cssi/SciSciGPT-SciSciNet huggingface dataset:
Progress toward source-to-target simulation☆

Abstract Source-to-target simulation of an accelerator provides a thorough check on the consistency of the design as well as a detailed understanding of the beam behavior. Issues such as envelope mismatch and emittance growth can be examined in a self-consistent manner, including the details of accelerator transitions, long-term transport, and longitudinal compression. The large range in scales, from centimeter-scale transverse beam size and applied field scale-length, to meter-scale beam length, to kilometer-scale accelerator length, poses a significant computational challenge. The ever-increasing computational power that is becoming available through massively parallel computers is making such simulation realizable. This paper discusses the progress toward source-to-target simulation using the WARP particle-in-cell code. Representative examples are shown, including 3-D, long-term transport simulations of Integrated Research Experiment (IRE) scale accelerators.
Photodetectors: UV to IR

This paper surveys recent work in several photodetector areas including high-speed, low-noise avalanche photodiodes, solar-blind ultra-violet PIN photodiodes, and quantum dot infrared photodetectors (QDIPs).
Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns

Despite their discovery over 25 years ago, the Marine Group II Euryarchaea (MGII) remain a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world, and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present a comparative genomic analysis of 250 MGII genomes, providing a comprehensive investigation of these mesophilic archaea. This analysis identifies 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera reveals distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins, common in all other subclades. The physiology and ecology of many yet-uncultured microorganisms, such as the Marine Group II Euryarchaea (MGII), is unclear. Here, Benjamin Tully analyses 250 MGII genomes, identifies 17 distinct subclades, and provides a detailed view of the metabolic potential and distribution of these archaea.
Harnessing the opportunities of inclusive technologies in a global economy

In this paper the authors propose that G20 countries endorse and facilitate the creation of a T20 digital platform for 'Accelerating the Jobs of the Future'. In a world driven by a new wave of technological change, the platform would revalue the role of think tanks, research institutions and knowledge hubs to move the global agenda in an issue of central importance for the future of society: the creation of the jobs of the future. Building on and complementing existing experiences, the T20 platform would be a digital hub for producing knowledge, informing policies and connecting potential partners to accelerate the jobs of the future, within the context of an increasing integrated global economy. It would also contribute to the development of consensual views among the research community, allowing to discard extreme visions about the jobs of the future, dispelling both overly optimistic visions with no evidence base and unwarranted fears.
Proceedings of the 2009 ACM workshop on Cognitive radio networks

On behalf of the organizing and technical committees of CoRoNet'09, we would like to welcome you to the 2009 ACM Workshop on Cognitive Radio Networks (CoRoNet), which is being held in conjunction with the 15th Annual International Conference on Mobile Computing and Networking (MobiCom). The workshop will take place on September 21 in Beijing, China, at the InterContinental Hotel Beijing Beichen inside the Beijing Olympic Park. The workshop received 21 valid submissions. Following a thorough review process, 8 papers were accepted as full papers, and 6 were accepted for poster presentations. Including an invited paper, a total of 15 papers will be presented at the workshop. We would like to take this opportunity to thank the Publicity Chair, Dr. Przemyslaw Pawelczak, and all Technical Program Committee members for their dedication and help. The program of CoRoNet'09 includes plenary talks, three oral presentation sessions, and a poster session. These talks and sessions cover recent developments in cognitive radio networks on topics ranging from spectrum measurements, cooperative sensing, interference management, to cognitive access and networking. We welcome you to CoRoNet 2009 and are looking forward to meeting you in Beijing.
Portfolio manager home‐country culture and mutual fund risk‐taking

I find that home‐country culture affects portfolio managers’ investment risk‐taking and performance. I focus on security value, which measures the degree to which people in a country assign importance to security, safety, and stability. Funds managed by managers from countries with higher security value exhibit lower fund return volatility, trade less frequently, and follow benchmarks more closely. These funds also tend to avoid lottery‐type stocks and hence perform significantly better. However, the impact of home‐country security value decays as managers spend more time away from their home countries.
Jonckheere–Terpstra Test†

For the one-way design, the Jonckheere-Terpstra procedure tests the null hypothesis of no difference in response magnitude across treatments against an ordered alternative, that response magnitude increases over a pre-specified ordering of the treatments. Where the treatment levels can be ordered according to expected response magnitude (e.g., drug dosages, stimulus intensities, and hours of practice), the Jonckheere–Terpstra test (1954) employs a more coherent, directional alternative hypothesis, that is, the response magnitude does not decrease for any treatment level increase and actually increases for one or more treatment level increases. Keywords: one-way design; ordered treatments; Kruskal–Wallis test; permutation test
Exercise intensity and middle cerebral artery dynamics in humans

Abstract Despite its necessity for understanding healthy brain aging, the influence of exercise intensity on cerebrovascular kinetics is currently unknown. We, therefore characterized middle cerebral artery blood flow velocity (MCAv) kinetics associated with two exercise intensities: low and moderate. We hypothesized that increasing exercise intensity would increase the MCAv amplitude response (Amp) and that age and estimated fitness (VO2max) would be related to Amp. Baseline (BL) values were collected for 90-seconds followed by a 6-minute exercise bout. Heart rate, end-tidal CO2, mean arterial pressure and MCAv were recorded throughout. MCAv kinetics were described by Amp, time delay (TD) and time constant (τ). Sixty-four adults completed the study. Amp was greater during moderate compared to low exercise intensity (p
Economic policy uncertainty and dollar-pound exchange rate return volatility

