cssi/SciSciGPT-SciSciNet huggingface dataset:
Real-time computability of real numbers by chemical reaction networks

We explore the class of real numbers that are computed in real time by deterministic chemical reaction networks that are integral in the sense that all their reaction rate constants are positive integers. We say that such a reaction network computes a real number $$\alpha$$ in real time if it has a designated species X such that, when all species concentrations are set to zero at time $$t = 0$$ , the concentration x(t) of X is within $$2^{-t}$$ of $$|\alpha |$$ at all times $$t \ge 1$$ , and the concentrations of all other species are bounded. We show that every algebraic number and some transcendental numbers are real time computable by chemical reaction networks in this sense. We discuss possible implications of this for the 1965 Hartmanis–Stearns conjecture, which says that no irrational algebraic number is real time computable by a Turing machine.
Statistical Methods without Estimating the Missingness Mechanism: A Discussion of "Statistical Inference for Nonignorable Missing Data Problems: A Selective Review" by Niansheng Tang and Yuanyuan Ju.

First of all, I wholeheartedly congratulate Tang and Ju (referred to as TJ hereafter) on a well-written comprehensive review paper that surveys cutting-edge statistical theory and methodology relev...
Additive Guarantees for Degree-Bounded Directed Network Design

We present polynomial-time approximation algorithms for some degree-bounded directed network design problems. Our main result is for intersecting supermodular connectivity requirements with degree bounds: given a directed graph $G=(V,E)$ with nonnegative edge-costs, a connectivity requirement specified by an intersecting supermodular function $f$, and upper bounds $\{a_v,b_v\}_{v\in V}$ on in-degrees and out-degrees of vertices, find a minimum-cost $f$-connected subgraph of $G$ that satisfies the degree bounds. We give a bicriteria approximation algorithm for this problem using the natural LP relaxation and show that our guarantee is the best possible relative to this LP relaxation. We also obtain similar results for the (more general) class of crossing supermodular requirements. In the absence of edge-costs, our result gives the first additive $O(1)$-approximation guarantee for degree-bounded intersecting/crossing supermodular connectivity problems. We also consider the minimum crossing spanning tree problem: Given an undirected edge-weighted graph $G$, edge-subsets $\{E_i\}_{i=1}^k$, and nonnegative integers $\{b_i\}_{i=1}^k$, find a minimum-cost spanning tree (if it exists) in $G$ that contains at most $b_i$ edges from each set $E_i$. We obtain a $+(r-1)$ additive approximation for this problem, when each edge lies in at most $r$ sets. A special case of this problem is the degree-bounded minimum spanning tree, and our techniques give a substantially shorter proof of the recent $+1$ approximation of Singh and Lau [in Proceedings of the 40th Annual ACM Symposium on Theory of Computing, 2007, pp. 661-670].
Integrated ownership and managerial incentives with endogenous project risk

Integrated ownership is often seen as a way to foster specific investments. However, even in integrated firms, managers invest to maximize their compensation, which is chiefly driven by divisional income. Thus it is not clear that integration has any effect on investments in a world of decentralized decision-making. Building on recent findings that efficiency-enhancing investments raise not only the expected value of a project but also its variance, we show that, under plausible conditions, integration calls for low-powered incentive contracts: the managers invest more as they are less exposed to the investment-related (endogenous) risk, and the principal of an integrated firm has more to gain from greater investment. On the other hand, integration may result in higher-powered incentives if the project is inherently very risky or if the project-specific input is personally costly to the managers (rather than a monetary investment). The qualitative takeaway remains, however, that the contract adjustments under integration mitigate any input distortions present under non-integration. We also allow for firmwide performance evaluation under integration and show that it may lead to larger input distortions, but those are outweighed by improved risk sharing.
A system for acquiring, processing, and rendering panoramic light field stills for virtual reality

