cssi/SciSciGPT-SciSciNet huggingface dataset:
The Thalamus Regulates Retinoic Acid Signaling and Development of Parvalbumin Interneurons in Postnatal Mouse Prefrontal Cortex

GABAergic inhibitory neurons in the prefrontal cortex (PFC) play crucial roles in higher cognitive functions. Despite the link between aberrant development of PFC interneurons and a number of psychiatric disorders, mechanisms underlying the development of these neurons are poorly understood. Here we show that the retinoic acid (RA)-degrading enzyme CYP26B1 (cytochrome P450 family 26, subfamily B, member 1) is transiently expressed in the mouse frontal cortex during postnatal development, and that medial ganglionic eminence (MGE)-derived interneurons, particularly in parvalbumin (PV)-expressing neurons, are the main cell type that has active RA signaling during this period. We found that frontal cortex-specific Cyp26b1 knock-out mice had an increased density of PV-expressing, but not somatostatin-expressing, interneurons in medial PFC, indicating a novel role of RA signaling in controlling PV neuron development. The initiation of Cyp26b1 expression in neonatal PFC coincides with the establishment of connections between the thalamus and the PFC. We found that these connections are required for the postnatal expression of Cyp26b1 in medial PFC. In addition to this region-specific role in postnatal PFC that regulates RA signaling and PV neuron development, the thalamocortical connectivity had an earlier role in controlling radial dispersion of MGE-derived interneurons throughout embryonic neocortex. In summary, our results suggest that the thalamus plays multiple, temporally separate roles in interneuron development in the PFC.
Synthesis and unexpected reactions of 2‐Hydroxy‐3‐pyridinylacetic hydrazides. Formation of 2H‐Pyrrolo[2,3‐b]pyridin‐2‐ones

Treatment of 2-hydroxy-3-pyridinylacetic hydrazides under mild mesylation conditions provided 2H-pyrrolo[2,3-b]pyridin-2-ones as unexpected products. This rearrangement is believed to result from an intramolecular attack of the hydrazide on a reactive pyridinium species formed under the reaction conditions.
Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney

The mammalian kidney develops through reciprocal interactions between the ureteric bud and the metanephric mesenchyme to give rise to the entire collecting system and the nephrons. Most of our knowledge of the developmental regulators driving this process arises from the study of gene expression and functional genetics in mice and other animal models. In order to shed light on human kidney development, we have used single-cell transcriptomics to characterize gene expression in different cell populations, and to study individual cell dynamics and lineage trajectories during development. Single-cell transcriptome analyses of 6414 cells from five individual specimens identified 11 initial clusters of specific renal cell types as defined by their gene expression profile. Further subclustering identifies progenitors, and mature and intermediate stages of differentiation for several renal lineages. Other lineages identified include mesangium, stroma, endothelial and immune cells. Novel markers for these cell types were revealed in the analysis, as were components of key signaling pathways driving renal development in animal models. Altogether, we provide a comprehensive and dynamic gene expression profile of the developing human kidney at the single-cell level.
Synthesis, asymmetric aldol reactions, and x-ray crystallography of some oxadiazinanone derivatives

A series of N4-substituted oxadiazinanones have been synthesized from (1R,2S)-norephedrine by a process of either reductive alkylation or arylation, N-nitrosation, reduction and cyclization. These derivatives (R = -CH2Ph, -CH2C(CH3)3, -cyclo-C6H11, -C6H5) have been acylated with propanoyl chloride and employed in the asymmetric Aldol reaction. The observed diastereoselectivities for the formation of the “non-Evans” syn-adduct ranged from 88:12 to 99:1. The hydrolysis of the Aldol adducts varied with the nature of the nitrogen substituent.
Facile Synthesis of 2,4-Disubstituted Thiooxazoles and 2,4-Disubstituted Oxazole Sulfonyl Chlorides via Acyl Isothiocyanates and TMS-Diazomethane

An expedient method for the direct conversion of acyl isothiocyanates to 2,4-disubstitued thiooxazoles and 2,4-disubstituted oxazole sulfonyl chlorides is described. The method takes advantage of an early observation by Sheehan and the reaction of diazomethane with isocyanates to form oxazolones. However, in this case an acyl isothiocyanate is utilized as well as the readily available TMS-diazomethane to provide access to the desired 4-substituted sulfur derivatives. The 2,4-disubstituted oxazole systems synthesized represent novel thiooxazoles and oxazole sulfonyl chlorides not previously described.
A three dimensional multiplane kinematic model for bilateral hind limb gait analysis in cats

Background Kinematic gait analysis is an important noninvasive technique used for quantitative evaluation and description of locomotion and other movements in healthy and injured populations. Three dimensional (3D) kinematic analysis offers additional outcome measures including internal-external rotation not characterized using sagittal plane (2D) analysis techniques. Methods The objectives of this study were to 1) develop and evaluate a 3D hind limb multiplane kinematic model for gait analysis in cats using joint coordinate systems, 2) implement and compare two 3D stifle (knee) prediction techniques, and 3) compare flexion-extension determined using the multiplane model to a sagittal plane model. Walking gait was recorded in 3 female adult cats (age = 2.9 years, weight = 3.5 ± 0.2 kg). Kinematic outcomes included flexion-extension, internal-external rotation, and abduction-adduction of the hip, stifle, and tarsal (ankle) joints. Results Each multiplane stifle prediction technique yielded similar findings. Joint angles determined using markers placed on skin above bony landmarks in vivo were similar to joint angles determined using a feline hind limb skeleton in which markers were placed directly on landmarks ex vivo. Differences in hip, stifle, and tarsal joint flexion-extension were demonstrated when comparing the multiplane model to the sagittal plane model. Conclusions This multiplane cat kinematic model can predict joint rotational kinematics as a tool that can quantify frontal, transverse, and sagittal plane motion. This model has multiple advantages given its ability to characterize joint internal-external rotation and abduction-adduction. A further, important benefit is greater accuracy in representing joint flexion-extension movements.
A new halo aldol reaction: three-component reaction via 1,4-robust activation of ethynyl alkyl ketones for stereoselective formations of versatile aldol adducts.

