cssi/SciSciGPT-SciSciNet huggingface dataset:
A Computational Approach to Estimating Nondisjunction Frequency in Saccharomyces cerevisiae

Errors segregating homologous chromosomes during meiosis result in aneuploid gametes and are the largest contributing factor to birth defects and spontaneous abortions in humans. Saccharomyces cerevisiae has long served as a model organism for studying the gene network supporting normal chromosome segregation. Measuring homolog nondisjunction frequencies is laborious, and involves dissecting thousands of tetrads to detect missegregation of individually marked chromosomes. Here we describe a computational method (TetFit) to estimate the relative contributions of meiosis I nondisjunction and random-spore death to spore inviability in wild type and mutant strains. These values are based on finding the best-fit distribution of 4, 3, 2, 1, and 0 viable-spore tetrads to an observed distribution. Using TetFit, we found that meiosis I nondisjunction is an intrinsic component of spore inviability in wild-type strains. We show proof-of-principle that the calculated average meiosis I nondisjunction frequency determined by TetFit closely matches empirically determined values in mutant strains. Using these published data sets, TetFit uncovered two classes of mutants: Class A mutants skew toward increased nondisjunction death, and include those with known defects in establishing pairing, recombination, and/or synapsis of homologous chromosomes. Class B mutants skew toward random spore death, and include those with defects in sister-chromatid cohesion and centromere function. Epistasis analysis using TetFit is facilitated by the low numbers of tetrads (as few as 200) required to compare the contributions to spore death in different mutant backgrounds. TetFit analysis does not require any special strain construction, and can be applied to previously observed tetrad distributions.
The mechanical microenvironment regulates ovarian cancer cell morphology, migration, and spheroid disaggregation

There is growing appreciation of the importance of the mechanical properties of the tumor microenvironment on disease progression. However, the role of extracellular matrix (ECM) stiffness and cellular mechanotransduction in epithelial ovarian cancer (EOC) is largely unknown. Here, we investigated the effect of substrate rigidity on various aspects of SKOV3 human EOC cell morphology and migration. Young's modulus values of normal mouse peritoneum, a principal target tissue for EOC metastasis, were determined by atomic force microscopy (AFM) and hydrogels were fabricated to mimic these values. We find that cell spreading, focal adhesion formation, myosin light chain phosphorylation, and cellular traction forces all increase on stiffer matrices. Substrate rigidity also positively regulates random cell migration and, importantly, directional increases in matrix tension promote SKOV3 cell durotaxis. Matrix rigidity also promotes nuclear translocation of YAP1, an oncogenic transcription factor associated with aggressive metastatic EOC. Furthermore, disaggregation of multicellular EOC spheroids, a behavior associated with dissemination and metastasis, is enhanced by matrix stiffness through a mechanotransduction pathway involving ROCK, actomyosin contractility, and FAK. Finally, this pattern of mechanosensitivity is maintained in highly metastatic SKOV3ip.1 cells. These results establish that the mechanical properties of the tumor microenvironment may play a role in EOC metastasis.
Titanocene(III)-promoted Reformatsky additions.

A novel method for the promotion of Reformatsky-like reactions is presented. The technique employs titanocene(III) chloride as a mild and homogeneous single-electron reductant. The reactions are rapid, operationally simple, and compatible with a wide range of functionalities. These additions are also anti diastereoselective.
Signatures of an emergent gravity from black hole entropy

The existence of a thermodynamic description of horizons indicates that spacetime has a microstructure. While the “fundamental” degrees of freedom remain elusive, quantizing Einstein’s gravity provides some clues about their properties. A quantum AdS black hole possesses an equispaced mass spectrum, independent of Newton’s constant, G, when its horizon radius is large compared to the AdS length. Moreover, the black hole’s thermodynamics in this limit is inextricably connected with its thermodynamics in the opposite (Schwarzschild) limit by a duality of the Bose partition function. G, absent in the mass spectrum, reemerges in the thermodynamic description through the Schwarzschild limit, which should be viewed as a natural “ground state”. It seems that the Hawking-Page phase transition separates fundamental, “particle-like” degrees of freedom from effective, “geometric” ones.
Multifunctional CRISPR-Cas9 with engineered immunosilenced human T cell epitopes

The CRISPR-Cas9 system has raised hopes for developing personalized gene therapies for complex diseases. Its application for genetic and epigenetic therapies in humans raises concerns over immunogenicity of the bacterially derived Cas9 protein. Here we detect antibodies to Streptococcus pyogenes Cas9 (SpCas9) in at least 5% of 143 healthy individuals. We also report pre-existing human CD8+T cell immunity in the majority of healthy individuals screened. We identify two immunodominant SpCas9 T cell epitopes for HLA-A*02:01 using an enhanced prediction algorithm that incorporates T cell receptor contact residue hydrophobicity and HLA binding and evaluated them by T cell assays using healthy donor PBMCs. In a proof-of-principle study, we demonstrate that Cas9 protein can be modified to eliminate immunodominant epitopes through targeted mutation while preserving its function and specificity. Our study highlights the problem of pre-existing immunity against CRISPR-associated nucleases and offers a potential solution to mitigate the T cell immune response. Possible immunogenicity of the Cas9 protein raises concerns about therapeutic applications. Here the authors identify pre-existing CD8+T-cell immunity in healthy individuals and in response modify Cas9 to remove the immunodominant epitopes.
A new, mild synthesis of N-sulfonyl ketimines via the palladium-catalyzed isomerization of aziridines.

