cssi/SciSciGPT-SciSciNet huggingface dataset:
Classical Lower Bounds from Quantum Upper Bounds

We prove lower bounds on complexity measures, such as the approximate degree of a Boolean function and the approximate rank of a Boolean matrix, using quantum arguments. We prove these lower bounds using a quantum query algorithm for the combinatorial group testing problem. We show that for any function f, the approximate degree of computing the OR of n copies of f is Omega(sqrt n) times the approximate degree of f, which is optimal. No such general result was known prior to our work, and even the lower bound for the OR of ANDs function was only resolved in 2013. We then prove an analogous result in communication complexity, showing that the logarithm of the approximate rank (or more precisely, the approximate gamma-2 norm) of F: X x Y to 0,1 grows by a factor of Omega (sqrtn) when we take the OR of n copies of F, which is also essentially optimal. As a corollary, we give a new proof of Razborov's celebrated Omega(sqrtn) lower bound on the quantum communication complexity of the disjointness problem. Finally, we generalize both these results from composition with the OR function to composition with arbitrary symmetric functions, yielding nearly optimal lower bounds in this setting as well.
Achieving Fair Treatment in Algorithmic Classification

Fairness in classification has become an increasingly relevant and controversial issue as computers replace humans in many of today’s classification tasks. In particular, a subject of much recent debate is that of finding, and subsequently achieving, suitable definitions of fairness in an algorithmic context. In this work, following the work of Hardt et al. (NIPS’16), we consider and formalize the task of sanitizing an unfair classifier \(\mathcal {C}\) into a classifier \(\mathcal {C}'\) satisfying an approximate notion of “equalized odds” or fair treatment. Our main result shows how to take any (possibly unfair) classifier \(\mathcal {C}\) over a finite outcome space, and transform it—by just perturbing the output of \(\mathcal {C}\)—according to some distribution learned by just having black-box access to samples of labeled, and previously classified, data, to produce a classifier \(\mathcal {C}'\) that satisfies fair treatment; we additionally show that our derived classifier is near-optimal in terms of accuracy. We also experimentally evaluate the performance of our method.
The Evolving Distribution of Giving in the United States

I compute the share of U.S. household giving accounted for by the American tax units donating the largest amounts over the 1960–2012 period from repeated cross-sectional samples of federal income t...
Predicting retinal tissue oxygenation using an image-based theoretical model

Abstract Impaired oxygen delivery and tissue perfusion have been identified as significant factors that contribute to the loss of retinal ganglion cells in glaucoma patients. This study predicts retinal blood and tissue oxygenation using a theoretical model of the retinal vasculature based on confocal microscopy images of the mouse retina. These images reveal a complex and heterogeneous geometry of vessels that are distributed non-uniformly into multiple distinct retinal layers at varying depths. Predicting oxygen delivery and distribution in this irregular arrangement of retinal microvessels requires the use of an efficient theoretical model. The model employed in this work utilizes numerical methods based on a Green's function approach to simulate the spatial distribution of oxygen levels in a network of retinal blood vessels and the tissue surrounding them. Model simulations also predict the blood flow rates and pressures in each of the microvessels throughout the entire network. As expected, the model predicts that average vessel PO2 decreases as oxygen demand is increased. However, the standard deviation of PO2 in the vessels nearly doubles as oxygen demand is increased from 1 to 8 cm3 O2/100 cm3/min, indicating a very wide spread in the predicted PO2 levels, suggesting that average PO2 is not a sufficient indicator of oxygenation in a heterogeneous vascular network. Ultimately, the development of this mathematical model will help to elucidate the important factors associated with blood flow and metabolism that contribute to the vision loss characteristic of glaucoma.
Paleomagnetic Biases Inferred From Numerical Dynamos and the Search for Geodynamo Evolution

The paleomagnetic record is central to our understanding of the history of the Earth. The orientation and intensity of magnetic minerals preserved in ancient rocks indicate the geodynamo has been alive since at least the Archean and possibly the Hadean. A paleomagnetic signature of the solidification of the inner core, arguably the singular most important event in core history, however, has remained elusive. In pursuit of this signature we investigate a suite of numerical dynamo simulations from a paleomagnetic perspective to explore how long the field should be time-averaged to obtain stable paleomagnetic pole directions and intensities. We find that running averages over $20-40$ kyr are needed to obtain stable paleomagnetic poles with $\alpha_{95}<10^\circ$, and over $40-120$ kyr for $\alpha_{95}<5^\circ$, depending on the variability of the field. We find that models with higher heat flux and more frequent polarity reversals require longer time averages, and that obtaining stable intensities requires longer time averaging than obtaining stable directions. Running averages of local field intensity and inclination produce reliable estimates of the underlying dipole moment when reversal frequency is low. However, when heat flux and reversal frequency are increased we find that local observations tend to underestimate virtual dipole moment (VDM) by up to $50\%$ and overestimate virtual axial dipole moment (VADM) by up to $150\%$. A latitudinal dependence is found where VDM underestimates the true dipole moment more at low latitudes, while VADM overestimates the true axial dipole moment more at high latitudes. The cause for these observed intensity biases appears to be a contamination of the time averaged field by non-GAD terms, which grows with reversal frequency. We derive a scaling law connecting reversal frequency and site paleolatitude to paleointensity bias (ratio of observed to the true value). Finally we apply this adjustment to the PINT paleointensity record. These biases produce little change to the overall trend of a relatively flat but scattered intensity over the last 3.5 Ga. A more careful intensity adjustment applied during periods when the reversal frequency is known could reveal previously obscured features in the paleointensity record.
Perspectives on mental accounting: An exploration of budgeting and investing

