cssi/SciSciGPT-SciSciNet huggingface dataset:
PRACTICAL SYNTHESIS OF ()-CHLOROVULONE II

We describe a total synthesis of (±)-chlorovulone II that is 10 steps shorter than the best alternative currently available (nine vs 19 steps). The key event of the synthesis is an aldol addition of the enolate of ethyl acetate into 4-cyclopentene-1,3-dione, a substance that has received little attention as an educt for prostanoid synthesis and for which little is known about carbonyl 1,2-addition with enolates. In addition, we provide chemical and stereochemical details of a route to a key intermediate toward the title compound that involves a carbonyl−ene reaction and a radical addition to an aldehyde carbonyl.
Syntheses, addition–eliminations, and addition–displacements of 5-(bromomethylene)hydantoins

Abstract 5-(Bromomethylene)hydantoins, prepared from bromopyruvic acid and ureas in the presence of BF3, react with various nitrogen, phosphorus, sulfur, and carbon nucleophiles by addition–elimination to give the corresponding 5-(substituted-methylene)hydantoins. The 5-(bromomethylene)hydantoins also undergo acid-catalyzed reactions with nucleophiles by addition–displacement and addition–elimination processes.
Chronic Intermittent Ethanol Exposure Selectively Increases Synaptic Excitability in the Ventral Domain of the Rat Hippocampus.

Abstract Many studies have implicated hippocampal dysregulation in the pathophysiology of alcohol use disorder (AUD). However, over the past twenty years, a growing body of evidence has revealed distinct functional roles of the dorsal (dHC) and ventral (vHC) hippocampal subregions, with the dHC being primarily involved in spatial learning and memory and the vHC regulating anxiety- and depressive-like behaviors. Notably, to our knowledge, no rodent studies have examined the effects of chronic ethanol exposure on synaptic transmission along the dorsal/ventral axis. To that end, we examined the effects of the chronic intermittent ethanol vapor exposure (CIE) model of AUD on dHC and vHC synaptic excitability. Adult male Long–Evans rats were exposed to CIE or AIR for 10 days (12 h/day; targeting blood ethanol levels of 175–225 mg%) and recordings were made 24 h into withdrawal. As expected, this protocol increased anxiety-like behaviors on the elevated plus-maze and successive alleys test. Extracellular recordings revealed marked CIE-associated increases in synaptic excitation in the CA1 region that were exclusively restricted to the ventral domain of the hippocampus. Western blot analysis of synaptoneurosomal fractions revealed that the expression of two proteins that regulate synaptic strength, GluA2 and SK2, were dysregulated in the vHC, but not the dHC, following CIE. Together, these findings suggest that the ventral CA1 region may be particularly sensitive to the maladaptive effects of chronic ethanol exposure and provide new insight into some of the neural substrates that may contribute to the negative affective state that develops during withdrawal.
Efficient Syntheses of 2-Functionalized Thiophenes, Cyclopent[b]thiophenes, and Polysubstituted Benzo[b]thiophenes from 2-(Benzotriazol-1-ylmethyl)thiophenes

Diverse 2-(functionalized-alkyl)- and 2-alkenylthiophenes 2a,b, 4a,b, and 6a−d are prepared via the side chain elaboration of 2-(benzotriazol-1-ylmethyl)thiophenes 3a,b, themselves readily available from the condensation of 1-(hydroxymethyl)benzotriazole with thiophenes 1a,b. Treatment of 2-(benzotriazol-1-ylmethyl)thiophenes 3b and 5g,j with styrenes in the presence of zinc bromide results in formal [3 + 2] cycloaddition to give in good yields substituted cyclopent[b]thiophenes 16a/17a, 16b/17b, and 18. Lithiation and 1,4-addition to a variety of α,β-unsaturated ketones and aldehydes, and subsequent acid-catalyzed intramolecular cyclization followed by debenzotriazolylation−dehydration converts 3 and 5 to a range of polysubstituted benzo[b]thiophenes 19a−d and 25a−e in moderate to excellent yields. NOE difference spectroscopy and NMR 1H−13C long-range correlation support structures of types 19 and 25 and exclude those of type 26, thus confirming the cyclization pathway.
SYNTHESIS OF AL(N3)3 AND THE DEPOSITION OF ALN THIN FILMS

Al(N3)3 is produced by the stoichiometric reaction between Al(CH3)3 and excess HN3 at room temperature. The reaction is thought to proceed by the addition of HN3 to Al(CH3)3 followed by elimination of CH4, repeated three times to produce the fully azidified Al(N3)3. The product Al(N3)3 is nonvolatile and condenses as a film on the walls of the reaction vessel. The reaction products were observed in the gas phase and in low-temperature argon matrices by FTIR spectroscopy. Ab initio methods were used to compute the geometry and frequencies of Al(N3)3 , and the results are in good agreement with experimental data. The films produced upon condensation of Al(N3)3 contain the Al−N2 complex and AlN as well as the azide. Heating the films to 400 K removes the azide and the Al−N2, leaving AlN. This method may be useful as a low-temperature route to the synthesis of AlN thin films.
Pacific geoduck (Panopea generosa) resilience to natural pH variation.

