cssi/SciSciGPT-SciSciNet huggingface dataset:
Preliminary assessment of the occurrence and possible sources of MTBE in groundwater in the United States, 1993-1994

The 1990 Clean Air Act Amendments require fuel oxygenates to be added to gasoline used in some metropolitan areas to reduce atmospheric concentrations of carbon monoxide or ozone. Methyl tert-butyl ether (MTBE) is the most commonly used fuel oxygenate and is a relatively new gasoline additive. Nevertheless, out of 60 volatile organic chemicals analyzed, MTBE was the second most frequently detected chemical in samples of shallow ambient groundwater from urban areas that were collected during 1993-1994 as part of the U.S. Geological Survey's National Water-Quality Assessment program. Samples were collected from five drinking water wells, 12 springs, and 193 monitoring wells in urban areas. No MTBE was detected in drinking water wells. At a reporting level of 0.2 μg/L, MTBE was detected most frequently in shallow groundwater from urban areas (27% of 210 wells and springs sampled in eight areas) as compared to shallow groundwater from agricultural areas (1.3% of 549 wells sampled in 21 areas) or deeper groundwater from major aquifers (1.0% of 412 wells sampled in nine areas). Only 3% of the shallow wells sampled in urban areas had concentrations of MTBE that exceed 20 μg/L, which is the estimated lower limit of the United States Environmental Protection Agency draft drinking water health advisory. Because MTBE is persistent and mobile in groundwater, it can move from shallow to deeper aquifers with time. In shallow urban groundwater, MTBE generally was not found with benzene, toluene, ethylbenzene, or xylene (BTEX) compounds, which commonly are associated with gasoline spills. This disassociation causes uncertainty as to the source of MTBE. Possible sources of MTBE in groundwater include point sources, such as leaking storage tanks, and non-point sources, such as recharge of precipitation and stormwater runoff.
Robust Dynamic Pricing with Strategic Customers

We consider the canonical revenue management (RM) problem wherein a seller must sell an inventory of some product over a finite horizon via an anonymous, posted price mechanism. Unlike typical mode...
Excess Volatility: Beyond Discount Rates

We document a form of excess volatility that is difficult to reconcile with standard models of prices, even after accounting for variation in discount rates. We compare prices of claims on the same cash flow stream but with different maturities. Standard models impose precise internal consistency conditions on the joint behavior of long- and short-maturity claims and these are strongly rejected in the data. In particular, long-maturity prices are significantly more variable than justified by the behavior at short maturities. We reject internal consistency conditions in all term structures that we study, including equity options, currency options, credit default swaps, commodity futures, variance swaps, and inflation swaps.
Liouville metric of star-scale invariant fields: tails and Weyl scaling

We study the Liouville metric associated to an approximation of a log-correlated Gaussian field with short range correlation. We show that below a parameter $$\gamma _c >0$$, the left–right length of rectangles for the Riemannian metric $$e^{\gamma \phi _{0,n}} ds^2$$ with various aspect ratio is concentrated with quasi-lognormal tails, that the renormalized metric is tight when $$\gamma < \min ( \gamma _c, 0.4)$$ and that subsequential limits are consistent with the Weyl scaling.
A Capacity Allocation Planning Model for Integrated Care and Access Management

The prevailing first-come-first-served approach to outpatient appointment scheduling ignores differing urgency levels, leading to unnecessarily long waits for urgent patients. In data from a partner healthcare organization, we found in some departments that urgent patients were inadvertently waiting longer for an appointment than non-urgent patients. This paper develops a capacity allocation optimization methodology that reserves appointment slots based on urgency in a complicated, integrated care environment where multiple specialties serve multiple types of patients. This optimization reallocates network capacity to limit access delays (indirect waiting times) for initial and downstream appointments differentiated by urgency. We formulate this problem as a queueing network optimization and approximate it via deterministic linear optimization to simultaneously smooth workloads and guarantee access delay targets. In a case study of our industry partner we demonstrate the ability to (1) reduce urgent patient mean access delay by 27% with only a 7% increase in mean access delay for non-urgent patients, and (2) increase throughput by 31% with the same service levels and overtime.
Pair and many-body interactions between ligated Au nanoparticles