A new three-component halo aldol reaction has been discovered for the tandem formations of I−C/C−C bonds by activating the α‘,β-positions of α,β-acetylenic ketones. The key intermediates, 1-iodo-3-siloxy-1,3-butadienes, were generated from allenolates and directly monitored by 1H NMR spectroscopic analysis. Excellent geometric selectivity (>95%) and good yields (65−82%) have been achieved for 10 examples.
The Synthesis of Phosphonate Ester Containing Fluorinated Vinyl Ethers.

Three novel perfluorovinyl ethers containing phosphonate ester groups, diethyl 1,1,2,2,3,3,5,6,6-nonafluoro-4-oxa-5-hexenylphosphonate, (EtO)2P(O)(CF2)3OCFCF2 (1), diethyl 1,1,2,2,4,5,5-heptafluoro-3-oxa-4-pentenylphosphonate, (EtO)2P(O)(CF2)2OCFCF2 (2), and diethyl 1,1,2,2,4,5,5,7,8,8-decafluoro-4-trifluoromethyl-3,6-dioxa-7-octenylphosphonate, CF2CFOCF2CF(CF3)O(CF2)2P(O)(OEt)2 (3), have been synthesized. Perfluorovinyl ethers 1 and 2 were synthesized from methyl 4-trifluoroethenoxy-2,2,3,3,4,4-hexafluorobutanoate and methyl 3-trifluoroethenoxy-2,2,3,3-tetrafluoropropanoate, respectively, while perfluorovinyl ether 3 was synthesized either from 5-trifluoroethenoxy-4-trifluoromethyl-3-oxa-1,1,2,2,4,5,5-heptafluoropentylsulfonyl fluoride or methyl 6-trifluoroethenoxy-5-trifluoromethyl-4-oxa-2,2,3,3,5,6,6-heptafluorohexanoate. The carboxylate esters were converted to the corresponding fluoroalkyl iodides via a free-radical iododecarboxylation. The sulfonyl fluoride was converted to its corresponding fluoroa...
Synthetically Useful Mono-Functionalizations of Dihaloarenes via Rieke Metals

Abstract Reaction of dihalobenzenes and 2, 5-dibromothiophene with Rieke magnesium, Rieke zinc, and Rieke calcium at low temperature affords a mono-organometallic intermediate which upon subsequent treatment with an electrophile provides a mono-functionalized aromatic product in excellent chemical yield.
Efficient synthesis of bicyclic oxazolino- and thiazolino[3,2- c ]pyrimidine-5,7-diones and its application to the synthesis of GnRH antagonists

Treatment of various 2-methyl oxazolines or thiazolines with chlorocarbonyl isocyanate gives the corresponding bicyclic oxazolino- or thiazolino[3,2-c]pyrimidin-5,7-dione derivatives in very good yield. This reaction has been applied to the rapid syntheses of human gonadotropin-releasing hormone (hGnRH) receptor antagonists for SAR study, resulting in 13e with binding affinity in the low nanomolar range (4.5 nM).
Spherically averaging ellipsoidal galaxy clusters in X-ray and Sunyaev–Zel’dovich studies – II. Biases

This is the second of two papers investigating the spherical averaging of ellipsoidal galaxy clusters in the context of X-ray and Sunyaev–Zel’dovich (SZ) observations. In the present study, we quantify the orientation-average bias and scatter in observables that result from spherically averaging clusters described by either ellipsoidal generalizations of the Navarro–Frenk–White (NFW) profile or a nearly scale-free logarithmic potential. Although the mean biases are small and mostly <1 per cent, the flattest cluster models generally have a significant mean bias; i.e. averaging over all orientations does not always eliminate projection biases. Substantial biases can result from different viewing orientations, where the integrated Compton-y parameter (YSZ) and the concentration have the largest scatter (as large as σ∼ 10 per cent for YSZ), and the emission-weighted temperature (TX) has the smallest (σ≲ 0.5 per cent). The very small scatter for TX leads to YX and Mgas having virtually the same orientation biases. Substantial scatter is expected for individual clusters (up to σ∼ 8 per cent) in the correlation between YSZ and YX in comparison to the small mean bias (σ≲ 1 per cent) applicable to a random sample of clusters of sufficient size. For ellipsoidal NFW models, we show that the orientation bias for the total cluster mass attains a minimum near the radius r2500 so that the spherically averaged mass computed at this radius is always within ≈0.5 per cent of the true value for any orientation. Finally, to facilitate the accounting for orientation bias in X-ray and SZ cluster studies, we provide cubic polynomial approximations to the mean orientation bias and 1σ scatter for each cluster observable as a function of axial ratio for the ellipsoidal NFW models.
LimoRhyde: A Flexible Approach for Differential Analysis of Rhythmic Transcriptome Data:

Unraveling the effects of genetic or environmental perturbations on biological rhythms requires detecting changes in rhythmicity across multiple conditions. Although methods to detect rhythmicity i...
Total Synthesis of the Anti Methicillin-Resistant Staphylococcus aureus Peptide Antibiotics TAN-1057A-D

TAN-1057A−D, dipeptides isolated from bacteria Flexibacter sp. PK-74 and PK-176, are new antibiotics with potent antibacterial activity against methicillin-resistant Staphylococcus aureus. We describe, in detail, the total synthesis of TAN-1057A−D by a convergent route featuring a new method to construct the cyclic amidinourea functional group.
W-LIKE MAPS WITH VARIOUS INSTABILITIES OF ACIM'S

This paper generalizes the results of [Li et al., 2011] and then provides an interesting example. We construct a family of W-like maps {Wa} with a turning fixed point having slope s1 on one side and –s2 on the other. Each Wa has an absolutely continuous invariant measure μa. Depending on whether is larger, equal or smaller than 1, we show that the limit of μa is a singular measure, a combination of singular and absolutely continuous measure or an absolutely continuous measure, respectively. It is known that the invariant density of a single piecewise expanding map has a positive lower bound on its support. In Sec. 4 we give an example showing that in general, for a family of piecewise expanding maps with slopes larger than 2 in modulus and converging to a piecewise expanding map, their invariant densities do not necessarily have a uniform positive lower bound on the support.
Synthesis of β,β-Disubstituted γ-Butyrolactones by Chemo­selective Oxidation of 1,4-Diols and γ-Hydroxy Olefins with RuCl3/NaIO4

Substituted γ-butyrolactones represent an important group of structural fragments commonly found in natural products, receptor ligands, and drug molecules. Interest in preparing a library of substituted γ-butyrolactones and finding that limited routes to β-substituted lactones exist, led to the development of an efficient approach for the synthesis of β,β-disubstituted γ-butyrolactones. Readily prepared substituted 1,4-diols and γ-hydroxy olefins were treated with the ­RuCl3/NaIO4 oxidation system to provide the target β,β-disubstituted γ-butyrolactones in modest to good yields. The reaction goes through a lactol intermediate that was isolated and characterized for selected compounds. The approach supplies an efficient and versatile method for the synthesis of these important heterocyclic structures. Importantly, the present work is the first report that demonstrates the ability of RuCl3/NaIO4 to selectively oxidize primary hydroxyl groups in the presence of secondary alcohols to prepare lactones in good yields.
Synthesis and characterization of Te2SeO7 : A powder second-harmonic-generating study of TeO2, Te2SeO7, Te2O5, and TeSeO4

The synthesis and characterization of a noncentrosymmetric tellurium selenate, Te2SeO7, is reported. In addition, the powder second-harmonic-generating (SHG) properties of TeO2, Te2SeO7, Te2O5, and TeSeO4 have been measured, using 1064 nm radiation. Through the powder SHG experiments, we are able to determine that TeO2 is not phase-matchable, whereas Te2SeO7, Te2O5, and TeSeO4 are phase-matchable. Also, TeO2, Te2SeO7, Te2O5, and TeSeO4 have SHG efficiencies of 5, 200, 400, and 400 times SiO2, respectively. The relative SHG efficiencies may be understood by examining the structure of each material. Through the powder SHG measurements, we estimate the average nonlinear optical bond susceptibility, 〈d2ωijk〉, for each material.
Synthesis of 3‐substituted‐1‐methylpyrazoles

Reaction of 3-bromo-1-methylpyrazole 1 with t-butyllithium at -100 o followed by quenching of the lithiopyrazole intermediate allows regiospecific introduction of substituents into the 3-position of the 1-methylpyrazole ring
Targeting IDH1 as a Prosenescent Therapy in High-grade Serous Ovarian Cancer

Epithelial ovarian cancer (EOC) is the deadliest gynecologic cancer. High-grade serous carcinoma (HGSC) is the most frequently diagnosed and lethal histosubtype of EOC. A significant proportion of patients with HGSC relapse with chemoresistant disease. Therefore, there is an urgent need for novel therapeutic strategies for HGSC. Metabolic reprogramming is a hallmark of cancer cells, and targeting metabolism for cancer therapy may be beneficial. Here, we found that in comparison with normal fallopian tube epithelial cells, HGSC cells preferentially utilize glucose in the TCA cycle and not for aerobic glycolysis. This correlated with universally increased TCA cycle enzyme expression in HGSC cells under adherent conditions. HGSC disseminates as tumor cell spheroids within the peritoneal cavity. We found that wild-type isocitrate dehydrogenase I (IDH1) is the only TCA cycle enzyme upregulated in both adherent and spheroid conditions and is associated with reduced progression-free survival. IDH1 protein expression is also increased in patients with primary HGSC tumors. Pharmacologic inhibition or knockdown of IDH1 decreased proliferation of multiple HGSC cell lines by inducing senescence. Mechanistically, suppression of IDH1 increased the repressive histone mark H3K9me2 at multiple E2F target gene loci, which led to decreased expression of these genes. Altogether, these data suggest that increased IDH1 activity is an important metabolic adaptation in HGSC and that targeting wild-type IDH1 in HGSC alters the repressive histone epigenetic landscape to induce senescence. IMPLICATIONS: Inhibition of IDH1 may act as a novel therapeutic approach to alter both the metabolism and epigenetics of HGSC as a prosenescent therapy.
Conformational Study of the Intramolecular Diels−Alder Reaction of a Pentadienyl Acrylate. Theoretical Evaluation of Kinetic and Thermodynamic Control

Acrylate 4, prepared from diacetylrhamnal, underwent intramolecular Diels−Alder cycloaddition to give the thermodynamically disfavored trans-fused γ-lactone 15 as the major product, along with two stereoisomeric cycloadducts. A computational analysis of each of the four transition states arising from 4 and the corresponding cycloadducts permits an understanding of the contrasting requirements for kinetic versus thermodynamic control of the reaction.
Neurotoxicity to dopamine neurons after the serial exposure to alcohol and methamphetamine: Protection by COX-2 antagonism.