A new method for the synthesis of N-tosylketimines via the palladium-catalyzed isomerization of N-tosylaziridines is described. The mild reaction conditions tolerate the presence of a variety of functional groups including ketones, esters, and acetals. The reactions are believed to proceed via the oxidative addition of the aziridine to Pd(0) and represent the first examples of transformations involving Pd(0)-mediated oxidative additions of aziridines that do not proceed through allylpalladium intermediates.
Combinatorial Chemical Vapor Deposition of Metal Dioxides Using Anhydrous Metal Nitrates

Modification of a low-pressure CVD reactor and the similar deposition chemistries of Ti(NO3)4, Sn(NO3)4, and Hf(NO3)4 allowed the growth of films on silicon exhibiting a compositional spread of the...
Ni(cod)2/PCy3-Catalyzed Cross-Coupling Reactions of Dihaloarenes with Arylboronic Acids

The Ni(0)-catalyzed cross-coupling reactions of dihaloarenes with one equivalent of arylboronic acids is described. The Ni(cod)2/PCy3 was identified as the best catalyst system to achieve a double cross-coupling reaction, likely via an efficient preferential oxidative addition.
The syntheses and structures of iron carbonyl adducts of tricoordinated hypervalent phosphorus compounds

The hypervalent phosphorus compound 3,7-di-t-butyl-5-aza-2,8-dioxa-1-phosphabicyclo[3.3.0]octa-2,4,6-triene(ADPO), forms a monosubstituted adduct, ADPO·Fe(CO)4, by direct reaction of 10-P-3 ADPO with Fe2(CO)9 or Fe(CO)5, as well as by reaction of 1,1-dichloro-3,7-di-t-butyl-5-aza-2,8-dioxa-1-phosphabicyclo[3.3.0]octa-3, 6-diene(ADPO·Cl2) with Na2[Fe(CO)4]. The X-ray crystal structure of ADPO·Fe(CO)4 shows that ADPO is coordinated to the iron through the phosphorus. The phosphorus of the adduct has a tetrahedral 8-P-4 geometry in contrast to the planar T-shaped geometry of uncomplexed 10-P-3 ADPO. Ultraviolet photolysis of ADPO·Fe(CO)4 yields the disubstituted species (ADPO)2·e(CO)3 wherein ADPO has dimerized via P–O bond cleavage to form a bidentate (ADPO)2 ligand containing a 10-membered ring that bridges axial and equatorial positions at the trigonal bipyramidal iron center.
Theoretical Study of HmGaPHn. Characteristics of Gallium-Phosphorus Multiple Bonds

Equilibrium structures, harmonic vibrational frequencies, and relative energies of 12 neutral or ionic gallium phosphorus hydrides are reported and analyzed. Hartree−Fock (HF), Becke's three-parameter exchange with Lee, Yang, and Parr correlation DFT (B3LYP), and second-order Moller−Plesset (MP2) calculations using the 6-311++G(d,p) basis set were performed on all molecules. Gallium−phosphorus bond energies were determined based on the MP2/6-311++G(d,p) calculations of the equilibrium structures and of their decomposition products. We find that the gallium−phosphorus double bond is, perhaps, surprisingly strong (i.e., 93 ± 2 kcal/mol) and short (2.128 ± 0.018 A); CCSD(T)/6-311++G(3df,3dp) single-point calculations on HGaPH corroborate the prediction of a strong double bond. Bond order analysis of some of the neutral species revealed that these compounds satisfy a Pauling relation between bond length and bond order, and also bond energy and bond order. CASSCF(8|8) calculations on H2PGa show that the surpri...
Aziridine-allylsilane-mediated synthesis of exocyclic γ-amino olefins and azabicyclo[x.y.1]-systems

Abstract We have shown that connection of C -2 of an allylsilane to a tethered aziridine ring yields exocyclic γ-amino olefins and desilylated azabicyclo[ x .2.1]-systems upon cyclization with BF 3 ·OEt 2 . Furthermore, manipulation of a specific exocyclic γ-amino olefin provided access to an azabicyclo[3.3.1]nonane. This methodology should be useful for the preparation of natural products and pharmacologically active agents containing these bicyclic heterocyclic systems.
Synthesis of (±)-plakoridine A lactam

Abstract A stereocontrolled synthesis of plakoridine A lactam, a degradation product of the marine alkaloid plakoridine A, is described.
$W/Z$ properties and $V+$jets at the Tevatron