We report the results of molecular dynamics simulations of the properties of a pseudo-atom (united atom) model of dodecane thiol ligated 5-nm diameter gold nanoparticles (AuNPs) in a vacuum as a function of ligand coverage and particle separation in three states of aggregation, namely, the isolated AuNPs, the isolated pair of AuNPs, and a square lattice of four AuNPs. Our calculations show that the ligand density along a radius emanating from the core of an isolated AuNP has the same gross features for all values of the coverage; it oscillates around a constant value up to a distance along the chain corresponding to the position of the fourth pseudo-atom and then smoothly decays to zero, reflecting both the restricted conformations of the chain near the core surface and the larger numbers of conformations available further from the core. Interaction between two AuNPs generates changes in the ligand distributions of each. We examine the structure and general shape of the ligand envelope as a function of the coverage and demonstrate that the equilibrium structure of the envelope and the deformation of that envelope generated by interaction between the NPs are coverage-dependent so that the shape, depth, and position of the minimum of the potential of mean force display a systematic dependence on the ligand coverage. We propose an accurate analytical description of the calculated potential of mean force as a function of a set of parameters that scale linearly with the ligand coverage. Noting that the conformational freedom of the ligands implies that multiparticle induced deviations from additivity of the pair potential of mean force are likely important; we define and calculate a "bond stretching" effective pair potential of mean force for a square lattice of particles that contains, implicitly, both the three- and four-NP contributions. We find that the bond stretching effective pair potential of mean force in this cluster has a different minimum and a different well depth from the isolated pair potential of mean force. Previous work has found that the three-particle contribution to deviation from pair additivity is monotonically repulsive, whereas we find that the combined three- and four-particle contributions have an attractive well, implying that the three- and four-particle contributions are of comparable magnitude but opposite sign, thereby suggesting that even higher order correction terms likely play a significant role in the behavior of dense assemblies of many nanoparticles.
Geometry-Aware Recurrent Neural Networks for Active Visual Recognition

We present recurrent geometry-aware neural networks that integrate visual in- formation across multiple views of a scene into 3D latent feature tensors, while maintaining an one-to-one mapping between 3D physical locations in the world scene and latent feature locations. Object detection, object segmentation, and 3D reconstruction is then carried out directly using the constructed 3D feature memory, as opposed to any of the input 2D images. The proposed models are equipped with differentiable egomotion-aware feature warping and (learned) depth-aware unprojection operations to achieve geometrically consistent mapping between the features in the input frame and the constructed latent model of the scene. We empirically show the proposed model generalizes much better than geometry- unaware LSTM/GRU networks, especially under the presence of multiple objects and cross-object occlusions. Combined with active view selection policies, our model learns to select informative viewpoints to integrate information from by “undoing" cross-object occlusions, seamlessly combining geometry with learning from experience.
International Comparisons in Underserved Health: Issues, Policies, Needs and Projections

Health care globally has made great strides; for example, there are lower rates of infant and maternal mortality. Increased incomes have led to lower rates of diseases accompanying poverty and hunger. There has been a shift away from the infectious diseases so deadly in developing nations toward first-world conditions. This article presents health care statistics across age groups and geographic areas to help the primary care physician understand these changes. There is a special focus on underserved populations. New technologies in health and health care spending internationally are addressed, emphasizing universal health care. The article concludes with recommendations for the future.
Deep late-time observations of the supernova impostors SN 1954J and SN 1961V

SN 1954J in NGC 2403 and SN 1961V in NGC 1058 were two luminous transients whose definitive classification as either non-terminal eruptions or supernovae remains elusive. A critical question is whether a surviving star can be significantly obscured by dust formed from material ejected during the transient. We use three lines of argument to show that the candidate surviving stars are not significantly optically extincted ($\tau \lesssim 1$) by dust formed in the transients. First, we use SED fits to new HST optical and near-IR photometry. Second, neither source is becoming brighter as required by absorption from an expanding shell of ejected material. Third, the ejecta masses implied by the H$\alpha$ luminosities are too low to produce significant dust absorption. The latter two arguments hold independent of the dust properties. The H$\alpha$ fluxes should also be declining with time as $t^{-3}$, and this seems not to be observed. As a result, it seems unlikely that recently formed dust can be responsible for the present faintness of the sources compared to their progenitors, although this can be verified with \textit{JWST}. This leaves three possibilities: 1) the survivors were misidentified; 2) they are intrinsically less luminous; 3) SN 1954J and SN 1961V were true supernovae.
Impact of Beam Misalignment on Hybrid Beamforming NOMA for mmWave Communications

The effect of beam misalignment on rate performance of the downlink hybrid beamforming-based non-orthogonal multiple access (HB-NOMA) systems is analyzed in this paper. First, an HB-NOMA framework is introduced in the context of multiuser millimeter wave (mmWave) communications, a sum-rate maximization problem is formulated for that, and an algorithm is introduced to design digital and analog precoders and power allocation. Then, a lower bound for the achievable rate of the perfectly aligned line-of-sight (LoS) channels is derived. Subsequently, the impact of beam misalignment is evaluated when the users experience misaligned LoS or non-LoS channels. To this end, a misalignment factor is modeled and each misaligned effective channel is described in terms of the perfectly aligned effective channel parameters and the misalignment factor. Furthermore, a lower bound for the achievable rate, and an upper bound for the rate gap expression between the aligned and misaligned HB-NOMA systems are established. The analyses reveal that a large misalignment can remarkably degrade the rate. Extensive numerical simulations are conducted to verify the findings.
Review of the Empirical Evidence for Superluminal Particles and the 3 + 3 Model of the Neutrino Masses

A review is given of hypothetical faster-than-light tachyons and the development of the author’s model of the neutrino mass states, which includes one tachyonic mass state doublet. Published empirical evidence for the model is summarized, including an interpretation of the mysterious Mont Blanc neutrino burst from SN 1987A as being due to tachyonic neutrinos having This possibility requires an 8 MeV antineutrino line from SN 1987A, which a new dark matter model has been found to support. Furthermore, this dark matter model is supported by several datasets: rays from the galactic center, and the Kamiokande-II neutrino data on the day of SN 1987A. The KATRIN experiment should serve as the unambiguous test of the model and its tachyonic mass state.
The role of glacial-interglacial climate change in shaping the genetic structure of eastern subterranean termites in the southern Appalachian Mountains, USA.

