from chronic periodontitis versus periodontally healthy subjects: a pilot study.

This study aimed to (1) compare the amounts of growth factors from platelet-rich fibrin (PRF) between chronic periodontitis and periodontally healthy subjects and (2) evaluate the relationships between the amounts of growth factors from PRF with complete blood counts (white blood cell (WBC) and platelet counts) and the serum concentrations of IL-1β, IL-6, and tumor necrosis factor-α (TNF-α). Venous blood was collected from chronic periodontitis (test) and periodontally healthy subjects (control). PRF and serum were collected from the centrifuged blood. Liquid exudates from the compression of PRF were collected. The compressed PRF membranes were incubated in saline, and eluted aliquots were collected at 1, 24, and 72 h, and the membranes were then digested with trypsin. Epidermal growth factor, insulin-like growth factor-1, platelet-derived growth factor-BB, transforming growth factor-β1, and vascular endothelial growth factor in the exudates and eluents were quantified by ELISA. Serum was used for IL-1β, IL-6, and TNF-α quantifications. Complete blood counts were measured. There were no significant differences in the amounts of growth factors from PRF exudates and membranes measured between groups (all p > 0.05). The test group had significantly higher WBC (p 0.05). PRF can be utilized as an autologous source of growth factors not affected by periodontal condition and WBC level. The amounts of growth factors from PRF were not affected by the periodontal condition of the patient.
Paclitaxel from primary taxanes: a perspective on creative invention in organozirconium chemistry.

In this Perspective, which describes the achievements recognized by the 2007 ACS Award for Creative Invention, we discuss the discovery of a new synthetic reaction and its translation into a substantially improved method for manufacturing a major pharmaceutical productthe blockbuster anticancer drug, paclitaxel. The role of creativity in the discovery and invention processes is also discussed. As is often the case, chance discovery and serendipitous findings played a role in the evolution of this work. Translation of the basic research into a commercially viable paclitaxel semisynthesis is also described. The final manufacturing process illustrates the enormous impact that the globalization of markets has had on chemical and pharmaceutical manufacturing.
A continuation method for Nash equilibria in structured games

Structured game representations have recently attracted interest as models for multi-agent artificial intelligence scenarios, with rational behavior most commonly characterized by Nash equilibria. This paper presents efficient, exact algorithms for computing Nash equilibria in structured game representations, including both graphical games and multi-agent influence diagrams (MAIDs). The algorithms are derived from a continuation method for normal-form and extensive-form games due to Govindan and Wilson; they follow a trajectory through a space of perturbed games and their equilibria, exploiting game structure through fast computation of the Jacobian of the payoff function. They are theoretically guaranteed to find at least one equilibrium of the game, and may find more. Our approach provides the first efficient algorithm for computing exact equilibria in graphical games with arbitrary topology, and the first algorithm to exploit fine-grained structural properties of MAIDs. Experimental results are presented demonstrating the effectiveness of the algorithms and comparing them to predecessors. The running time of the graphical game algorithm is similar to, and often better than, the running time of previous approximate algorithms. The algorithm for MAIDs can effectively solve games that are much larger than those solvable by previous methods.
4′-Aminomethyl-2,2′-bipyridyl-4-carboxylic Acid (Abc) and Related Derivatives: Novel Bipyridine Amino Acids for the Solid-Phase Incorporation of a Metal Coordination Site Within a Peptide Backbone

Abstract The novel bipyridyl amino acid, 4′-aminomethyl-2,2′-bipyridyl-4-carboxylic acid (Abc), and related Boc- and Fmoc-protected derivatives were synthesized to provide high-affinity bidentate metal-binding amino acid modules for the solid-phase peptide synthesis (SPPS) of metallopeptides. Since the bipyridyl group of Abc is inserted into the peptide mainchain and not in the sidechain, its presence in a peptide should impart distinct conformational constraints to the backbone geometry, influencing local secondary structure. To demonstrate its amenability for SPPS and its capacity for metal complexation, Abc was incorporated into the hexapeptide Ac-Ala-Abc-Ahx-Ahx-Abc-Gly-NH2 (peptide Aha; where Ahx=aminohexanoic acid) and subsequently used as a tetradentate ligand to octahedrally coordinate and asymmetrically encapsulate a ruthenium(II) ion, creating a novel peptide-caged redox-active metal complex.
Radical cyclization strategies for the formation of ring constrained tricyclic tropane analogues

Abstract A concise and efficient method for the construction of N,C3-constrained tropane derivatives has been developed. The key step of the reaction sequence involves either a 6- or a 7-trig radical cyclization.
A SIMPLE Pipeline for Mapping Point Mutations

A forward genetic screen is one of the best methods for revealing the function of genes. In plants, this technique is highly efficient, as it is relatively easy to grow and screen hundreds or thousands of individuals. The cost efficiency and ease of data production afforded by next-generation sequencing have created new opportunities for rapid mapping of induced mutations. Current mapping tools are often not user friendly, are complicated, or require extensive preparation steps. To simplify the process of mapping new mutations, we developed a pipeline that takes next-generation sequencing fastq files as input, calls on several well-established and freely available genome-analysis tools, and outputs the most likely causal DNA changes. The pipeline has been validated in Arabidopsis thaliana (Arabidopsis) and can be readily applied to other species, with the possibility of mapping either dominant or recessive mutations.
CARBON-CARBON BOND FORMATION BY ELECTROCHEMICAL CATALYSIS IN CONDUCTIVE MICROEMULSIONS

Bicontinuous microemulsions made from oil, water, and surfactants were examined as substitutes for organic solvents in carbon−carbon bond-forming reactions. Conjugated additions of primary alkyl iodides 3a−c to 2-cyclohexen-1-one (4) to give 3-alkyl cyclohexanones 5a−c and cyclization of 2-(4-bromobutyl)-2-cyclohexen-1-one (9) to 1-decalone (10) were mediated by the Co(I)L complex vitamin B12s generated at carbon cloth electrodes under mild conditions. Reaction of the Co(I)L nucleophile with the alkyl halides gives a Co−alkyl complex. Cleavage of the Co−alkyl complexes by using an electrode potential of −0.85 V (all vs SCE) and irradiation with visible light, or a potential of −1.45 V in the dark, were compared. Addition of the resulting alkyl radicals to the activated double bonds gave comparable yields of 3-alkylcyclohexanone 5a−c (70−80% using −0.85 V + light) and 1-decalone (90%, both cleavage modes) 10 in microemulsions and in DMF. Microemulsions containing hexadecyltrimethylammonium bromide (CTAB) g...