We present a summary of recent measurements of W and Z properties and W /Z production in association with jets in collisions at √s = 1.96 TeV with the CDF and DO detectors. Latest measurements of Z /γ * transverse momentum and are presented along with new measurements of the angular distributions of final state electrons from Drell Yan events as a way to probe Z boson production mechanisms. The mass dependence of the forward-backward asymmetry in → Z /γ* → e+ e− . interactions is measured, the effective weak mixing angle extracted, and the most precise direct measurement of the vector and axial-vector couplings of u and d quarks to the Z boson presented. New measurements of jets produced in association with Z and W bosons for inclusive, beauty and charm jets are also discussed.
Toward Collaborative Information Seeking (CIS)

It is natural for humans to collaborate while dealing with complex problems. In this article I consider this process of collaboration in the context of information seeking. The study and discussion presented here are driven by two dissatisfactions: (1) the majority of IR systems today do not facilitate collaboration directly, and (2) the concept of collaboration itself is not well-understood. I begin by probing the notion of collaboration and propose a model that helps us understand the requirements for a successful collaboration. A model of a Collaborative Information Seeking (CIS) environment is then rendered based on an extended model of information seeking.
Synthesis of substituted 1H‐pyrrolo[3,2‐c]quinolines

1H-2-Phenylpyrrolo[3,2-c]quinoline (1a) is made by thermal cyclization of quinol-4-yl hydrazone. Subsequent substitution of the C-3 hydrogen atom of the pyrrole ring of 1a with chlorine and a formyl group is easily achieved by reacting 1a with trichloroacetyl chloride and phosphorus oxychloride in DMF, respectively.
A computational model to understand mouse iron physiology and disease

It is well known that iron is an essential element for life but is toxic when in excess or in certain forms. Accordingly there are many diseases that result directly from either lack or excess of iron. Yet many molecular and physiological aspects of iron regulation have only been discovered recently and others are still elusive. There is still no good quantitative and dynamic description of iron absorption, distribution, storage and mobilization that agrees with the wide array of phenotypes presented in several iron-related diseases. The present work addresses this issue by developing a mathematical model of iron distribution in mice calibrated with ferrokinetic data and subsequently validated against data from mouse models of iron disorders, such as hemochromatosis, β-thalassemia, atransferrinemia and anemia of inflammation. To adequately fit the ferrokinetic data required inclusion of the following mechanisms: a) transferrin-mediated iron delivery to tissues, b) induction of hepcidin by transferrin-bound iron, c) ferroportin-dependent iron export regulated by hepcidin, d) erythropoietin regulation of erythropoiesis, and e) liver uptake of NTBI. The utility of the model to simulate disease interventions was demonstrated by using it to investigate the outcome of different schedules of transferrin treatment in β-thalassemia.
Synthesis of 4-Substituted Phthalazin-1(2H)-ones from 2-Acylbenzoic Acids: Controlling Hydrazine in a Pharmaceutical Intermediate through PAT-Guided Process Development

A simple one-pot, two-step process for the conversion of 2-acylbenzoic acids to phthalazin-1(2H)-ones was developed. A robust process was required that delivered the final isolated solid with consistently low levels of residual hydrazine, for further processing to the final drug substance. An in situ formed intermediate was critical to control reactivity and allowed for the controlled crystallization that prevented entrainment of hydrazine. Leveraging Process Analytical Technology (PAT), we investigated the reaction profile with in situ IR and Power Compensation Calorimetry (PCC) to aid development prior to a successful scale-up.
A Facile Cascade Synthesis of 5,6-Diaryldibenzo[a,e]cyclooctenes from (Z,Z)-1-Aryl-3,5-octadiene-1,7-diynes†

Sequential treatment of (Z)-3-methyl-2-penten-4-ynal (10) with the allenylborane 2 and 2-aminoethanol furnished 11. The use of 11 for cross-coupling with aryl iodides followed by the KH-induced syn elimination of the coupled adducts 13 provided easy access to a variety of dienediynes 14 for subsequent conversions to dibenzo[a,e]cyclooctenes (sym-dibenzocyclooctatetraenes) 17. By cross-coupling with 1,2- and 1,4-diiodobenzene, it was possible to obtain 19 and 25 having two dienediynyl moieties. It was anticipated that the oligomers 21 and 26 containing multiple dibenzo[a,e]cyclooctenyl units could thus be synthesized. The 1H NMR spectrum of 32 having three dibenzo[a,e]cyclooctenyl units indicates the presence of three diastereomers 32a−c in a random statistical distribution of 2:1:1. Similarly, the 1H NMR spectrum of 33 having two dibenzo[a,e]cyclooctenyl units exhibits signals that support the presence of two diastereomers 33a and 33b in a 1:1 ratio.
Alkali-metal thiogermanates: sodium channels and variations on the La3CuSiS7 structure type.