Abstract Pacific geoduck aquaculture is a growing industry, however, little is known about how geoduck respond to varying environmental conditions, or how the industry will fare under projected climate conditions. To understand how geoduck production may be impacted by low pH associated with ocean acidification, multi-faceted environmental heterogeneity needs to be included to understand species and community responses. In this study, eelgrass habitats and environmental heterogeneity across four estuarine bays were leveraged to examine low pH effects on geoduck under different natural regimes, using targeted proteomics to assess physiology. Juvenile geoduck were deployed in eelgrass and adjacent unvegetated habitats for 30 days while pH, temperature, dissolved oxygen, and salinity were monitored. Across the four bays, pH was lower in unvegetated habitats compared to eelgrass habitats. However this did not impact geoduck growth, survival, or proteomic abundance patterns in gill tissue. Temperature and dissolved oxygen differences across all locations corresponded to differences in growth and targeted protein abundance patterns. Specifically, three protein abundance levels (trifunctional-enzyme β-subunit, puromycin-sensitive aminopeptidase, and heat shock protein 90-α) and shell growth positively correlated with dissolved oxygen variability and inversely correlated with mean temperature. These results demonstrate that geoduck may be resilient to low pH in a natural setting, but other abiotic factors (i.e. temperature, dissolved oxygen variability) may have a greater influence on geoduck physiology. In addition this study contributes to the understanding of how eelgrass patches influences water chemistry.
A convenient synthesis of the thieno[3,2‐c]pyridine nucleus

The unsubstituted thieno[3,2-c]pyridine ring system was prepared from thiophene-3-carboxaldehyde in 4 steps. The sequence is suitable for scale-up.
Total synthesis of smenochromene B through ring contraction

A total synthesis of racemic smenochromene B has been achieved. The synthesis proceeds through an unusual rearrangement of smenochromene D with concomitant ring contraction and double bond isomerization.
Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy

Identifying functional enhancer elements in metazoan systems is a major challenge. Large-scale validation of enhancers predicted by ENCODE reveal false-positive rates of at least 70%. We used the pregrastrula-patterning network of Drosophila melanogaster to demonstrate that loss in accuracy in held-out data results from heterogeneity of functional signatures in enhancer elements. We show that at least two classes of enhancers are active during early Drosophila embryogenesis and that by focusing on a single, relatively homogeneous class of elements, greater than 98% prediction accuracy can be achieved in a balanced, completely held-out test set. The class of well-predicted elements is composed predominantly of enhancers driving multistage segmentation patterns, which we designate segmentation driving enhancers (SDE). Prediction is driven by the DNA occupancy of early developmental transcription factors, with almost no additional power derived from histone modifications. We further show that improved accuracy is not a property of a particular prediction method: after conditioning on the SDE set, naive Bayes and logistic regression perform as well as more sophisticated tools. Applying this method to a genome-wide scan, we predict 1,640 SDEs that cover 1.6% of the genome. An analysis of 32 SDEs using whole-mount embryonic imaging of stably integrated reporter constructs chosen throughout our prediction rank-list showed >90% drove expression patterns. We achieved 86.7% precision on a genome-wide scan, with an estimated recall of at least 98%, indicating high accuracy and completeness in annotating this class of functional elements.
Donor layer-acceptor chain formation in the LaNiGe2 structure : A crystallographic and computational study

Synthesis, and single-crystal X-ray diffraction and computational studies were carried out for the title compound. LaNiGe2 crystallizes in the orthorhombic lattice Cmcm (a = 4.3040(6) A, b = 16.892(10) A, c = 4.2367(5) A, Z = 4). It consists of a Ni-capped Ge square lattice and Ge zigzag chains. A unique structural feature is the formation of the square lattice by the more electronegative Ge instead of by Ni atoms as in several other phases such as La3Ni4Ge4. Computational analysis indicates that the Ge square lattice acts as an electron donor while the Ge zigzag chain acts as electron acceptor. A donor−acceptor interaction similar to that in the CaBe2Ge2 phase stabilizes the Ge square lattice.
Substituent-controlled domino-Henry-hetero Diels–Alder reaction: synthesis of polycyclic nitronates

Syntheses of hitherto unreported 5-aryl-3,3-dimethylchromeno[2,3-b]furo[3,4-d]pyridine-1,11-diones and 6-aryl-4,4-dimethyl-12-oxochromeno[2,3:2′,3′]pyridino[4′,5′-d][1,2]oxazine-2-N-oxide have been accomplished by a metal-free domino-Henry-hetero Diels–Alder reaction.
Cyclin D-Cdk4,6 Drives Cell-Cycle Progression via the Retinoblastoma Protein's C-Terminal Helix.