The eastern subterranean termite, Reticulitermes flavipes, currently inhabits previously glaciated regions of the northeastern U.S., as well as the unglaciated southern Appalachian Mountains and surrounding areas. We hypothesized that Pleistocene climatic fluctuations have influenced the distribution of R. flavipes, and thus the evolutionary history of the species. We estimated contemporary and historical geographic distributions of R. flavipes by constructing Species Distribution Models (SDM). We also inferred the evolutionary and demographic history of the species using mitochondrial (cytochrome oxidase I and II) and nuclear (endo-beta-1,4-glucanase) DNA sequence data. To do this, genetic populations were delineated using Bayesian spatial-genetic clustering, competing hypotheses about population divergence were assessed using approximate Bayesian computation (ABC), and changes in population size were estimated using Bayesian skyline plots. SDMs identified areas in the north with suitable habitat during the transition from the Last Interglacial to the Last Glacial Maximum, as well as an expanding distribution from the mid-Holocene to the present. Genetic analyses identified three geographically cohesive populations, corresponding with northern, central, and southern portions of the study region. Based on ABC analyses, divergence between the Northern and Southern populations was the oldest, estimated to have occurred 64.80 thousand years ago (kya), which corresponds with the timing of available habitat in the north. The Central and Northern populations diverged in the mid-Holocene, 8.63 kya, after which the Central population continued to expand. Accordingly, phylogeographic patterns of R. flavipes in the southern Appalachians appear to have been strongly influenced by glacial-interglacial climate change. Open research badges This article has been awarded Open Materials, Open Data Badges. All materials and data are publicly accessible via the Open Science Framework at https://doi.org/10.5061/dryad.5hr7f31.
Medication Adherence Prediction Through Online Social Forums: A Case Study of Fibromyalgia

Background: Medication nonadherence can compound into severe medical problems for patients. Identifying patients who are likely to become nonadherent may help reduce these problems. Data-driven machine learning models can predict medication adherence by using selected indicators from patients’ past health records. Sources of data for these models traditionally fall under two main categories: (1) proprietary data from insurance claims, pharmacy prescriptions, or electronic medical records and (2) survey data collected from representative groups of patients. Models developed using these data sources often are limited because they are proprietary, subject to high cost, have limited scalability, or lack timely accessibility. These limitations suggest that social health forums might be an alternate source of data for adherence prediction. Indeed, these data are accessible, affordable, timely, and available at scale. However, they can be inaccurate. Objective: This paper proposes a medication adherence machine learning model for fibromyalgia therapies that can mitigate the inaccuracy of social health forum data. Methods: Transfer learning is a machine learning technique that allows knowledge acquired from one dataset to be transferred to another dataset. In this study, predictive adherence models for the target disease were first developed by using accurate but limited survey data. These models were then used to predict medication adherence from health social forum data. Random forest, an ensemble machine learning technique, was used to develop the predictive models. This transfer learning methodology is demonstrated in this study by examining data from the Medical Expenditure Panel Survey and the PatientsLikeMe social health forum. Results: When the models are carefully designed, less than a 5% difference in accuracy is observed between the Medical Expenditure Panel Survey and the PatientsLikeMe medication adherence predictions for fibromyalgia treatments. This design must take into consideration the mapping between the predictors and the outcomes in the two datasets. Conclusions: This study exemplifies the potential and limitations of transfer learning in medication adherence–predictive models based on survey data and social health forum data. The proposed approach can make timely medication adherence monitoring cost-effective and widely accessible. Additional investigation is needed to improve the robustness of the approach and extend its applicability to other therapies and other sources of data.
The planet nine hypothesis

Over the course of the past two decades, observational surveys have unveiled the intricate orbital structure of the Kuiper Belt, a field of icy bodies orbiting the Sun beyond Neptune. In addition to a host of readily-predictable orbital behavior, the emerging census of trans-Neptunian objects displays dynamical phenomena that cannot be accounted for by interactions with the known eight-planet solar system alone. Specifically, explanations for the observed physical clustering of orbits with semi-major axes in excess of ∼250AU, the detachment of perihelia of select Kuiper belt objects from Neptune, as well as the dynamical origin of highly inclined/retrograde long-period orbits remain elusive within the context of the classical view of the solar system. This newly outlined dynamical architecture of the distant solar system points to the existence of a new planet with mass of m_g ∼5−10M⊕, residing on a moderately inclined orbit (i_g∼15−25deg) with semi-major axis a_g∼400−800AU and eccentricity between e_g∼0.2−0.5. This paper reviews the observational motivation, dynamical constraints, and prospects for detection of this proposed object known as Planet Nine.
Giant Conductivity Modulation of Aluminum Oxide Using Focused Ion Beam