This article provides an overview of recent advances in the literature on mental accounting within the context of consumer financial decision‐making. We first discuss the categorization process that underlies mental accounting and the methods people use to categorize funds. We then highlight some of the notable work that examines how mental accounting influences budgeting, spending, and investment decisions. The article concludes by proposing an agenda for future research, focusing on current gaps in our knowledge and promising areas to explore. Full Text Available Here: https://doi.org/10.1002/cfp2.1011
Issues Encountered Deploying Differential Privacy

When differential privacy was created more than a decade ago, the motivating example was statistics published by an official statistics agency. In attempting to transition differential privacy from the academy to practice, the U.S. Census Bureau has encountered many challenges unanticipated by differential privacy's creators. These challenges include obtaining qualified personnel and a suitable computing environment, the difficulty accounting for all uses of the confidential data, the lack of release mechanisms that align with the needs of data users, the expectation on the part of data users that they will have access to micro-data, and the difficulty in setting the value of the privacy-loss parameter, ? (epsilon), and the lack of tools and trained individuals to verify the correctness of differential privacy implementations.
Novel Single View Constraints for Manhattan 3D Line Reconstruction

This paper proposes a novel and exact method to reconstruct line-based 3D structure from a single image using Manhattan world assumption. This problem is a distinctly unsolved problem because there can be multiple 3D reconstructions from a single image. Thus, we are often forced to look for priors on Manhattan world and common scene structures. In addition to the standard orthogonality, linear perspective, and parallelism constraints, we investigate a few novel constraints based on the physical realizability of the scene structure. We treat the line segments in the image to be part of a graph similar to \emph{\bf straws and connectors game}, where the goal is to back-project the line segments in 3D space and while ensuring that some of these 3D line segments connect with each other (i.e., truly intersect in 3D space) to form the 3D structure. We consider three sets of novel constraints while solving the reconstruction: (1) constraints on a series of Manhattan line intersections that form cycles, but are not all physically realizable, (2) constraints on true and false intersections in the case of nearby lines lying on the same Manhattan plane, and (3) constraints on the intersections of boundary and non-boundary line segments. The reconstruction is achieved using mixed integer linear programming (MILP), and we show compelling results on real images. Along with this paper, we release a challenging Single View Line Reconstruction dataset with ground truth 3D line models for research purposes.
Filtration Simplification for Persistent Homology via Edge Contraction

Persistent homology is a popular data analysis technique that is used to capture the changing topology of a filtration associated with some simplicial complex K. These topological changes are summarized in persistence diagrams. We propose two contraction operators which when applied to K and its associated filtration, bound the perturbation in the persistence diagrams. The first assumes that the underlying space of K is a 2-manifold and ensures that simplices are paired with the same simplices in the contracted complex as they are in the original. The second is for arbitrary d-complexes, and bounds the bottleneck distance between the initial and contracted p-dimensional persistence diagrams. This is accomplished by defining interleaving maps between persistence modules which arise from chain maps defined over the filtrations. In addition, we show how the second operator can efficiently compose with itself across multiple contractions. The paper concludes with experiments demonstrating the second operator’s utility on manifolds and a brief discussion of future directions for research.
Total-internal-reflection elastic metasurfaces: Design and application to structural vibration isolation

This letter presents the concept of the Total Internal Reflection metasurface (TIR-MS) which supports the realization of structure-embedded subwavelength acoustic shields for elastic waves propagating in thin waveguides. The proposed metasurface design exploits extreme phase gradients, implemented via locally resonant elements, in order to achieve operating conditions that are largely beyond the critical angle. Such artificial discontinuity is capable of producing complete reflection of the incoming waves regardless of the specific angle of incidence. From a practical perspective, the TIR-MS behaves as a sound hard barrier that is impenetrable to long-wavelength modes at a selected frequency. The TIR metasurface concept is first conceived for a flat interface embedded in a rectangular waveguide and designed to block longitudinal S0-type guided modes. Then, it is extended to circular plates in order to show how enclosed areas can be effectively shielded by incoming waves. Given the same underlying physics, an equivalent dynamic behavior was also numerically and experimentally illustrated for flexural A0-type guided modes. This study shows numerical and experimental evidence that, when the metasurface is excited at the target frequency, significant vibration isolation can be achieved in the presence of waves having any arbitrary angle of incidence. These results open interesting paths to achieve vibration isolation and energy filtering in certain prototypical structures of interest for practical engineering applications.
Dynamics of Ion Beam Charge Neutralization by Ferroelectric Plasma Sources