The cyclin-dependent kinases Cdk4 and Cdk6 form complexes with D-type cyclins to drive cell proliferation. A well-known target of cyclin D-Cdk4,6 is the retinoblastoma protein Rb, which inhibits cell-cycle progression until its inactivation by phosphorylation. However, the role of Rb phosphorylation by cyclin D-Cdk4,6 in cell-cycle progression is unclear because Rb can be phosphorylated by other cyclin-Cdks, and cyclin D-Cdk4,6 has other targets involved in cell division. Here, we show that cyclin D-Cdk4,6 docks one side of an alpha-helix in the Rb C terminus, which is not recognized by cyclins E, A, and B. This helix-based docking mechanism is shared by the p107 and p130 Rb-family members across metazoans. Mutation of the Rb C-terminal helix prevents its phosphorylation, promotes G1 arrest, and enhances Rb's tumor suppressive function. Our work conclusively demonstrates that the cyclin D-Rb interaction drives cell division and expands the diversity of known cyclin-based protein docking mechanisms.
Growth of new ternary intermetallic phases from Ca/Zn eutectic flux

Abstract The eutectic 7.3:2.7 molar ratio mixture of calcium and zinc metal melts at 394 °C and was explored as a solvent for the growth of new intermetallic phases for potential use as hydrogen storage materials. The reaction of nickel in this molten mixture produces two new phases—the CaCu 5 -related structure CaNi 2 Zn 3 ( P 6/ mmm , a =8.9814(5) A, c =4.0665(5) A) and a new cubic structure Ca 21 Ni 2 Zn 36 ( Fd– 3 m , a =21.5051(4) A). Palladium-containing reactions produced CaPd 0.85 Zn 1.15 with the orthorhombic TiNiSi structure type ( Pnma , a =7.1728(9) A, b =4.3949(5) A, c =7.7430(9) A). Reactions of platinum in the Ca/Zn mixture produce Ca 6 Pt 3 Zn 5 , with an orthorhombic structure related to that of W 3 CoB 3 ( Pmmn , a =13.7339(9) A, b =4.3907(3) A, c =10.7894(7) A).
Kinetics and Mechanisms of the Reactions of Hypochlorous Acid, Chlorine, and Chlorine Monoxide with Bromite Ion

The reaction between BrO2- and excess HOCl (p[H+] 6−7, 25.0 °C) proceeds through several pathways. The primary path is a multistep oxidation of HOCl by BrO2- to form ClO3- and HOBr (85% of the initial 0.15 mM BrO2-). Another pathway produces ClO2 and HOBr (8%), and a third pathway produces BrO3- and Cl- (7%). With excess HOCl concentrations, Cl2O also is a reactive species. In the proposed mechanism, HOCl and Cl2O react with BrO2- to form steady-state species, HOClOBrO- and ClOClOBrO-. Acid facilitates the conversion of HOClOBrO- and ClOClOBrO- to HOBrOClO-. These reactions require a chainlike connectivity of the intermediates with alternating halogen−oxygen bonding (i.e. HOBrOClO-) as opposed to Y-shaped intermediates with a direct halogen−halogen bond (i.e. HOBrCl(O)O-). The HOBrOClO- species dissociates into HOBr and ClO2- or reacts with general acids to form BrOClO. The distribution of products suggests that BrOClO exists as a BrOClO·HOCl adduct in the presence of excess HOCl. The primary products, Cl...
SPRING: a kinetic interface for visualizing high dimensional single-cell expression data.

Motivation Single-cell gene expression profiling technologies can map the cell states in a tissue or organism. As these technologies become more common, there is a need for computational tools to explore the data they produce. In particular, visualizing continuous gene expression topologies can be improved, since current tools tend to fragment gene expression continua or capture only limited features of complex population topologies. Results Force-directed layouts of k-nearest-neighbor graphs can visualize continuous gene expression topologies in a manner that preserves high-dimensional relationships and captures complex population topologies. We describe SPRING, a pipeline for data filtering, normalization and visualization using force-directed layouts and show that it reveals more detailed biological relationships than existing approaches when applied to branching gene expression trajectories from hematopoietic progenitor cells and cells of the upper airway epithelium. Visualizations from SPRING are also more reproducible than those of stochastic visualization methods such as tSNE, a state-of-the-art tool. We provide SPRING as an interactive web-tool with an easy to use GUI. Availability and implementation https://kleintools.hms.harvard.edu/tools/spring.html, https://github.com/AllonKleinLab/SPRING/. Contact calebsw@gmail.com or allon_klein@hms.harvard.edu. Supplementary information Supplementary data are available at Bioinformatics online.
Ferromagnetic Coupling in Hexanuclear Gadolinium Clusters

The magnetic susceptibilities of hexanuclear gadolinium clusters in the compounds Gd(Gd6ZI12) (Z = Co, Fe, or Mn) and CsGd(Gd6CoI12)2 are reported and subjected to theoretical analysis with the help of density functional theory (DFT) computations. The single-crystal structure of Gd(Gd6CoI12) is reported here as well. We find that the compound with a closed shell of cluster bonding electrons, Gd(Gd6CoI12), exhibits the effects of antiferromagnetic coupling over the entire range of temperatures measured (4−300 K). Clusters with unpaired, delocalized cluster bonding electrons (CBEs) exhibit enhanced susceptibilities consistent with strong ferromagnetic coupling, except at lower temperatures (less than 30 K) where intercluster antiferromagnetic coupling suppresses the susceptibilities. The presence of two unpaired CBEs, as in [Gd6MnI12]3-, yields stronger coupling than when just one unpaired CBE is present, as in [Gd6FeI12]3- or [Gd6CoI12]2-. DFT calculations on model molecular systems, [Gd6CoI12](OPH3)6 and ...
SYNTHESIS OF INOSITOL PHOSPHODIESTERS BY PHOSPHOLIPASE C-CATALYZED TRANSESTERIFICATION