Five new isotypic quaternary chalcogenides containing rare-earth metal atoms crystallizing in the hexagonal noncentrosymmetric space group P6(3) (No. 173) with the La(3)CuSiS(7) structure type have been synthesized by reacting the appropriate anhydrous rare-earth trichloride with sodium thiogermanate, Na(2)GeS(3). The reaction between LnCl(3) and Na(2)GeS(3) in an evacuated fused-silica ampule produced high yields of good-quality crystals of NaLn(3)GeS(7) [Ln = Ce (I), Nd (II), Sm (III), Gd (IV), and Yb (V)], while a similar reaction between EuCl(3) and Na(2)GeS(3) yielded a quinary chloride thiogermanate, Na(1.2)Eu(3.4)Cl(2)Ge(3)S(9) (VI), incorporating a cyclic trimeric Ge(3)S(9) building unit and adopting a structure related to La(3)CuSiS(7). The crystal structure of the compounds comprises a complex network of bicapped trigonal-prismatic LnS(8) and GeS(4) tetrahedra, which creates channels along the [001] direction. The Na(+) cations reside in these channels within trigonally distorted octahedral coordination environments, surrounded by six S atoms. For compounds III-V, the temperature dependence of the magnetic susceptibility indicates that these compounds are paramagnetic with μ(eff). = 1.86, 8.01, and 3.87 μ(B), for III-V, respectively. The experimental μ(eff) for IV is close to the theoretical value of 7.94 for free Gd(3+) ions, while μ(eff) values for III and V deviate from their theoretical values of 0.86 and 4.54 μ(B) for Sm(3+) and Yb(3+) ions, respectively. These compounds are semiconductors with optical band gaps of around 1.3 eV for III and V. Extended Huckel calculations suggest that the valence band comprises primarily S 3p and the bottom of the conduction band is dominated by empty rare-earth 5d orbitals. Compound VI exhibits a sharp optical absorption of around 2.18 eV, which is attributed to the f → d transition of Eu(II). The effective magnetic moment of 7.94 μ(B)/Eu is in excellent agreement with the theoretical value of 7.94 μ(B) for the free Eu(2+) ion.
Synthesis of 7‐benzoxazol‐2‐yl and 7‐benzothiazol‐2‐yl‐6‐fluoroquinolones

The fluoroquinolones, 7-benzoxazol-2-yl-1-ethyl-6-fluoro-1,4-dihydro-4-oxoquinoline-3-carboxylic acid and 7-benzothiazol-2-yl-1-ethyl-6-fluoro-1,4-dihydro-4-oxoquinoline-3-carboxylic acid, were synthesized. The compounds were obtained by use of the Gould-Jacobs route to the quinoline ring system. The required anilines, 3-benzoxazol-2-yl-4-fluorophenylamine and 3-benzothiazol-2-yl-4-fluorophenylamine were obtained by the cyclodehydration reaction of 5-amino-2-fluorobenzoic acid with 2-aminophenol or 2-aminothiophenol respectively using polyphosphoric acid.
Kinetic pathways of topology simplification by Type-II topoisomerases in knotted supercoiled DNA

The topological state of covalently closed, double-stranded DNA is defined by the knot type $K$ and the linking-number difference $\Delta Lk$ relative to unknotted relaxed DNA. DNA topoisomerases are essential enzymes that control the topology of DNA in all cells. In particular, type-II topoisomerases change both $K$ and $\Delta Lk$ by a duplex-strand-passage mechanism and have been shown to simplify the topology of DNA to levels below thermal equilibrium at the expense of ATP hydrolysis. It remains a key question how small enzymes are able to preferentially select strand passages that result in topology simplification in much larger DNA molecules. Using numerical simulations, we consider the non-equilibrium dynamics of transitions between topological states $(K,\Delta Lk)$ in DNA induced by type-II topoisomerases. For a biological process that delivers DNA molecules in a given topological state $(K,\Delta Lk)$ at a constant rate we fully characterize the pathways of topology simplification by type-II topoisomerases in terms of stationary probability distributions and probability currents on the network of topological states $(K,\Delta Lk)$. In particular, we observe that type-II topoisomerase activity is significantly enhanced in DNA molecules that maintain a supercoiled state with constant torsional tension. This is relevant for bacterial cells in which torsional tension is maintained by enzyme-dependent homeostatic mechanisms such as DNA-gyrase activity.
An improved coupling procedure for the barton-zard pyrrole synthesis

An improved final step in the Barton-Zard pyrrole synthesis uses inexpensive potassium carbonate as base in the coupling-cyclization reaction of vic-nitro-acetates with isocyanides. In this modification the isolated yields of synthetically useful 2-carboalkoxypyrroles (1a,b and 3) and 2-(p-toluenesulfonyl)pyrroles (2a,b) consistently rise to the 78-89% range. Conversion of 2a to 5-(p-toluenesulfonyl)-2-pyrrolinone 4 is conveniently and directly achieved by reaction with 30% hydrogen peroxide in acetic acid, thus circumventing the commonly used two step procedure involving bromination followed by solvolysis.
Conformational effects on the excited state 1,2-hydrogen migration in alkyldiazomethanes

Abstract Excited state rearrangements of alkyldiazo compounds are well-known. In particular, 1,2-hydrogen migrations to give carbene products are common. In this communication we provide evidence showing the migration in the diazo excited state is dependent upon the dihedral angle formed between the migrating hydrogen and the diazo carbon.
cis-regulatory architecture of a short-range EGFR organizing center in the Drosophila melanogaster leg