Ferroelectric Plasma Sources (FEPS) can generate plasma that provides effective space-charge neutralization of intense high-perveance ion beams. Here we present experimental results on charge neutralization of a high-perveance 38 keV Ar+ beam by a FEPS plasma. By comparing the measured beam radius with the envelope model for space-charge expansion, it is shown that a charge neutralization fraction of 98% is attainable. The transverse electrostatic potential of the ion beam is reduced from 15 V before neutralization to 0.3 V, implying that the energy of the neutralizing electrons is below 0.3 eV. Near-complete charge neutralization is established in approximately 5 μs after the driving pulse is applied to the FEPS, and can last for 35 μs. It is argued that the duration of neutralization is much longer than a reasonable lifetime of the plasma produced in the sub-μs surface discharge. Measurements of current flow in the driving circuit of the FEPS suggest that plasma can be generated for tens of μs after the high voltage pulse is applied. This is confirmed by fast photography of the plasma in the 1-meter long FEPS on the Neutralized Drift Compression Experiment-II at LBL, where effective charge neutralization of the ion beam pulse was achieved with the optimized FEPS timing.
How Much of Barrier to Entry is Occupational Licensing

We exploit state variation in licensing laws to study the effect of licensing on occupational choice using a boundary discontinuity design. We find that licensing reduces equilibrium labour supply by an average of 17–27 per cent.
Structural basis of tubulin recruitment and assembly by microtubule polymerases with Tumor Overexpressed Gene (TOG) domain arrays.

XMAP215/Stu2/Alp14 proteins accelerate microtubule plus-end polymerization by recruiting tubulins via arrays of tumor overexpressed gene (TOG) domains, yet their mechanism remains unknown. Here, we describe the biochemical and structural basis for TOG arrays in recruiting and polymerizing tubulins. Alp14 binds four tubulins via dimeric TOG1-TOG2 subunits, in which each domain exhibits a distinct exchange rate for tubulin. X-ray structures revealed square-shaped assemblies composed of pseudo-dimeric TOG1-TOG2 subunits assembled head-to-tail, positioning four unpolymerized tubulins in a polarized wheel-like configuration. Crosslinking and electron microscopy show Alp14-tubulin forms square assemblies in solution, and inactivating their interfaces destabilize this organization without influencing tubulin binding. An X-ray structure determined using approach to modulate tubulin polymerization revealed an unfurled assembly, in which TOG1-TOG2 uniquely bind to two polymerized tubulins. Our findings suggest a new microtubule polymerase model in which TOG arrays recruit tubulins by forming square assemblies that then unfurl, facilitating their concerted polymerization into protofilaments.
How Does Cilium Length Affect Beating

Abstract The effects of cilium length on the dynamics of cilia motion were investigated by high-speed video microscopy of uniciliated mutants of the swimming alga, Chlamydomonas reinhardtii. Cells with short cilia were obtained by deciliating cells via pH shock and allowing cilia to reassemble for limited times. The frequency of cilia beating was estimated from the motion of the cell body and of the cilium. Key features of the ciliary waveform were quantified from polynomial curves fitted to the cilium in each image frame. Most notably, periodic beating did not emerge until the cilium reached a critical length between 2 and 4 μm. Surprisingly, in cells that exhibited periodic beating, the frequency of beating was similar for all lengths with only a slight decrease in frequency as length increased from 4 μm to the normal length of 10–12 μm. The waveform average curvature (rad/μm) was also conserved as the cilium grew. The mechanical metrics of ciliary propulsion (force, torque, and power) all increased in proportion to length. The mechanical efficiency of beating appeared to be maximal at the normal wild-type length of 10–12 μm. These quantitative features of ciliary behavior illuminate the biophysics of cilia motion and, in future studies, may help distinguish competing hypotheses of the underlying mechanism of oscillation.
Zero-shot Deep Reinforcement Learning Driving Policy Transfer for Autonomous Vehicles based on Robust Control

Although deep reinforcement learning (deep RL) methods have lots of strengths that are favorable if applied to autonomous driving, real deep RL applications in autonomous driving have been slowed down by the modeling gap between the source (training) domain and the target (deployment) domain. Unlike current policy transfer approaches, which generally limit to the usage of uninterpretable neural network representations as the transferred features, we propose to transfer concrete kinematic quantities in autonomous driving. The proposed robust-control-based (RC) generic transfer architecture, which we call RL-RC, incorporates a transferable hierarchical RL trajectory planner and a robust tracking controller based on disturbance observer (DOB). The deep RL policies trained with known nominal dynamics model are transfered directly to the target domain, DOB-based robust tracking control is applied to tackle the modeling gap including the vehicle dynamics errors and the external disturbances such as side forces. We provide simulations validating the capability of the proposed method to achieve zero-shot transfer across multiple driving scenarios such as lane keeping, lane changing and obstacle avoidance.
Emergent Properties of a Market-based Digital Library with Strategic Agents

The University of Michigan Digital Library (UMDL) is designed as an open system that allows third parties to build and integrate their own profit-seeking agents into the marketplace of information goods and services. The profit-seeking behavior of agents, however, risks inefficient allocation of goods and services, as agents take strategic stances that might backfire. While it would be good if we could impose mechanisms to remove incentives for strategic reasoning, this is not possible in the UMDL. Therefore, our approach has instead been to study whether encouraging the other extreme—making strategic reasoning ubiquitous—provides an answer. Toward this end, we have designed a strategy (called the p-strategy) that uses a stochastic model of the market to find the best offer price. We have then examined the collective behavior of p-strategy agents in the UMDL auction. Our experiments show that strategic thinking is not always beneficial and that the advantage of being strategic decreases with the arrival of equally strategic agents. Furthermore, a simpler strategy can be as effective when enough other agents use the p-strategy. Consequently, we expect the UMDL is likely to evolve to a point where some agents use simpler strategies and some use the p-strategy.
Financial crises: past and future

