cssi/SciSciGPT-SciSciNet huggingface dataset:
Toxoplasma gondii AP2IX-4 Regulates Gene Expression during Bradyzoite Development

Toxoplasma gondii is a protozoan parasite of great importance to human and animal health. In the host, this obligate intracellular parasite persists as a tissue cyst that is imperceptible to the immune response and unaffected by current therapies. The tissue cysts facilitate transmission through predation and give rise to chronic cycles of toxoplasmosis in immunocompromised patients. Transcriptional changes accompany conversion of the rapidly replicating tachyzoites into the encysted bradyzoites, and yet the mechanisms underlying these alterations in gene expression are not well defined. Here we show that AP2IX-4 is a nuclear protein exclusively expressed in tachyzoites and bradyzoites undergoing division. Knockout of AP2IX-4 had no discernible effect on tachyzoite replication but resulted in a reduced frequency of tissue cyst formation following alkaline stress induction-a defect that is reversible by complementation. AP2IX-4 has a complex role in regulating bradyzoite gene expression, as the levels of many bradyzoite mRNAs dramatically increased beyond those seen under conditions of normal stress induction in AP2IX-4 knockout parasites exposed to alkaline media. The loss of AP2IX-4 also resulted in a modest virulence defect and reduced cyst burden in chronically infected mice, which was reversed by complementation. These findings illustrate that the transcriptional mechanisms responsible for tissue cyst development operate across the intermediate life cycle from the dividing tachyzoite to the dormant bradyzoite. IMPORTANCEToxoplasma gondii is a single-celled parasite that persists in its host as a transmissible tissue cyst. How the parasite converts from its replicative form to the bradyzoites housed in tissue cysts is not well understood, but the process clearly involves changes in gene expression. Here we report that parasites lacking a cell cycle-regulated transcription factor called AP2IX-4 display reduced frequencies of tissue cyst formation in culture and in a mouse model of infection. Parasites missing AP2IX-4 lose the ability to regulate bradyzoite genes during tissue cyst development. Expressed in developing bradyzoites still undergoing division, AP2IX-4 may serve as a useful marker in the study of transitional forms of the parasite.
Sex-biased transcriptomic response of the reproductive axis to stress.

Abstract Stress is a well-known cause of reproductive dysfunction in many species, including birds, rodents, and humans, though males and females may respond differently. A powerful way to investigate how stress affects reproduction is by examining its effects on a biological system essential for regulating reproduction, the hypothalamic-pituitary-gonadal (HPG) axis. Often this is done by observing how a stressor affects the amount of glucocorticoids, such as cortisol or corticosterone, circulating in the blood and their relationship with a handful of known HPG-producing reproductive hormones, like testosterone and estradiol. Until now, we have lacked a full understanding of how stress affects all genomic activity of the HPG axis and how this might differ between the sexes. We leveraged a highly replicated and sex-balanced experimental approach to test how male and female rock doves (Columba livia) respond to restraint stress at the level of their transcriptome. Females exhibit increased genomic responsiveness to stress at all levels of their HPG axis as compared to males, and these responsive genes are mostly unique to females. Reasons for this may be due to fluctuations in the female endocrine environment over the reproductive cycle and/or their evolutionary history, including parental investment and the potential for maternal effects. Direct links between genome to phenome cause and effect cannot be ascertained at this stage; however, the data we report provide a vital genomic foundation on which sex-specific reproductive dysfunction and adaptation in the face of stress can be further experimentally studied, as well as novel gene targets for genetic intervention and therapy investigations.
Structure/Enantioselectivity Study of the Asymmetric Addition of Trimethylsilylcyanide to Benzaldehyde Catalyzed by Ti(IV)−Schiff Base Complexes

In the presence of titanium tetraisopropoxide, tridentate salen ligands derived from cis-1-amino-2-indanol have been utilized in the asymmetric addition of trimethylsilylcyanide to benzaldehyde, which gave the cyanohydrins in up to 85% ee. We have examined the reaction of titanium tetraisopropoxide with these salen ligands by NMR spectrometry and X-ray crystallography. Reaction of ligands derived from salicylaldehydes with bulky substituents in the 3-position with titanium tetraisopropoxide gave the L*Ti(O-i-Pr)2 complexes, which are the proposed precatalysts in the asymmetric addition reaction. These ligands give good to very good enantioselectivity in the asymmetric trimethylsilylcyanation reaction. However, with groups smaller than tert-butyl in the 3-position, substantial amounts (up to 73%) of the catalytically inactive L2*Ti species are formed, resulting in large drops in the ee's of the cyanohydrins. The L2*Ti species were formed as mixtures of diastereomers, one of which has been characterized by ...
TalkSumm: A Dataset and Scalable Annotation Method for Scientific Paper Summarization Based on Conference Talks.