Transesterification of primary alcohols with inositol 1,2-cyclic phosphate (IcP) in the presence of phosphatidylinositol-specific phospholipase C (PI-PLC) resulted in the formation of O-alkyl inositol 1-phosphates. The starting IcP was obtained in a single step by PI-PLC catalyzed cleavage of phosphatidylinositol from the soybean phospholipid. The transesterification reaction was performed with a series of 20 structurally diverse hydroxyl compounds, ranging in the structural complexity from methanol to the serine-containing Ser-Tyr-Ser-Met tetrapeptide, to give the corresponding phosphodiesters with 20−80% yields, depending mainly on the solubility of alcohols in water. The rates of transesterifications, and of the competing hydrolysis of IcP to inositol 1-phosphate (IP), were relatively insensitive to the alcohol structure. With polyhydroxyl compounds such as glycerol and hexitols, the enzyme displayed complete preference toward formation of the inositol phosphate derivatives of the primary hydroxyl grou...
Filling in the Holes: Structural and Magnetic Properties of the Chemical Pressure Stabilized LnMnxGa3 (Ln = Ho–Tm; x < 0.15)

Single crystals of LnMnxGa3 (Ln = Ho–Tm; x < 0.15) were grown from a Ga self-flux. These compounds crystallize in a variant of the AuCu3 structure type where Mn partially occupies the Ga6 octahedral holes. Introduction of the Mn guest atoms allows for modulation of the structures and magnetic properties of their hosts: While TmGa3 orders antiferromagnetically at ∼4.2 K, TmMnxGa3 (x = 0.05, 0.10) remains paramagnetic down to 1.8 K. Ho and Er analogs order antiferromagnetically, with effective moments and Neel temperatures, respectively, decreasing and increasing as a function of Mn concentration. DFT–chemical pressure analysis elucidates the trends in the stability of LnGa3 AuCu3-type phases and their stuffed derivatives. Guest atom insertion supports expansion of the filled octahedra, allowing the relief of negative chemical pressures in the surrounding Ga–Ga contacts.
Fluorescence-Based Screening of Asymmetric Acylation Catalysts through Parallel Enantiomer Analysis. Identification of a Catalyst for Tertiary Alcohol Resolution

A technique for high-throughput screening of kinetic resolution catalysts is reported. The method relies on carrying simultaneous kinetic resolutions in a multiwell plate format wherein each well contains a unique catalyst and a small amount of a pH-activated fluorescent sensor (3). By conducting experiments such that each catalyst is evaluated in parallel in the presence of each isolated enantiomer, an indication of catalyst activity is obtained on a per enantiomer basis. Catalysts that are highly active for one enantiomer but modestly active for another are then reevaluated in conventional kinetic resolutions. From these screens, a highly selective (krel = 46) pentapeptide (4) was obtained for a model secondary alcohol (1). In addition, peptide 10 was found to afford excellent selectivities (krel > 20) for a number of alcohol substrates (9a−9f) in the traditionally challenging tertiary class.
Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan (Hexacorallia: Actiniaria).

Sympatric diversification is recognized to have played an important role in the evolution of biodiversity. However, an in situ sympatric origin for codistributed taxa is difficult to demonstrate because different evolutionary processes can lead to similar biogeographic outcomes, especially in ecosystems that can readily facilitate secondary contact due to a lack of hard barriers to dispersal. Here we use a genomic (ddRADseq), model-based approach to delimit a species complex of tropical sea anemones that are codistributed on coral reefs throughout the Tropical Western Atlantic. We use coalescent simulations in fastsimcoal2 and ordinary differential equations in Moments to test competing diversification scenarios that span the allopatric-sympatric continuum. Our results suggest that the corkscrew sea anemone Bartholomea annulata is a cryptic species complex whose members are codistributed throughout their range. Simulation and model selection analyses from both approaches suggest these lineages experienced historical and contemporary gene flow, supporting a sympatric origin, but an alternative secondary contact model receives appreciable model support in fastsimcoal2. Leveraging the genome of the closely related Exaiptasia diaphana, we identify five loci under divergent selection between cryptic B. annulata lineages that fall within mRNA transcripts or CDS regions. Our study provides a rare empirical, genomic example of sympatric speciation in a tropical anthozoan and the first range-wide molecular study of a tropical sea anemone, underscoring that anemone diversity is under-described in the tropics, and highlighting the need for additional systematic studies into these ecologically and economically important species.
Design and evaluation of a high throughput QoS-aware and congestion-aware router architecture for Network-on-Chip

Abstract This paper proposes a novel QoS-aware and congestion-aware Network-on-Chip architecture that not only enables quality-oriented network transmission and maintains a feasible implementation cost but also well balance traffic load inside the network to enhance overall throughput. By differentiating application traffic into different service classes, bandwidth allocation is managed accordingly to fulfill QoS requirements. Incorporating with congestion control scheme which consists of dynamic arbitration and adaptive routing path selection, high priority traffic is directed to less congested areas and is given preference to available resources. Simulation results show that average latency of high priority and overall traffic is improved dramatically for various traffic patterns. Cost evaluation results also show that the proposed router architecture requires negligible cost overhead but provides better performance for both advanced mesh NoC platforms.
Changing Trends in the Types of Intrauterine Illicit Drug Exposures in neonates admitted to our Neonatal Intensive Care Unit (NICU)

Background: A variety of illicit drugs abused by women during pregnancy cross the placenta. All of these may be associated with short-term deleterious effects on birth outcomes that are often drug specific. For instance, maternal cocaine use may result in catastrophic birth outcomes like placental abruption, maternal opiate use in neonatal abstinence syndrome and maternal marijuana use in preterm birth. Prevalence of maternal use of specific drugs has probably shifted over the years in keeping with the popularity or access to these substances in …
Upper-Level Physics Students' Perceptions of Physicists.