We present a system for acquiring, processing, and rendering panoramic light field still photography for display in Virtual Reality (VR). We acquire spherical light field datasets with two novel light field camera rigs designed for portable and efficient light field acquisition. We introduce a novel real-time light field reconstruction algorithm that uses a per-view geometry and a disk-based blending field. We also demonstrate how to use a light field prefiltering operation to project from a high-quality offline reconstruction model into our real-time model while suppressing artifacts. We introduce a practical approach for compressing light fields by modifying the VP9 video codec to provide high quality compression with real-time, random access decompression.We combine these components into a complete light field system offering convenient acquisition, compact file size, and high-quality rendering while generating stereo views at 90Hz on commodity VR hardware. Using our system, we built a freely available light field experience application called Welcome to Light Fields featuring a library of panoramic light field stills for consumer VR which has been downloaded over 15,000 times.
Attention and Anticipation in Fast Visual-Inertial Navigation

We study a visual-inertial navigation (VIN) problem in which a robot needs to estimate its state using an on-board camera and an inertial sensor, without any prior knowledge of the external environment. We consider the case in which the robot can allocate limited resources to VIN, due to tight computational constraints. Therefore, we answer the following question: under limited resources, what are the most relevant visual cues to maximize the performance of VIN? Our approach has four key ingredients. First, it is task-driven , in that the selection of the visual cues is guided by a metric quantifying the VIN performance. Second, it exploits the notion of anticipation , since it uses a simplified model for forward-simulation of robot dynamics, predicting the utility of a set of visual cues over a future time horizon. Third, it is efficient and easy to implement , since it leads to a greedy algorithm for the selection of the most relevant visual cues. Fourth, it provides formal performance guarantees : we leverage submodularity to prove that the greedy selection cannot be far from the optimal (combinatorial) selection. Simulations and real experiments on agile drones show that our approach ensures state-of-the-art VIN performance while maintaining a lean processing time. In the easy scenarios, our approach outperforms appearance-based feature selection in terms of localization errors. In the most challenging scenarios, it enables accurate VIN while appearance-based feature selection fails to track robot's motion during aggressive maneuvers.
Development of a pediatric asthma predictive index for hospitalization

Abstract Background Variation in emergency department (ED) management for asthma exacerbation leads to disparities in care. Current asthma severity scores are insufficient to be used for hospitalization decisions. Objective To develop and internally validate an asthma predictive index for hospitalization (APIH) to guide practitioners in their admission decision for children with asthma exacerbations. Methods Data were collected from 12,066 children between 5 and 18 years old diagnosed with asthma exacerbation in the ED. Epidemiologic findings, number of inhaled corticosteroid canisters, short-acting β-blocker canisters, oral steroids, coexisting atopy, family history of atopy, insurance, and prior asthma ED visits or hospitalizations were compared between patients hospitalized and discharged. We used univariate analysis and multivariate analysis to determine the best predictor variables for hospitalization. Our study internally validated the prediction index to estimate future performance of the prediction rule. Results The highest risk factors associated with asthma hospitalization from the ED are oxygen saturation less than 94%, respiratory rate greater than 31/min, history of pneumonia, and asthma ED visits in past 12 months. With a reduced predictive model that combined these risk factors, the odds ratio was 44.9 (95% CI, 32.8-61.4), which is extremely significant. Our C index of discrimination of 0.77 was similar to the validation C index of 0.78, which confirms a solid prediction model. Conclusion We have developed and internally validated a pediatric hospitalization prediction index for acute asthma exacerbation in the ED. Further studies are needed to externally validate the APIH before its implementation into clinical practice.
The Unsound Theory Behind the Consumer (and Total) Welfare Goal in Antitrust

This is the first installment of a two-part commentary on the New Brandeis School (the “New Brandeisians”) in Antitrust. In this first part, I examine why the New Brandeisians are correct to reject...
Domain topology, stability, and translation speed determine mechanical force generation on the ribosome