Currently, no large-scale training data is available for the task of scientific paper summarization. In this paper, we propose a novel method that automatically generates summaries for scientific papers, by utilizing videos of talks at scientific conferences. We hypothesize that such talks constitute a coherent and concise description of the papers’ content, and can form the basis for good summaries. We collected 1716 papers and their corresponding videos, and created a dataset of paper summaries. A model trained on this dataset achieves similar performance as models trained on a dataset of summaries created manually. In addition, we validated the quality of our summaries by human experts.
Alternate Syntheses Of Pyrromethanes And Porphyrins Using Acid-Modified Montmorillonite K-10 Clay

Abstract A variety of porphyrins and pyrromethanes are prepared using Montmorillonite clay mixed with a variety of acids (p-TsOH, BF3 Et2O).The ease of use of the naturally occurring clay as a co-catalyst makes it an attractive reagent for use in synthesis.
New cycloaddition/fragmentation strategies for preparing 5-7-5 and 5-7-6 fused tricyclic ring systems

Abstract Tethering additional functionality to cyclobutadienyl iron tricarbonyl complexes provides new opportunities for the rapid construction of medium-ring-containing polycyclic compounds. Specifically, an intramolecular cycloaddition between cyclobutadiene and a tethered olefin, followed by an intramolecular cyclopropanation of the resulting cyclobutene-containing adduct generates highly strained pentacyclic intermediates. These compounds can then be relaxed thermally to generate 5-7-5 and 5-7-6 fused tricyclic ring systems that are shared with numerous natural products.
Inferring Tumor Evolution from Longitudinal Samples.

Background: Determining the clonal composition and somatic evolution of a tumor greatly aids in accurate prognosis and effective treatment for cancer. In order to understand how a tumor evolves over time and/or in response to treatment, multiple recent studies have performed longitudinal DNA sequencing of tumor samples from the same patient at several different time points. However, none of the existing algorithms that infer clonal composition and phylogeny using several bulk tumor samples from the same patient integrate the information that these samples were obtained from longitudinal observations. Results: We introduce a model for a longitudinally-observed phylogeny and derive constraints that longitudinal samples impose on the reconstruction of a phylogeny from bulk samples. These constraints form the basis for a new algorithm, Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction (CALDER), which infers phylogenetic trees from longitudinal bulk DNA sequencing data. We show on simulated data that constraints from longitudinal sampling can substantially reduce ambiguity when deriving a phylogeny from multiple bulk tumor samples, each a mixture of tumor clones. On real data, where there is often considerable uncertainty in the clonal composition of a sample, longitudinal constraints yield more parsimonious phylogenies with fewer tumor clones per sample. We demonstrate that CALDER reconstructs more plausible phylogenies than existing methods on two longitudinal DNA sequencing datasets from chronic lymphocytic leukemia patients. These findings show the advantages of directly incorporating temporal information from longitudinal sampling into tumor evolution studies. Availability: CALDER is available at https://github.com/raphael-group.
Fine-scale temporal analysis of genotype-dependent mortality at settlement in the Pacific oyster Crassostrea gigas

Abstract Settlement and metamorphosis mark a critical transition in the life cycle of marine invertebrates, during which substantial mortality occurs in both field and laboratory settings. Previous pair-crossing experiments with the Pacific oyster Crassostrea gigas have revealed significant selective or genotype-dependent mortality around the metamorphic transition, but the fine-scale nature and timing of this mortality is not known, particularly whether it occurs before, during or after metamorphosis. In this laboratory study, microsatellite marker segregation ratios were followed daily throughout the settlement and metamorphosis of an F 2 cross of the Pacific oyster to examine the fine-scale patterns of genotype dependent mortality at this transition and whether settlement timing (early vs. late) might be under genetic control and affect inference of genotype dependent mortality. Settlement occurred over nine days (day 18 to day 27 post-fertilization) with 68% of individuals settling either early (day 19) or late (day 24). Tracking the survival of spat for 40 days after initial settlement revealed almost no mortality and thus no appreciable genetic mortality. Temporal genetic analysis revealed that 3/11 loci exhibited genotype dependent mortality around the metamorphic transition, one of which (Cg205) was followed throughout settlement and metamorphosis. Alternative temporal patterns of strong selection against each homozygous genotype at Cg205 revealed possible defects in both the competency pathway (inability to initiate metamorphosis) and the morphogenesis pathway (mortality during the metamorphic transition). Quantitative trait locus (QTL) mapping of settlement timing identified three individual and one epistatic QTL with significant genetic effects on this trait (29% of the variance explained in total); however, two of these loci were linked to markers exhibiting selective mortality at metamorphosis, potentially confounding their apparent association with settlement timing. Overall, the results of this study highlight the complex nature of mortality and behavior during settlement and metamorphosis in oysters and suggest that endogenous sources of mortality at settlement may play an important role in the recruitment dynamics of oysters and possibly other broadcast spawning marine invertebrates.
Open-source food: Nutrition, toxicology, and availability of wild edible greens in the East Bay.

