cssi/SciSciGPT-SciSciNet huggingface dataset:
Take-up and Targeting: Experimental Evidence from SNAP

This paper develops a framework for evaluating the welfare impact of various interventions designed to increase take-up of social safety net programs in the presence of potential behavioral biases. We calibrate the key parameters using a randomized field experiment in which 30,000 elderly individuals not enrolled in  but likely eligible for  the Supplemental Nutrition Assistance Program (SNAP) are either provided with information that they are likely eligible, provided with this information and also offered assistance in applying, or are in a "status quo" control group. Only 6 percent of the control group enrolls in SNAP over the next 9 months, compared to 11 percent of the Information Only group and 18 percent of the Information Plus Assistance group. The individuals who apply or enroll in response to either intervention receive lower benefits and are less sick than the average enrollee in the control group. The results are consistent with the existence of optimization frictions that are greater for needier individuals, suggesting that the poor targeting properties of the interventions reduce their welfare gains.
Learning in the zone: toward workforce development of evidence-based public policy communication.

Evidence-based policy communication (EBPC) is an important, emerging focus in public health research. However, we have yet to understand public health workforce ability to develop and/or use it. The study objective was to characterize capacity to develop and use EBPC and identify cooperative learning and development opportunities using the case of Human papillomavirus (HPV). Vygotsky’s Zone of Proximal Development (ZPD) informed guided interviews with 27 advocates in Indiana from government, industry, research, state associations and individuals. Participants focused on HPV, cancer, women’s health, school health and minority health. Capacity to develop and use EBPC was reported to develop through cooperative learning opportunities on the job or in advocacy focused coalitions. Coalition learning appeared to translate across health topics. Notably, policy experience did not assure understanding or use of EBPC. The ZPD framework can inform workforce EBPC interventions by focusing on actual development, potential development and factors for learning and development in the ZPD. Future studies should further clarify and evaluate emerging indicators in additional public health policy areas with a larger sample.
A National Pragmatic Safety Limit for Nuclear Weapon Quantities

This study determines the nuclear pragmatic limit where the direct physical negative consequences of nuclear weapons use are counter to national interests, by assuming all unknowns are conservatively optimistic. The only effect considered is nuclear winter (“nuclear autumn” in the low weapons limits) and the resultant effects on the aggressor nation. First, the ability of low nuclear weapon limits is probed for maintaining deterrence in the worst-case scenario of attacking the most-populous nation. Second, the ability of aggressor nations to feed themselves is assessed without trade and industry resultant from a nuclear attack causing “nuclear autumn” (10% global agricultural shortfall). Third, the best-case wealthy aggressor nation with abundant arable land is analyzed for starvation and economic impacts given 7000, 1000, and 100 nuclear weapons scenarios. The results found that 100 nuclear warheads is adequate for nuclear deterrence in the worst case scenario, while using more than 100 nuclear weapons by any aggressor nation (including the best positioned strategically to handle the unintended consequences) even with optimistic assumptions (including no retaliation) would cause unacceptable damage to their own society. Thus, 100 nuclear warheads is the pragmatic limit and use of government funds to maintain more than 100 nuclear weapons does not appear to be rational.
Delegated Search Approximates Efficient Search

There are many settings in which a principal performs a task by delegating it to an agent, who searches over possible solutions and proposes one to the principal. This describes many aspects of the workflow within organizations, as well as many of the activities undertaken by regulatory bodies, who often obtain relevant information from the parties being regulated through a process of delegation. A fundamental tension underlying delegation is the fact that the agent's interests will typically differ -- potentially significantly -- from the interests of the principal, and as a result the agent may propose solutions based on their own incentives that are inefficient for the principal. A basic problem, therefore, is to design mechanisms by which the principal can constrain the set of proposals they are willing to accept from the agent, to ensure a certain level of quality for the principal from the proposed solution. In this work, we investigate how much the principal loses -- quantitatively, in terms of the objective they are trying to optimize -- when they delegate to an agent. We develop a methodology for bounding this loss of efficiency, and show that in a very general model of delegation, there is a family of mechanisms achieving a universal bound on the ratio between the quality of the solution obtained through delegation and the quality the principal could obtain in an idealized benchmark where they searched for a solution themself. Moreover, it is possible to achieve such bounds through mechanisms with a natural threshold structure, which are thus structurally simpler than the optimal mechanisms typically considered in the literature on delegation. At the heart of our framework is an unexpected connection between delegation and the analysis of prophet inequalities, which we leverage to provide bounds on the behavior of our delegation mechanisms.
Prefix and Suffix Sequential Pattern Mining

Sequential pattern mining is a challenging problem that has received much attention in the past few decades. The mining of large sequential databases can be very time consuming and produces a large number of unrelated patterns that must be evaluated. In this paper, we explore the problems of frequent prefix, prefix-closed, and prefix-maximal pattern mining along with their suffix variants. By constraining the pattern mining task, we are able to reduce the mining time required while obtaining patterns of interest. We introduce notations related to prefix/suffix sequential pattern mining while providing theorems and proofs that are key to our proposed algorithms. We show that the use of projected databases can greatly reduce the time required to mine the complete set of frequent prefix/suffix patterns, prefix/suffix-closed patterns, and prefix/suffix-maximal patterns. Theoretical analysis shows that our approach is better than the current existing approach, and empirical analysis on various datasets is used to support these conclusions.
Physics-based scene-level reasoning for object pose estimation in clutter:

This paper focuses on vision-based pose estimation for multiple rigid objects placed in clutter, especially in cases involving occlusions and objects resting on each other. Progress has been achiev...
The Role of Statistical Learning in Understanding and Treating Spoken Language Outcomes in Deaf Children With Cochlear Implants

Purpose Statistical learning—the ability to learn patterns in environmental input—is increasingly recognized as a foundational mechanism necessary for the successful acquisition of spoken language....
GeneSys: enabling continuous learning through neural network evolution in hardware

Modern deep learning systems rely on (a) a hand-tuned neural network topology, (b) massive amounts of labelled training data, and (c) extensive training over large-scale compute resources to build a system that can perform efficient image classification or speech recognition. Unfortunately, we are still far away from implementing adaptive general purpose intelligent systems which would need to learn autonomously in unknown environments and may not have access to some or any of these three components. Reinforcement learning and evolutionary algorithm (EA) based methods circumvent this problem by continuously interacting with the environment and updating the models based on obtained rewards. However, deploying these algorithms on ubiquitous autonomous agents at the edge (robots/drones) demands extremely high energy-efficiency due to (i) tight power and energy budgets, (ii) continuous / lifelong interaction with the environment, (iii) intermittent or no connectivity to the cloud to offloadheavy-weight processing. To address this need, we present Genesys, a HW-SW prototype of a EA-based learning system, that comprises of a closed loop learning engine called EvE and an inference engine called ADAM. EvE can evolve the topology and weights of neural networks completely in hardware for the task at hand, without requiring hand-optimization or backpropogation training. ADAM continuously interacts with the environment and is optimized for efficiently running the irregular neural networks generated by EvE. Genesys identifies and leverages multiple unique avenues of parallelism unique to EAs that we term "gene"-level parallelism, and "population"-level parallelism. We ran Genesys with a suite of environments from OpenAI gym and observed 2--5 orders of magnitude higher energy-efficiency over state-of-the-art embedded and desktop CPU and GPU systems.
Analysis of optical data using extended Drude model and generalized Allen’s formulas

Extended Drude model formalism has been successfully utilized for analyzing optical spectra of strongly correlated electron systems including heavy-fermion systems and high-T c superconducting iron pnictides and cuprates. Furthermore, generalized Allen's formulas have been developed and applied to extract the electron-boson spectral density function from measured optical data of high temperature superconductors including cuprates in various material phases. Here we used a reverse process to obtain various optical quantities starting from two typical electron-boson spectral density model functions for three intriguing (normal, pseudogap, and d-wave superconducting) material phases in cuprates. We also assigned the calculated optical results to designated regions in the phase diagram of hole-doped cuprates and compared them with the corresponding measured optical spectra of Bi2Sr2CaCu2 [Formula: see text] (Bi-2212). This comparison suggested that this way of optical data analysis can be a convincing method to study correlated electrons in the copper oxide superconductors and other superconducting systems as well.
Optimal Dynamic Appointment Scheduling of Base and Surge Capacity

Problem definition: We study dynamic stochastic appointment scheduling when delaying appointments increases the risk of incurring costly failures, such as readmissions in healthcare or engine failu...
A Cryptographic Escrow for Treaty Declarations and Step-by-Step Verification

AbstractThe verification of arms-control and disarmament agreements requires states to provide declarations, including information on sensitive military sites and assets. There are important cases,...
Quasi-universality in single-cell sequencing data

The development of single-cell technologies provides the opportunity to identify new cellular states and reconstruct novel cell-to-cell relationships. Applications range from understanding the transcriptional and epigenetic processes involved in metazoan development to characterizing distinct cells types in heterogeneous populations like cancers or immune cells. However, analysis of the data is impeded by its unknown intrinsic biological and technical variability together with its sparseness; these factors complicate the identification of true biological signals amidst artifact and noise. Here we show that, across technologies, roughly 95% of the eigenvalues derived from each single-cell data set can be described by universal distributions predicted by Random Matrix Theory. Interestingly, 5% of the spectrum shows deviations from these distributions and present a phenomenon known as eigenvector localization, where information tightly concentrates in groups of cells. Some of the localized eigenvectors reflect underlying biological signal, and some are simply a consequence of the sparsity of single cell data; roughly 3% is artifactual. Based on the universal distributions and a technique for detecting sparsity induced localization, we present a strategy to identify the residual 2% of directions that encode biological information and thereby denoise single-cell data. We demonstrate the effectiveness of this approach by comparing with standard single-cell data analysis techniques in a variety of examples with marked cell populations.
Exact Replication of the Best Rebalancing Rule in Hindsight