Abstract The extent to which economic policy uncertainty (EPU) amplifies exchange rate volatility has been an important research question for at least a decade. Previous research has investigated this relationship using monthly data, concluding that EPU imparts an effect on exchange rate volatility either contemporaneously, or with a one month lag. The use of monthly frequency, however, may not provide an accurate causal interpretation, and may even compromise the accuracy of the estimates if the natural cycles of EPU are shorter than a month. To address this econometric concern I construct uncertainty measures at a daily frequency, and estimate a GARCH model using daily USD/British pound returns. The evidence indicates that EPU contributes to exchange rate volatility much more quickly than monthly data can detect. Using a regression technique for separating EPU from non-policy economic uncertainty, I find that non-policy market uncertainty increases volatility more than EPU does.
Repairing without Retraining: Avoiding Disparate Impact with Counterfactual Distributions

When the performance of a machine learning model varies over groups defined by sensitive attributes (e.g., gender or ethnicity), the performance disparity can be expressed in terms of the probability distributions of the input and output variables over each group. In this paper, we exploit this fact to reduce the disparate impact of a fixed classification model over a population of interest. Given a black-box classifier, we aim to eliminate the performance gap by perturbing the distribution of input variables for the disadvantaged group. We refer to the perturbed distribution as a counterfactual distribution, and characterize its properties for common fairness criteria. We introduce a descent algorithm to learn a counterfactual distribution from data. We then discuss how the estimated distribution can be used to build a data preprocessor that can reduce disparate impact without training a new model. We validate our approach through experiments on real-world datasets, showing that it can repair different forms of disparity without a significant drop in accuracy.
Fracton fusion and statistics

Universal properties of quasiparticle excitations, such as fusion and statistics of anyons in two dimensions, play a central role in characterizing quantum phases of matter. Here, the authors develop a systematic framework to describe fusion and statistical processes of fractons and other quasiparticle excitations with subdimensional mobility. The restricted mobility of excitations leads to statistical processes that differ dramatically from more familiar braiding processes of anyons.
An inner model theoretic proof of Becker’s theorem

We re-prove Becker’s theorem from Becker (Isr J Math 40(3–4):229–234, 1981) by showing that $$AD^{L({\mathbb {R}})}$$ implies that $$L({\mathbb {R}})\vDash ``\omega _2$$ is -supercompact”. Our proof uses inner model theoretic tools instead of Baire category. We also show that $$\omega _2$$ is $$<\Theta $$ -strongly compact.
Crowdfunding via Revenue-Sharing Contracts

Problem definition: We analyze a new model of crowdfunding recently introduced by Bolstr, Localstake, and Startwise. A platform acts as a matchmaker between a firm needing funds and a crowd of inve...
Self-organization of spindle-like microtubule structures

Microtubule self-organization is an essential physical process underlying several essential cellular functions, including cell division. In cell division, the dominant arrangement is the mitotic spindle, a football-shaped microtubule-based machine responsible for separating the chromosomes. We are interested in the underlying fundamental principles behind the self-organization of the spindle shape. Prior biological works have hypothesized that motor proteins control the proper formation of the spindle. Many of these motor proteins are also microtubule-crosslinkers, so it is unclear if the critical aspect is the motor activity or the crosslinking. In this study, we seek to address this question by examining the self-organization of microtubules using crosslinkers alone. We use a minimal system composed of tubulin, an antiparallel microtubule-crosslinking protein, and a crowding agent to explore the phase space of organizations as a function of tubulin and crosslinker concentration. We find that the concentration of the antiparallel crosslinker, MAP65, has a significant effect on the organization and resulted in spindle-like arrangements at relatively low concentration without the need for motor activity. Surprisingly, the length of the microtubules only moderately affects the equilibrium phase. We characterize both the shape and dynamics of these spindle-like organizations. We find that they are birefringent homogeneous tactoids. The microtubules have slow mobility, but the crosslinkers have fast mobility within the tactoids. These structures represent a first step in the recapitulation of self-organized spindles of microtubules that can be used as initial structures for further biophysical and active matter studies relevant to the biological process of cell division.
Generalized gene co-expression analysis via subspace clustering using low-rank representation

Gene Co-expression Network Analysis (GCNA) helps identify gene modules with potential biological functions and has become a popular method in bioinformatics and biomedical research. However, most current GCNA algorithms use correlation to build gene co-expression networks and identify modules with highly correlated genes. There is a need to look beyond correlation and identify gene modules using other similarity measures for finding novel biologically meaningful modules. We propose a new generalized gene co-expression analysis algorithm via subspace clustering that can identify biologically meaningful gene co-expression modules with genes that are not all highly correlated. We use low-rank representation to construct gene co-expression networks and local maximal quasi-clique merger to identify gene co-expression modules. We applied our method on three large microarray datasets and a single-cell RNA sequencing dataset. We demonstrate that our method can identify gene modules with different biological functions than current GCNA methods and find gene modules with prognostic values. The presented method takes advantage of subspace clustering to generate gene co-expression networks rather than using correlation as the similarity measure between genes. Our generalized GCNA method can provide new insights from gene expression datasets and serve as a complement to current GCNA algorithms.
Determination of the magnetic field dependence of the surface resistance of superconductors from cavity tests