Abstract A significant co-morbidity exists between alcohol and methamphetamine (Meth) in humans but the consequences and mechanisms underlying their co-morbid effects remain to be identified. A consequence associated with the abuse of either alcohol or Meth involves inflammation but little is known about the role of inflammation in a possible neurotoxicity arising from their co-exposure. Sprague Dawley rats were allowed 28 days of intermittent, voluntary access to 10% ethanol (EtOH) followed by a neurotoxic binge administration of Meth. EtOH drinking followed by Meth increased microglial cell counts and produced morphological changes in microglia of the substantia nigra pars compacta 2 h after Meth administration that were distinct from those produced by either EtOH or Meth alone. These effects preceded the activation of cleaved caspase-3 in dopamine cell bodies, as well as decreases in tyrosine hydroxylase (TH) immunoreactivity in the substantia nigra and dopamine transporter (DAT) immunoreactivity in the striatum measured at 7 days after Meth. Intervention with a selective COX-2 inhibitor during EtOH drinking prevented the changes in microglia, and attenuated the increase in cleaved caspase-3, and decreases in TH and DAT after Meth administration. Furthermore, motor dysfunction measured by a rotarod test was evident but only in rats that were exposed to both EtOH and Meth. The motor dysfunction was ameliorated by prior inhibition of COX-2 during EtOH drinking. The exaggerated neurochemical and behavioral deficits indicate that the comorbidity of EtOH and Meth induces a degeneration of the nigrostriatal pathway and support the role of inflammation produced by EtOH drinking that primes and mediates the neurotoxic consequences associated with the common co-morbidity of these drugs.
Samarium-Promoted Coupling of 1,10-Phenanthroline with Carbonyl Compounds for Synthesis of New Ligands†

1,10-Phenanthroline reacts with aldehydes and ketones in the presence of samarium diiodide to produce 2-(1-hydroxyalkyl)-1,10-phenanthrolines. The hydroxyalkyl substituent can be functionalized in numerous ways or removed to permit further ligand variation. The carbonyl coupling reaction can also be repeated to provide 2,9-disubstituted phenanthrolines. Taken together, these operations provide ready access to a large number of phenanthroline derivatives to serve as ligand libraries for catalyst exploration.
Development of Greenbiochemistry

The present situation and the development of Japanese green chemistry are discussed.Subjects to be solved and the strategy to be adopted are discussed. Several examples of industrial biotechnology are described.
Normalization of the microbiota in patients after treatment for colonic lesions

Colorectal cancer is a worldwide health problem. Despite growing evidence that members of the gut microbiota can drive tumorigenesis, little is known about what happens to it after treatment for an adenoma or carcinoma. This study tested the hypothesis that treatment for adenoma or carcinoma alters the abundance of bacterial populations associated with disease to those associated with a normal colon. We tested this hypothesis by sequencing the 16S rRNA genes in the feces of 67 individuals before and after treatment for adenoma (N = 22), advanced adenoma (N = 19), and carcinoma (N = 26). There were small changes to the bacterial community associated with adenoma or advanced adenoma and large changes associated with carcinoma. The communities from patients with carcinomas changed significantly more than those with adenoma following treatment (P value 0.05). Because the distribution of OTUs across patients and diagnosis groups was irregular, we used the random forest machine learning algorithm to identify groups of OTUs that could be used to classify pre and post-treatment samples for each of the diagnosis groups. Although the adenoma and carcinoma models could reliably differentiate between the pre- and post-treatment samples (P value 0.05). By better understanding the response of the microbiota to treatment for adenomas and carcinomas, it is likely that biomarkers will eventually be validated that can be used to quantify the risk of recurrence and the likelihood of survival. Although it was difficult to identify significant differences between pre- and post-treatment samples from patients with adenoma and advanced adenoma, this was not the case for carcinomas. Not only were there large changes in pre- versus post-treatment samples for those with carcinoma, but also these changes were toward a more normal microbiota.
LeafNATS: An Open-Source Toolkit and Live Demo System for Neural Abstractive Text Summarization

Neural abstractive text summarization (NATS) has received a lot of attention in the past few years from both industry and academia. In this paper, we introduce an open-source toolkit, namely LeafNATS, for training and evaluation of different sequence-to-sequence based models for the NATS task, and for deploying the pre-trained models to real-world applications. The toolkit is modularized and extensible in addition to maintaining competitive performance in the NATS task. A live news blogging system has also been implemented to demonstrate how these models can aid blog/news editors by providing them suggestions of headlines and summaries of their articles.
Chemical vapor deposition of iron and iron oxide thin films from Fe(II) dihydride complexes