As part of a longitudinal study into identity development in upper-level physics students, we used a phenomenographic research method to examine students’ perceptions of what it means to be a physicist. The results revealed four different categories. We find a clear distinction in the exclusivity students associate with being a physicist and the differences in the importance of research and its association with being a physicist. A relationship between perceptions of physicists and goal orientation is indicated.
Prior Information Guided Regularized Deep Learning for Cell Nucleus Detection

Cell nuclei detection is a challenging research topic because of limitations in cellular image quality and diversity of nuclear morphology, i.e., varying nuclei shapes, sizes, and overlaps between multiple cell nuclei. This has been a topic of enduring interest with promising recent success shown by deep learning methods. These methods train convolutional neural networks (CNNs) with a training set of input images and known, labeled nuclei locations. Many such methods are supplemented by spatial or morphological processing. Using a set of canonical cell nuclei shapes, prepared with the help of a domain expert, we develop a new approach that we call shape priors (SPs) with CNNs (SPs-CNN). We further extend the network to introduce an SP layer and then allowing it to become trainable (i.e., optimizable). We call this network as tunable SP-CNN (TSP-CNN). In summary, we present new network structures that can incorporate “expected behavior” of nucleus shapes via two components: learnable layers that perform the nucleus detection and a fixed processing part that guides the learning with prior information. Analytically, we formulate two new regularization terms that are targeted at: 1) learning the shapes and 2) reducing false positives while simultaneously encouraging detection inside the cell nucleus boundary. Experimental results on two challenging datasets reveal that the proposed SP-CNN and TSP-CNN can outperform the state-of-the-art alternatives.
Khovanov homology, Lee homology and a Rasmussen invariant for virtual knots

The paper contains an essentially self-contained treatment of Khovanov homology, Khovanov–Lee homology as well as the Rasmussen invariant for virtual knots and virtual knot cobordisms which directly applies as well to classical knots and classical knot cobordisms. We give an alternate formulation for the Manturov definition [34] of Khovanov homology [25], [26] for virtual knots and links with arbitrary coefficients. This approach uses cut loci on the knot diagram to induce a conjugation operator in the Frobenius algebra. We use this to show that a large class of virtual knots with unit Jones polynomial is non-classical, proving a conjecture in [20] and [10]. We then discuss the implications of the maps induced in the aforementioned theory to the universal Frobenius algebra [27] for virtual knots. Next we show how one can apply the Karoubi envelope approach of Bar-Natan and Morrison [3] on abstract link diagrams [17] with cross cuts to construct the canonical generators of the Khovanov–Lee homology [30]. Using these canonical generators we derive a generalization of the Rasmussen invariant [39] for virtual knot cobordisms and generalize Rasmussen’s result on the slice genus for positive knots to the case of positive virtual knots. It should also be noted that this generalization of the Rasmussen invariant provides an easy to compute obstruction to knot cobordisms in Sg × I × I in the sense of Turaev [42].
Maximal tori in contactomorphism groups

Abstract I describe a general scheme which associates conjugacy classes of tori in the contactomorphism group to transverse almost complex structures on a compact contact manifold. Moreover, to tori of Reeb type whose Lie algebra contains a Reeb vector field one can associate a Sasaki cone. Thus, for contact structures D of K-contact type one obtains a configuration of Sasaki cones called a bouquet such that each Sasaki cone is associated with a conjugacy class of tori of Reeb type.
The minimum rank of a sign pattern matrix with a 1-separation

Abstract A sign pattern matrix is a matrix whose entries are from the set { + , − , 0 } . If A is an m × n sign pattern matrix, the qualitative class of A, denoted Q ( A ) , is the set of all real m × n matrices B = [ b i , j ] with b i , j positive (respectively, negative, zero) if a i , j is + (respectively, −, 0). The minimum rank of a sign pattern matrix A, denoted mr ( A ) , is the minimum of the ranks of the real matrices in Q ( A ) . Determination of the minimum rank of a sign pattern matrix is a longstanding open problem. For the case that the sign pattern matrix has a 1-separation, we present a formula to compute the minimum rank of a sign pattern matrix using the minimum ranks of certain generalized sign pattern matrices associated with the 1-separation.
Accurate Inference for Adaptive Linear Models

Estimators computed from adaptively collected data do not behave like their non-adaptive brethren. Rather, the sequential dependence of the collection policy can lead to severe distributional biases that persist even in the infinite data limit. We develop a general method — W-decorrelation — for transforming the bias of adaptive linear regression estimators into variance. The method uses only coarse-grained information about the data collection policy and does not need access to propensity scores or exact knowledge of the policy. We bound the finite-sample bias and variance of W-decorrelation and develop asymptotically correct confidence intervals based on a novel martingale central limit theorem. We then demonstrate the empirical benefits of the generic W-decorrelation procedure in two different adaptive data settings: the multi-armed bandit and the autoregressive time series settings.
On the limited communication analysis and design for decentralized estimation