This article prices and replicates the financial derivative whose payoff at T is the wealth that would have accrued to a $1 deposit into the best continuously-rebalanced portfolio (or fixed-fraction betting scheme) determined in hindsight. For the single-stock Black–Scholes market, Ordentlich and Cover (1998) only priced this derivative at time-0, giving . Of course, the general time-t price is not equal to . The author completes the Ordentlich–Cover (1998) analysis by deriving the price at any time t. By contrast, the author also studies the more natural case of the best-levered rebalancing rule in hindsight. This yields , where b(S, t) is the best rebalancing rule in hindsight over the observed history [0, t]. The author shows that the replicating strategy amounts to betting the fraction b(S, t) of wealth on the stock over the interval [t, t + dt]. This fact holds for the general market with n correlated stocks in geometric Brownian motion: C(S, t) = (T/t)n/2 exp(rt + b′Σb·t/2), where Σ is the covariance of instantaneous returns per unit time. This result matches the O(Tn/2) “cost of universality” derived by Cover in his “universal portfolio theory” (1986, 1991, 1996, 1998), which super-replicates the same derivative in discrete-time. The replicating strategy compounds its money at the same asymptotic rate as the best-levered rebalancing rule in hindsight, thereby beating the market asymptotically. Naturally enough, the American-style version of Cover’s Derivative is never exercised early in equilibrium. TOPICS:Derivatives, portfolio construction, performance measurement, statistical methods
Impact of mandated exclusive territories in the US brewing industry: Evidence from scanner level data

Abstract I examine the competitive effects of mandated exclusive territories in the US beer industry. Theory is ambiguous as to the competitive impacts of this vertical practice. Using scanner data from a large number of grocery stores, I empirically examine the impact on beer prices, quantities, and number of brands sold after Wisconsin mandated that brewers must assign exclusive wholesale territories in 2006. Reduced form results from a differences-in-differences model using several control groups and a synthetic control show that the mandates increased prices and reduced quantity of craft beer. Overall number of brands sold decreased as well and craft brewers were the most negatively impacted. Findings suggest that the mandate gave protection to wholesalers and caused an increase in the costs of distribution and reduced competition in the brewing industry.
Topological Data Analysis for the String Landscape

Persistent homology computes the multiscale topology of a data set by using a sequence of discrete complexes. In this paper, we propose that persistent homology may be a useful tool for studying the structure of the landscape of string vacua. As a scaled-down version of the program, we use persistent homology to characterize distributions of Type IIB flux vacua on moduli space for three examples: the rigid Calabi-Yau, a hypersurface in weighted projective space, and the symmetric six-torus T6 = (T2)3. These examples suggest that persistence pairing and multiparameter persistence contain useful information for characterization of the landscape in addition to the usual information contained in standard persistent homology. We also study how restricting to special vacua with phenomenologically interesting low-energy properties affects the topology of a distribution.
SRPT for Multiserver Systems

The Shortest Remaining Processing Time (SRPT) scheduling policy and its variants have been extensively studied in both theoretical and practical settings. While beautiful results are known for single-server SRPT, much less is known for multiserver SRPT. In particular, stochastic analysis of the M/G/k under SRPT is entirely open. Intuition suggests that multiserver SRPT should be optimal or near-optimal for minimizing mean response time. However, the only known analysis of multiserver SRPT is in the worst-case adversarial setting, where SRPT can be far from optimal. In this paper, we give the first stochastic analysis bounding mean response time of the M/G/k under SRPT. Using our response time bound, we show that multiserver SRPT has asymptotically optimal mean response time in the heavy-traffic limit. The key to our bounds is a strategic combination of stochastic and worst-case techniques. Beyond SRPT, we prove similar response time bounds and optimality results for several other multiserver scheduling policies. This article is an introduction to our longer paper, [1].
Clustering, Single Linkage†

Single linkage clustering is used in hierarchical clustering analysis to partition a set of n observations into g groups or clusters on the basis of p variables measured on the n observations. The analysis is performed on an n × n matrix of pairwise distance measures between observations. The procedure starts by combining the two observations with the smallest distance between them. The procedure continues to combine clusters with the smallest distances until only one cluster, including the entire sample, remains. The number of groups, g, is determined to represent the final number of clusters to retain. Keywords: hierarchical methods; similarity; dissimilarity; distance measures
Japanese regulation of truck transport

Since 1951 the Japanese Ministry of Transport has been vested with sweeping authority to restrict entry and set prices in commercial trucking, but the standard price schedules that it continues to publicize and periodically revise are in fact widely disregarded by commercial trucking firms. There are no economies or diseconomies of scale and firms have expanded until industry profits are exhausted. The changes in truck transport regulation introduced in 1991 were mainly directed at freeing a new activity, parcel delivery service, from regulatory constraints and spreading some of the benefits to others in the industry. J. Japan. Int. Econ., March 2001, 15(1), pp. 1–28. Department of Economics, North Carolina State University, Raleigh, North Carolina 27695-8110. Copyright 2001 Academic Press. Journal of Economic Literature Classification Numbers: L92, L51.
Developments in accounting regulation: A synthesis and annotated bibliography of evidence and commentary in the academic literature (1999–2000)