This article takes a selective global tour of some of the prominent economic and financial risks in advanced, emerging, and low-income developing economies. The primary emphasis is on near-term risks. The discussion covers areas where vulnerabilities have either already become manifest, or those where risks are mounting but have not yet sounded a glaring alarm. For the advanced economies, the topics cover aspects of the recent surge in collateralized lending obligations in the United States and Europe that are reminiscent of the pre-crisis boom in mortgage-backed securities as well as Italy’s unresolved debt overhang. On emerging markets (EMs) and developing economies, the themes cover the curious case of the missing defaults (2011–2018); global factors and EM turbulence; and China’s international lending to low-income countries and its consequences. A brief discussion of some persistent medium-to-long-term concerns about the rising levels of US public debt and the tensions that arise from internal economic objectives and the external pressures associated with the US dollar’s role as the world’s principal reserve currency completes the discussion.
Projection Learning

A method of combining learning algorithms is described that preserves attribute-efficiency. It yields learning algorithms that require a number of examples that is polynomial in the number of relevant variables and logarithmic in the number of irrelevant ones. The algorithms are simple to implement and realizable on networks with a number of nodes linear in the total number of variables. They include generalizations of Littlestone‘s Winnow algorithm, and are, therefore, good candidates for experimentation on domains having very large numbers of attributes but where nonlinear hypotheses are sought.
Knowledge Graph Fact Prediction via Knowledge-Enriched Tensor Factorization

Abstract We present a family of novel methods for embedding knowledge graphs into real-valued tensors. These tensor-based embeddings capture the ordered relations that are typical in the knowledge graphs represented by semantic web languages like RDF. Unlike many previous models, our methods can easily use prior background knowledge provided by users or extracted automatically from existing knowledge graphs. In addition to providing more robust methods for knowledge graph embedding, we provide a provably-convergent, linear tensor factorization algorithm. We demonstrate the efficacy of our models for the task of predicting new facts across eight different knowledge graphs, achieving between 5% and 50% relative improvement over existing state-of-the-art knowledge graph embedding techniques. Our empirical evaluation shows that all of the tensor decomposition models perform well when the average degree of an entity in a graph is high, with constraint-based models doing better on graphs with a small number of highly similar relations and regularization-based models dominating for graphs with relations of varying degrees of similarity.
Endowment Taxation and Equality of Resources

This Article has two primary aims. The first is to provide an in-depth survey of recent legal academic literature on endowment (or ability) taxation, which is a tax on a person’s maximum potential earnings over a given period. This scheme of taxation, which has for some time enjoyed favor as an ideal among economists, has recently gained significant support from tax law scholars as well. The second aim is to demonstrate that a seemingly elegant justification for the endowment tax, which attempts to reconcile the demands of equity and liberty within a certain luck egalitarian framework—Ronald Dworkin’s “equality of resources”—is not ultimately successful. Thus, the firmness of the endowment tax’s normative foundations remains far from settled.
Radiographic abnormalities, bladder interventions, and bladder surgery in the first decade of life in children with spina bifida

Spina bifida (SB) patients are at increased risk for hydronephrosis, bladder storage and emptying problems, and renal failure that may require multiple bladder surgeries. We retrospectively reviewed patients born with SB 2005–2009, presenting to our institution within 1 year of birth. Outcomes at 8–11 years old included final renal/bladder ultrasound (RBUS) results, clean intermittent catheterization (CIC) use, anticholinergic use, surgical interventions, and final renal function. We excluded those without follow-up past age 8 and/or no RBUS or fluoroscopic urodynamic images (FUI) within the first year of life. Imaging was independently reviewed by four pediatric urologists blinded to radiologists’ interpretation and initial findings compared with final outcomes. Of 98 children, 62 met inclusion criteria (48% male, 76% shunted). Median age at last follow-up was 9.6 years. Upon initial imaging, 74% had hydronephrosis (≥ SFU grade 1), decreasing to 5% at 10 years (p < 0.0001). Initially, 9% had ≥ SFU grade 3 hydronephrosis, decreasing to 2% (p = 0.13). CIC and anticholinergic use increased from 61% and 37% to 87% and 86%, respectively (p = 0.001 and p < 0.0001, respectively). With follow-up, 55% had surgical intervention and 23% had an augmentation. Of children with a serum creatinine/cystatin-C at 8–11 years old, one had confirmed chronic kidney disease (stage 2). Despite initial high incidence of hydronephrosis, this was low grade and resolved in the first decade of life. Additionally, the 8–11-year incidence of kidney disease and upper tract changes was low due to aggressive medical management.
Effects of repeated injection of sublethal doses of soman on behavior and on brain acetylcholine and choline concentrations in the rat.