Precise control of the conductivity of semiconductors through doping has enabled the creation of advanced electronic devices; similarly, the ability to control the conductivity in oxides can enable...
Input Substitutability and Cross-Country Variation in Sectoral Linkages

Using panel data on input-output intensities and expenditure prices from 28 countries, this paper finds the elasticity of substitution across sectoral inputs to be less than one in each of the three broad sectors of the economy. Intermediates are most complementary in the production of services while it is easiest to substitute across intermediates in the production of agricultural goods. Differences in relative prices alone account for a non-trivial fraction of the cross-country variation in sectoral linkages. Abstracting from the price channel that allows for substitution across inputs in response to changes in relative prices delivers biased aggregate implications of changes in productivity and distortions.
The science process for selecting the landing site for the 2020 Mars rover

The process of identifying the landing site for NASA's Mars 2020 rover began in 2013 by defining threshold mission science criteria related to seeking signs of ancient habitable conditions, searching for biosignatures of past microbial life, assembling a returnable cache of samples for possible future return to Earth, and collecting data for planning eventual human missions to the surface of Mars. Mission engineering constraints on elevation and latitude were used to identify candidate landing sites that addressed the scientific objectives of the mission. However, for the first time these constraints did not have a major influence on the viability of candidate sites and, with the new entry, descent, and landing capabilities included in the baseline mission, the vast majority of sites were evaluated and down-selected on the basis of science merit. More than 30 candidate sites with likely acceptable surface and atmospheric conditions were considered at a series of open workshops in the years leading up to the launch. During that period, iteration between engineering constraints and the evolving relative science potential of candidate sites led to the identification of three final candidate sites: Jezero crater (18.4386°N, 77.5031°E), northeast (NE) Syrtis (17.8899°N,77.1599°E) and Columbia Hills (14.5478°S, 175.6255°E). The final landing site will be selected by NASA's Associate Administrator for the Science Mission Directorate. This paper serves as a record of landing site selection activities related primarily to science, an inventory of the number and variety of sites proposed, and a summary of the science potential of the highest-ranking sites.
Operative time as a marker of quality in bariatric surgery

Abstract Background Few studies have examined the effect of prolonged operative time (OT) on outcomes in laparoscopic bariatric surgery. Existing studies mostly focus on 30-day complications, whereas serious complications may not occur until well after 30 days from the index operation. Objective To determine the effect of prolonged OT on 1-year morbidity and mortality after laparoscopic Roux-en-Y gastric bypass (LRYGB) and laparoscopic sleeve gastrectomy (LSG). Setting The Bariatric Outcomes Longitudinal Database (BOLD). Methods Data on primary LRYGB and LSG cases performed between 2008 and 2012 in the BOLD were analyzed. Converted cases and cases concurrent with other procedures were excluded. Multivariate logistic regression was used to assess the association between OT and 1-year morbidity and mortality, with adjustment for preoperative demographic and clinical characteristics. Results A total of 93,051 cases were examined, including 74,745 (80.3%) LRYGB and 18,306 (19.7%) LSG cases. For LRYGB, mean OT was 104 minutes (standard deviation [SD] 46.6). Every additional 10 minutes of OT was associated with increased odds of 1-year mortality (adjusted odds ratio [AOR] 1.04; P = .02), leak (AOR 1.07; P Conclusion Prolonged operative time is associated with a significant increase in the odds of mortality and serious complications after laparoscopic bariatric surgery. Operative time may be a useful marker of quality in primary laparoscopic bariatric surgery.
Metamorphic Testing for Quality Assurance of Protein Function Prediction Tools

Proteins are the workhorses of life and gaining insight on their functions is of paramount importance for applications such as drug design. However, the experimental validation of functions of proteins is highly-resource consuming. Therefore, recently, automated protein function prediction (AFP) using machine learning has gained significant interest. Many of these AFP tools are based on supervised learning models trained using existing gold-standard functional annotations, which are known to be incomplete. The main challenge associated with conducting systematic testing on AFP software is the lack of a test oracle, which determines passing or failing of a test case; unfortunately, due to the incompleteness of gold-standard data, the exact expected outcomes are not well defined for the AFP task. Thus, AFP tools face the oracle problem. In this work, we use metamorphic testing (MT) to test nine state-of-the-art AFP tools by defining a set of metamorphic relations (MRs) that apply input transformations to protein sequences. According to our results, we observe that several AFP tools fail all the test cases causing concerns over the quality of their predictions.
Scaffold-free bioprinting of mesenchymal stem cells using the Regenova printer: Spheroid characterization and osteogenic differentiation