Abstract In this article, we synthesize in annotated bibliography form, recent regulation-related findings and commentaries in the academic literature. This annotated bibliography is the fourth in a series of bibliographies that will summarize regulation-related academic research for at least the period 1990 and forward. We reviewed academic outlets such as The Accounting Review, The Journal of Accounting Research, The Journal of Accounting and Economics, Accounting Horizons, The Journal of Accounting, Auditing & Finance, The Journal of Accounting and Public Policy, The Journal of Business, Finance & Accounting, Auditing: A Journal of Practice and Theory, and Research in Accounting Regulation. We annotate results of regulation-related research studies and key points from regulation-related commentaries.
How to recognize a Leonard pair

Let V denote a vector space with finite positive dimension. We consider an ordered pair of linear transformations A : V → V and A ∗ : V → V that satisfy (i) and (ii) below. There exists a basis for...
Exploration of the "traceless" reductive ligation of S-nitrosothiols.

The first “traceless” reductive ligation of S-nitrosothiols using phosphine ester/thioester conjugates is reported. Experiments also show that stable thioimidate compounds could be formed in the reaction between S-nitrosothiols and some phosphine−thioester substrates.
The use of aluminum and gallium hydrides in materials science

Abstract The use of aluminum and gallium hydrides as molecular precursors has been an important development in the field of materials science. Alanes and gallanes have been used in a variety of techniques, such as chemical vapor deposition and solution-based methodologies, to synthesize materials ranging from aluminum thin films to nanocrystalline 13–15 materials. This review is intended to capture the general features of the use of alanes and gallanes in the synthesis of solid state materials.
A likelihood ratio test for changes in homeolog expression bias

Gene duplications are a major source of raw material for evolution and a likely contributor to the diversity of life on earth. Duplicate genes (i.e., homeologs, in the case of a whole genome duplication) may retain their ancestral function, sub- or neofunctionalize, or be lost entirely. A primary way that duplicate genes evolve new functions is by altering their expression patterns. Comparing the expression patterns of duplicate genes gives clues as to whether any of these evolutionary processes have occurred. We develop a likelihood ratio test for the analysis of the expression ratios of duplicate genes across two conditions (e.g., tissues). We demonstrate an application of this test by comparing homeolog expression patterns of 1448 homeologous gene pairs using RNA-seq data generated from leaves and petals of an allotetraploid monkeyflower (Mimulus luteus). We assess the sensitivity of this test to different levels of homeolog expression bias and compare the method to several alternatives. The likelihood ratio test derived here is a direct, transparent, and easily implemented method for detecting changes in homeolog expression bias that outperforms alternative approaches. While our method was derived with homeolog analysis in mind, this method can be used to analyze changes in the ratio of expression levels between any two genes in any two conditions.
Disease-associated mutations in human BICD2 hyperactivate motility of dynein-dynactin.

Bicaudal D2 (BICD2) joins dynein with dynactin into a ternary complex (termed DDB) capable of processive movement. Point mutations in the BICD2 gene have been identified in patients with a dominant form of spinal muscular atrophy, but how these mutations cause disease is unknown. To investigate this question, we have developed in vitro motility assays with purified DDB and BICD2’s membrane vesicle partner, the GTPase Rab6a. Rab6a–GTP, either in solution or bound to artificial liposomes, released BICD2 from an autoinhibited state and promoted robust dynein–dynactin transport. In these assays, BICD2 mutants showed an enhanced ability to form motile DDB complexes. Increased retrograde transport by BICD2 mutants also was observed in cells using an inducible organelle transport assay. When overexpressed in rat hippocampal neurons, the hyperactive BICD2 mutants decreased neurite growth. Our results reveal that dominant mutations in BICD2 hyperactivate DDB motility and suggest that an imbalance of minus versus plus end–directed microtubule motility in neurons may underlie spinal muscular atrophy.
Combined cluster and atomic displacement expansion for solid solutions and magnetism

Finite-temperature disordered solid solutions and magnetic materials are difficult to study directly using first-principles calculations, due to the large unit cells and many independent samples that are required. In this work, we develop a combined cluster expansion and atomic displacement expansion, which we fit to first-principles energies, forces, and stresses. We then use the expansion to calculate thermodynamic quantities at nearly first-principles levels of accuracy. Our model naturally includes both configurational and vibrational entropy, including anharmonic contributions and structural phase transitions. In addition, we can treat coupling between atomic displacement and chemical or magnetic degrees of freedom. As examples, we use our expansion to calculate properties of ${\mathrm{Si}}_{1\ensuremath{-}x}{\mathrm{Ge}}_{x}$, magnetic MnO, Al with vacancies, and ${\mathrm{Ba}}_{x}{\mathrm{Sr}}_{1\ensuremath{-}x}{\mathrm{TiO}}_{3}$. Finally, we demonstrate that by treating all the relevant degrees of freedom explicitly, we can in some cases achieve improved convergence of fitting parameters versus distance as compared to a pure cluster expansion.
Superacid-promoted reactions of pyrazolecarboxaldehydes and the role of dicationic electrophiles

Abstract Pyrazolecarboxaldehydes react in the Bronsted superacid triflic acid (CF3SO3H, TfOH) to generate electrophilic intermediates capable of reacting with benzene in condensation reactions. Appropriately substituted pyrazoles may also undergo intramolecular Friedel–Crafts-type reactions. It is proposed that the pyrazolecarboxaldehydes and related systems form diprotonated intermediates in these reactions.
A convergent approach for the synthesis of ara-neplanocin a analogues under subzero microwave assisted conditions.