We characterized the establishment of an Epidermal Growth Factor Receptor (EGFR) organizing center (EOC) during leg development in Drosophila melanogaster. Initial EGFR activation occurs in the center of leg discs by expression of the EGFR ligand Vn and the EGFR ligand-processing protease Rho, each through single enhancers, vnE and rhoE, that integrate inputs from Wg, Dpp, Dll and Sp1. Deletion of vnE and rhoE eliminates vn and rho expression in the center of the leg imaginal discs, respectively. Animals with deletions of both vnE and rhoE (but not individually) show distal but not medial leg truncations, suggesting that the distal source of EGFR ligands acts at short-range to only specify distal-most fates, and that multiple additional ‘ring’ enhancers are responsible for medial fates. Further, based on the cis-regulatory logic of vnE and rhoE we identified many additional leg enhancers, suggesting that this logic is broadly used by many genes during Drosophila limb development.
Random sequences rapidly evolve into de novo promoters

How new functions arise de novo is a fundamental question in evolution. We studied de novo evolution of promoters in Escherichia coli by replacing the lac promoter with various random sequences of the same size (~100 bp) and evolving the cells in the presence of lactose. We find that ~60% of random sequences can evolve expression comparable to the wild-type with only one mutation, and that ~10% of random sequences can serve as active promoters even without evolution. Such a short mutational distance between random sequences and active promoters may improve the evolvability, yet may also lead to accidental promoters inside genes that interfere with normal expression. Indeed, our bioinformatic analyses indicate that E. coli was under selection to reduce accidental promoters inside genes by avoiding promoter-like sequences. We suggest that a low threshold for functionality balanced by selection against undesired targets can increase the evolvability by making new beneficial features more accessible. Bacterial promoters initiate gene transcription and have distinct sequence features. Here, the authors show that random sequences that contain no information are just on the verge of functioning as promoters in Escherichia coli.
An asymmetric synthesis of a 3-hydroxy-β-lactam by ketene-imine cycloaddition: utilization of chiral ketenes from carbohydrates

Abstract The Staudinger reaction of a chiral carbohydrate-based ketene and an imine proceeds to give, after removal of the sugar, cis-3-hydroxy-β-lactam 7 in moderate yield with good asymmetric induction (70% e.e.).
A First Course in Data Science

Data science is a discipline that provides principles, methodology, and guidelines for the analysis of data for tools, values, or insights. Driven by a huge workforce demand, many academic institut...
Ligand effects in the Rh(II) catalyzed reaction of α-diazo ketoamides

Abstract The rhodium(II) catalyzed decomposition of several α-diazo ketoamides resulted in either formation of a push–pull carbonyl ylide intermediate followed by intramolecular [3+2]-cycloaddition across the tethered π-bond or C–H insertion of the initially formed rhodium carbenoid into the C5-position of the lactam ring followed by a carboethoxy-decarboxylation reaction. The chemoselectivity exhibited by the rhodium carbenoid intermediate was found to be markedly dependent on the metal ligands employed.
Uncertain seas: probabilistic modeling of future coastal flood zones

ABSTRACTFuture sea-level rise will likely expand the inland extent of storm surge inundation and, in turn, increase the vulnerability of the people, properties and economies of coastal communities....
SPECTRAL STATISTICS OF DIRECTED NETWORKS WITH RANDOM LINK MODEL TRANSPOSE-ASYMMETRY

Stochastic network influences complicate graph filter design by producing uncertainty in network iteration matrix eigenvalues, the points at which the graph filter response is defined. While joint statistics for the eigenvalues typically elude analysis, predictable spectral asymptotics can emerge for large scale networks. Previously published works successfully analyze large-scale networks described by undirected graphs and directed graphs with transpose-symmetric distributions, focusing on consensus acceleration filter design for time-invariant networks as an application. This work expands upon these results by enabling analysis of certain large-scale directed networks described by transpose-asymmetric distributions. Specifically, efficiently computable spectral density approximations are possible for transpose-asymmetric percolation network models with node-transitive symmetry group and normal mean matrix. Numerical simulations support the derived approximations and application to consensus filters.
Indicators of Hopf algebras in positive characteristic

The notion of n-th indicator for a finite-dimensional Hopf algebra was introduced by Kashina, Montgomery, and Ng as invariance of the tensor category of its representations. In this short note, we show that the indicators appearing in positive characteristic all share the same sequence pattern if we assume the coradical of the Hopf algebra is a local Hopf subalgebra.
Eigenfunctions and Nodal sets

This is a survey of recent results on eigenfunctions of the Laplacian on compact Riemannian manifolds and their nodal sets. It is the write-up of my talk at JDG 2011.
CT-Realistic Lung Nodule Simulation from 3D Conditional Generative Adversarial Networks for Robust Lung Segmentation