Under some reasonable assumptions, the rf surface resistance of superconducting cavities for different surface magnetic fields can be reconstructed from an experimentally measured $Q$ curve.
Bimodal Bandgaps in Mixed Cesium Methylammonium Lead Bromide Perovskite Single Crystals

Alloying inorganic cations such as Cs+ or Rb+ into hybrid lead halide perovskites has been shown to provide long-term material stability critical to the implementation in solar cells, but little is...
Eyeriss v2: A Flexible Accelerator for Emerging Deep Neural Networks on Mobile Devices

A recent trend in deep neural network (DNN) development is to extend the reach of deep learning applications to platforms that are more resource and energy-constrained, e.g., mobile devices. These endeavors aim to reduce the DNN model size and improve the hardware processing efficiency and have resulted in DNNs that are much more compact in their structures and/or have high data sparsity . These compact or sparse models are different from the traditional large ones in that there is much more variation in their layer shapes and sizes and often require specialized hardware to exploit sparsity for performance improvement. Therefore, many DNN accelerators designed for large DNNs do not perform well on these models. In this paper, we present Eyeriss v2, a DNN accelerator architecture designed for running compact and sparse DNNs. To deal with the widely varying layer shapes and sizes, it introduces a highly flexible on-chip network, called hierarchical mesh, that can adapt to the different amounts of data reuse and bandwidth requirements of different data types, which improves the utilization of the computation resources. Furthermore, Eyeriss v2 can process sparse data directly in the compressed domain for both weights and activations and therefore is able to improve both processing speed and energy efficiency with sparse models. Overall, with sparse MobileNet, Eyeriss v2 in a 65-nm CMOS process achieves a throughput of 1470.6 inferences/s and 2560.3 inferences/J at a batch size of 1, which is $12.6\times $ faster and $2.5\times $ more energy-efficient than the original Eyeriss running MobileNet.
Revisiting the softmax bellman operator: New benefits and new perspective

The impact of softmax on the value function itself in reinforcement learning (RL) is often viewed as problematic because it leads to sub-optimal value (or Q) functions and interferes with the contraction properties of the Bellman operator. Surprisingly, despite these concerns, and independent of its effect on exploration, the softmax Bellman operator when combined with Deep Q-learning, leads to Q-functions with superior policies in practice, even outperforming its double Q-learning counterpart. To better understand how and why this occurs, we revisit theoretical properties of the softmax Bellman operator, and prove that $(i)$ it converges to the standard Bellman operator exponentially fast in the inverse temperature parameter, and $(ii)$ the distance of its Q function from the optimal one can be bounded. These alone do not explain its superior performance, so we also show that the softmax operator can reduce the overestimation error, which may give some insight into why a sub-optimal operator leads to better performance in the presence of value function approximation. A comparison among different Bellman operators is then presented, showing the trade-offs when selecting them.
Robust Bio-Inspired Routing Protocol in MANETs Using Ant Approach

This paper discusses about developing a routing protocol for mobile ad-hoc networks in a bio-inspired manner. Algorithms inspired by collective behavior of social insect colonies, bird flocking, honey bee dancing, etc., promise to be capable of catering to the challenges faced by tiny wireless sensor networks. We propose an energy efficient multi-path routing algorithm based on foraging nature of ant colonies. This paper considers many meta-heuristic factors to provide good robust paths from source node to destination node in a hope to overcome the challenges posed by resource-constrained sensors. The performance of proposed ant colony routing algorithm is compared against well-known AODV routing protocol.
Do 40-Year-Old Facts Still Matter? Long-Run Effects of Federal Oversight under the Voting Rights Act

In 2013, the Supreme Court struck down parts of the Voting Rights Act that mandated federal oversight of election laws in discriminatory jurisdictions, prompting a spate of controversial new voting rules. Utilizing difference-in-differences to examine the act's 1975 revision, I provide the first estimates of the effects of "preclearance" oversight. I find that preclearance increased long-run voter turnout by 4-8 percentage points, due to lasting gains in minority participation. Surprisingly, Democratic support dropped sharply in areas subject to oversight. Using historical survey and newspaper data, I provide evidence that this was the result of political backlash among racially conservative whites.
Syntheses of unstable diol epoxide metabolites of the potent carcinogens 7- and 12-methylbenz[a]anthracene

Abstract Stereospecific syntheses of the anti- and syn-diol epoxides of 7- and 12-methylbenz[a]anthracene, suspected as active metabolites of the parent PAHs but previously thought to be too chemically reactive and unstable to isolate, are described and the pure compounds are shown to be moderately stable.
Synthesis and intracrystalline oxidation of nitrite-intercalated layered double hydroxides