The concomitant folding of a nascent protein domain with its synthesis can generate mechanical forces that act on the ribosome and alter translation speed. Such changes in speed can affect the structure and function of the newly synthesized protein as well as cellular phenotype. The domain properties that govern force generation have yet to be identified and understood, and the influence of translation speed is unknown because all reported measurements have been carried out on arrested ribosomes. Here, using coarse-grained molecular simulations and statistical mechanical modeling of protein synthesis, we demonstrate that force generation is determined by a domain’s stability and topology, as well as translation speed. The statistical mechanical models we create predict how force profiles depend on these properties. These results indicate that force measurements on arrested ribosomes will not always accurately reflect what happens in a cell, especially for slow-folding domains, and suggest the possibility that certain domain properties may be enriched or depleted across the structural proteome of organisms through evolutionary selection pressures to modulate protein synthesis speed and posttranslational protein behavior.
Relative sensitivity of explicit reaiming and implicit motor adaptation.

This paper provides the first psychometric sensitivity function for explicit reaiming. Additionally, we show that the sensitivities of both implicit adaptation and explicit reaiming are influenced ...
Detection of Instrument Gain Problems Based on Body‐Wave Polarization: Application to the Hi‐Net Array

Monitoring and assessing instrument performance and response are crucial to various seismological analyses that utilize the seismic signal recorded by the instrument. One of the important components of the instrument response is the gain or the amplification factor that determines the amplitude of the recorded wave arrival. We introduce a new method to detect problems in the gain of three‐component seismographs by examining the body‐wave polarization. Anomalous gain of a certain component causes P‐ and S‐wave polarization to be distinct from expected values, allowing one to identify the issue in the instrument. The method is applied to the High‐Sensitivity Seismograph Network (Hi‐net) stations between 2004 and 2016, and 305 out of 790 stations are identified to have issues at various time periods. The detections are confirmed by comparison with the Hi‐net daily calibration pulses. Utilization of teleseismic body‐wave polarization information is an effective way to detect instrument gain problems without physically examining the instrument, which is particularly advantageous for instruments such as borehole or ocean‐bottom sensors that cannot be accessed easily.
On the Similarities of Low-Temperature Plasma Discharges

In similar discharges, the physical characteristics of the plasma in one gap are proportional to those in the others. The similarities of the gas discharge enable scaling discharge features, particularly useful for those scales for which experimental studies are not feasible. In this paper, the history of the similarity theory is revisited, and recent studies of the similarities of low-temperature plasma discharges, including scaling laws for the gas breakdown and steady-state discharges, are reported according to both experiments and numerical simulations. The validity of similarity laws is evaluated from low- to high-pressure discharge regimes, and violations of similarity laws are discussed when the nonlinear processes cannot be ignored, especially in the high-pressure regime. The impact factors, including the nonlinear processes and the scaling factors, for the similarity laws are also discussed. Several applications of the similarity law are explored for the related plasma physics issues.
Causal approximations

Adequate problem representations require the identification of abstractions and approximations that are well suited to the task at hand. In this paper we introduce a new class of approximations, called causal approximations, that are commonly found in modeling the physical world. Causal approximations support the efficient generation of parsimonious causal explanations, which play an important role in reasoning about engineered devices. The central problem to be solved in generating parsimonious causal explanations is the identification of a simplest model that explains the phenomenon of interest. We formalize this problem and show that it is, in general, intractable. In this formalization, simplicity of models is based on the intuition that using more approximate models of fewer phenomena leads to simpler models. We then show that when all the approximations are causal approximations, the above problem can be solved in polynomial time.
Regulation of myofilament force and loaded shortening by skeletal myosin binding protein C