A convergent strategy for the synthesis of ara-neplanocin A analogues has been developed. Microwave assisted Mitsunobu reaction proved to be an essential tool both for the 2′-β-hydroxy inversion and for the coupling reaction with the heterocyclic bases. The exploitation of the present approach allowed generating a family of ara-neplanocins which biological potential is still unexplored.
Toward Practical Homomorphic Evaluation of Block Ciphers Using Prince.

We present the homomorphic evaluation of the Prince block cipher. Our leveled implementation is based on a generalization of NTRU. We are motivated by the drastic bandwidth savings that may be achieved by scheme conversion. To unlock this advantage we turn to lightweight ciphers such as Prince. These ciphers were designed from scratch to yield fast and compact implementations on resource-constrained embedded platforms. We show that some of these ciphers have the potential to enable near practical homomorphic evaluation of block ciphers. Indeed, our analysis shows that Prince can be implemented using only a 24 level deep circuit. Using an NTRU based implementation we achieve an evaluation time of 3.3 seconds per Prince block – one and two orders of magnitude improvement over homomorphic AES implementations achieved using NTRU, and BGV-style homomorphic encryption libraries, respectively.
Forty-eight hour conditioning produces a robust long lasting flavor preference in rats

Conditioned flavor preference (CFP) learning is a form of associative learning in ingestive behavior. CFP Learning can be rapid and produces preferences of varying strengths that can be exceptionally persistent. We sought to establish a method to produce a robust long-lasting CFP in rats. Rats were given 48-h access (conditioning) to a CS+ flavor (grape or cherry 0.05% Kool-Aid, counterbalanced) mixed with 8% glucose and 0.05% saccharin. In order to determine the strength of conditioning rats were given 14 consecutive days of 24-h access to CS+ and CS- flavors mixed only with 0.05% Kool-Aid and 0.05% saccharin (extinction), then further tested 34 days after the last extinction test (48 days post conditioning) for 2 consecutive days with the CS+ and CS-. We found that not only did the learned CFP fail to extinguish over 14 days of testing, but it also persisted for at least 48 days after conditioning. These data provide a method to produce a robust, long lasting and persistent CFP for use in future ingestive behavior research.
Lepadiformine: a case study of the value of total synthesis in natural product structure elucidation.

Since the emergence of routine X-ray crystallography and high-field FT NMR in the mid-twentieth century, the importance of total synthesis in structure elucidation has become underappreciated by most organic chemists. However, the limitations and fallibility of spectral methodology has recently been highlighted by the mischaracterization of a number of complex natural products, the correct structures of which were all ultimately assigned by total synthesis. This Account describes how total synthesis was not only instrumental in disproving the erroneously assigned structure of the marine alkaloid, lepadiformine, but also was also pivotal in establishing the correct structure and absolute configuration.
CRISPR/Cas9 gene editing for the creation of an MGAT1-deficient CHO cell line to control HIV-1 vaccine glycosylation

Over the last decade, multiple broadly neutralizing monoclonal antibodies (bN-mAbs) to the HIV-1 envelope protein (Env) gp120 have been described. Many of these recognize epitopes consisting of both amino acid and glycan residues. Moreover, the glycans required for binding of these bN-mAbs are early intermediates in the N-linked glycosylation pathway. This type of glycosylation substantially alters the mass and net charge of Envs compared to molecules with the same amino acid sequence but possessing mature, complex (sialic acid–containing) carbohydrates. Since cell lines suitable for biopharmaceutical production that limit N-linked glycosylation to mannose-5 (Man5) or earlier intermediates are not readily available, the production of vaccine immunogens displaying these glycan-dependent epitopes has been challenging. Here, we report the development of a stable suspension-adapted Chinese hamster ovary (CHO) cell line that limits glycosylation to Man5 and earlier intermediates. This cell line was created using the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing system and contains a mutation that inactivates the gene encoding Mannosyl (Alpha-1,3-)-Glycoprotein Beta-1,2-N-Acetylglucosaminyltransferase (MGAT1). Monomeric gp120s produced in the MGAT1− CHO cell line exhibit improved binding to prototypic glycan-dependent bN-mAbs directed to the V1/V2 domain (e.g., PG9) and the V3 stem (e.g., PGT128 and 10–1074) while preserving the structure of the important glycan-independent epitopes (e.g., VRC01). The ability of the MGAT1− CHO cell line to limit glycosylation to early intermediates in the N-linked glycosylation pathway without impairing the doubling time or ability to grow at high cell densities suggests that it will be a useful substrate for the biopharmaceutical production of HIV-1 vaccine immunogens.
Neighboring Carboxyl Group Participation in the Hydrolysis of Acetals. Hydrolysis of o-Carboxybenzaldehyde cis- and trans-1,2-Cyclohexanediyl Acetals