Author(s): Stark, Philip B; Miller, Daphne; Carlson, Thomas J; de Vasquez, Kristen Rasmussen | Abstract: Significance Foraged leafy greens are consumed around the globe, including in urban areas, and may play a larger role when food is scarce or expensive. It is thus important to assess the safety and nutritional value of wild greens foraged in urban environments. Methods Field observations, soil tests, and nutritional and toxicology tests on plant tissue were conducted for three sites, each roughly 9 square blocks, in disadvantaged neighborhoods in the East San Francisco Bay Area in 2014–2015. The sites included mixed-use areas and areas with high vehicle traffic. Results Edible wild greens were abundant, even during record droughts. Soil at some survey sites had elevated concentrations of lead and cadmium, but tissue tests suggest that rinsed greens of the tested species are safe to eat. Daily consumption of standard servings comprise less than the EPA reference doses of lead, cadmium, and other heavy metals. Pesticides, glyphosate, and PCBs were below detection limits. The nutrient density of 6 abundant species compared favorably to that of the most nutritious domesticated leafy greens. Conclusions Wild edible greens harvested in industrial, mixed-use, and high-traffic urban areas in the San Francisco East Bay area are abundant and highly nutritious. Even grown in soils with elevated levels of heavy metals, tested species were safe to eat after rinsing in tap water. This does not mean that all edible greens growing in contaminated soil are safe to eat—tests on more species, in more locations, and over a broader range of soil chemistry are needed to determine what is generally safe and what is not. But it does suggest that wild greens could contribute to nutrition, food security, and sustainability in urban ecosystems. Current laws, regulations, and public-health guidance that forbid or discourage foraging on public lands, including urban areas, should be revisited.
Synthesis of trans‐dihydrodiol derivatives of phenanthro[3,4‐b]‐thiophene and phenanthro[4,3‐b]thiophene

The present study describes the synthesis of phenanthro[3,4-b]thiophene (3), phenanthro[4,3-b]thiophene (4) and its potential dihydrodiol metabolites, trans-6,7-dihydroxy-6,7-dihydrophenanthro[3,4-b]thiophene (5) and trans-8,9-dihydroxy-8,9-dihydrophenanthro[3,4-b]thiophene (6), trans–6,7-dihydroxy-6,7-dihydro-phenanthro[4,3-b]thiophene (7) and trans-8,9-dihydroxy-8,9-dihydrophenanthro[4,3-b]thiophene (8) from Suzuki coupled intermediates. The UV spectra of these dihydrodiols are presented. These spectra are useful tools for identifying these dihydrodiols among unknown metabolites of 1 and 2 produced in vitro or in vivo.
Kinpute: using identity by descent to improve genotype imputation.

Motivation Genotype imputation, though generally accurate, often results in many genotypes being poorly imputed, particularly in studies where the individuals are not well represented by standard reference panels. When individuals in the study share regions of the genome identical by descent (IBD), it is possible to use this information in combination with a study-specific reference panel (SSRP) to improve the imputation results. Kinpute uses IBD information-due to recent, familial relatedness or distant, unknown ancestors-in conjunction with the output from linkage disequilibrium (LD) based imputation methods to compute more accurate genotype probabilities. Kinpute uses a novel method for IBD imputation, which works even in the absence of a pedigree, and results in substantially improved imputation quality. Results Given initial estimates of average IBD between subjects in the study sample, Kinpute uses a novel algorithm to select an optimal set of individuals to sequence and use as an SSRP. Kinpute is designed to use as input both this SSRP and the genotype probabilities output from other LD-based imputation software, and uses a new method to combine the LD imputed genotype probabilities with IBD configurations to substantially improve imputation. We tested Kinpute on a human population isolate where 98 individuals have been sequenced. In half of this sample, whose sequence data was masked, we used Impute2 to perform LD-based imputation and Kinpute was used to obtain higher accuracy genotype probabilities. Measures of imputation accuracy improved significantly, particularly for those genotypes that Impute2 imputed with low certainty. Availability and implementation Kinpute is an open-source and freely available C++ software package that can be downloaded from. Supplementary information Supplementary data are available at Bioinformatics online.
Dileptons in high-energy heavy-ion collisions

The current status of our understanding of dilepton production in ultra-relativistic heavyion collisions is discussed with special emphasis on signals from the (approach towards) chirally restored and deconfined phases. In particular, recent results of the CERN-SPS low-energy runs are compared to model predictions and interpreted. Prospects for RHIC experiments are given.
Highly active palladium catalysts supported by bulky proazaphosphatrane ligands for Stille cross-coupling: coupling of aryl and vinyl chlorides, room temperature coupling of aryl bromides, coupling of aryl triflates, and synthesis of sterically hindered biaryls.

A family of proazaphosphatrane ligands [P(RNCH2CH2)2N(R‘NCH2CH2): R = R‘ = i-Bu, 1; R = Bz, R‘ = i-Bu, 3; R = R‘ = Bz, 4] for palladium-catalyzed Stille reactions of aryl chlorides is described. Catalysts derived from ligands 1 and 4 efficiently catalyze the coupling of electronically diverse aryl chlorides with an array of organotin reagents. The catalyst system based on the ligand 3 is active for the synthesis of sterically hindered biaryls (di-, tri-, and tetra-ortho substituted). The use of ligand 4 allows room-temperature coupling of aryl bromides and it also permits aryl triflates and vinyl chlorides to participate in Stille coupling.
Preparation and Spectroscopic Characterization of [Pt(en)2I2][Pt(CN)4]: A New Quasi-One-Dimensional Mixed Valence Chain Material in a Completely Ordered Lattice