This paper pertains to the analysis and design of decentralized estimation schemes that make use of limited communication. Briefly, these schemes equip the sensors with scalar states that iteratively merge the measurements and the state of other sensors to be used for state estimation. Contrarily to commonly used distributed estimation schemes, the only information being exchanged are scalars, there is only one common time-scale for communication and estimation, and the retrieval of the state of the system and sensors is achieved in finite-time. We extend previous work to a more general setup and provide necessary and sufficient conditions required for the communication between the sensors that enable the use of limited communication decentralized estimation schemes. Additionally, we discuss the cases where the sensors are memoryless, and where the sensors might not have the capacity to discern the contributions of other sensors. Based on these conditions and the fact that communication channels incur a cost, we cast the problem of finding the minimum cost communication graph that enables limited communication decentralized estimation schemes as an integer programming problem.
Analysis of Transmission Rate of Wireless Networks Under the Broadcast Approach With Continuum of Transmission Layers

In this letter, we characterize the performance of broadcast approach with continuum of transmission layers in random wireless networks where the channel state information (CSI) is assumed to be known only at the receiver. By modeling the transmitter-receiver pairs using bipolar Poisson point process, we derive analytical expressions for the mean and variance of achievable transmission rate and the network transmission capacity under broadcast approach. Our analysis shows that the broadcast approach provides better mean transmission rate with lower variance compared to outage strategy.
Shape dynamics of growing cell walls

We introduce a general theoretical framework to study the shape dynamics of actively growing and remodeling surfaces. Using this framework we develop a physical model for growing bacterial cell walls and study the interplay of cell shape with the dynamics of growth and constriction. The model allows us to derive constraints on cell wall mechanical energy based on the observed dynamics of cell shape. We predict that exponential growth in cell size requires a constant amount of cell wall energy to be dissipated per unit volume. We use the model to understand and contrast growth in bacteria with different shapes such as spherical, ellipsoidal, cylindrical and toroidal morphologies. Coupling growth to cell wall constriction, we predict a discontinuous shape transformation, from partial constriction to cell division, as a function of the chemical potential driving cell wall synthesis. Our model for cell wall energy and shape dynamics relates growth kinetics with cell geometry, and provides a unified framework to describe the interplay between shape, growth and division in bacterial cells.
Estimating tail probabilities of the ratio of the largest eigenvalue to the trace of a Wishart matrix

Abstract This paper develops an efficient Monte Carlo method to estimate the tail probabilities of the ratio of the largest eigenvalue to the trace of the Wishart matrix, which plays an important role in multivariate data analysis. The estimator is constructed based on a change-of-measure technique and it is proved to be asymptotically efficient for both the real and complex Wishart matrices. Simulation studies further show the improved performance of the proposed method over existing approaches based on asymptotic approximations, especially when estimating probabilities of rare events.
Identification of relevant subtypes via preweighted sparse clustering

Cluster analysis methods are used to identify homogeneous subgroups in a data set. In biomedical applications, one frequently applies cluster analysis in order to identify biologically interesting subgroups. In particular, one may wish to identify subgroups that are associated with a particular outcome of interest. Conventional clustering methods generally do not identify such subgroups, particularly when there are a large number of high-variance features in the data set. Conventional methods may identify clusters associated with these high-variance features when one wishes to obtain secondary clusters that are more interesting biologically or more strongly associated with a particular outcome of interest. A modification of sparse clustering can be used to identify such secondary clusters or clusters associated with an outcome of interest. This method correctly identifies such clusters of interest in several simulation scenarios. The method is also applied to a large prospective cohort study of temporomandibular disorders and a leukemia microarray data set.
Sample complexity of the distinct elements problem

We consider the distinct elements problem, where the goal is to estimate the number of distinct colors in an urn containing $ k $ balls based on $n$ samples drawn with replacements. Based on discrete polynomial approximation and interpolation, we propose an estimator with additive error guarantee that achieves the optimal sample complexity within $O(\log\log k)$ factors, and in fact within constant factors for most cases. The estimator can be computed in $O(n)$ time for an accurate estimation. The result also applies to sampling without replacement provided the sample size is a vanishing fraction of the urn size. One of the key auxiliary results is a sharp bound on the minimum singular values of a real rectangular Vandermonde matrix, which might be of independent interest.
The Higgs and WIMP DM Lamp Posts for New Weak Scale Physics: EFT Perspectives and the NMSSM