Data availability plays a critical role for the performance of deep learning systems. This challenge is especially acute within the medical image domain, particularly when pathologies are involved, due to two factors: (1) limited number of cases, and (2) large variations in location, scale, and appearance. In this work, we investigate whether augmenting a dataset with artificially generated lung nodules can improve the robustness of the progressive holistically nested network (P-HNN) model for pathological lung segmentation of CT scans. To achieve this goal, we develop a 3D generative adversarial network (GAN) that effectively learns lung nodule property distributions in 3D space. In order to embed the nodules within their background context, we condition the GAN based on a volume of interest whose central part containing the nodule has been erased. To further improve realism and blending with the background, we propose a novel multi-mask reconstruction loss. We train our method on over 1000 nodules from the LIDC dataset. Qualitative results demonstrate the effectiveness of our method compared to the state-of-art. We then use our GAN to generate simulated training images where nodules lie on the lung border, which are cases where the published P-HNN model struggles. Qualitative and quantitative results demonstrate that armed with these simulated images, the P-HNN model learns to better segment lung regions under these challenging situations. As a result, our system provides a promising means to help overcome the data paucity that commonly afflicts medical imaging.
On the Energy Spectrum of Strong Magnetohydrodynamic Turbulence

Department of Astronomy and Astrophysics, University of Chicago, 5640 S. Ellis Ave, Chicago, Illinois 60637, USA(Received 27 October 2011; revised manuscript received 12 August 2012; published 25 October 2012)The energy spectrum of magnetohydrodynamic turbulence attracts interest due to its fundamentalimportance and its relevance for interpreting astrophysical data. Here we present measurements of theenergy spectra from a series of high-resolution direct numerical simulations of magnetohydrodynamicsturbulence with a strong guide ﬁeld and for increasing Reynolds number. The presented simulations, withnumerical resolutions up to 2048
Tree-dependent component analysis

We present a generalization of independent component analysis (ICA), where instead of looking for a linear transform that makes the data components independent, we look for a transform that makes the data components well fit by a tree-structured graphical model. Treating the problem as a semiparametric statistical problem, we show that the optimal transform is found by minimizing a contrast function based on mutual information, a function that directly extends the contrast function used for classical ICA. We provide two approximations of this contrast function, one using kernel density estimation, and another using kernel generalized variance. This tree-dependent component analysis framework leads naturally to an efficient general multivariate density estimation technique where only bivariate density estimation needs to be performed.
The power allocation game on a network: a paradox

The well-known Braess paradox in congestion games states that adding an additional road to a transportation network may increase the total travel time, and consequently decrease the overall efficiency. This paper presents a paradox in a similar spirit and involves a distributed resource allocation game on networks, namely the power allocation game between countries developed in Li and Morse &#x0028 2017 &#x0029. The paradox is that by having additional friends may actually decrease a country &#x02BC s total welfare in equilibrium. Conditions for this paradox to occur as well as the price of anarchy results are also derived.
Bounded Turing Reductions and Data Processing Inequalities for Sequences

A data processing inequality states that the quantity of shared information between two entities (e.g. signals, strings) cannot be significantly increased when one of the entities is processed by certain kinds of transformations. In this paper, we prove several data processing inequalities for sequences, where the transformations are bounded Turing functionals and the shared information is measured by the lower and upper mutual dimensions between sequences. We show that, for all sequences X, Y, and Z, if Z is computable Lipschitz reducible to X, then $$mdim(Z:Y) \leq mdim(X:Y) \text{ and} \ Mdim(Z:Y) \leq Mdim(X:Y). $$ We also show how to derive different data processing inequalities by making adjustments to the computable bounds of the use of a Turing functional. The yield of a Turing functional Φ S with access to at most n bits of the oracle S is the smallest input $m \in \mathbb {N}$ such that ${\Phi }^{S \upharpoonright n}(m)\uparrow $ . We show how to derive reverse data processing inequalities (i.e., data processing inequalities where the transformation may significantly increase the shared information between two entities) for sequences by applying computable bounds to the yield of a Turing functional.
Natural Analysts in Adaptive Data Analysis.

Adaptive data analysis is frequently criticized for its pessimistic generalization guarantees. The source of these pessimistic bounds is a model that permits arbitrary, possibly adversarial analysts that optimally use information to bias results. While being a central issue in the field, still lacking are notions of natural analysts that allow for more optimistic bounds faithful to the reality that typical analysts aren't adversarial. In this work, we propose notions of natural analysts that smoothly interpolate between the optimal non-adaptive bounds and the best-known adaptive generalization bounds. To accomplish this, we model the analyst's knowledge as evolving according to the rules of an unknown dynamical system that takes in revealed information and outputs new statistical queries to the data. This allows us to restrict the analyst through different natural control-theoretic notions. One such notion corresponds to a recency bias, formalizing an inability to arbitrarily use distant information. Another complementary notion formalizes an anchoring bias, a tendency to weight initial information more strongly. Both notions come with quantitative parameters that smoothly interpolate between the non-adaptive case and the fully adaptive case, allowing for a rich spectrum of intermediate analysts that are neither non-adaptive nor adversarial. Natural not only from a cognitive perspective, we show that our notions also capture standard optimization methods, like gradient descent in various settings. This gives a new interpretation to the fact that gradient descent tends to overfit much less than its adaptive nature might suggest.
New CLEO II results on charm hadron decays