Limitations in scaffold material properties, such as sub-optimal degradation time, highlight the need for alternative approaches to engineer de novo tissues. One emerging solution for fabricating tissue constructs is scaffold-free tissue engineering. To facilitate this approach, three-dimensional (3D) bioprinting technology (Regenova Bio 3D Printer) has been developed to construct complex geometric shapes from discrete cellular spheroids without exogenous scaffolds. Optimizing spheroid fabrication and characterizing cellular behavior in the spheroid environment are important first steps prior to printing larger constructs. Here, we characterized spheroids of immortalized mouse bone marrow stromal cells (BMSCs) that were differentiated to the osteogenic lineage. Immortalized BMSCs were seeded in low attachment 96-well plates in various numbers to generate self-aggregated spheroids either under the force of gravity or centrifugation. Cells were cultured in control or osteogenic media for up to 28 days. Spheroid diameter, roundness and smoothness were measured. Cell viability, DNA content and alkaline phosphatase activity were assessed at multiple time points. Additionally, expression of osteogenic markers was determined using real time qPCR. Spheroids formed under gravity with 20 K, 30 K and 40 K cells had average diameters of 498.5 ± 8.3 μm, 580.0 ± 32.9 μm and 639.2 ± 54.0 μm, respectively, while those formed under 300G centrifugation with the same numbers of cells had average diameters of 362.3 ± 3.5 μm, 433.1 ± 6.4 μm and 491.2 ± 8.0 μm. Spheroids formed via centrifugation were superior to those formed by gravity, as evidenced by better roundness and smoothness and double the retention of DNA (cellular) content. Cells in spheroids exhibited a robust osteogenic response to the differentiation medium, including higher mRNA expression of alkaline phosphatase, collagen type I, and osteocalcin than those cultured in control medium, as well as greater alkaline phosphatase activity. The optimal spheroid fabrication technique from this study was to aggregate 40K cells under 150-300G centrifugation. In future investigations, these spheroids will be 3D printed into larger tissue constructs.
Use of the g-index for assessment of citation-based scholarly activity of United States radiation oncology residents and subsequent choice of academic versus private practice career.

Abstract Introduction The Hirsch index (h-index) evaluates citation-based scholarly activity, but has limited ability to acknowledge those publishing a smaller number of manuscripts with exceedingly high citations. The g-index addresses this limitation by assessing the largest number of manuscripts (g) by an author cited at least (g × g) times, but has yet to be applied to radiation oncology resident productivity. Methods A list of recent radiation oncology resident graduates (comprising 86% of the 2016 graduating class) and their post-residency career choice was compiled. The Scopus bibliometric citation database was searched to collect and calculate g-index data for each resident. Results The mean g-index score for all resident graduates was 7.16. Residents with a PhD had significantly higher g-index scores (11.97 versus 5.80; p Conclusion Radiation oncology resident graduates published on average a minimum of seven manuscripts cited at least 49 times. PhD-degree graduates had significantly higher g-index scores, as did residents choosing academic over private practice careers. There was no significant gender-related difference in g-index score regardless of career choice. The majority of academic careers are produced from programs graduating at least three residents.
Entanglement Wedge Reconstruction and the Information Paradox

When absorbing boundary conditions are used to evaporate a black hole in AdS/CFT, we show that there is a phase transition in the location of the quantum Ryu-Takayanagi surface, at precisely the Page time. The new RT surface lies slightly inside the event horizon, at an infalling time approximately the scrambling time β/2πlogSBH into the past. We can immediately derive the Page curve, using the Ryu-Takayanagi formula, and the Hayden-Preskill decoding criterion, using entanglement wedge reconstruction. Because part of the interior is now encoded in the early Hawking radiation, the decreasing entanglement entropy of the black hole is exactly consistent with the semiclassical bulk entanglement of the late-time Hawking modes, despite the absence of a firewall. By studying the entanglement wedge of highly mixed states, we can understand the state dependence of the interior reconstructions. A crucial role is played by the existence of tiny, non-perturbative errors in entanglement wedge reconstruction. Directly after the Page time, interior operators can only be reconstructed from the Hawking radiation if the initial state of the black hole is known. As the black hole continues to evaporate, reconstructions become possible that simultaneously work for a large class of initial states. Using similar techniques, we generalise Hayden-Preskill to show how the amount of Hawking radiation required to reconstruct a large diary, thrown into the black hole, depends on both the energy and the entropy of the diary. Finally we argue that, before the evaporation begins, a single, state-independent interior reconstruction exists for any code space of microstates with entropy strictly less than the Bekenstein-Hawking entropy, and show that this is sufficient state dependence to avoid the AMPSS typical-state firewall paradox.
Synthesis of D2-symmetric 5,10,15,20-tetraarylporphyrins from C2-symmetric benzaldehydes and achiral aryldipyrromethanes

Abstract A series of new enantiomerically pure D 2 - symmetric 5,10,15,20-tetraarylporphyrins has been synthesized by condensation of C 2 -symmetric substiuted benzaldehydes with achiral aryldipyrromethanes in 22–40% yield. The mild conditions used enable selective incorporation of the chiral arenes at the 5,15-positions and the achiral arenes at the 10,20-positions. Due to the incorporation of the C 2 -symmetric chiral arenes, no atropisomers are possible in these D 2 -symmetric ligands. Manganse complexes of these ligands are catalysts for the enantioselective epoxidation of cis-β-methylstyrene.
Why Concatenation Fails Near the Anomaly Zone