H2Fe[P(CH3)3]4 produced crystalline films α-Fe without O2 and Fe3O4 with O2, where H2Fe[P(OCH3)3]4 produced amorphous films Fe−Fe3O4 without O2 and Fe2O3 with O2 at substrate temperatures as low as 230 °C. The crystalline Fe3O4 film exhibited higher values of saturation magnetization, remanent magnetization, and coercivity than the amorphous Fe−Fe3O4 film.
Astrin-SKAP complex reconstitution reveals its kinetochore interaction with microtubule-bound Ndc80

Chromosome segregation requires robust interactions between the macromolecular kinetochore structure and dynamic microtubule polymers. A key outstanding question is how kinetochore-microtubule attachments are modulated to ensure that bi-oriented attachments are selectively stabilized and maintained. The Astrin-SKAP complex localizes preferentially to properly bi-oriented sister kinetochores, representing the final outer kinetochore component recruited prior to anaphase onset. Here, we reconstitute the 4-subunit Astrin-SKAP complex, including a novel MYCBP subunit. Our work demonstrates that the Astrin-SKAP complex contains separable kinetochore localization and microtubule binding domains. In addition, through cross-linking analysis in human cells and biochemical reconstitution, we show that the Astrin-SKAP complex binds synergistically to microtubules with the Ndc80 complex to form an integrated interface. We propose a model in which the Astrin-SKAP complex acts together with the Ndc80 complex to stabilize correctly formed kinetochore-microtubule interactions.
Look4TRs: a de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models.

MOTIVATION Simple tandem repeats, microsatellites in particular, have regulatory functions, links to several diseases and applications in biotechnology. There is an immediate need for an accurate tool for detecting microsatellites in newly sequenced genomes. The current available tools are either sensitive or specific but not both; some tools require adjusting parameters manually. RESULTS We propose Look4TRs, the first application of self-supervised hidden Markov models to discovering microsatellites. Look4TRs adapts itself to the input genomes, balancing high sensitivity and low false positive rate. It auto-calibrates itself. We evaluated Look4TRs on 26 eukaryotic genomes. Based on F measure, which combines sensitivity and false positive rate, Look4TRs outperformed TRF and MISA-the most widely used tools-by 78 and 84%. Look4TRs outperformed the second and the third best tools, MsDetector and Tantan, by 17 and 34%. On eight bacterial genomes, Look4TRs outperformed the second and the third best tools by 27 and 137%. AVAILABILITY AND IMPLEMENTATION https://github.com/TulsaBioinformaticsToolsmith/Look4TRs. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
ABSTRACT COMMENSURATORS OF RIGHT-ANGLED ARTIN GROUPS AND MAPPING CLASS GROUPS

We prove that, aside from the obvious exceptions, the mapping class group of a compact orientable surface is not abstractly commensurable with any right-angled Artin group. Our argument applies to various sub- groups of the mapping class group—the subgroups generated by powers of Dehn twists and the terms of the Johnson filtration—and additionally to the outer automorphism group of a free group and to certain linear groups. There are many analogies and interconnections between the theories of right- angled Artin groups on one hand and mapping class groups on the other hand. For instance, by the work of Crisp and Wiest (13), the work of Koberda (27), and the work of the first two authors with Mangahas (12), there is an abundance of injective homomorphisms from right-angled Artin groups to mapping class groups. Also, the last two authors proved (30) that any two elements of the pure braid group either generate a free group or a free abelian group—a property shared by all right-angled Artin groups (4, Theorem 1.2). We are thus led to ask to what extent mapping class groups are the same as right-angled Artin groups. It is straightforward to see that most mapping class groups are not isomorphic to right-angled Artin groups, for instance because right-angled Artin groups are torsion free. On the other hand, mapping class groups have finite-index sub- groups that are torsion free, and so this leaves open the possibility that mapping class groups are abstractly commensurable to right-angled Artin groups, that is, that they have isomorphic finite-index subgroups. We prove that, aside from a small number of exceptions, this is not the case. We also extend this result to several classes of groups related to mapping class groups. We start by recalling some definitions. To a finite graph , we can associate a right-angled Artin grou p: this is the group with one generator for each vertex of , and one defin ing relator for each edge, namely, the commutator of the two generators corresponding to the endpoints. Let Sg,n denote a closed, connected, orientable surface of genus g with n marked points. The mapping class group Mod(Sg,n) is the group of homotopy classes of orientation-preserving homeomorphisms of Sg,n preserving the set of marked points. As discussed in Koberda's paper (27, Theorem 1.5), no finite-index subgroup of Mod(Sg,n) injects into a right-angled Artin group if g ≥ 2 and (g,n) 6 (2,0); see
Tithonus: A Bitcoin Based Censorship Resilient System

Providing reliable and surreptitious communications is difficult in the presence of adaptive and resourceful state level censors. In this paper we introduce Tithonus, a framework that builds on the Bitcoin blockchain and network to provide censorship-resistant communication mechanisms. In contrast to previous approaches, we do not rely solely on the slow and expensive blockchain consensus mechanism but instead fully exploit Bitcoin's peer-to-peer gossip protocol. We develop adaptive, fast and cost effective data communication solutions that camouflage client requests into inconspicuous Bitcoin transactions. We propose solutions to securely request and transfer content, with unobservability and censorship resistance, and free, pay-per-access and subscription based payment options. When compared to state-of-the-art Bitcoin writing solutions, Tithonus reduces the cost of transferring data to censored clients by 2 orders of magnitude and increases the goodput by 3 to 5 orders of magnitude. We show that Tithonus client initiated transactions are hard to detect, while server initiated transactions cannot be censored without creating split world problems to the Bitcoin blockchain.
Optimal bilinear restriction estimates for general hypersurfaces and the role of the shape operator