The unique linear chain compound [Pt(en){sub 2}I{sub 2}][Pt(CN){sub 4}] {l{underscore}brace}where en = ethylenediamine{r{underscore}brace} has been synthesized through a standard method. The results of a structural analysis by X-ray crystallography reveal this new MX compound to be quasi-one-dimensional with complete chain-to-chain registry to give a completely ordered structure. The results of resonance Raman, IR, diffuse reflectance, and X-ray crystallography reveal that the Pt centers are highly charge disproportionated with a large commensurate distortion of the iodide sublattice about the Pt center of higher charge. These results reveal that this material is the strongest CDW MX compound, containing iodide bridges, reported to date. Resonance Raman experiments have shown that five A{sub g} (C{sub 2h} site symmetry) Raman bands are strongly enhanced. These correspond to three in-chain Pt-I modes and two (chain perpendicular) CN stretches and are interpreted in terms of strong phonon coupling to the IVCT band.
Recent advances in zeolite science based on advance characterization techniques

Abstract This short review summarizes recent research highlights that manifest the progress that is currently experienced in the field of zeolite synthesis, characterization and catalysis as reported in the period of January 2012 to June, 2013 and with emphasis in the application and development of advanced characterization techniques. The review is divided into three sections that focus on New Materials Synthesis, Advances in Characterization and Catalysis.
Samarium Metal in Organic Synthesis

Recently organolanthanides have been widely employed as useful reagents in organic synthesis. Since the pioneering studies by Kagan and his co-workers demonstrated the effectiveness of samarium diiodide as a strong one-electron transfer reducing agent, the utility of this reagent in organic synthesis has been dramatically documented. There is increasing attention to performing synthetic transformation by direct reaction of metals. This represents an advantageous approach that avoids the use of sensitive and expensive organometallic compounds. For example, we have demonstrated the direct use of samarium metal in organic synthesis in recent publications. Parallel to our research, several other groups also have demonstrated new chemistry by samarium-induced reactions. This review is focused on the application of samarium-induced organic reactions. The advantages of using samarium metal in terms of reactivity, yield of the products, and selectivity in several organic transformations are discussed. Special attention is paid to the chemistry developed in our laboratory. A suggestion of reactive intermediates is also presented. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)
Preparation of 3-aryl-substituted salicylaldehydes via Suzuki coupling

Abstract An efficient method for the preparation of 3-arylsalicylaldehydes by palladium-catalyzed cross-coupling reaction of arylboronic acids and 3-bromo-5-tert-butylsalicylaldehyde is described. Parallel catalyst screening allowed rapid optimization of the reaction conditions.
Optimal Pricing in Markets with Non-Convex Costs

We consider a market run by an operator who seeks to satisfy a given consumer demand for a commodity by purchasing the needed amount from a group of competing suppliers with non-convex cost functions. The operator knows the suppliers' cost functions and announces a price/payment function for each supplier, which determines the payment to that supplier for producing different quantities. Each supplier then makes an individual decision about how much to produce (and whether to participate at all), in order to maximize its own profit. The key question is how to design the price functions. This problem is relevant for many applications, including electricity markets. The main contribution of this paper is the introduction of a new pricing scheme, \name (\acr ) pricing, which is applicable to general non-convex costs, allows using general parametric price functions, and guarantees market clearing, revenue adequacy, and ecomonic efficiency while supporting comptitive euqilibrium. The name of this scheme stems from the fact that we directly impose all the equilibrium conditions as constraints in the optimization problem for finding the best allocations, as opposed to adjusting the prices later to make the allocations an equilibrium. While the optimization problem is, of course, non-convex, and non-convex problems are intractable in general, we present a tractable approximation algorithm for solving the proposed optimization problem. Our framework extends to the case of networked markets, which, to the best of our knowledge, has not been considered in previous work.
Structural periodicity in plutonium(IV) sulfates.

The chemistry of tetravalent Pu with sulfate is explored in a series of single-crystal X-ray diffraction studies of the alkali metal plutonium sulfate compounds. Five new structures of Pu(IV) sulfa...
Constant-Error Pseudorandomness Proofs from Hardness Require Majority

Research in the 1980s and 1990s showed how to construct a pseudorandom generator from a function that is hard to compute on more than 99% of the inputs. A more recent line of works showed, however, that if the generator has small error, then the proof of correctness cannot be implemented in subclasses of TC0, and hence the construction cannot be applied to the known hardness results. This article considers a typical class of pseudorandom generator constructions, and proves an analogous result for the case of large error.
What About the Five-Membered Ring? Cyclopenta-fused Polycyclic Aromatic Hydrocarbons as a Building Block for Functional Materials

There has been recent interest in creating new functional materials based on cyclopenta-fused polycyclic aromatic hydrocarbons (CP-PAH) that can be integrated into organic electronic devices. These five-membered-ring-containing materials are appealing because the electronic properties that are associated with their nonalternate PAH ring structure are not typically accessible by alternate PAH composed solely of six-membered rings. This paper highlights some recent synthetic advances for new CP-PAH systems and describes work from our lab that we believe has helped advance the methodology to create new CP-PAH-containing small molecules and polymeric materials.
A New Application of Dimethyl Trithiocarbonate. Methylthiothiocarbonylation of 2,4-Pentanedione and Some β-Oxoesters