Myosin binding protein C (MyBP-C) is a 125-140-kD protein located in the C-zone of each half-thick filament. It is thought to be an important regulator of contraction, but its precise role is unclear. Here we investigate mechanisms by which skeletal MyBP-C regulates myofilament function using rat permeabilized skeletal muscle fibers. We mount either slow-twitch or fast-twitch skeletal muscle fibers between a force transducer and motor, use Ca2+ to activate a range of forces, and measure contractile properties including transient force overshoot, rate of force development, and loaded sarcomere shortening. The transient force overshoot is greater in slow-twitch than fast-twitch fibers at all Ca2+ activation levels. In slow-twitch fibers, protein kinase A (PKA) treatment (a) augments phosphorylation of slow skeletal MyBP-C (sMyBP-C), (b) doubles the magnitude of the relative transient force overshoot at low Ca2+ activation levels, and (c) increases force development rates at all Ca2+ activation levels. We also investigate the role that phosphorylated and dephosphorylated sMyBP-C plays in loaded sarcomere shortening. We test the hypothesis that MyBP-C acts as a brake to filament sliding within the myofilament lattice by measuring sarcomere shortening as thin filaments traverse into the C-zone during lightly loaded slow-twitch fiber contractions. Before PKA treatment, shortening velocity decelerates as sarcomeres traverse from ∼3.10 to ∼3.00 µm. After PKA treatment, sarcomeres shorten a greater distance and exhibit less deceleration during similar force clamps. After sMyBP-C dephosphorylation, sarcomere length traces display a brief recoil (i.e., "bump") that initiates at ∼3.06 µm during loaded shortening. Interestingly, the timing of the bump shifts with changes in load but manifests at the same sarcomere length. Our results suggest that sMyBP-C and its phosphorylation state regulate sarcomere contraction by a combination of cross-bridge recruitment, modification of cross-bridge cycling kinetics, and alteration of drag forces that originate in the C-zone.
CDASH: Community Data Analytics for Social Harm Prevention

Communities are adversely affected by heterogeneous social harm events (e.g., crime, traffic crashes, medical emergencies, drug use) and police, fire, health and social service departments are tasked with mitigating social harm through various types of interventions. Smart cities of the future will need to leverage IoT, data analytics, and government and community human resources to most effectively reduce social harm. Currently, methods for collection, analysis, and modeling of heterogeneous social harm data to identify government actions to improve quality of life are needed. In this paper we propose a system, CDASH, for synthesizing heterogeneous social harm data from multiples sources, identifying social harm risks in space and time, and communicating the risk to the relevant community resources best equipped to intervene. We discuss the design, architecture, and performance of CDASH. CDASH allows users to report live social harm events using mobile hand-held devices and web browsers and flags high risk areas for law enforcement and first responders. To validate the methodology, we run simulations on historical social harm event data in Indianapolis illustrating the advantages of CDASH over recently introduced social harm indices and existing point process methods used for predictive policing.
Feeling the Bern: Adaptive Estimators for Bernoulli Probabilities of Pairwise Comparisons

We study methods for aggregating pairwise comparison data among a collection of $n$ items with the goal of estimating the outcome probabilities for future comparisons. Working within a flexible model that only imposes a form of strong stochastic transitivity, we introduce an “adaptivity index” which compares the risk of our estimator to that of an oracle, over appropriate sub-models, where the oracle knows the specific sub-model in the ground truth. In addition to measuring the usual worst-case risk of an estimator, this adaptivity index also captures the extent to which the estimator adapts to instance-specific difficulty relative to an oracle estimator. First, we propose a three-step estimator termed count-randomize-least squares, and show that it has adaptivity index upper bounded by $\sqrt {n}$ up to logarithmic factors. We then show that conditional on the planted clique hypothesis, no computationally efficient estimator can achieve an adaptivity index smaller than $\sqrt {n}$ . Second, we show that a regularized least squares estimator can achieve a poly-logarithmic adaptivity index, thereby demonstrating a $\sqrt {n}$ -gap between optimal and computationally achievable adaptivity. Finally, we prove that the standard least squares estimator, which is known to be optimally adaptive in several closely related problems, fails to adapt in the context of estimating pairwise probabilities.
Cross-lingual Transfer Learning for Spoken Language Understanding