We present new results on charm hadron decays from the CLEO II experiment. The D∗+ width is measured for the first time, Γ(D∗+) = 96 ± 4 ± 22 keV. The semileptonic decay branching fractions are determined to be B(D → K∗0e+νe) = (6.7± 0.4± 0.5± 0.4)% and B(D → K∗0μ+νμ) = (6.5± 0.9± 0.5± 0.4)%. We observe evidence for Ωc → Ω−e+νe and measure the product of the branching fraction and cross section, B(Ωc → Ω−e+νe) · σ(e+e− → ΩcX) = 42.2± 14.1 ± 11.9 fb. Within the framework of Heavy Quark Effective Theory, we measure in the decay Λc → Λeνe the form factor ratio, R = f2/f1 = −0.31 ± 0.06 ± 0.06. This provides strong evidence that the form factor f2 describing spin interaction of the s quark is non-zero. The Ξ + c lifetime is measured to be 503 ± 47 ± 18 fs. The results on branching fractions, cross section, and form factor ratio are preliminary. We present new results on charm hadron decays from the CLEO II experiment [1] at the Cornell Electron Storage Ring (CESR). The data were collected at the Υ(4S) ( √ s ∼ 10.6 GeV) resonance and at energies just below. In this paper, we begin with the presentation of the first measurement of the D∗+ width. We then report the measurement of the branching fractions for the semileptonic decays D+ → K∗0e+νe and K∗0μ+νμ. We then present evidence for the decay Ωc → Ω−e+νe and measurement of the product of the branching fraction and cross section. This is followed by the measurement of form factor ratio in the decay Λc → Λeνe within the framework of Heavy Quark Effective Theory. Finally, we present the measurement of Ξc lifetime. 1. First Measurement of D∗+ Width A measurement of D∗+ width provides a test of the non-perturbative strong physics involving heavy quarks. The predictions for the width range from 15 to 150 keV [2]. The level splittings in the B sector are not large enough for strong transitions. Therefore a measurement of the D∗+ width gives unique information about the strong coupling constant ∗Speaker. †Representing the CLEO Collaboration. P r H E P h e p 2 0 0 1 International Europhysics Conference on HEP K.K. Gan in heavy-light meson systems. The width depends only on g, a universal strong coupling between heavy vector and pseudoscaler mesons to the pion, since the small contribution of the electromagnetic decay can be neglected, yielding Γ(D∗+) = g2 12πf2 π (2pπ+ + p 3 π0), (1.1) where fπ is the pion decay constant and the momentum is for the pion in the D ∗+ rest frame [3] for the decay D∗+ → D0π+ and D+π0, respectively. The width is measured from the distribution of the energy Events Signal Signal Background Mis-meas. 10
Anisotropic functional Laplace deconvolution

Abstract In the present paper we consider the problem of estimating a three-dimensional function f based on observations from its noisy Laplace convolution. Our study is motivated by the analysis of Dynamic Contrast Enhanced (DCE) imaging data. We construct an adaptive wavelet-Laguerre estimator of f , derive minimax lower bounds for the L 2 -risk when f belongs to a three-dimensional Laguerre–Sobolev ball and demonstrate that the wavelet-Laguerre estimator is adaptive and asymptotically near-optimal in a wide range of Laguerre–Sobolev spaces. We carry out a limited simulations study and show that the estimator performs well in a finite sample setting. Finally, we use the technique for the solution of the Laplace deconvolution problem on the basis of DCE Computerized Tomography data.
High order correctors and two-scale expansions in stochastic homogenization

In this paper, we study high order correctors in stochastic homogenization. We consider elliptic equations in divergence form on $$\mathbb {Z}^d$$ , with the random coefficients constructed from i.i.d. random variables. We prove moment bounds on the high order correctors and their gradients under dimensional constraints. It implies the existence of stationary correctors and stationary gradients in high dimensions. As an application, we prove a two-scale expansion of the solutions to the random PDE, which identifies the first and higher order random fluctuations in a strong sense.
A Bio-inspired Redundant Sensing Architecture

Sensing is the process of deriving signals from the environment that allows artificial systems to interact with the physical world. The Shannon theorem specifies the maximum rate at which information can be acquired. However, this upper bound is hard to achieve in many man-made systems. The biological visual systems, on the other hand, have highly efficient signal representation and processing mechanisms that allow precise sensing. In this work, we argue that redundancy is one of the critical characteristics for such superior performance. We show architectural advantages by utilizing redundant sensing, including correction of mismatch error and significant precision enhancement. For a proof-of-concept demonstration, we have designed a heuristic-based analog-to-digital converter - a zero-dimensional quantizer. Through Monte Carlo simulation with the error probabilistic distribution as a priori, the performance approaching the Shannon limit is feasible. In actual measurements without knowing the error distribution, we observe at least 2-bit extra precision. The results may also help explain biological processes including the dominance of binocular vision, the functional roles of the fixational eye movements, and the structural mechanisms allowing hyperacuity.
Unperturbed: spectral analysis beyond Davis-Kahan