Abstract 2,4-Pentanedione, ethyl acetoacetate, benzoyl acetate and diethyl malonate 1a-d react with sodium acetate and dimethyl trithiocarbonate in dimethylformamide to afford methyl-β,β′-dicarbonyldithiocarboxylate derivatives 2a-d in moderate yield.
Temporal evolution of cortical ensembles promoting remote memory retrieval

Memories of fearful events can last a lifetime. The prelimbic (PL) cortex, a subregion of prefrontal cortex, plays a critical role in fear memory retrieval over time. Most studies have focused on acquisition, consolidation, and retrieval of recent memories, but much less is known about the neural mechanisms of remote memory. Using a new knock-in mouse for activity-dependent genetic labeling (TRAP2), we demonstrate that neuronal ensembles in the PL cortex are dynamic. PL neurons TRAPed during later memory retrievals are more likely to be reactivated and make larger behavioral contributions to remote memory retrieval compared to those TRAPed during learning or early memory retrieval. PL activity during learning is required to initiate this time-dependent reorganization in PL ensembles underlying memory retrieval. Finally, while neurons TRAPed during earlier and later retrievals have similar broad projections throughout the brain, PL neurons TRAPed later have a stronger functional recruitment of cortical targets.
Synthesis and Thermodynamics of Porous Metal Oxide Nanomaterials

Porous metal oxide nanoparticles is a new class of material of great scientific and technological importance with a wide range of applications. In this article, we briefly review the synthetic methods and thermodynamic properties of such materials. We compare and summarize common synthetic routes of such materials including solid-state, solution- phase (co-precipitation, sol-gel, microemulsion, solvothermal/hydrothermal, non-aqueous), and vapor-phase methods. As for the thermodynamics of porous metal oxide nanoparticles, we review experimental determinations, mainly by calorime- try, on surface and interfaces energetics. The interplay among particle size, surface area, morphology, surface stabilizer, phase stability, and redox potentials is discussed.
Analysis of Copy Number Variants on Chromosome 21 in Down Syndrome-Associated Congenital Heart Defects

One in five people with Down syndrome (DS) are born with an atrioventricular septal defect (AVSD), an incidence 2000 times higher than in the euploid population. The genetic loci that contribute to this risk are poorly understood. In this study, we tested two hypotheses: (1) individuals with DS carrying chromosome 21 copy number variants (CNVs) that interrupt exons may be protected from AVSD, because these CNVs return AVSD susceptibility loci back to disomy, and (2) individuals with DS carrying chromosome 21 genes spanned by microduplications are at greater risk for AVSD because these microduplications boost the dosage of AVSD susceptibility loci beyond a tolerable threshold. We tested 198 case individuals with DS+AVSD, and 211 control individuals with DS and a normal heart, using a custom microarray with dense probes tiled on chromosome 21 for array CGH (aCGH). We found that neither an individual chromosome 21 CNV nor any individual gene intersected by a CNV was associated with AVSD in DS. Burden analyses revealed that African American controls had more bases covered by rare deletions than did African American cases. Inversely, we found that Caucasian cases had more genes intersected by rare duplications than did Caucasian controls. We also showed that previously DS+AVSD (DS and a complete AVSD)-associated common CNVs on chromosome 21 failed to replicate. This research adds to the swell of evidence indicating that DS-associated AVSD is similarly heterogeneous, as is AVSD in the euploid population.
Low-Background Acyl-Biotinyl Exchange Largely Eliminates the Coisolation of Non- S-Acylated Proteins and Enables Deep S-Acylproteomic Analysis

Protein S-acylation (also called palmitoylation) is a common post-translational modification whose deregulation plays a key role in the pathogenesis of many diseases. Acyl-biotinyl exchange (ABE), ...
Two Accessory Proteins Govern MmpL3 Mycolic Acid Transport in Mycobacteria

Mycolic acids are the signature lipid of mycobacteria and constitute an important physical component of the cell wall, a target of mycobacterium-specific antibiotics and a mediator of Mycobacterium tuberculosis pathogenesis. Mycolic acids are synthesized in the cytoplasm and are thought to be transported to the cell wall as a trehalose ester by the MmpL3 transporter, an antibiotic target for M. tuberculosis However, the mechanism by which mycolate synthesis is coupled to transport, and the full MmpL3 transport machinery, is unknown. Here, we identify two new components of the MmpL3 transport machinery in mycobacteria. The protein encoded by MSMEG_0736/Rv0383c is essential for growth of Mycobacterium smegmatis and M. tuberculosis and is anchored to the cytoplasmic membrane, physically interacts with and colocalizes with MmpL3 in growing cells, and is required for trehalose monomycolate (TMM) transport to the cell wall. In light of these findings, we propose MSMEG_0736/Rv0383c be named "TMM transport factor A", TtfA. The protein encoded by MSMEG_5308 also interacts with the MmpL3 complex but is nonessential for growth or TMM transport. However, MSMEG_5308 accumulates with inhibition of MmpL3-mediated TMM transport and stabilizes the MmpL3/TtfA complex, indicating that it may stabilize the transport system during stress. These studies identify two new components of the mycobacterial mycolate transport machinery, an emerging antibiotic target in M. tuberculosis IMPORTANCE The cell envelope of Mycobacterium tuberculosis, the bacterium that causes the disease tuberculosis, is a complex structure composed of abundant lipids and glycolipids, including the signature lipid of these bacteria, mycolic acids. In this study, we identified two new components of the transport machinery that constructs this complex cell wall. These two accessory proteins are in a complex with the MmpL3 transporter. One of these proteins, TtfA, is required for mycolic acid transport and cell viability, whereas the other stabilizes the MmpL3 complex. These studies identify two new components of the essential cell envelope biosynthetic machinery in mycobacteria.
On the Weil–Petersson Curvature of the Moduli Space of Riemann Surfaces of Large Genus