The effects of repeated exposure to a sublethal dose (60 µg/kg; 0.4 LD50) of soman on brain regional acetylcholine (ACh) and choline (Ch) levels, spinal cord cholinesterase (ChE) activity and on water consumption, body weight and gross behavioral changes were examined. Male rats were dosed once a week or three times a week and at 24 h after 2, 4 or 6 weeks of dosing, selected brain tissues and behavior were examined. During the 6-week period, there was no difference between control and soman-dosed rats in water consumption or body weight under either treatment regimen. The animals treated once a week adapted to this exposure regimen well. They exhibited no change in the levels of ACh or Ch in any of the brain areas when examined at the end of 2, 4 or 6 weeks, nor did they show any obvious signs of poisoning. The total ChE activity fluctuated between 70 and 100% of control. When treated three times a week, however, survivors (90%) of the somantreated rats developed signs that progressed in severity to a hyper-reactivity syndrome which consisted of an exaggerated reaction to mild tactile stimuli. Brain ACh levels did not change and ChE activity showed inhibition of 40, 58 and 75% when measured at 2, 4 and 6 weeks, respectively. At the end of 6 weeks, the levels of Ch, except in the striatum, were significantly elevated in brainstem, cerebral cortex, hippocampus, midbrain, and cerebellum (52%, 147%, 68%, 46%, and 91%, respectively), indicating that Ch metabolism in neuronal membranes may be altered following more frequent low-dose soman exposures.
Constraints on the number of X-ray pulsars in IC 10 from a deep XMM-Newton observation

We report the most sensitive search yet for X-ray pulsars in the dwarf starburst galaxy IC 10, which is known to contain a population of young high mass X-ray binaries. We searched for pulsations in 207 point-like X-ray sources in the direction of IC 10 by a 2012 \xmm~observation with a total exposure time of 134.5 ks. Pulsation searches in faint objects can be sensitive to the energy bands of the light curves, and the source and background extraction areas. We analyzed separately the PN and MOS barycenter corrected 0.2-12 keV data, with good time interval filtering. Different schemes for source and background extraction were compared, and the search was repeated in the narrower 0.5-8 keV energy band to increase the signal-to-noise ratio. For the most conservative parameters, 5 point sources produced significant peaks in the Lomb-Scargle periodogram (99\% significance, single trial, assuming white noise). A similar number of different candidates result from alternative analyses. A $\sim$4100 s period seen in all 3 instruments for the black hole (BH) + Wolf-Rayet (WR) binary IC 10 X-1 is probably due to red noise of astrophysical origin. Considering the periods, luminosities, and spatial distribution of the pulsar candidates in the direction of IC 10, they do not belong to the same distribution as the ones in the Magellanic Clouds and Milky Way. This result holds even if the candidates are spurious, since if the Small Magellanic Cloud were placed at the distance of IC 10, we would expect to see $\sim$5 pulsars at $L_x>10^{36}$ \lx ~inside the $D_{25}$ contour, and their periods would be of order 100 seconds, rather than the mostly $\sim$1 s periods for the candidates reported here, which lie outside the main body of the galaxy.
Return of the Campus Speech Wars

In this review of Free Speech on Campus by Erwin Chemerinsky and Howard Gillman, I consider the evidence behind the claim that there is a free speech crisis on university campuses; analyze the scope of campus speech rights for students, faculty, and outside speakers; and discuss the options available for university administrators who want to protect free speech while also creating an inclusive environment for an increasingly diverse student population.
Improving Natural Language Interaction with Robots Using Advice

Over the last few years, there has been growing interest in learning models for physically grounded language understanding tasks, such as the popular blocks world domain. These works typically view this problem as a single-step process, in which a human operator gives an instruction and an automated agent is evaluated on its ability to execute it. In this paper we take the first step towards increasing the bandwidth of this interaction, and suggest a protocol for including advice, high-level observations about the task, which can help constrain the agent’s prediction. We evaluate our approach on the blocks world task, and show that even simple advice can help lead to significant performance improvements. To help reduce the effort involved in supplying the advice, we also explore model self-generated advice which can still improve results.
Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis

The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes (cis-eQTLs). More research is needed to identify effects of genetic variation on distant genes (trans-eQTLs) and understand their biological mechanisms. One common trans-eQTLs mechanism is "mediation" by a local (cis) transcript. Thus, mediation analysis can be applied to genome-wide SNP and expression data in order to identify transcripts that are "cis-mediators" of trans-eQTLs, including those "cis-hubs" involved in regulation of many trans-genes. Identifying such mediators helps us understand regulatory networks and suggests biological mechanisms underlying trans-eQTLs, both of which are relevant for understanding susceptibility to complex diseases. The multitissue expression data from the Genotype-Tissue Expression (GTEx) program provides a unique opportunity to study cis-mediation across human tissue types. However, the presence of complex hidden confounding effects in biological systems can make mediation analyses challenging and prone to confounding bias, particularly when conducted among diverse samples. To address this problem, we propose a new method: Genomic Mediation analysis with Adaptive Confounding adjustment (GMAC). It enables the search of a very large pool of variables, and adaptively selects potential confounding variables for each mediation test. Analyses of simulated data and GTEx data demonstrate that the adaptive selection of confounders by GMAC improves the power and precision of mediation analysis. Application of GMAC to GTEx data provides new insights into the observed patterns of cis-hubs and trans-eQTL regulation across tissue types.
A modified Curtius reaction: an efficient and simple method for direct isolation of free amine