Classical matrix perturbation results, such as Weyl's theorem for eigenvalues and the Davis-Kahan theorem for eigenvectors, are general purpose. These classical bounds are tight in the worst case, but in many settings sub-optimal in the typical case. In this paper, we present perturbation bounds which consider the nature of the perturbation and its interaction with the unperturbed structure in order to obtain significant improvements over the classical theory in many scenarios, such as when the perturbation is random. We demonstrate the utility of these new results by analyzing perturbations in the stochastic blockmodel where we derive much tighter bounds than provided by the classical theory. We use our new perturbation theory to show that a very simple and natural clustering algorithm -- whose analysis was difficult using the classical tools -- nevertheless recovers the communities of the blockmodel exactly even in very sparse graphs.
Bayesian random fields: the Bethe-Laplace approximation

While learning the maximum likelihood value of parameters of an undirected graphical model is hard, modelling the posterior distribution over parameters given data is harder. Yet, undirected models are ubiquitous in computer vision and text modelling (e.g. conditional random fields). But where Bayesian approaches for directed models have been very successful, a proper Bayesian treatment of undirected models in still in its infant stages. We propose a new method for approximating the posterior of the parameters given data based on the Laplace approximation. This approximation requires the computation of the covariance matrix over features which we compute using the linear response approximation based in turn on loopy belief propagation. We develop the theory for conditional and "unconditional" random fields with or without hidden variables. In the conditional setting we introduce a new variant of bagging suitable for structured domains. Here we run the loopy max-product algorithm on a "super-graph" composed of graphs for individual models sampled from the posterior and connected by constraints. Experiments on real world data validate the proposed methods.
Quantum partial search for uneven distribution of multiple target items

Quantum partial search algorithm is an approximate search. It aims to find a target block (which has the target items). It runs a little faster than full Grover search. In this paper, we consider quantum partial search algorithm for multiple target items unevenly distributed in a database (target blocks have different number of target items). The algorithm we describe can locate one of the target blocks. Efficiency of the algorithm is measured by number of queries to the oracle. We optimize the algorithm in order to improve efficiency. By perturbation method, we find that the algorithm runs the fastest when target items are evenly distributed in database.
How to escape saddle points efficiently

This paper shows that a perturbed form of gradient descent converges to a second-order stationary point in a number iterations which depends only poly-logarithmically on dimension (i.e., it is almost "dimension-free"). The convergence rate of this procedure matches the well-known convergence rate of gradient descent to first-order stationary points, up to log factors. When all saddle points are non-degenerate, all second-order stationary points are local minima, and our result thus shows that perturbed gradient descent can escape saddle points almost for free. Our results can be directly applied to many machine learning applications, including deep learning. As a particular concrete example of such an application, we show that our results can be used directly to establish sharp global convergence rates for matrix factorization. Our results rely on a novel characterization of the geometry around saddle points, which may be of independent interest to the non-convex optimization community.
Koszul duality and the PBW theorem in symmetric tensor categories in positive characteristic

Abstract We generalize the theory of Koszul complexes and Koszul algebras to symmetric tensor categories. In characteristic zero the generalization is routine, while in characteristic p there is a subtlety – the symmetric algebra of an object is not always Koszul (i.e., its Koszul complex is not always exact). Namely, this happens in the Verlinde category Ver p in any characteristic p ≥ 5 . We call an object Koszul if its symmetric algebra is Koszul, and show that the only Koszul objects of Ver p are usual supervector spaces, i.e., a non-invertible simple object L m ( 2 ≤ m ≤ p − 2 ) is not Koszul. We show, however, that the symmetric algebra S L m is almost Koszul in the sense of Brenner, Butler and King (namely, ( p − m , m ) -Koszul), and compute the corresponding internal Yoneda algebra (i.e., the internal Ext-algebra from the trivial module to itself). We then proceed to discuss the PBW theorem for operadic Lie algebras (i.e., algebras over the operad Lie). This theorem is well known to fail for vector spaces in characteristic 2 (as one needs to require that [ x , x ] = 0 ), and for supervector spaces in characteristic 3 (as one needs to require that [ [ x , x ] , x ] = 0 for odd x), but it holds in these categories in any characteristic p ≥ 5 ; there is a well known proof based on Koszul duality. However, we show that in the category Ver p , because of failure of Koszul duality, the PBW theorem can fail in any characteristic p ≥ 5 . Namely, one needs to impose the p-Jacobi identity, a certain generalization to characteristic p of the identities [ x , x ] = 0 and [ [ x , x ] , x ] = 0 . On the other hand, our main result is that once the p-Jacobi identity is imposed, the PBW theorem holds. This shows that the correct definition of a Lie algebra in Ver p is an algebra over Lie which satisfies the p-Jacobi identity. This also applies to any symmetric tensor category that admits a symmetric tensor functor to Ver p (e.g., a symmetric fusion category, see [19] , Theorem 1.5). Finally, we prove the PBW theorem for Lie algebras in any quasi-semisimple symmetric tensor category.
Weyl asymptotics of the transmission eigenvalues for a constant index of refraction

We prove Weyl-type asymptotic formulas for the real and the complex internal transmission eigenvalues when the domain is a ball and the index of refraction is constant.