Nitrite-intercalated LDHs could be prepared by a two-stage process that involves coprecipitation in the presence of nitrite ions followed by stirring the product with excess of nitrite ions. The nitrite ion lies flat in these LDHs with its c{sub 2}-axis lying approximately perpendicular to the crystallographic c-axis. The interlayer nitrite ions in these LDHs could be quantitatively oxidized to nitrate ions using H{sub 2}O{sub 2} solution. In the LDHs thus obtained the nitrate ion lies flat with its c{sub 3}-axis parallel to the crystallographic c-axis (D{sub 3h} symmetry) in the interlayer region resulting in lower basal spacing. - Graphical abstract: Nitrite-intercalated LDHs could be prepared by a two-stage process that involves coprecipitation in the presence of nitrite ions followed by stirring the product with excess of nitrite ions. The interlayer nitrite ions in these LDHs could be quantitatively oxidized to nitrate ions.
Boron trifluoride induced fragmentation of β-aryl-β-hydroxyketones

Abstract β-Aryl-β-hydroxy ketones are readily cleaved by boron trifluoride in non-protic solvents. The reaction appears to proceed via a non-synchronous Grobe fragmentation pathway.
The Cell Cycle Browser: An Interactive Tool for Visualizing, Simulating, and Perturbing Cell-Cycle Progression.

Summary The cell cycle is driven by precise temporal coordination among many molecular activities. To understand and explore this process, we developed the Cell Cycle Browser (CCB), an interactive web interface based on real-time reporter data collected in proliferating human cells. This tool facilitates visualizing, organizing, simulating, and predicting the outcomes of perturbing cell-cycle parameters. Time-series traces from individual cells can be combined to build a multi-layered timeline of molecular activities. Users can simulate the cell cycle using computational models that capture the dynamics of molecular activities and phase transitions. By adjusting individual expression levels and strengths of molecular relationships, users can predict effects on the cell cycle. Virtual assays, such as growth curves and flow cytometry, provide familiar outputs to compare cell-cycle behaviors for data and simulations. The CCB serves to unify our understanding of cell-cycle dynamics and provides a platform for generating hypotheses through virtual experiments.
New regional isomers of 1-methyl-5-(trifluoromethyl)pyrazoles

Utilizing the recently reported compound, 1-methyl-5-(trifluoromethyl)-2,3,4,5-tetrahydropyrazol-3-one, 4, a series of regional isomers of 1-methyl-5-(trifluoromethyl)-3-chloropyrazole, newly substituted in the 4-position were prepared by original syntheses. Chief among them was the new regional 4-hydroxy isomer, 3a, a linkage reagent valuable for preparing new SAR candidates in the bio-active pyrazole phenyl ether series.
A new algorithm for decremental single-source shortest paths with applications to vertex-capacitated flow and cut problems

We study the vertex-decremental Single-Source Shortest Paths (SSSP) problem: given an undirected graph G=(V,E) with lengths l(e)≥ 1 on its edges that undergoes vertex deletions, and a source vertex s, we need to support (approximate) shortest-path queries in G: given a vertex v, return a path connecting s to v, whose length is at most (1+є) times the length of the shortest such path, where є is a given accuracy parameter. The problem has many applications, for example to flow and cut problems in vertex-capacitated graphs. Decremental SSSP is a fundamental problem in dynamic algorithms that has been studied extensively, especially in the more standard edge-decremental setting, where the input graph G undergoes edge deletions. The classical algorithm of Even and Shiloach supports exact shortest-path queries in O(mn) total update time. A series of recent results have improved this bound to O(m1+o(1)logL), where L is the largest length of any edge. However, these improved results are randomized algorithms that assume an oblivious adversary. To go beyond the oblivious adversary restriction, recently, Bernstein, and Bernstein and Chechik designed deterministic algorithms for the problem, with total update time O(n2logL), that by definition work against an adaptive adversary. Unfortunately, their algorithms introduce a new limitation, namely, they can only return the approximate length of a shortest path, and not the path itself. Many applications of the decremental SSSP problem, including the ones considered in this paper, crucially require both that the algorithm returns the approximate shortest paths themselves and not just their lengths, and that it works against an adaptive adversary. Our main result is a randomized algorithm for vertex-decremental SSSP with total expected update time O(n2+o(1)logL), that responds to each shortest-path query in O(nlogL) time in expectation, returning a (1+є)-approximate shortest path. The algorithm works against an adaptive adversary. The main technical ingredient of our algorithm is an O(|E(G)|+ n1+o(1))-time algorithm to compute a core decomposition of a given dense graph G, which allows us to compute short paths between pairs of query vertices in G efficiently. We use our result for vertex-decremental SSSP to obtain (1+є)-approximation algorithms for maximum s-t flow and minimum s-t cut in vertex-capacitated graphs, in expected time n2+o(1), and an O(log4n)-approximation algorithm for the vertex version of the sparsest cut problem with expected running time n2+o(1). These results improve upon the previous best known algorithms for these problems in the regime where m= ω(n1.5 + o(1)).
Phase-Transfer Catalysts in the O-Alkylation of 2-Hydroxynaphthoquinones

A mild procedure has been developed for the O-alkyl­ation of 2-hydroxynaphthoquinones by using phase-transfer catalysts. Optimal yields were obtained when 18-crown-6 (10 mol%) and tetrabutylammonium iodide (10 mol% ) were used as cocatalysts in refluxing tetrahydrofuran containing potassium carbonate. Variability in the product yields (0–82%) was attributed to differences in the reactivity of the alkylating agent and to resonance stabilization of the 2-hydroxynaphthoquinone anion. Comparisons of the UV–visible spectra suggest that the degree of electron delocalization has a marked effect on the outcome of the reaction. Quinoid π-electrons were more delocalized in the absence of a stabilizing counteraction, resulting in lower yields. In the presence of tetrabutylammonium iodide, reduced levels of electron delocalization were detected, possibly as a result of ion pairing between the tetrabutylammonium cation and the C-2 oxygen anion. Enhanced reactivity correlates to a lower level of delocalization, and a combination of both catalysts is necessary to facilitate the O-alkylation.
Practical Yet Universally Composable Two-Server Password-Authenticated Secret Sharing.