The Curtius rearrangement and related reactions are often used to convert carboxylic acids to the corresponding primary amines. However, this reaction often requires harsh conditions for hydrolysis of the isocyanate intermediates to amines, and can also be contaminated by the formation of corresponding ureas due to the reactive nature of the intermediates. We have discovered that by quenching the isocyanate intermediates with sodium trimethylsilanolate, the free amines can be isolated after aqueous workup. This mild and fast procedure provides free amines in one pot with good yields.
Improved Synthesis of CsN3

Abstract : Cesium azide can conveniently be prepared from anhydrous CsF and (CH3)3SiN3 in SO2 solvent in high purity and yield. In this reaction, the initially generated SO2F(-) anion is converted in SO2 solvent to solvated azide, (SO2)(sub n)N3(-), which is labile and releases S02 under dynamic vacuum yielding pure CsN3.
mol2sphere: spherical decomposition of multi-domain molecules for visualization and coarse grained spatial modeling.

Motivation Proteins, especially those involved in signaling pathways are composed of functional modules connected by linker domains with varying degrees of flexibility. To understand the structure-function relationships in these macromolecules, it is helpful to visualize the geometric arrangement of domains. Furthermore, accurate spatial representation of domain structure is necessary for coarse-grain models of the multi-molecular interactions that comprise signaling pathways. Results We introduce a new tool, mol2sphere, that transforms the atomistic structure of a macromolecule into a series of linked spheres corresponding to domains. It does this with a k-means clustering algorithm. It may be used for visualization or for coarse grain modeling and simulation. Availability and implementation PyMOL plugin, source, and documentation. https://nmrbox.org/registry/mol2sphere. SpringSaLaD executables and documentation: http://vcell.org/ssalad, SpringSaLaD v.2 source: https://github.com/jmasison/SpringSaLaD.
Photo-Arbuzov Rearrangements of Benzylic Phosphites. Stereochemistry at Migratory Carbon

The stereochemistry of the photo-Arbuzov rearrangement of the benzylic phosphite trans-(R,R‘)-10 to the corresponding phosphonate, 11, has been determined by 31P NMR spectroscopy and X-ray crystallography. The reaction is shown to occur with predominant retention of configuration at the stereogenic migratory carbon center of configuration R‘ in starting trans-(R,R‘)-10 and the predominant product cis-(R,R‘)-11. Thus, reaction of optically active phosphoramidite 13 (R/S ratio 98/2, 96% ee) with 1-phenylethanol of high optical purity (R‘/S‘ ratio, 97/3, 94% ee) gives phosphite trans-10 (cis/trans ratio ≥ 97/3) almost entirely as the single enantiomer, trans-(R,R‘)-10. Irradiation of trans-(R,R‘)-10 in acetonitrile with 254 nm ultraviolet light converted it cleanly to two diastereomers of phosphonate cis-11 in 80/20 ratio (31P NMR). The major (80%) isomer was isolated, recrystallized, and shown by X-ray crystallography to be cis-(R,R‘)-11. The lesser (20%) product is identified, on the basis of its 31P NMR c...
pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive

The NCBI Sequence Read Archive (SRA) is the primary archive of next-generation sequencing datasets. SRA makes metadata and raw sequencing data available to the research community to encourage reproducibility and to provide avenues for testing novel hypotheses on publicly available data. However, methods to programmatically access this data are limited. We introduce the Python package, pysradb, which provides a collection of command line methods to query and download metadata and data from SRA, utilizing the curated metadata database available through the SRAdb project. We demonstrate the utility of pysradb on multiple use cases for searching and downloading SRA datasets. It is available freely at https://github.com/saketkc/pysradb.
Chronic, low-level oral exposure to marine toxin, domoic acid, alters whole brain morphometry in nonhuman primates.

Abstract Domoic acid (DA) is an excitatory neurotoxin produced by marine algae and responsible for Amnesiac Shellfish Poisoning in humans. Current regulatory limits (˜0.075-0.1 mg/kg/day) protect against acute toxicity, but recent studies suggest that the chronic consumption of DA below the regulatory limit may produce subtle neurotoxicity in adults, including decrements in memory. As DA-algal blooms are increasing in both severity and frequency, we sought to better understand the effects of chronic DA exposure on reproductive and neurobehavioral endpoints in a preclinical nonhuman primate model. To this end, we initiated a long-term study using adult, female Macaca fascicularis monkeys exposed to daily, oral doses of 0.075 or 0.15 mg/kg of DA for a range of 321–381, and 346–554 days, respectively. This time period included a pre-pregnancy, pregnancy, and postpartum period. Throughout these times, trained data collectors observed intentional tremors in some exposed animals during biweekly clinical examinations. The present study explores the basis of this neurobehavioral finding with in vivo imaging techniques, including diffusion tensor magnetic resonance imaging and spectroscopy. Diffusion tensor analyses revealed that, while DA exposed macaques did not significantly differ from controls, increases in DA-related tremors were negatively correlated with fractional anisotropy, a measure of structural integrity, in the internal capsule, fornix, pons, and corpus callosum. Brain concentrations of lactate, a neurochemical closely linked with astrocytes, were also weakly, but positively associated with tremors. These findings are the first documented results suggesting that chronic oral exposure to DA at concentrations near the current human regulatory limit are related to structural and chemical changes in the adult primate brain.
A symmetric monoidal and equivariant Segal infinite loop space machine