Genome-scale sequencing has been of great benefit in recovering species trees but has not provided final answers. Despite the rapid accumulation of molecular sequences, resolving short and deep branches of the tree of life has remained a challenge and has prompted the development of new strategies that can make the best use of available data. One such strategy-the concatenation of gene alignments-can be successful when coupled with many tree estimation methods, but has also been shown to fail when there are high levels of incomplete lineage sorting. Here, we focus on the failure of likelihood-based methods in retrieving a rooted, asymmetric four-taxon species tree from concatenated data when the species tree is in or near the anomaly zone-a region of parameter space where the most common gene tree does not match the species tree because of incomplete lineage sorting. First, we use coalescent theory to prove that most informative sites will support the species tree in the anomaly zone, and that as a consequence maximum-parsimony succeeds in recovering the species tree from concatenated data. We further show that maximum-likelihood tree estimation from concatenated data fails both inside and outside the anomaly zone, and that this failure cannot be easily predicted from the topology of the most common gene tree. We demonstrate that likelihood-based methods often fail in a region partially overlapping the anomaly zone, likely because of the lower relative cost of substitutions on discordant gene tree branches that are absent from the species tree. Our results confirm and extend previous reports on the performance of these methods applied to concatenated data from a rooted, asymmetric four-taxon species tree, and highlight avenues for future work improving the performance of methods aimed at recovering species tree.
Total synthesis of the latrunculins

The total syntheses of (+)-latrunculin A (1) and (+)-latrunculin B (2), two architecturally novel toxins isolated from the Red Sea sponge Latrunculia magnifica (Keller), have been achieved via highly convergent and stereocontrolled routes (longest linear sequences, 16 and 12 steps, respectively). Formal syntheses of scalemic latrunculins C (3) and M (5) also derive from the construction of 2. Central features of the unified synthetic strategy include the aldol reaction of aldehyde (-)-12 with methyl ketone (-)-13, a novel acid-catalyzed reorganization-equilibration of ortho ester (-)-11, and Mitsunobu macrolide cyclization
Selectfluor-mediated mild oxidative halogenation and thiocyanation of 1-aryl-allenes with TMSX (X = Cl, Br, I, NCS) and NH4SCN

Abstract Presence of TMSX (X = Cl, Br, I) unleashes the oxidative character of Selectfluor and provides a mild dihalogenation method for 1-arylallenes. Preference for 2,3-addition was observed with TMSCl in MeCN irrespective of the nature of the substituent on the aryl moiety, whereas 1,2-addition was preferred in [BMIM][BF4]. With TMSBr and TMSI only products corresponding to 2,3-addition were observed. Reactions carried out with TMSBr in IL solvents gave the corresponding monobromoalkenes as a major product along with the isomeric dibromo-alkenes. Reaction with NH4SCN provided convenient access to dithiocyanate derivatives. The same products were formed via TMS-NCS/Selectfluor. Formation of common products via TMSNCS and NH4SCN points to the formation and interplay of SCN+/NCS+ as incipient electrophiles.
Arylsulfenium Ion Promoted Cascade Cyclizations of Deactivated Aryldienes. An Investigation into Reagent-Based Acceleration of Cationic Annulation

The efficiency of sulfenylative cyclization has been shown to be strongly influenced by both substrate substitution pattern and the structure of the external sulfenium ion source. Of the various reagents examined, 2-methoxyethyl 4-chlorobenzenesulfenate (9b) has been found a particularly effective initiator for the regioselective cyclization of a range of aryldienes at low temperature.
Synthetic applications of lithiated N-Boc allylic amines as asymmetric homoenolate equivalents.

Lithiation of N-(Boc)-N-(p-methoxyphenyl) allylic amines in the presence of (−)-sparteine provides asymmetric homoenolate equivalents which react with electrophiles to provide highly enantioenriched enecarbamates. Acidic hydrolysis of the enecarbamates can provide the corresponding β-substituted aldehydes. A synthetic sequence that involves a stereocontrolled intramolecular nitrone−olefin dipolar cycloaddition has been developed for the preparation of enantioenriched 2-formyl-4-phenyl-1-aminocyclopentanes from one β-allyl-substituted aldehyde. Further manipulations allow access to an enantioenriched β-lactam. In another synthetic sequence, transmetalation of the lithiated intermediates and reactions with aldehyde electrophiles can be controlled to afford highly enantioenriched anti homoaldol products. Use of an anti aldehyde homoaldol product as the chiral electrophile in an iterative reaction provides a double homoaldol product containing four stereogenic centers with high diastereoselectivity and enanti...
Impacts of a millennium drought on butterfly faunal dynamics

Climate change is challenging plants and animals not only with increasing temperatures, but also with shortened intervals between extreme weather events. Relatively little is known about diverse assemblages of organisms responding to extreme weather, and even less is known about landscape and life history properties that might mitigate effects of extreme weather. Our aim was to address this knowledge gap using a multi-decadal dataset of 163 butterfly species that recently experienced a millennium-scale drought. To understand faunal dynamics in the context of the millennium drought, we investigated the behavior of phenology (including date of first flight), species richness and diversity indices through time at 10 study sites spanning an elevational gradient. Linear models were developed to understand the differential sensitivity of butterflies to climate at low and high elevations. Dates of first flight advanced across the elevational gradient during the drought, leading to an overall expansion of the flight window at low elevations and a compression of the flight window in the mountains. The number of species observed per year increased at lower elevations but decreased at higher elevations, apparently as a consequence of extreme sensitivity to hot and dry conditions. Montane populations may be more sensitive to climatic extremes than expected based on availability of microclimates and spatial heterogeneity, while low-elevation populations (despite existing in degraded habitats) are buffered by life history plasticity.
An efficient, asymmetric synthesis of (+)-euphococcinine†