Password-authenticated secret sharing (PASS) schemes, first introduced by Bagherzandi et al. at CCS 2011, allow users to distribute data among several servers so that the data can be recovered using a single humanmemorizable password, but no single server (or collusion of servers up to a certain size) can mount an off-line dictionary attack on the password or learn anything about the data. We propose a new, universally composable (UC) security definition for the two-server case (2PASS) in the public-key setting that addresses a number of relevant limitations of the previous, non-UC definition. For example, our definition makes no prior assumptions on the distribution of passwords, preserves security when honest users mistype their passwords, and guarantees secure composition with other protocols in spite of the unavoidable non-negligible success rate of online dictionary attacks. We further present a concrete 2PASS protocol and prove that it meets our definition. Given the strong security guarantees, our protocol is surprisingly efficient: in its most efficient instantiation under the DDH assumption in the random-oracle model, it requires fewer than twenty elliptic-curve exponentiations on the user’s device. We achieve our results by careful protocol design and by exclusively focusing on the two-server public-key setting.
Interfaces in Diblocks: A Study of Miktoarm Star Copolymers

We study ABn miktoarm star block copolymers in the strong segregation limit, focusing on the role that the AB interface plays in determining the phase behavior. We develop an extension of the kinked-path approach which allows us to explore the energetic dependence on interfacial shape. We consider a one-parameter family of interfaces to study the columnar to lamellar transition in asymmetric stars. We compare with recent experimental results. We discuss the stability of the A15 lattice of spherelike micelles in the context of interfacial energy minimization. We corroborate our theory by implementing a numerically exact self-consistent-field theory to probe the phase diagram and the shape of the AB interface.
Yb(OTf)(3)-Catalyzed oxymercuration of homoallylic alcohol-derived hemiacetals and hemiketals.

1,3-Diol synthons, protected as acetonides or benzylidene acetals, may be synthesized efficiently from homoallylic alcohols and acetone or benzaldehyde by oxymercuration of the derived hemiketals and hemiacetals with HgClOAc. The use of catalytic amounts of Yb(OTf)3 is crucial to the success of the reaction, which was determined to be reversible.
Analogues of 10-deazaaminopterin and 5-alkyl-5,10-dideazaaminopterin with the 4-substituted 1-naphthoyl group in the place of 4-substituted benzoyl.

10-Deaza modifications of classical antifolate analogues bearing the 1,4-disubstituted naphthalene ring in place of the 1,4-disubstituted benzene ring were prepared and tested for antitumor activity. Naphthalene analogues (9a−c, respectively) of 10-deazaaminopterin, 5-methyl-5,10-dideazaaminopterin, and 5-ethyl-5,10-dideazaaminopterin were prepared by a route consisting of C-alkylations of the anion derived from 4-carboxy-1-naphthaleneacetic acid dimethyl ester (2) by 6-(bromomethyl)-2,4-diaminopteridine (1a) and 6-(bromomethyl)-2,4-diamino-5-methyl- and -5-ethyl-5-deazapteridines (1b and 1c, respectively) followed by ester hydrolysis and subsequent decarboxylation to give naphthalene analogues (7a−c, respectively) of 4-amino-4-deoxy-10-deazapteroic acid and 4-amino-4-deoxy-5-methyl- and -5-ethyl-5,10-dideazapteroic acids. Peptide coupling of 7a−c with l-glutamic acid dialkyl ester followed by mild ester hydrolysis gave target compounds 9a−c. The key advantage of this route is circumvention of a hydrogena...
Soft supersymmetry breaking and the supersymmetric standard model

Abstract We recall how the idea of Softly Broken Supersymmetry led to the construction of the Supersymmetric Standard Model in 1981. Its first prediction, the supersymmetric unification of gauge couplings, was conclusively verified by the LEP and SLC experiments 10 years later. Its other predictions include: the existence of superparticles at the electroweak scale; a stable lightest superparticle (LSP) with a mass of ∼ 100 GeV, anticipated to be a neutral electroweak gaugino; the universality of scalar and gaugino masses at the unification scale. The original motivation for the model, solving the hierarchy problem, indicates that the superparticles should be discovered at the LHC or the TeVatron.
Cobalt carbonyl-mediated carbocyclizations of enynes: generation of bicyclooctanones or monocyclic alkenes.