Abstract In [12] , we reworked and generalized equivariant infinite loop space theory, which shows how to construct G-spectra from G-spaces with suitable structure. In this paper, we construct a new variant of the equivariant Segal machine that starts from the category of finite sets rather than from the category of finite G-sets and which is equivalent to the machine studied in [19] , [12] . In contrast to the machine in [19] , [12] , the new machine gives a lax symmetric monoidal functor from the symmetric monoidal category of –G-spaces to the symmetric monoidal category of orthogonal G-spectra. We relate it multiplicatively to suspension G-spectra and to Eilenberg–Mac Lane G-spectra via lax symmetric monoidal functors from based G-spaces and from abelian groups to –G-spaces. Even non-equivariantly, this gives an appealing new variant of the Segal machine. This new variant makes the equivariant generalization of the theory essentially formal, hence likely to be applicable in other contexts.
Tin dithiocarbamates: applications and structures

The uses and potential utility of tin/organotin dithiocarbamate, −S2CNR′2, compounds are reviewed. Various derivatives exhibit exciting potential as anti-cancer agents, anti-microbial agents and insecticides, e.g. against mosquito larvae. Tin dithiocarbamates have also proven useful as precursors for tin sulfide nanoparticles. There is a wealth of structural data available for such compounds and with the exception of the diorganotin bis(dithiocarbamate) compounds, R2Sn(S2CNR′2)2, compounds for which different structural motifs are evident, there is a certain degree of homogeneity in the molecular structures for each class of compound unless there are additional coordination sites on the R and/or R′ groups. Owing to the strong coordination potential of the dithiocarbamate ligand for tin, supramolecular aggregates involving secondary Sn…S interactions are the exception rather than the norm. Copyright © 2008 John Wiley & Sons, Ltd.
X-ray and Neutron Diffraction Studies on “Li4.4Sn”

A chemical analysis and detailed structural characterization, using X-ray single crystal and neutron powder diffraction, of the binary lithium-tin compound "Li(4.4)Sn" is presented. Phase analyses and subsequent structural refinements result in the reformulation of "Li(4.4)Sn" as Li(17)Sn(4). The lithium-rich binary phase crystallizes with a complex cubic structure in the space group Ffourmacr;3m, with a = 19.6907(11) A, Z = 20. The improved crystal structure determination indicates well-defined lithium atom positions, some of which differ from those previously reported. The nearly Zintl phase Li(17)Sn(4) exhibits poor metallic behavior similar to that of heavily doped semiconductors. Comparisons of the refined crystal structure with previously reported X-ray crystal structures associated with "Li(4.4)Sn" are discussed.
SYNTHESIS OF A MEXICAN BEAN BEETLE AZAMACROLIDE ALLOMONE VIA A NOVEL LACTAM TO LACTONE RING EXPANSION

The Mixican bean beetle (Epilachna varivestis) defensive secretion azamacrolide 1 has been synthesized via the novel ring expansion of N-hydroxyethyl lactam 12, which was prepared in seven steps from cyclooctanone (6).
Synthesis of Cytotoxic Indenoisoquinoline Topoisomerase I Poisons

A number of indenoisoquinolines were prepared and evaluated for cytotoxicity in human cancer cell cultures and for activity vs topoisomerase 1 (top1). The two most cytotoxic indenoisoquinolines proved to be cis-6-ethyl-5,6,12,13-tetrahydro-2,3-dimethoxy-8,9-(methylenedioxy)-5,11-dioxo-11H-indeno[1,2-c]isoquinoline (21) and cis-6-allyl-5,6,12,13-tetrahydro-2,3-dimethoxy-8,9-(methylenedioxy)-5,11-dioxo-11H-indeno[1,2-c]isoquinoline (22), both of which displayed submicromolar mean graph midpoints when tested in 55 human cancer cell cultures. Two of the most potent top1 inhibitors were 6-(3-carboxy-1-propyl)-5,6-dihydro-5,11-dioxo-11H-indeno[1,2-c]isoquinoline (26) and 6-ethyl-2,3-dimethoxy-8,9-(methylenedioxy)-11H-indeno[1,2-c]isoquinolinium chloride (27), both of which also inhibited top2, unwound DNA, and are assumed to be DNA intercalators. However, two additional potent top1 inhibitors, 6-allyl-5,6-dihydro-2,3-dimethoxy-8,9-(methylenedioxy)-5,11-dioxo-11H-indeno[1,2-c]isoquinoline (13c) and 5,6-dihydro-6...
Total Synthesis of the Coccinellid Alkaloid (±)-Adalinine Utilizing a Nitrenium Ion Cyclization

The total synthesis of (′) -adalinine, a piperidine alkaloid from the European two-spotted ladybird Adalia bipunctata, is reported. Central to this undertaking are (i) the use of an N-alkoxy-N-acylnitrenium ion-induced spirocyclization to rapidly access the 6,6'-disubstituted piperidinone ring of the natural product and (ii) exploitation of the cyclohexa-2,5-dienone system generated in this process as a latent 1,6-ketoaldehyde.
Imidazolium-based polymer supported gadolinium triflate as a heterogeneous recyclable Lewis acid catalyst for Michael additions