Let $S_g$ be a closed surface of genus $g$ and $\mathbb{M}_g$ be the moduli space of $S_g$ endowed with the Weil-Petersson metric. In this paper we investigate the Weil-Petersson curvatures of $\mathbb{M}_g$ for large genus $g$. First, we study the asymptotic behavior of the extremal Weil-Petersson holomorphic sectional curvatures at certain thick surfaces in $\mathbb{M}_g$ as $g \to \infty$. Then we prove two curvature properties on the whole space $\mathbb{M}_g$ as $g\to \infty$ in a probabilistic way.
On the first solution of a long standing problem: Uniqueness of the phaseless quantum inverse scattering problem in 3-d

Abstract After publishing his recent paper in SIAM J. Appl. Math. 74, 392–410, 2014 the author has realized that actually he has addressed in that paper, for the first time, a long standing open question being unaware about this. This question is about the uniqueness of a 3-d inverse scattering problem without the phase information. Thus, it makes sense in the current paper to explicitly make the latter statement and to formulate corresponding uniqueness theorems.
Coordinated AC/DC microgrid optimal scheduling

This paper proposes a coordinated optimal scheduling model for hybrid AC/DC microgrids. The objective of the proposed model is to minimize the total microgrid operation cost when considering interactions between AC and DC subsystems of the microgrid network. Nonlinear power flow equations for AC and DC networks have been linearized through a proposed model to enable formulating the problem by mixed integer linear programming (MILP) which expedites the solution process and ensures better solutions in terms of optimality. The proposed model is tested on the modified IEEE 33-bus test system. Numerical simulations exhibit the merits of the proposed coordinated AC/DC optimal scheduling model and further analyze its sensitivity to various decisive operational parameters.
Intersection numbers in the curve graph with a uniform constant

Abstract We derive various inequalities involving the intersection number of the curves contained in geodesics and tight geodesics in the curve graph. While there already exist such inequalities on tight geodesics, our method applies in the setting of geodesics. Furthermore, the method gives inequalities with a uniform constant depending only on the topology of the surface.
Level set estimation from compressive measurements using box constrained total variation regularization

Estimating the level set of a signal from measurements is a task that arises in a variety of fields, including medical imaging, astronomy, and digital elevation mapping. Motivated by scenarios where accurate and complete measurements of the signal may not available, we examine here a simple procedure for estimating the level set of a signal from highly incomplete measurements, which may additionally be corrupted by additive noise. The proposed procedure is based on box-constrained Total Variation (TV) regularization. We demonstrate the performance of our approach, relative to existing state-of-the-art techniques for level set estimation from compressive measurements, via several simulation examples.
Frozen Gaussian approximation for high frequency wave propagation in periodic media

Propagation of high-frequency wave in periodic media is a challenging problem due to the existence of multiscale characterized by short wavelength, small lattice constant and large physical domain size. Conventional computational methods lead to extremely expensive costs, especially in high dimensions. In this paper, based on Bloch decomposition and asymptotic analysis in the phase space, we derive the frozen Gaussian approximation for high-frequency wave propagation in periodic media and establish its converge to the true solution. The formulation leads to efficient numerical algorithms, which are presented in a companion paper [Delgadillo, Lu and Yang, arXiv:1509.05552].
When Does the Set of (a, b, c)-Core Partitions Have a Unique Maximal Element?

In 2007, Olsson and Stanton gave an explicit form for the largest $(a, b)$-core partition, for any relatively prime positive integers $a$ and $b$, and asked whether there exists an $(a, b)$-core that contains all other $(a, b)$-cores as subpartitions; this question was answered in the affirmative first by Vandehey and later by Fayers independently. In this paper we investigate a generalization of this question, which was originally posed by Fayers: for what triples of positive integers $(a, b, c)$ does there exist an $(a, b, c)$-core that contains all other $(a, b, c)$-cores as subpartitions? We completely answer this question when $a$, $b$, and $c$ are pairwise relatively prime; we then use this to generalize the result of Olsson and Stanton.
Found Graph Data and Planted Vertex Covers

A typical way in which network data is recorded is to measure all interactions involving a specified set of core nodes, which produces a graph containing this core together with a potentially larger set of fringe nodes that link to the core. Interactions between nodes in the fringe, however, are not present in the resulting graph data. For example, a phone service provider may only record calls in which at least one of the participants is a customer; this can include calls between a customer and a non-customer, but not between pairs of non-customers. Knowledge of which nodes belong to the core is crucial for interpreting the dataset, but this metadata is unavailable in many cases, either because it has been lost due to difficulties in data provenance, or because the network consists of "found data" obtained in settings such as counter-surveillance. This leads to an algorithmic problem of recovering the core set. Since the core is a vertex cover, we essentially have a planted vertex cover problem, but with an arbitrary underlying graph. We develop a framework for analyzing this planted vertex cover problem, based on the theory of fixed-parameter tractability, together with algorithms for recovering the core. Our algorithms are fast, simple to implement, and out-perform several baselines based on core-periphery structure on various real-world datasets.
Algorithms for strongly stable ideals