The plot of log kobsd vs pH for the hydrolysis of o-carboxybenzaldehyde trans-1,2-cyclohexanediyl acetal at 50 °C in H2O has four unit changes of slope in the pH range 2−9. The plot is here described by proceeding from low pH to high pH. The observed hydronium ion- and water-catalyzed reactions at pH < 6 have rate constants that are similar, but not identical, to those for hydrolysis of the acylal 3-[(trans-2-hydroxycyclohexyl)oxy]phthalide, which was isolated from the reaction at pH 3, and synthesized independently. The pH−log rate constant profile for hydrolysis of the acetal bends downward near pH 6 to give a slope of −1.0. Oxocarbonium ion hydrolysis is then a water reaction. At pH 7 the mechanism of the reaction changes to attack of OH- on the oxocarbonium ion intermediate. A change in rate-determining step takes place at pH 8 to hydronium ion-catalyzed ring opening of the anionic species of the acetal, or the kinetically equivalent intramolecular general acid catalysis in ring opening of the neutral...
Enantioselective cyanocarbonation of ketones with chiral base

Abstract A highly enantioselective cyanocarbonation of dialkyl ketones catalyzed by commercially available and easily recyclable cinchona alkaloid derivatives has been developed. The reaction provides a useful approach for the enantioselective construction of tetrasubstituted carbon stereocenters. Mechanistic studies have been carried out to shed light on the origin of the catalytic activity of the cinchona alkaloid and the asymmetric induction step.
Evidence for the Priming Effect in a Planktonic Estuarine Microbial Community

The 'priming effect', in which addition of labile substances changes the remineralization rate of recalcitrant organic matter, has been intensively studied in soils, but is less well-documented in aquatic systems. We investigated the extent to which additions of nutrients or labile organic carbon could influence remineralization rates of 14C-labeled, microbially-degraded, phytoplankton-derived organic matter (OM) in microcosms inoculated with microbial communities drawn from Grove’s Creek Estuary in coastal Georgia, USA. We found that amendment with labile protein plus phosphorus increased remineralization rates of degraded, phytoplankton-derived OM by up to 100%, whereas acetate slightly decreased remineralization rates relative to an unamended control. Addition of ammonium and phosphate induced a smaller effect, whereas addition of ammonium alone had no effect. Counterintuitively, alkaline phosphatase activities increased in response to the addition of protein under P-replete conditions, indicating that production of enzymes unrelated to the labile priming compound may be a mechanism for the priming effect. The observed priming effect was transient: after 36 days of incubation roughly the same quantity of organic carbon had been mineralized in all treatments including no-addition controls. This timescale is on the order of the typical hydrologic residence times of well-flushed estuaries suggesting that priming in estuaries has the potential to influence whether OC is remineralized in situ or exported to the coastal ocean.
Efficient profile maximum likelihood for universal symmetric property estimation

Estimating symmetric properties of a distribution, e.g. support size, coverage, entropy, distance to uniformity, are among the most fundamental problems in algorithmic statistics. While these properties have been studied extensively and separate optimal estimators have been produced, in striking recent work Acharya et al. provided a single estimator that is competitive for each. They showed that the value of the property on the distribution that approximately maximizes profile likelihood (PML), i.e. the probability of observed frequency of frequencies, is sample competitive with respect to a broad class of estimators. Unfortunately, prior to this work, there was no known polynomial time algorithm to compute such an approximation or use PML to obtain a universal plug-in estimator. In this paper we provide an algorithm that, given n samples from a distribution, computes an approximate PML distribution up to a multiplicative error of exp(n2/3poly log(n)) in nearly linear time. Generalizing work of Acharya et al. we show that our algorithm yields a universal plug-in estimator that is competitive with a broad range of estimators up to accuracy є = Ω(n−0.166). Further, we provide efficient polynomial-time algorithms for computing a d-dimensional generalization of PML (for constant d) that allows for universal plug-in estimation of symmetric relationships between distributions.
Integral Field Spectroscopy of the Extended Emission-Line Region of 4C 37.43*

We present Gemini Multiobject Spectrograph integral field spectroscopy of the extended emission-line region associated with quasar 3C 249.1. The kinematics of the ionized gas measured from the [O III] λ5007 line is rather complex and cannot be explained globally by a simple dynamical model, but some clouds can be modeled individually as having locally linear velocity gradients. The temperatures of the ionized gas appear uniform (varying from ~12,000 to 15,000 K), while the densities vary from a few tens to a few hundred per cubic centimeter. The emission mechanism of all of the emission clouds, as indicated by the line-ratio diagnostics, is consistent with both "shock + precursor" and pure photoionization models. The total mass of the ionized gas is on the order of 109 M☉. We estimate a bulk kinetic energy and momentum of the extended emission-line region of 2.5 × 1057 ergs and 1050 dyn s, and a dynamical timescale of ~10 Myr. By comparing the injection rates of kinetic energy and momentum of different galactic wind models with the observation, we argue that the emission-line clouds are most likely a direct result of the feedback of the quasar. We also discuss the nature of the extended X-ray emission surrounding the quasar.
UPS-indel: a Universal Positioning System for Indels