Abstract I will show, via effective field theory (EFT) techniques, that obtaining an observationally consistent relic density while evading stringent direct detection limits and maintaining h125 phenomenology in an extended Higgs sector can be easily achieved. I will then map such an EFT to the low energy limit of the NMSSM with the Higgsinos integrated out. Both the singlino and the singlet-like CP-odd and even scalars in the NMSSM may play a relevant role in such a scenario, while being difficult to probe via conventional searches. The singlet sector of the general NMSSM can be mapped on to a 2HDM+S, and I will discuss prospects of probing this at the LHC using signatures such as mono-Higgs and mono-Z. This proceeding is mostly based on Refs. [S. Baum, M. Carena, N.R. Shah, C.E.M. Wagner, Higgs portals for thermal Dark Matter. EFT perspectives and the NMSSM, JHEP 04 (2018) 069. arXiv:1712.09873 , doi: 10.1007/JHEP04(2018)069 ] and [S. Baum, N.R. Shah, Two Higgs Doublets and a Complex Singlet: Disentangling the Decay Topologies and Associated Phenomenology. arXiv:1808.02667 ].
Modular Representations and Branching Rules for Wreath Hecke Algebras

We introduce a generalization of degenerate affine Hecke algebra, called wreath Hecke algebra, associated with an arbitrary finite group G. The simple modules of the wreath Hecke algebra and of its associated cyclotomic algebras are classified over an algebraically closed field of any characteristic p ≥ 0. The modular branching rules for these algebras are obtained, and when p does not divide the order of G, they are further identified with crystal graphs of integrable modules for quantum affine algebras. The key is to establish an equivalence between a module category of the (cyclotomic) wreath Hecke algebra and its suitable counterpart for the degenerate affine Hecke algebra.
Correction and strengthening of “How large are the level sets of the Takagi function?”

The purpose of this note is to correct an error in an earlier paper by the author about the level sets of the Takagi function (Monatsh Math 167:311–331, 2012), and to prove a stronger form of one of the main results of that paper.
An Empirical Study of the Manipulability of Single Transferable Voting

Voting is a simple mechanism to combine together the preferences of multiple agents. Agents may try to manipulate the result of voting by mis-reporting their preferences. One barrier that might exist to such manipulation is computational complexity. In particular, it has been shown that it is NP-hard to compute how to manipulate a number of different voting rules. However, NP-hardness only bounds the worst-case complexity. Recent theoretical results suggest that manipulation may often be easy in practice. In this paper, we study empirically the manipulability of single transferable voting (STV) to determine if computational complexity is really a barrier to manipulation. STV was one of the first voting rules shown to be NP-hard. It also appears one of the harder voting rules to manipulate. We sample a number of distributions of votes including uniform and real world elections. In almost every election in our experiments, it was easy to compute how a single agent could manipulate the election or to prove that manipulation by a single agent was impossible.
Stirring two grains of sand

Consider two unit balls in a $d$-dimensional flat torus with edge length $r$, for $d\geq 2$. The balls do not move by themselves but they are pushed by a Brownian motion. The balls never intersect---they reflect if they touch. It is proved that the joint distribution of the processes representing the centers of the balls converges to the distribution of two independent Brownian motions when $r\to \infty$, assuming that we use a proper clock and proper scaling. The diffusion coefficient of the limit process depends on the dimension. The positions of the balls are asymptotically independent also in the following sense. The rescaled stationary distributions of the centers of the balls converge to the product of the stationary (hence uniform) distributions for each ball separately, as $r\to\infty$.
Bifurcations of edge states—topologically protected and non-protected—in continuous 2D honeycomb structures

Edge states are time-harmonic solutions to energy-conserving wave equations, which are propagating parallel to a line-defect or 'edge' and are localized transverse to it. This paper summarizes and extends the authors' work on the bifurcation of topologically protected edge states in continuous two-dimensional (2D) honeycomb structures. We consider a family of Schrodinger Hamiltonians consisting of a bulk honeycomb potential and a perturbing edge potential. The edge potential interpolates between two different periodic structures via a domain wall. We begin by reviewing our recent bifurcation theory of edge states for continuous 2D honeycomb structures (http://arxiv.org/abs/1506.06111). The topologically protected edge state bifurcation is seeded by the zero-energy eigenstate of a one-dimensional Dirac operator. We contrast these protected bifurcations with (more common) non-protected bifurcations from spectral band edges, which are induced by bound states of an effective Schrodinger operator. Numerical simulations for honeycomb structures of varying contrasts and 'rational edges' (zigzag, armchair and others), support the following scenario: (a) for low contrast, under a sign condition on a distinguished Fourier coefficient of the bulk honeycomb potential, there exist topologically protected edge states localized transverse to zigzag edges. Otherwise, and for general edges, we expect long lived edge quasi-modes which slowly leak energy into the bulk. (b) For an arbitrary rational edge, there is a threshold in the medium-contrast (depending on the choice of edge) above which there exist topologically protected edge states. In the special case of the armchair edge, there are two families of protected edge states; for each parallel quasimomentum (the quantum number associated with translation invariance) there are edge states which propagate in opposite directions along the armchair edge.
Inner functions on the bidisk and associated Hilbert spaces

Abstract Matrix valued inner functions on the bidisk have a number of natural subspaces of the Hardy space on the torus associated to them. We study their relationship to Agler decompositions, regularity up to the boundary, and restriction maps into one variable spaces. We give a complete description of the important spaces associated to matrix rational inner functions. The dimension of some of these spaces can be computed in a straightforward way, and this ends up having an application to the study of three variable rational inner functions. Examples are included to highlight the differences between the scalar and matrix cases.
Character varieties and actions on products of trees