Abstract A heterogeneous Lewis acid catalytic system has been developed by incorporating gadolinium triflate on to poly[styrene- co -(1-((4-vinylphenyl)methyl)-3-methylimidazolium) tetrafluoroborate] ( 1 -Gd(OTf) 3 ), and the catalytic activity of this system has been examined for Michael additions of amines and thiols to α,β-unsaturated esters and acrylonitrile. The reactions proceed in moderate to excellent yields in the presence of catalytic system 1 -Gd(OTf) 3 . The catalytic system could be efficiently recycled and reused.
A new route to alkoxysilanes and alkoxysiloxanes of use for the preparation of ceramics by the sol-gel technique

The preparation of (EtO) 4 Si from Ca 3 (SiO 4 )O, Ca 2 SiO 4 , and portland cement, (EtO) 3 SiOSi(OEt) 3 from Ca 2 Zn(SiO 3 ) 2 O, (n-PrO) 3 SiOSi(O-n-Pr) 2 OSi(O-n-Pr) 3 from Ca 3 (SiO 3 ) 3 , [(EtO) 2 SiO] 4 from Ca 8 (SiO 3 ) 4 Cl 8 , and the bicyclic [5.5.1]- and [5.3.3]-isomers of (EtO) 10 Si 6 O 7 from Cu 6 (SiO 3 ) 6 •6H 2 O and Na 4 Ca 4 (SiO 3 ) 6 is described. The route employed in these preparations has two variations. Both can be described in terms of three steps
Chloroaluminate ionic liquids as reagents for isolating soluble hexanuclear zirconium halide cluster compounds.

Ambient-temperature chloroaluminate molten salts, mixtures of aluminum trichloride (AlCl3) and 1-ethyl-3-methylimidazolium chloride (ImCl), have been used as solvents to excise and isolate centered hexanuclear zirconium halide clusters from their solid-state precursors. Cluster compounds synthesized via high-temperature reactions, KZr6CCl15 and Li2Zr6MnCl15, were dissolved into basic molten salts at 100−110 °C. The C-centered cluster compound, Im4Zr6CCl18, was isolated in 70% yield, and the Mn-centered cluster compound, Im5Zr6MnCl18·C7H8·2CH3CN, was isolated in 54% yield. Im5Zr6BCl18 is efficiently oxidized by ferrocenium tetrafluoroborate, and one-electron-oxidized B-centered cluster, [(Zr6B)Cl18]4-, was isolated in 90% yield as the salt Im4Zr6BCl18.
Genomic and epigenomic mapping of leptin-responsive neuronal populations involved in body weight regulation

Genome wide association studies (GWAS) in obesity have identified a large number of noncoding loci located near genes expressed in the central nervous system. However, due to the difficulties in isolating and characterizing specific neuronal subpopulations, few obesity-associated SNPs have been functionally characterized. Leptin responsive neurons in the hypothalamus are essential in controlling energy homeostasis and body weight. Here, we combine FACS-sorting of leptin-responsive hypothalamic neuron nuclei with genomic and epigenomic approaches (RNA-seq, ChIP-seq, ATAC-seq) to generate a comprehensive map of leptin-response specific regulatory elements, several of which overlap obesity-associated GWAS variants. We demonstrate the usefulness of our leptin-response neuron regulome, by functionally characterizing a novel enhancer near Socs3, a leptin response-associated transcription factor. We envision our data to serve as a useful resource and a blueprint for functionally characterizing obesity-associated SNPs in the hypothalamus.
An Early Devonian permineralized rhyniopsid from the Battery Point Formation of Gaspé (Canada)

The Emsian deposits of the Battery Point Formation (Gaspe, Canada) host the most diverse Early Devonian flora in North America. While most of this diversity has been described from plant compressions, the permineralized component of the flora is incompletely explored. Based on >15 axes studied in serial sections, we describe a new anatomically preserved rhyniopsid from the Battery Point Formation, Eddianna gaspiana gen. & sp. nov. Eddianna axes are up to 2 mm in diameter and have a well-developed terete xylem strand with potential centrarch maturation (comprising 80% of the cross sectional surface area) that features Sennicaulis-type tracheid wall thickenings. A thin layer interpreted as phloem is preserved around the central xylem and an irregular sclerenchymatous cortex forms longitudinal anastomosing ridges on the outside of the axes. The anatomy of Eddianna axes suggests that they represent lower portions, specialized in efficient water transfer, of a larger plant whose distal regions have yet to be discovered. Eddianna, the first permineralized rhyniopsid described from the Battery Point Formation, is one of only four anatomically preserved plants reported from this unit. These fossils reiterate the potential for additional discoveries of anatomically preserved plants in the Battery Point Formation.
Interactions of Hydrogen with CeO2

The interactions of hydrogen with ceria have been the subject of several experimental studies, but whether hydrogen atoms enter the bulk or are merely chemisorbed on the surfaces is disputed. We combine first-principles calculations with thermodynamic arguments and conclude that the uptake of small amounts of hydrogen by ceria is spontaneous below 665 K. The calculations also predict that hydrogen atoms within the bulk form hydroxyl groups and slightly expand the lattice. The predicted hydrogen content, OH vibrational frequency, and ceria lattice expansion upon hydrogen uptake are consistent with available data.