It is known that under some transversality and curvature assumptions on the hypersurfaces involved, the bilinear restriction estimate holds true with better exponents than what would trivially follow from the corresponding linear estimates. This subject was extensively studied for conic and parabolic surfaces with sharp results proved by Wolff and Tao, and with later generalizations by Lee. In this paper we provide a unified theory for general hypersurfaces and clarify the role of curvature in this problem, by making statements in terms of the shape operators of the hypersurfaces involved.
Community Recovery in a Preferential Attachment Graph

A message passing algorithm is derived for recovering communities within a graph generated by a variation of the Barabasi–Albert preferential attachment model. The estimator is assumed to know the arrival times, or order of attachment, of the vertices. The derivation of the algorithm is based on belief propagation under an independence assumption. Two precursors to the message passing algorithm are analyzed: the first is a degree thresholding (DT) algorithm and the second is an algorithm based on the arrival times of the children (C) of a given vertex, where the children of a given vertex are the vertices that attached to it. Comparison of the performance of the algorithms shows it is beneficial to know the arrival times, not just the number, of the children. The probability of correct classification of a vertex is asymptotically determined by the fraction of vertices arriving before it. Two extensions of Algorithm C are given: the first is based on joint likelihood of the children of a fixed set of vertices; it can sometimes be used to seed the message passing algorithm. The second is the message passing algorithm. Simulation results are given.
Positive entropy equilibrium states

For transitive shifts of finite type, and more generally for shifts with specification, it is well-known that every equilibrium state for a Holder continuous potential has positive entropy as long as the shift has positive topological entropy. We give a non-uniform specification condition under which this property continues to hold, and demonstrate that it does not necessarily hold for other non-uniform versions of specification that have been introduced elsewhere.
Convex functions and geodesic connectedness of space-times

Abstract This paper explores the relation between convex functions and the geometry of space-times and semi-Riemannian manifolds. Specifically, we study geodesic connectedness. We give geometric–topological proofs of geodesic connectedness for classes of space-times to which known methods do not apply. For instance: A null-disprisoning space-time is geodesically connected if it supports a proper, nonnegative strictly convex function whose critical set is a point. Timelike strictly convex hypersurfaces of Minkowski space are geodesically connected. We also give a criterion for the existence of a convex function on a semi-Riemannian manifold. We compare our work with previously known results.
Studies of parton propagation and hadron formation in the space-time domain

Over the past decade, new data from HERMES, Jefferson Lab, Fermilab, and RHIC that connect to parton propagation and hadron formation have become available. Semi‐inclusive DIS on nuclei, the Drell‐Yan reaction, and heavy‐ion collisions all bring different kinds of information on parton propagation within a medium, while the most direct information on hadron formation comes from the DIS data. Over the next decade one can hope to begin to understand these data within a unified picture. We briefly survey the most relevant data and the common elements of the physics picture, then highlight the new Jefferson Lab data, and close with a prospective for the future.
Topological superfluidity with repulsive alkaline-earth atoms in optical lattices

Topological superfluids are of technological relevance since they are believed to host Majorana bound states, a powerful resource for quantum computation and memory. Here we propose to realize topological superfluidity with fermionic atoms in an optical lattice. We consider a situation where atoms in two internal states experience different lattice potentials: one species is localized and the other itinerant, and show how quantum fluctuations of the localized fermions give rise to an attraction and strong spin-orbit coupling in the itinerant band. At low temperature, these effects stabilize a topological superfluid of mobile atoms even if their bare interactions are repulsive. This emergent state can be engineered with ${}^{87}$Sr atoms in a superlattice with a dimerized unit cell. To probe its unique properties we describe protocols that use high spectral resolution and controllability of the Sr clock transition, such as momentum-resolved spectroscopy and supercurrent response to a synthetic (laser-induced) magnetic field.
r-Robustness and (r, s)-robustness of circulant graphs

There has been recent growing interest in graph theoretical properties known as r- and (r, s) -robustness. These properties serve as sufficient conditions guaranteeing the success of certain consensus algorithms in networks with misbehaving agents present. Due to the complexity of determining the robustness for an arbitrary graph, several methods have previously been proposed for identifying the robustness of specific classes of graphs or constructing graphs with specified robustness levels. The majority of such approaches have focused on undirected graphs. In this paper we identify a class of scalable directed graphs whose edge set is determined by a parameter k and prove that the robustness of these graphs is also determined by k. We support our results through computer simulations.
On periodic critical points and local minimizers of the Ohta–Kawasaki functional

Abstract In this paper we collect some new observations about periodic critical points and local minimizers of a nonlocal isoperimetric problem arising in the modeling of diblock copolymers. In the main result, by means of a purely variational procedure, we show that it is possible to construct (locally minimizing) periodic critical points whose shape resemble that of any given strictly stable constant mean curvature (periodic) hypersurface. Along the way, we establish several auxiliary results of independent interest.
Automorphisms of decompositions