Abstract The enantioselective synthesis of (+)-euphococcinine (1), a homotropane alkaloid, has been achieved in five steps from bicyclic lactam 5.
The reaction of N-phenylsulfonimidoyl chloride with trimethylsilylethene. A new route to 2-alkenylanilines

Abstract N-Phenylsulfonimidoyl chloride reacts with trimethylsilylethene in the presence of aluminum chloride to give two product benzothiazines, one of which has been desilylated. The silylated benzothiazine can be deprotonated and alkylated, sometimes with very high diastereocontrol. Upon treatment with fluoride, these silylated benzothiazines undergo desilylation with concomitant cleavage of the carbon-sulfur bond to give 2-alkenylsulfinanilides which can be hydrolyzed to the corresponding anilines.
Total synthesis of (+/-)-hedychilactone B: stepwise allenoate diene cycloaddition to prepare trimethyldecalin systems.

The total synthesis of the diterpene hedychilactone B 1 is reported. The exo adduct 4x, the major product of the stepwise [4+2] cycloaddition of the diene 2 and the allenoate 3, has been converted into 1 via 7 steps, among them a key nonconjugative hydrolysis of a γ-methylene silyl enol ether and an E-selective olefination.
Adaptive-Price Combinatorial Auctions

This work introduces a novel iterative combinatorial auction that aims to achieve both high efficiency and fast convergence across a wide range of valuation domains. We design the first fully adaptive-price combinatorial auction that gradually extends price expressivity as the rounds progress. We implement our auction design using polynomial prices and show how to detect when the current price structure is insufficient to clear the market, and how to expand the polynomial structure to guarantee progress. An experimental evaluation confirms that our auction is competitive with bundle-price auctions in regimes where these excel, namely multi-minded valuations, but also performs well in regimes favorable to linear prices, such as valuations with pairwise synergy.
Stereoselective conjugate additions of Grignard reagents to cyclopentadienones

Abstract Conjugate addition reactions of Grignard reagents with cyclopentadienones having trimethylsilyl groups at the α and α′ positions, and 1-hydroxyethyl substitutents at the β and β′ positions, are reported; excellent stereoselectivity was observed and the relative stereochemistry of three of the products was determined by X-ray methods.
LSALSA: accelerated source separation via learned sparse coding

We propose an efficient algorithm for the generalized sparse coding (SC) inference problem. The proposed framework applies to both the single dictionary setting, where each data point is represented as a sparse combination of the columns of one dictionary matrix, as well as the multiple dictionary setting as given in morphological component analysis (MCA), where the goal is to separate a signal into additive parts such that each part has distinct sparse representation within an appropriately chosen corresponding dictionary. Both the SC task and its generalization via MCA have been cast as $$\ell _1$$ -regularized optimization problems of minimizing quadratic reconstruction error. In an effort to accelerate traditional acquisition of sparse codes, we propose a deep learning architecture that constitutes a trainable time-unfolded version of the split augmented lagrangian shrinkage algorithm (SALSA), a special case of the alternating direction method of multipliers (ADMM). We empirically validate both variants of the algorithm, that we refer to as learned-SALSA (LSALSA), on image vision tasks and demonstrate that at inference our networks achieve vast improvements in terms of the running time and the quality of estimated sparse codes on both classic SC and MCA problems over more common baselines. We also demonstrate the visual advantage of our technique on the task of source separation. Finally, we present a theoretical framework for analyzing LSALSA network: we show that the proposed approach exactly implements a truncated ADMM applied to a new, learned cost function with curvature modified by one of the learned parameterized matrices. We extend a very recent stochastic alternating optimization analysis framework to show that a gradient descent step along this learned loss landscape is equivalent to a modified gradient descent step along the original loss landscape. In this framework, the acceleration achieved by LSALSA could potentially be explained by the network’s ability to learn a correction to the gradient direction of steeper descent.
Targeted Reactivation of FMR1 Transcription in Fragile X Syndrome Embryonic Stem Cells