Storing biologically equivalent indels as distinct entries in databases causes data redundancy, and misleads downstream analysis. It is thus desirable to have a unified system for identifying and representing equivalent indels. Moreover, a unified system is also desirable to compare the indel calling results produced by different tools. This paper describes UPS-indel, a utility tool that creates a universal positioning system for indels so that equivalent indels can be uniquely determined by their coordinates in the new system, which also can be used to compare different indel calling results. UPS-indel identifies 15% redundant indels in dbSNP, 29% in COSMIC coding, and 13% in COSMIC noncoding datasets across all human chromosomes, higher than previously reported. Comparing the performance of UPS-indel with existing variant normalization tools vt normalize, BCFtools, and GATK LeftAlignAndTrimVariants shows that UPS-indel is able to identify 456,352 more redundant indels in dbSNP; 2,118 more in COSMIC coding, and 553 more in COSMIC noncoding indel dataset in addition to the ones reported jointly by these tools. Moreover, comparing UPS-indel to state-of-the-art approaches for indel call set comparison demonstrates its clear superiority in finding common indels among call sets. UPS-indel is theoretically proven to find all equivalent indels, and thus exhaustive.
Alkenenitriles: Annulations with ω-Chloro Grignard Reagents

ω-Chloro Grignard reagents chelate with cyclic γ-hydroxy-α,β-alkenenitriles to trigger a conjugate addition−alkylation annulation. The chelation-controlled conjugate addition−alkylation is the firs...
A facile synthesis of dragmacidin B and 2,5-bis(6'-bromo-3'-indolyl)piperazine.

A short synthesis of dragmacidin B (1), 2,5-bis(6‘-bromo-3‘-indolyl)piperazine (2), and corresponding didebromo analogues 8 and 9 is described. The key steps involve the dimerization of oxotryptamines 4 and 11 to give bis(indolyl)pyrazines 5 and 12, which upon selective reduction and reductive methylation with sodium cyanoborohydride afforded the requisite piperazine natural products.
Zeolite supported permanganate: An efficient catalyst for selective oxidation of enamines, alkylarenes and unsaturated alcohols

Abstract Potassium permanganate supported on zeolite can be used for the selective oxidation of various enamines, alkylarenes and unsaturated alcohols to the corresponding ketones, in good yield. Arenes were selectively oxidized at the benzylic position. If the benzylic carbon is secondary, ketones are obtained, and alcohols are produced if the benzylic position is tertiary. In contrast unsaturated secondary alcohols selectively undergo oxidation to the corresponding olefinic ketones without affecting the carbon-carbon double bonds.
The synthesis of ring‐expanded analogues of xanthine containing the imidazo[4,5‐e][1,4]diazepine ring system

The synthesis of 4,5,7,8-tetrahydro-6H-imidazo[4,5-e][1,4]diazepine-5,8-dione and its several 1- and 3-alkyl (aralkyl) derivatives 2 has been reported. Mechanistic explorations of the final synthetic step as well as structural confirmation of a final product 2d by single-crystal X-ray diffraction analyses have also been presented.
Inferring Identical-by-Descent Sharing of Sample Ancestors Promotes High-Resolution Relative Detection.

As genetic datasets increase in size, the fraction of samples with one or more close relatives grows rapidly, resulting in sets of mutually related individuals. We present DRUID—deep relatedness utilizing identity by descent—a method that works by inferring the identical-by-descent (IBD) sharing profile of an ungenotyped ancestor of a set of close relatives. Using this IBD profile, DRUID infers relatedness between unobserved ancestors and more distant relatives, thereby combining information from multiple samples to remove one or more generations between the deep relationships to be identified. DRUID constructs sets of close relatives by detecting full siblings and also uses an approach to identify the aunts/uncles of two or more siblings, recovering 92.2% of real aunts/uncles with zero false positives. In real and simulated data, DRUID correctly infers up to 10.5% more relatives than PADRE when using data from two sets of distantly related siblings, and 10.7%–31.3% more relatives given two sets of siblings and their aunts/uncles. DRUID frequently infers relationships either correctly or within one degree of the truth, with PADRE classifying 43.3%–58.3% of tenth degree relatives in this way compared to 79.6%–96.7% using DRUID.
Development of efficient new methodology for generation, cyclization and functional trapping of iminyl and amidyl radicals