Harding showed that the direct product decompositions of many different types of structures, such as sets, groups, vector spaces, topological spaces, and relational structures, naturally form orthomodular posets. When applied to the direct product decompositions of a Hilbert space, this construction yields the familiar orthomodular lattice of closed subspaces of the Hilbert space. In this note we consider orthomodular posets Fact X of decompositions of a finite set X. We consider the structure of these orthomodular posets, such as their size, shape, and connectedness, states, and begin a study of their automorphism groups in the context of the natural map \Gamma from the group of permutations of X to the automorphism group of Fact X. We show \Gamma is an embedding except when |X| is prime or 4, and completely describe the situation when |X| has two or fewer prime factors, when |X|=8 and when |X|=27. The bulk of our effort lies in a series of combinatorial arguments to show \Gamma is an isomorphism when |X|=27. We conjecture that this is the case whenever |X| has sufficiently many prime factors of sufficient size, and hope that our arguments here might be adapted to the general case.
Structure–function relationships of fullerene esters in polymer solar cells: unexpected structural effects on lifetime and efficiency

We report both transport measurements and spectroscopic data of polymer/fullerene blend photovoltaics using a small library of fullerene esters to correlate device properties with a range of functionality and structural diversity of the ester substituent. We observe that minor structural changes can lead to significant differences in device efficiency and lifetime. Surprisingly, we have found that isomeric R-groups in the fullerene ester-based devices we have studied have very different efficiencies. The characteristic lifetimes derived from both transport and spectroscopic measurements are generally comparable, however some more rapid effects in specific fullerene esters are not observed spectroscopically. Our results support using a library approach for optimizing device performance in these systems.
An extension of the Bianchi–Egnell stability estimate to Bakry, Gentil, and Ledoux's generalization of the Sobolev inequality to continuous dimensions

Abstract This paper extends a stability estimate of the Sobolev Inequality established by Bianchi and Egnell in [3] . Bianchi and Egnell's Stability Estimate answers the question raised by H. Brezis and E.H. Lieb in [5] : “Is there a natural way to bound ‖ ∇ φ ‖ 2 2 − C N 2 ‖ φ ‖ 2 N N − 2 2 from below in terms of the ‘distance’ of φ from the manifold of optimizers in the Sobolev Inequality?” Establishing stability estimates – also known as quantitative versions of sharp inequalities – of other forms of the Sobolev Inequality, as well as other inequalities, is an active topic. See [9] , [11] , and [12] , for stability estimates involving Sobolev inequalities and [6] , [11] , and [14] for stability estimates on other inequalities. In this paper, we extend Bianchi and Egnell's Stability Estimate to a Sobolev Inequality for “continuous dimensions.” Bakry, Gentil, and Ledoux have recently proved a sharp extension of the Sobolev Inequality for functions on R + × R n , which can be considered as an extension to “continuous dimensions.” V.H. Nguyen determined all cases of equality. The present paper extends the Bianchi–Egnell stability analysis for the Sobolev Inequality to this “continuous dimensional” generalization.
Process-Oriented Iterative Multiple Alignment for Medical Process Mining

Adapted from biological sequence alignment, trace alignment is a process mining technique used to visualize and analyze workflow data. Any analysis done with this method, however, is affected by the alignment quality. The best existing trace alignment techniques use progressive guide-trees to heuristically approximate the optimal alignment in O(N2L2) time. These algorithms are heavily dependent on the selected guide-tree metric, often return sum-of-pairs-score-reducing errors that interfere with interpretation, and are computationally intensive for large datasets. To alleviate these issues, we propose process-oriented iterative multiple alignment (PIMA), which contains specialized optimizations to better handle workflow data. We demonstrate that PIMA is a flexible framework capable of achieving better sum-of-pairs score than existing trace alignment algorithms in only O(NL2) time. We applied PIMA to analyzing medical workflow data, showing how iterative alignment can better represent the data and facilitate the extraction of insights from data visualization.
The Transition Matrix Between the Specht and Web Bases is Unipotent with Additional Vanishing Entries

We compare two important bases of an irreducible representation of the symmetric group: the web basis and the Specht basis. The web basis has its roots in the Temperley-Lieb algebra and knot-theoretic considerations. The Specht basis is a classic algebraic and combinatorial construction of symmetric group representations which arises in this context through the geometry of varieties called Springer fibers. We describe a graph that encapsulates combinatorial relations between each of these bases, prove that there is a unique way (up to scaling) to map the Specht basis into the web representation, and use this to recover a result of Garsia-McLarnan that the transition matrix between the Specht and web bases is upper-triangular with ones along the diagonal. We then strengthen their result to prove vanishing of certain additional entries unless a nesting condition on webs is satisfied. In fact we conjecture that the entries of the transition matrix are nonnegative and are nonzero precisely when certain directed paths exist in the web graph.
Phase Retrieval with Polarization

In many areas of imaging science, it is difficult to measure the phase of linear measurements. As such, one often wishes to reconstruct a signal from intensity measurements, that is, perform phase retrieval. In this paper, we provide a novel measurement design which is inspired by interferometry and exploits certain properties of expander graphs. We also give an efficient phase retrieval procedure, and use recent results in spectral graph theory to produce a stable performance guarantee which rivals the guarantee for PhaseLift in [Candes, Strohmer, and Voroninski, PhaseLift: Exact and Stable Signal Recovery from Magnitude Measurements via Convex Programming, preprint, arXiv:1109.4499, 2011]. We use numerical simulations to illustrate the performance of our phase retrieval procedure, and we compare reconstruction error and runtime with a common alternating-projections-type procedure.
Resolutions of Hilbert Modules and Similarity