Fragile X Syndrome (FXS) is the most common inherited cause of intellectual disability and autism. It results from expansion of a CGG nucleotide repeat in the 5' untranslated region (UTR) of FMR1. Large expansions elicit repeat and promoter hyper-methylation, heterochromatin formation, FMR1 transcriptional silencing and loss of the Fragile X protein, FMRP. Efforts aimed at correcting the sequelae resultant from FMRP loss have thus far proven insufficient, perhaps because of FMRP's pleiotropic functions. As the repeats do not disrupt the FMRP coding sequence, reactivation of endogenous FMR1 gene expression could correct the proximal event in FXS pathogenesis. Here we utilize the Clustered Regularly Interspaced Palindromic Repeats/deficient CRISPR associated protein 9 (CRISPR/dCas9) system to selectively re-activate transcription from the silenced FMR1 locus. Fusion of the transcriptional activator VP192 to dCas9 robustly enhances FMR1 transcription and increases FMRP levels when targeted directly to the CGG repeat in human cells. Using a previously uncharacterized FXS human embryonic stem cell (hESC) line which acquires transcriptional silencing with serial passaging, we achieved locus-specific transcriptional re-activation of FMR1 messenger RNA (mRNA) expression despite promoter and repeat methylation. However, these changes at the transcript level were not coupled with a significant elevation in FMRP protein expression in FXS cells. These studies demonstrate that directing a transcriptional activator to CGG repeats is sufficient to selectively reactivate FMR1 mRNA expression in Fragile X patient stem cells.
Reactions of N‐aryl‐1H‐benzotriazolyl‐1‐methanamines with allyl trimethylsilanes. A facile route to trialkylsilane tetrahydroquinolines

N-Aryl-1H-benzotriazolyl-1-methanamines 1, easily accessible from the condensation of anilines with formaldehyde and benzotriazole, undergo Lewis acid assisted reactions with allyl trimethylsilanes to give 4-(trimethylsilyl)methyl-1,2,3,4-tetrahydroquinolines 2 in good to high yields.
Effects of chronic spinal cord injury on relationships among ion channel and receptor mRNAs in mouse lumbar spinal cord

Spinal cord injury (SCI) causes widespread changes in gene expression of the spinal cord, even in the undamaged spinal cord below the level of the lesion. Less is known about changes in the correlated expression of genes after SCI. We investigated gene co-expression networks among voltage-gated ion channel and neurotransmitter receptor mRNA levels using quantitative RT-PCR in longitudinal slices of the mouse lumbar spinal cord in control and chronic SCI animals. These longitudinal slices were made from the ventral surface of the cord, thus forming slices relatively enriched in motor neurons or interneurons. We performed absolute quantitation of mRNA copy number for 50 ion channel or receptor transcripts from each sample, and used multiple correlation analyses to detect patterns in correlated mRNA levels across all pairs of genes. The majority of channels and receptors changed in expression as a result of chronic SCI, but did so differently across slice levels. Furthermore, motor neuron-enriched slices experienced an overall loss of correlated channel and receptor expression, while interneuron slices showed a dramatic increase in the number of positively correlated transcripts. These correlation profiles suggest that spinal cord injury induces distinct changes across cell types in the organization of gene co-expression networks for ion channels and transmitter receptors.
On the Structure of Total Synthesis of Complex Natural Products

A chemically intuitive measure (metric) for molecular complexity is described. It is then applied to several syntheses of complex natural products. We conclude that the metric corresponds well with chemical ideas of complexity, and that different syntheses do in fact have appreciably different logical structures as measured by this. Possible implications of this interesting observation are discussed.
Catalytic asymmetric synthesis of the central tryptophan residue of celogentin C.

Chiral phase-transfer catalyst 5 containing an electron-deficient trifluorobenzyl moiety promoted the alkylation of glycine derivative 6 with propargyl bromide 7a in good yield and excellent ee. The resulting propargyl glycine 8 was converted to 14, the central tryptophan residue of Celogentin C, in two steps, with the Pd-catalyzed heteroannulation as the key transformation. This method promises to be an efficient route for the preparation of tryptophan derivatives possessing substitution on the indole ring.
The Epstein-Barr virus miR-BHRF1 microRNAs regulate viral gene expression in cis

The Epstein-Barr virus (EBV) miR-BHRF1 microRNA (miRNA) cluster has been shown to facilitate B-cell transformation and promote the rapid growth of the resultant lymphoblastoid cell lines (LCLs). However, we find that expression of physiological levels of the miR-BHRF1 miRNAs in LCLs transformed with a miR-BHRF1 null mutant (∆123) fails to increase their growth rate. We demonstrate that the pri-miR-BHRF1-2 and 1-3 stem-loops are present in the 3'UTR of transcripts encoding EBNA-LP and that excision of pre-miR-BHRF1-2 and 1-3 by Drosha destabilizes these mRNAs and reduces expression of the encoded protein. Therefore, mutational inactivation of pri-miR-BHRF1-2 and 1-3 in the ∆123 mutant upregulates the expression of not only EBNA-LP but also EBNA-LP-regulated mRNAs and proteins, including LMP1. We hypothesize that this overexpression causes the reduced transformation capacity of the ∆123 EBV mutant. Thus, in addition to regulating cellular mRNAs in trans, miR-BHRF1-2 and 1-3 also regulate EBNA-LP mRNA expression in cis.
Synthesis of pyrinodemins A and B. Assignment of the double bond position of pyrinodemin A

Condensation of aldehyde 3a with hydroxylamine 4b afforded nitrone 2, which underwent an intramolecular cycloaddition to give 1b, the proposed structure of pyrinodemin A. A similar condensation of aldehyde 3a and hydroxylamine 4a provided pyrinodemin A (1a), which has the double bond one carbon further away from the isoxazolidine. An analogous sequence gave pyrinodemin B (21).