Strongly stable monomial ideals are important in algebraic geometry, commutative algebra, and combinatorics. Prompted, for example, by combinatorial approaches for studying Hilbert schemes and the existence of maximal total Betti numbers among saturated ideals with a given Hilbert polynomial, in this note we present three algorithms to produce all strongly stable ideals with certain prescribed properties: the saturated strongly stable ideals with a given Hilbert polynomial, the almost lexsegment ideals with a given Hilbert polynomial, and the saturated strongly stable ideals with a given Hilbert function. We also establish results for estimating the complexity of our algorithms.
Einstein solvmanifolds have maximal symmetry

All known examples of homogeneous Einstein metrics of negative Ricci curvature can be realized as left-invariant Riemannian metrics on solvable Lie groups. After defining a notion of maximal symmetry among left-invariant Riemannian metrics on a Lie group, we prove that any left-invariant Einstein metric of negative Ricci curvature on a solvable Lie group is maximally symmetric. This theorem is motivated both by the Alekseevskii Conjecture and by the question of stability of Einstein metrics under the Ricci flow. We also address questions of existence of maximally symmetric left-invariant Riemannian metrics more generally.
Monitoring in IOT enabled devices

---------------------------------------------------------------ABSTRACT-----------------------------------------------------------------As network size continues to grow exponentially, there has been a proportionate increase in the number of nodes in the corresponding network. With the advent of Internet of things (IOT), it is assumed that many more devices will be connected to the existing network infrastructure. As a result, monitoring is expected to get more complex for administrators as networks tend to become more heterogeneous. Moreover, the addressing for IOTs would be more complex given the scale at which devices will be added to the network and hence monitoring is bound to become an uphill task due to management of larger range of addresses. This paper will throw light on what kind of monitoring mechanisms can be deployed in internet of things (IOTs) and their overall effectiveness.
Refined comparison theorems for the Dirac equation in d dimensions

A single spin-$\frac{1}{2}$ particle obeys the Dirac equation in $d\ge 1$ spatial dimension and is bound by an attractive central monotone potential which vanishes at infinity (in one dimension the potential is even). This work refines the relativistic comparison theorems which were derived by Hall \cite{p75}. The new theorems allow the graphs of the two comparison potentials $V_a$ and $V_b$ to crossover in a controlled way and still imply the spectral ordering $E_a\le E_b$ for the eigenvalues at the bottom of each angular momentum subspace. More specifically in a simplest case we have: in dimension $d=1$, if $\int_0^x (V_b(t)-V_a(t)) dt\ge 0,\ x\in [0,\ \infty)$, then $E_a\le E_b$; and in $d>1$ dimensions, if $\int_0^r (V_b(t)-V_a(t))t^{2|k_d|} dt\ge 0,\ r\in [0,\ \infty)$, where $k_d=\tau\left(j+\frac{d-2}{2}\right)$ and $\tau=\pm 1$, then $E_a\le E_b$.
Hermitian Clifford analysis and its connections with representation theory

AbstractThis work reconsiders the holomorphic and anti-holomorphic Dirac operators of Hermitian Clifford analysis to determine whether or not they are the natural generalization of the orthogonal Dirac operator to spaces with complex structure. We argue the generalized gradient construction of Stein and Weiss based on representation theory of Lie groups is the natural way to construct such a Dirac-type operator because applied to a Riemannian spin manifold, it provides the Atiyah–Singer Dirac operator. This method, however, does not apply to these Hermitian Dirac operators because the representations of the unitary group used are not irreducible, causing problems in considering invariance under a group larger than U(n). This motivates either the development of Clifford analysis over a complex vector space with respect to a Hermitian inner product or the development of Dirac-type operators on Cauchy–Riemann structures.
Higher homotopy excision and Blakers–Massey theorems for structured ring spectra

Abstract Working in the context of symmetric spectra, we prove higher homotopy excision and higher Blakers–Massey theorems, and their duals, for algebras and left modules over operads in the category of modules over a commutative ring spectrum (e.g., structured ring spectra).
KEPLER ECLIPSING BINARIES WITH STELLAR COMPANIONS

Many short-period binary stars have distant orbiting companions that have played a role in driving the binary components into close separation. Indirect detection of a tertiary star is possible by measuring apparent changes in eclipse times of eclipsing binaries as the binary orbits the common center of mass. Here we present an analysis of the eclipse timings of 41 eclipsing binaries observed throughout the NASA Kepler mission of long duration and precise photometry. This subset of binaries is characterized by relatively deep and frequent eclipses of both stellar components. We present preliminary orbital elements for seven probable triple stars among this sample, and we discuss apparent period changes in seven additional eclipsing binaries that may be related to motion about a tertiary in a long period orbit. The results will be used in ongoing investigations of the spectra and light curves of these binaries for further evidence of the presence of third stars.
A Nested HDP for Hierarchical Topic Models