Let \(H^{2}_{m}\) be the Drury–Arveson (DA) module which is the reproducing kernel Hilbert space with the kernel function \((z, w) \in\mathbb{B}^{m} \times\mathbb{B}^{m} \rightarrow (1 - \sum_{i=1}^{m}z_{i} \bar{w}_{i})^{-1}\). We investigate for which multipliers \(\theta: \mathbb{B}^{m} \rightarrow \mathcal{L}(\mathcal{E}, \mathcal {E}_{*})\) with ran Mθ closed, the quotient module \(\mathcal{H}_{\theta}\), given by $$\cdots\longrightarrow H^2_m \otimes\mathcal{E} \stackrel{M_{\theta }}{\longrightarrow}H^2_m \otimes\mathcal{E}_* \stackrel{\pi_{\theta}}{\longrightarrow}\mathcal{H}_{\theta}\longrightarrow0,$$ is similar to \(H^{2}_{m} \otimes \mathcal {F}\) for some Hilbert space \(\mathcal{F}\). Here Mθ is the corresponding multiplication operator in \(\mathcal{L}(H^{2}_{m} \otimes\mathcal{E}, H^{2}_{m} \otimes\mathcal{E}_{*})\) for Hilbert spaces \(\mathcal{E}\) and \(\mathcal{E}_{*}\) and \(\mathcal {H}_{\theta}\) is the quotient module \((H^{2}_{m} \otimes\mathcal{E}_{*})/ M_{\theta}(H^{2}_{m} \otimes\mathcal{E})\), and πθ is the quotient map. We show that a necessary condition is the existence of a multiplier ψ in \(\mathcal{M}(\mathcal{E}_{*}, \mathcal{E})\) such that $$\theta\psi\theta= \theta.$$ Moreover, we show that the converse is equivalent to a structure theorem for complemented submodules of \(H^{2}_{m} \otimes\mathcal{E}\) for a Hilbert space \(\mathcal {E}\), which is valid for the case of m=1. The latter result generalizes a known theorem on similarity to the unilateral shift, but the above statement is new. Further, we show that a finite resolution of DA-modules of arbitrary multiplicity using partially isometric module maps must be trivial. Finally, we discuss the analogous questions when the underlying operator m-tuple (or algebra) is not necessarily commuting (or commutative). In this case the converse to the similarity result is always valid.
Cracking the cocktail party problem by multi-beam deep attractor network

While recent progresses in neural network approaches to singlechannel speech separation, or more generally the cocktail party problem, achieved significant improvement, their performance for complex mixtures is still not satisfactory. In this work, we propose a novel multi-channel framework for multi-talker separation. In the proposed model, an input multi-channel mixture signal is firstly converted to a set of beamformed signals using fixed beam patterns. For this beamforming, we propose to use differential beamformers as they are more suitable for speech separation. Then each beamformed signal is fed into a single-channel anchored deep attractor network to generate separated signals. And the final separation is acquired by post selecting the separating output for each beams. To evaluate the proposed system, we create a challenging dataset comprising mixtures of 2, 3 or 4 speakers. Our results show that the proposed system largely improves the state of the art in speech separation, achieving 11.5 dB, 11.76 dB and 11.02 dB average signal-to-distortion ratio improvement for 4, 3 and 2 overlapped speaker mixtures, which is comparable to the performance of a minimum variance distortionless response beamformer that uses oracle location, source, and noise information. We also run speech recognition with a clean trained acoustic model on the separated speech, achieving relative word error rate (WER) reduction of 45.76%, 59.40% and 62.80% on fully overlapped speech of 4, 3 and 2 speakers, respectively. With a far talk acoustic model, the WER is further reduced.
Deep Convolutional Ranking for Multilabel Image Annotation

Abstract: Multilabel image annotation is one of the most important challenges in computer vision with many real-world applications. While existing work usually use conventional visual features for multilabel annotation, features based on Deep Neural Networks have shown potential to significantly boost performance. In this work, we propose to leverage the advantage of such features and analyze key components that lead to better performances. Specifically, we show that a significant performance gain could be obtained by combining convolutional architectures with approximate top-$k$ ranking objectives, as thye naturally fit the multilabel tagging problem. Our experiments on the NUS-WIDE dataset outperforms the conventional visual features by about 10%, obtaining the best reported performance in the literature.
Controllability of Conjunctive Boolean Networks With Application to Gene Regulation

A Boolean network is a finite-state discrete-time dynamical system. At each step, each variable takes a value from a binary set. The value update rule for each variable is a local function which depends only on a selected subset of variables. Boolean networks have been used in modeling gene regulatory networks. In this paper, we focus on a special class of Boolean networks, namely, the conjunctive Boolean networks (CBNs), whose value update rule is comprised of only logic AND operations. It is known that any trajectory of a Boolean network will enter a periodic orbit. Periodic orbits of a CBN have been completely understood. In this paper, we investigate the orbit-controllability and state-controllability of a CBN: We ask the question of how one can steer a CBN to enter any periodic orbit or to reach any final state, from any initial state. We establish necessary and sufficient conditions for a CBN to be orbit-controllable and state-controllable. Furthermore, explicit control laws are presented along the analysis.
Cooperative Robot Localization Using Event-Triggered Estimation

This paper describes a novel communication-spare cooperative localization algorithm for a team of mobile unmanned robotic vehicles. Exploiting an event-based estimation paradigm, robots only send m...