It is well known that surface groups admit free and proper actions on finite products of infinite valence trees. In this note, we address the question of whether there can be a free and proper action on a finite product of bounded valence trees. We provide both some obstructions and an arithmetic criterion for existence. The bulk of the paper is devoted to an approach to verifying the arithmetic criterion which involves studying the character variety of certain surface groups over a field of positive characteristic. These methods may be useful for attempting to determine when groups admit good linear representations in other contexts.
Duality and socle generators for residual intersections

Paper has been accepted for publication in the Journal fur die reine und Angewandte Mathematik. This version contains the corrections and additional references made in the Galley proofs.
Aerial Vehicle Tracking by Adaptive Fusion of Hyperspectral Likelihood Maps

Hyperspectral cameras provide unique spectral signatures that can be used to solve surveillance tasks. This paper proposes a novel real-time hyperspectral likelihood maps-aided tracking method (HLT) inspired by an adaptive hyperspectral sensor. We focus on the target detection part of a tracking system and remove the necessity to build any offline classifiers and tune large amount of hyper-parameters, instead learning a generative target model in an online manner for hyperspectral channels ranging from visible to infrared wavelengths. The key idea is that our adaptive fusion method can combine likelihood maps from multiple bands of hyperspectral imagery into one single more distinctive representation increasing the margin between mean value of foreground and background pixels in the fused map. Experimental results show that the HLT not only outperforms all established fusion methods but is on par with the current state-of-the-art hyperspectral target tracking frameworks.
Weak containment rigidity for distal actions

Abstract We prove that if a measure distal action α of a countable group Γ is weakly contained in a strongly ergodic probability measure preserving action β of Γ, then α is a factor of β. In particular, this applies when α is a compact action. As a consequence, we show that the weak equivalence class of any strongly ergodic action completely remembers the weak isomorphism class of the maximal distal factor arising in the Furstenberg–Zimmer Structure Theorem.
A Stochastic View of Optimal Regret through Minimax Duality

We study the regret of optimal strategies for online convex optimization games. Using von Neumann's minimax theorem, we show that the optimal regret in this adversarial setting is closely related to the behavior of the empirical minimization algorithm in a stochastic process setting: it is equal to the maximum, over joint distributions of the adversary's action sequence, of the difference between a sum of minimal expected losses and the minimal empirical loss. We show that the optimal regret has a natural geometric interpretation, since it can be viewed as the gap in Jensen's inequality for a concave functional--the minimizer over the player's actions of expected loss--defined on a set of probability distributions. We use this expression to obtain upper and lower bounds on the regret of an optimal strategy for a variety of online learning problems. Our method provides upper bounds without the need to construct a learning algorithm; the lower bounds provide explicit optimal strategies for the adversary. Peter L. Bartlett, Alexander Rakhlin
EMBEDDED MODEL ERROR REPRESENTATION FOR BAYESIAN MODEL CALIBRATION

Model error estimation remains one of the key challenges in uncertainty quantification and predictive science. For computational models of complex physical systems, model error, also known as structural error or model inadequacy, is often the largest contributor to the overall predictive uncertainty. This work builds on a recently developed framework of embedded, internal model correction, in order to represent and quantify structural errors, together with model parameters, within a Bayesian inference context. We focus specifically on a Polynomial Chaos representation with additive modification of existing model parameters, enabling a non-intrusive procedure for efficient approximate likelihood construction, model error estimation, and disambiguation of model and data errors' contributions to predictive uncertainty. The framework is demonstrated on several synthetic examples, as well as on a chemical ignition problem.
Coinvariant algebras and fake degrees for spin Weyl groups of exceptional type

Abstract We compute all the spin fake degrees for the exceptional Weyl groups, which are by definition the graded multiplicities of the simple modules of a spin Weyl group in its spin coinvariant algebra. The spin fake degrees are all shown to be palindromic polynomials.
Quadratic twists of elliptic curves with small Selmer rank

Given an elliptic curve E over the rational with no rational 2-torsion points, we prove the existence of a quadratic twist of E for which the 2-Selmer rank is less than or equal to 1. By the author's earlier result, we establish a lower bound on the number of D's for which the twists E(D) have 2-Selmer rank <= 1. We include in the introduction our (brief) opinion about why it is supposed to be hard to push our technique to make the Selmer group trivial.
A New Functional-Logic Compiler for Curry: Sprite

We introduce a new native code compiler for Curry codenamed Sprite. Sprite is based on the Fair Scheme, a compilation strategy that provides instructions for transforming declarative, non-deterministic programs of a certain class into imperative, deterministic code. We outline salient features of Sprite, discuss its implementation of Curry programs, and present benchmarking results. Sprite is the first-to-date operationally complete implementation of Curry. Preliminary results show that ensuring this property does not incur a significant penalty.
Impact of contingent payments on systemic risk in financial networks

In this paper we study the implications of contingent payments on the clearing wealth in a network model of financial contagion. We consider an extension of the Eisenberg–Noe financial contagion model in which the nominal interbank obligations depend on the wealth of the firms in the network. We first consider the problem in a static framework and develop conditions for existence and uniqueness of solutions as long as no firm is speculating on the failure of other firms. In order to achieve existence and uniqueness under more general conditions, we introduce a dynamic framework. We demonstrate how this dynamic framework can be applied to problems that were ill-defined in the static framework.