Depending on the thermolytic conditions, dicobalthexacarbonyl-complexed enynes underwent cyclizations to provide different carbocyclic frameworks. Bicyclopentanones were formed from enyne−Co2(CO)6 complexes, or from enynes that were treated with Co2(CO)8, or more effectively, with Co4(CO)12 in an alcoholic solvent under a H2 or N2 atmosphere. This transformation proceeded via a sequential cyclocarbonylation and 1,4-reduction and is the first account using the cobalt carbonyl cluster. Under these conditions a cobalt hydride was presumably generated, which mediated reduction of the enone to the saturated ketone. In contrast, thermolysis of dicobalthexacarbonyl-complexed enynes under a hydrogen atmosphere in toluene resulted in their reductive cyclization to form monocyclic alkenes in moderate yields, in addition to the bicyclopentenone product. In some cases, addition of a hydrosilane to the reaction induced a complete suppression of the bicyclopentenone formation. While the former results demonstrate a rea...
The Design of Reagents for Photochemical and Thermal Multiple Electron Transfer Reactions

Abstract Most, if not all, electron transfer reactions involving more than one electron can be considered as a series of sequential one electron transfer steps when evaluated on an appropriate timescale. Once the critical activation barrier for the first electron transfer to occur has been surmounted, the ensuing electrons are generally transferred in rapid succession. A number of multiple electron, inorganic systems, particularly those containing platinum, are evaluated; and the underlying principles for the design of these systems are discussed. Both thermally and photochemically activated systems are considered. Additionally, new thermodynamic criteria are proposed for certain inner sphere electron transfer reactions.
Ab Initio Characterization of [H3N·BH3]2, [H3N·AlH3]2, and [H3N·GaH3]2

The dimers of [H3N·BH3]2, [H3N·AlH3]2, and [H3N·GaH3]2 are characterized as head-to-tail complexes with intermolecular H−H hydrogen bonding. In the case of [H3N·BH3]2, that hydrogen bonding is bifurcated resulting in four short (N)H−H(B) distances. For both [H3N·AlH3]2 and [H3N·GaH3]2, there are only two short (N)H−H(Al/Ga) distances, although the four-atom linkage remains far from linear. The binding energies that are calculated at the MP2 level of theory using polarized-double-ζ basis sets are −15.1, −11.8, and −10.7 kcal/mol for [H3N·BH3]2, [H3N·AlH3]2, and [H3N·GaH3]2, respectively. These energies appear converged to within 1 kcal/mol with respect to larger basis sets and more complete accounting for electron correlation effects. Binding energies from density functional calculations are within 0.3 kcal/mol of the MP2 results. All-electron and effective-core-potential basis sets for gallium provide similar predictions.
Interfacial Properties of Proteins/Spectroelectrochemical Studies

The sections in this article are Introduction Methodologies Surface-enhanced Resonance Raman Scattering Spectroscopy Electroreflectance (Potential-Modulated UV-vis Reflectance) Spectroscopy Infrared Reflection Absorption Spectroscopy Absorption Linear Dichroism and Total Internal Reflection Fluorescence Spectroscopies Redox Behavior of Heme- and Flavoproteins at Unmodified Electrode Surfaces Gold Electrode Cytochrome c Cytochrome c3 Silver Electrode Cytochrome c Cytochrome c3 Cytochrome c552 (Thermus thermophilus) Cytochrome b5 and Hemoglobin Myoglobin Flavoproteins Cytochrome P-450 Electrode Reaction of Electron Transfer Proteins at Modified Electrodes Cytochrome c at Pyridine Derivative-modified Electrodes ER Spectroscopic Studies SERRS Studies Stability of Bis-(4pyridyl) Disulfide and 4-Mercaptopyridine at Gold Electrodes Cytochrome c at ω-Functional Alkanethiol Modified Electrodes Cytochrome c at Iodine-modified Electrodes Cytochrome c3 at 4,4′-Bipyridyl and Carboxylic Acid-terminated Alkanethiol Modified Electrodes Proteins Cast in Lipid Bilayer Molecular Orientation of Proteins on Solid Substrates. Cytochrome c Immobilized on Self-assembled Monolayers IRRAS Studies Conformation of Cytochrome c on Carboxylic Acid-terminated SAM Electron Transfer Kinetics of Electron Transfer Proteins at Electrode Surfaces Electron Transfer Kinetics of Cytochrome c at Carboxylic Acid-terminated Alkanethiol SAM Electron Transfer Kinetics of Cytochromes c and c552 at Silver Electrode Electron Transfer Kinetics of Azurin at Methyl-terminated Alkanethiol Self-assembled Monolayers Recent review article related to this chapter
Mobile precursor mediated protein adsorption on solid surfaces

Abstract The interaction between a protein molecule and a surface is ubiquitous to a number of important technologies, such as bio-sensing, biomaterials, and nanomedicine. This process is also essential to complex biological functions, such as protein–cell surface interactions. Here we explore the application of fundamental concepts developed in the field of surface science to the understanding of protein–surface interactions. In particular, we focus on the role of mobile precursor states in the reversible and irreversible adsorption of protein molecules. We attempt to apply these simple concepts to the analysis of the kinetics and thermodynamics of protein–surface interactions. We conclude by discussing how one may take advantage of these simple concepts in designing and controlling protein–surface interactions for various bio-interface based technologies.
Solvent-dependent chemoselectivities in Ce(IV)-mediated oxidative coupling reactions.