New methodology has been devised for the generation and subsequent cyclization of iminyl and amidyl radicals under mild conditions. The process involves either the treatment of oximes with 2,6-dimethylbenzenesulfinyl chloride, or the treatment of hydroxamic acids with tert-butylsulfinyl chloride (−50°C to rt), to give the corresponding nitrogen radicals, followed by cyclization onto pendant olefins. Radical traps such as diphenyl diselenide, diphenyl disulfide, and TEMPO can be used to terminate the cyclizations, thus introducing functionality that provides multiple options for further manipulation. In a more convenient procedure, both iminyl and amidyl radical cyclizations can be initiated using commercially available diethyl chlorophosphite which generally provides similar (with diphenyl disulfide and TEMPO) or significantly higher (with diphenyl diselenide) yields of products.
Terminal Ligand Assignments Based on Trends in Metal−Ligand Bond Lengths of Cubane-Type [Fe4S4]2+,+ Clusters

Trends in Fe−L bond distances in [Fe4S4L4]2-,3- cubane-type clusters with L = Cl- and RS- are summarized. The compound (Et4N)3[Fe4S4(SH)4]·Et4NCl was prepared and structurally characterized. The Fe−SH bond lengths of this cluster and previously reported (Ph4P)2[Fe4S4(SH)4] fall in the ranges for clusters with alkyl- and arenethiolate terminal ligands. Upon slow crystallization from 1,2-dichloroethane/THF, the compound (Pr4N)2[Fe4S4(SH)4] undergoes chloride substitution to form (Pr4N)2[Fe4S4Cl4], which may be identified by its Fe−Cl distance. An X-ray structure recently attributed to (Pr4N)2[Fe4S4(SH)4] is that of (Pr4N)2[Fe4S4Cl4].
Synthesis and chemistry of new benzoporphyrins

Abstract Benzoporphyrins 5 and 6 are the major products obtained from the cycloaddition reactions of β-fused metallo-pyrroloporphyrins 1 and 2 with dimethyl acetylenedicarboxylate. In the presence of excess dienophile a bis-adduct is also obtained which undergoes retro-Diels-Alder reaction to produce 5. Benzoporphyrin 5 was converted into the first reported β-fused benzochlorins 9–11, and the free-base benzoporphyrin 12 was regioselectively brominated to afford 13. Exhaustive bromination also yields hexabromobenzoporphyrin 14.
Synthesis of 5-substituted 1H-tetrazoles catalyzed by ytterbium triflate hydrate

Various 5-substituted 1H-tetrazoles were synthesized from aryl nitriles, alkyl nitriles, and vinyl nitriles reacting with sodium azide. The tetrazoles were recovered in high yield under mild conditions when the reaction was catalyzed by ytterbium triflate hydrate in dimethylformamide. Other rare-earth and post-transition metal catalysts were also investigated.
Theory of Cytoskeletal Reorganization during Cross-Linker-Mediated Mitotic Spindle Assembly

Cells grow, move, and respond to outside stimuli by large-scale cytoskeletal reorganization. A prototypical example of cytoskeletal remodeling is mitotic spindle assembly, during which microtubules nucleate, undergo dynamic instability, bundle, and organize into a bipolar spindle. Key mechanisms of this process include regulated filament polymerization, cross-linking, and motor-protein activity. Remarkably, using passive cross-linkers, fission yeast can assemble a bipolar spindle in the absence of motor proteins. We develop a torque-balance model that describes this reorganization because of dynamic microtubule bundles, spindle-pole bodies, the nuclear envelope, and passive cross-linkers to predict spindle-assembly dynamics. We compare these results to those obtained with kinetic Monte Carlo-Brownian dynamics simulations, which include cross-linker-binding kinetics and other stochastic effects. Our results show that rapid cross-linker reorganization to microtubule overlaps facilitates cross-linker-driven spindle assembly, a testable prediction for future experiments. Combining these two modeling techniques, we illustrate a general method for studying cytoskeletal network reorganization.
Alkoxide precoordination to rhodium enables stereodirected catalytic hydrogenation of a dihydrofuranol precursor of the C29-40 F/G sector of pectenotoxin-2

Abstract An enantioselective synthesis of the stereochemically fully endowed C(29-40) fragment of pectenotoxin-2 is detailed. The highlight of the synthesis is an alkoxide-directed hydrogenation in which ionic complexation of the deprotonated substrate to [Rh(NBD)(DIPHOS-4)]BF4, accomplished by the co-addition of an equivalent of sodium hydride in THF, completely deters a kinetic tendency for dehydration and properly sets the critical stereochemistry at C-35. The dual objectives made possible by this catalytic technology are expected to have far-ranging applications.
InternalBrace has biomechanical properties comparable to suture button but less rigid than screw in ligamentous lisfranc model.

Abstract Purpose The aim of this study was to investigate the biomechanical properties of the InternalBrace for lisfranc injuries. Methods A Sawbone model was developed comparing screw, suture button and InternalBrace. Results When loaded in axial tension at 0.5 mm/s, the screw was stiffest (2,240 N/mm), while the InternalBrace (200 N/mm) was stiffer than the suture button (133 N/mm). Cyclic loading with 10,000 cycles of 69 N, 138 N, and 207 N showed the InternalBrace maintained stiffness, but fatigued earlier than the suture button. Conclusion The mechanical properties of the InternalBrace support clinical use, but further studies are needed regarding early weight bearing.