We develop a nested hierarchical Dirichlet process (nHDP) for hierarchical topic modeling. The nHDP is a generalization of the nested Chinese restaurant process (nCRP) that allows each word to follow its own path to a topic node according to a document-specific distribution on a shared tree. This alleviates the rigid, single-path formulation of the nCRP, allowing a document to more easily express thematic borrowings as a random effect. We demonstrate our algorithm on 1.8 million documents from The New York Times.1
Equivariant chromatic localizations and commutativity

In this paper, we study the extent to which Bousfield and finite localizations relative to a thick subcategory of equivariant finite spectra preserve various kinds of highly structured multiplications. Along the way, we describe some basic, useful results for analyzing categories of acyclics in equivariant spectra, and we show that Bousfield localization with respect to an ordinary spectrum (viewed as an equivariant spectrum with trivial action) always preserves equivariant commutative ring spectra.
Almost filling laminations and the connectivity of ending lamination space

We show that if S is a finite type orientable surface of negative Euler characteristic which is not the 3-holed sphere, 4-holed sphere or 1-holed torus, then the ending lamination space of S is connected, locally path connected and cyclic.
Preferential Affinity of Calcium Ions to Charged Phosphatidic Acid Surface from a Mixed Calcium/Barium Solution: X-ray Reflectivity and Fluorescence Studies

X-ray reflectivity and fluorescence near total reflection experiments were performed to examine the affinities of divalent ions (Ca2+ and Ba2+) from aqueous solution to a charged phosphatidic acid (PA) surface. A phospholipid (1,2-dimyristoyl-sn-glycero-3-phosphate, DMPA), spread as a monolayer at the air/water interface, was used to form and control the charge density at the interface. We find that, for solutions of the pure salts (i.e., CaCl2 and BaCl2), the number of bound ions per DMPA at the interface is saturated at concentrations that exceed 10−3 M. For 1:1 Ca2+/Ba2+ mixed solutions, we find that the bound Ca2+/Ba2+ ratio at the interface is 4:1. If the only property determining charge accumulation near PA were the ionic charges, the concentration of mixed Ca2+/Ba2+ at the interface would equal that of the bulk. Our results show a clear specific affinity of PA for Ca compared to Ba. We provide some discussion on this issue as well as some implications for biological systems. Although our results in...
A distributed one-step estimator

Distributed statistical inference has recently attracted enormous attention. Many existing work focuses on the averaging estimator, e.g., Zhang and Duchi (J Mach Learn Res 14:3321–3363, 2013) together with many others. We propose a one-step approach to enhance a simple-averaging based distributed estimator by utilizing a single Newton–Raphson updating. We derive the corresponding asymptotic properties of the newly proposed estimator. We find that the proposed one-step estimator enjoys the same asymptotic properties as the idealized centralized estimator. In particular, the asymptotic normality was established for the proposed estimator, while other competitors may not enjoy the same property. The proposed one-step approach merely requires one additional round of communication in relative to the averaging estimator; so the extra communication burden is insignificant. The proposed one-step approach leads to a lower upper bound of the mean squared error than other alternatives. In finite sample cases, numerical examples show that the proposed estimator outperforms the simple averaging estimator with a large margin in terms of the sample mean squared error. A potential application of the one-step approach is that one can use multiple machines to speed up large scale statistical inference with little compromise in the quality of estimators. The proposed method becomes more valuable when data can only be available at distributed machines with limited communication bandwidth.
Non-stochastic Best Arm Identification and Hyperparameter Optimization

Motivated by the task of hyperparameter optimization, we introduce the non-stochastic best-arm identification problem. Within the multi-armed bandit literature, the cumulative regret objective enjoys algorithms and analyses for both the non-stochastic and stochastic settings while to the best of our knowledge, the best-arm identification framework has only been considered in the stochastic setting. We introduce the non-stochastic setting under this framework, identify a known algorithm that is well-suited for this setting, and analyze its behavior. Next, by leveraging the iterative nature of standard machine learning algorithms, we cast hyperparameter optimization as an instance of non-stochastic best-arm identification, and empirically evaluate our proposed algorithm on this task. Our empirical results show that, by allocating more resources to promising hyperparameter settings, we typically achieve comparable test accuracies an order of magnitude faster than baseline methods.
On (Non)Supermodularity of Average Control Energy

Given a linear system, we consider the expected energy to move from the origin to a uniformly random point on the unit sphere as a function of the set of actuated variables. We prove that this function is not necessarily supermodular, correcting some claims in the existing literature.
Dispersive Behavior of an Energy-Conserving Discontinuous Galerkin Method for the One-Way Wave Equation

The dispersive behavior of the recently proposed energy-conserving discontinuous Galerkin (DG) method by Fu and Shu (Optimal energy-conserving discontinuous Galerkin methods for linear symmetric hyperbolic systems, 2018. arXiv:1804.10307 ) is analyzed and compared with the classical centered and upwinding DG schemes. It is shown that the new scheme gives a significant improvement over the classical centered and upwinding DG schemes in terms of dispersion error. Numerical results are presented to support the theoretical findings.