The oxidative coupling of 1,3-diketones, β-keto esters, and β-keto silyl enol ethers with allyl trimethylsilane in the presence of CTAN was investigated. In the case of acyclic diketones and esters, different chemoselectivities were observed in CH3CN and CH2Cl2 leading to good yields of allylation and dihydrofuran products, respectively.
Psymberin, A Potent Sponge-Derived Cytotoxin from Psammocinia Distantly Related to the Pederin Family

Bioassay-guided fractionation of the sponge Psammocinia sp. afforded psymberin (1) possessing 5S,8S,9S,11R,13R,15S,16R,17R stereochemistry. Psymberin exhibits structural similarities to the pederin family metabolites. The potent cytotoxicty and unique structural features of 1 make it a promising lead for therapeutic development.
Sterically shielded secondary N-tritylamines and N-tritylamide bases, readily available and useful synthetic reagents

t-Butyltritylamine (1) and lithium t-butyltritylamide (2) are introduced as readily available and useful superhindered bases.
Cascade Radical Cyclizations via Biradicals Generated from (Z)-1,2,4-Heptatrien-6-ynes

On heating in refluxing benzene, acyclic enyne−allene 4 underwent intramolecular transformations in a sequence with an initial Myers cycloaromatization to form α,3-didehydrotoluene biradical 5 followed by a 5-exo cyclization of the benzenoid radical center in 5 to produce 6. Biradical 6 then decayed through a 1,5-hydrogen shift to furnish o-quinodimethane 7, which in turn was captured in an intramolecular Diels−Alder reaction to afford 8 having the tetracyclic steroidal skeleton in a single step from 4 in 50% isolated yield. Similarly, acyclic enyne−allene 16 having one of the tethers shortened by one carbon atom furnished 18 having the fused 5,6,6,5-ring system. Tetracycle 19 substituted with an angular methyl group was obtained from 17. In the cases of 24 and 34, a predominant 1,5-hydrogen shift of an allylic hydrogen to the benzenoid radical center of biradicals 26 and 35 followed by a homolytic coupling produced spiro derivatives 31 and 40, respectively. On the other hand, a preferential 7-endo ring c...
An enantioselective synthesis of benzylidene-protected syn-3,5-dihydroxy carboxylate esters via osmium, palladium, and base catalysis.

The enantioselective syntheses of several protected syn-3,5-dihydroxy carboxylic esters have been achieved from the corresponding achiral 1,3-dieneoates. The route relies upon an enantio- and regioselective Sharpless dihydroxylation and a palladium-catalyzed reduction to form δ-hydroxy-1-enoates. The resulting δ-hydroxy-1-enoates are subsequently converted into benzylidene-protected 3,5-dihydroxy carboxylic esters in one step. The benzylidene-protected 3,5-dihydroxy carboxylic esters are produced in good overall yields (25% to 51%) and high enantiomeric excesses (80% to >95%).
Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins

To comprehensively study extracellular small RNAs (sRNA) by sequencing (sRNA-seq), we developed a novel pipeline to overcome current limitations in analysis entitled, "Tools for Integrative Genome analysis of Extracellular sRNAs (TIGER)". To demonstrate the power of this tool, sRNA-seq was performed on mouse lipoproteins, bile, urine and livers. A key advance for the TIGER pipeline is the ability to analyse both host and non-host sRNAs at genomic, parent RNA and individual fragment levels. TIGER was able to identify approximately 60% of sRNAs on lipoproteins and >85% of sRNAs in liver, bile and urine, a significant advance compared to existing software. Moreover, TIGER facilitated the comparison of lipoprotein sRNA signatures to disparate sample types at each level using hierarchical clustering, correlations, beta-dispersions, principal coordinate analysis and permutational multivariate analysis of variance. TIGER analysis was also used to quantify distinct features of exRNAs, including 5' miRNA variants, 3' miRNA non-templated additions and parent RNA positional coverage. Results suggest that the majority of sRNAs on lipoproteins are non-host sRNAs derived from bacterial sources in the microbiome and environment, specifically rRNA-derived sRNAs from Proteobacteria. Collectively, TIGER facilitated novel discoveries of lipoprotein and biofluid sRNAs and has tremendous applicability for the field of extracellular RNA.
Selective oxidation of canthines to canthin-6-ones with triethylbenzylammonium permanganate

Abstract Oxidation of canthines, prepared from intramolecular inverse electron demand Diels-Alder reactions of indole with tethered triazines, produced the corresponding canthin-6-ones regiospecifically, with no detected canthin-4-ones.
Enantioselective Synthesis of 1-Aryltetrahydroisoquinolines

1-Aryltetrahydroisoquinolines (1-arylTHIQs) are important structural motifs in many alkaloids and biologically active compounds. Ligand 2a promotes the enantioselective addition of arylzinc reagent...
Using competition assays to quantitatively model cooperative binding by transcription factors and other ligands.

Abstract Background The affinities of DNA binding proteins for target sites can be used to model the regulation of gene expression. These proteins can bind to DNA cooperatively, strongly impacting their affinity and specificity. However, current methods for measuring cooperativity do not provide the means to accurately predict binding behavior over a wide range of concentrations. Methods We use standard computational and mathematical methods, and develop novel methods as described in Results. Results We explore some complexities of cooperative binding, and develop an improved method for relating in vitro measurements to in vivo function, based on ternary complex formation. We derive expressions for the equilibria among the various complexes, and explore the limitations of binding experiments that model the system using a single parameter. We describe how to use single-ligand binding and ternary complex formation in tandem to determine parameters that have thermodynamic relevance. We develop an improved method for finding both single-ligand dissociation constants and concentrations simultaneously. We show how the cooperativity factor can be found when only one of the single-ligand dissociation constants can be measured. Conclusions The methods that we develop constitute an optimized approach to accurately model cooperative binding. General significance The expressions and methods we develop for modeling and analyzing DNA binding and cooperativity are applicable to most cases where multiple ligands bind to distinct sites on a common substrate. The parameters determined using these methods can be fed into models of higher-order cooperativity to increase their predictive power.
Synthesis and crystal structure of α-ThTe3

The binary thorium tritelluride, α-ThTe3, was synthesized by solid-state methods at 1223 K. From a single-crystal X-ray diffraction study the material crystallizes in the TiS3 structure type with two formula units in space group C22h–P21/m of the monoclinic system in a cell with lattice constants a = 6.1730 (4) A, b = 4.3625(3) A, c = 10.4161(6) A, and β = 97.756(3)° (at 100 K). The asymmetric unit of this compound comprises one Th atom and three Te atoms each with site symmetry m. Each Th atom is coordinated to eight Te atoms in a bicapped trigonal-pyramidal arrangement. Th–Te distances range from 3.1708(4) A to 3.2496(6) A. The structure features a Te–Te interaction 2.7631(8) A in length, which is typical for a Te–Te single bond. Thus α-ThTe3 may be charge balanced and formulated as Th4+Te2–Te22–.
Synthesis and biological evaluation of 4-deacetylpaclitaxel

Abstract 4-Deacetylpaclitaxel, prepared from baccatin III via two synthetic approaches and from paclitaxel via one synthetic approach, has minimal effects on tubulin polymerization and is not cytotoxic to human CA46 Burkitt lymphoma cells.
Highly Practical and Enantioselective Cu-Catalyzed Conjugate Addition of Alkylzinc Reagents to Cyclic Enones at Ambient Temperature

A new ligand for Cu-catalyzed enantioselective additions of dialkylzincs to cyclic enones has been developed. In addition to providing good to excellent enantioselectivities with a range of cyclic enones and dialkylzincs, the ligand has several notworthy features: it can be readily prepared in just two steps, is an air-stable crystalline solid, and provides optimal performance at ambient temperature.
Face Rings of Cycles, Associahedra, and Standard Young Tableaux

We show that $J_n$, the Stanley-Reisner ideal of the $n$-cycle, has a free resolution supported on the $(n-3)$-dimensional simplicial associahedron $A_n$. This resolution is not minimal for $n \geq 6$; in this case the Betti numbers of $J_n$ are strictly smaller than the $f$-vector of $A_n$. We show that in fact the Betti numbers $\beta_{d}$ of $J_n$ are in bijection with the number of standard Young tableaux of shape $(d+1, 2, 1^{n-d-3})$. This complements the fact that the number of $(d-1)$-dimensional faces of $A_n$ are given by the number of standard Young tableaux of (super)shape $(d+1, d+1, 1^{n-d-3})$; a bijective proof of this result was first provided by Stanley. An application of discrete Morse theory yields a cellular resolution of $J_n$ that we show is minimal at the first syzygy. We furthermore exhibit a simple involution on the set of associahedron tableaux with fixed points given by the Betti tableaux, suggesting a Morse matching and in particular a poset structure on these objects.
P-sets and minimal right ideals in N*

Recall that a $P$-set is a closed set $X$ such that the intersection of countably many neighborhoods of $X$ is again a neighborhood of $X$. We show that if $\mathfrak{t} = \mathfrak{c}$ then there is a minimal right ideal of $(\beta \mathbb N,+)$ that is also a $P$-set. We also show that the existence of such $P$-sets implies the existence of $P$-points; in particular, it is consistent with ZFC that no minimal right ideal is a $P$-set. As an application of these results, we prove that it is both consistent with and independent of ZFC that the shift map is (up to isomorphism) the unique chain transitive autohomeomorphism of $\mathbb N^*$.
Combinatorics of the K-theory of affine Grassmannians

Abstract We introduce a family of tableaux that simultaneously generalizes the tableaux used to characterize Grothendieck polynomials and k -Schur functions. We prove that the polynomials drawn from these tableaux are the affine Grothendieck polynomials and k - K -Schur functions – Schubert representatives for the K -theory of affine Grassmannians and their dual in the nil Hecke ring. We prove a number of combinatorial properties including Pieri rules.
Realization of Groups with Pairing as Jacobians of Finite Graphs

We study which groups with pairing can occur as the Jacobian of a finite graph. We provide explicit constructions of graphs whose Jacobian realizes a large fraction of odd groups with a given pairing. Conditional on the generalized Riemann hypothesis, these constructions yield all groups with pairing of odd order, and unconditionally, they yield all groups with pairing whose prime factors are sufficiently large. For groups with pairing of even order, we provide a partial answer to this question, for a certain restricted class of pairings. Finally, we explore which finite abelian groups occur as the Jacobian of a simple graph. There exist infinite families of finite abelian groups that do not occur as the Jacobians of simple graphs.