Typically, spoken language understanding (SLU) models are trained on annotated data which are costly to gather. Aiming to reduce data needs for bootstrapping a SLU system for a new language, we present a simple but effective weight transfer approach using data from another language. The approach is evaluated with our promising multi-task SLU framework developed towards different languages. We evaluate our approach on the ATIS and a real-world SLU dataset, showing that i) our monolingual models outperform the state-of-the-art, ii) we can reduce data amounts needed for bootstrapping a SLU system for a new language greatly, and iii) while multitask training improves over separate training, different weight transfer settings may work best for different SLU modules.
Effect Of AlGaN/GaN Strained Layer Superlattice Period On InGaN MQW Laser Diodes

AlGaN/GaN strained layer superlattices have been employed in the cladding layers of InGaN multi-quantum well laser diodes grown by metalorganic chemical vapor deposition (MOCVD). Superlattices have been investigated for strain relief of the cladding layer, as well as an enhanced hole concentration, which is more than ten times the value obtained for bulk AlGaN films. Laser diodes with strained layer superlattices as cladding layers were shown to have superior structural and electrical properties compared to laser diodes with bulk AlGaN cladding layers. As the period of the strained layer superlattices is decreased, the threshold voltage, as well as the threshold current density, is decreased. The resistance to vertical conduction through p-type superlattices with increasing superlattice period is not offset by the increase in hole concentration for increasing superlattice spacing, resulting in higher voltages.
Management of Autoimmune Pancreatitis.

The article contains modern data on such a chronic pancreatic disease as autoimmune pancreatitis (AIP). Statistical data on the prevalence and incidence of AIP are presented, the current international classification of this pathology is considered, the main features of type 1 AIP (lymphoplasmacytic sclerosing pancreatitis, LPSP) and type 2 AIP (idiopathic duct centric pancreatitis, IDCP) are put forward. The clinical manifestation of these types is different: obstructive jaundice develops more often in patients with LPSP, while patients with IDCP mostly have acute pancreatitis. The presence and variety of extrapancreatic manifestations of the disease with extremely frequent concomitant development of ulcerative colitis is emphasized. The features of serological diagnosis of AIP and the role of IgG4 level in determining the type of disease are considered. The proper techniques of AIP instrumental diagnostics are listed, the typical changes detected during computed tomography and the distinctive histological characteristics of LPSP and IDCP are considered. The feasibility of a differential diagnosis between AIP and pancreatic cancer is indicated by analyzing the results of serological, imaging, and histological studies. The algorithm of management of AIP patients depending on the type of disease is described, as well as the tactics of prescribing corticosteroids, immunomodulators upon LPSP and IDCP. Immunomodulators of choice (mycophenolate mofetil, azathioprine) are indicated, and rituximab administration features are considered. Possible signs of AI recurrence are listed (IgG4-sclerosing cholangitis, high IgE level).
Anomalies and similarities among consensus numbers of variously-relaxed queues

Shared data structures are a basic building block in distributed computing, but can be expensive to implement. One way to circumvent the high implementation cost of linearizability is to relax the sequential specification of the data type. This gives up some guarantees, for instance on the ordering of data elements, as a tradeoff against performance. We want to explore the effects of this tradeoff on the computational power of the shared data structures. In this paper, we characterize the effects of three different types of relaxation, chosen from the literature, on the computational power of FIFO queues. By parametrically relaxing each of the three operations on a queue (Enqueue, Dequeue, Peek), we obtain an infinite 3-dimensional space for each type of relaxation. We find the consensus number, a standard measure of the computational power of shared data types, of each point in these spaces, completely describing the effect of these three types of relaxation on the computational power of queues.
Factors Influencing the Impact of Depressive Symptoms on Physical Functional Capacity After Cardiac Rehabilitation.

Purpose This study aims to determine (1) if depressive symptoms in the year following completion of cardiac rehabilitation impact physical functional capacity and (2) if exercise, perceived benefits and barriers, self-efficacy, and social support moderate this relationship. Design This longitudinal correlational secondary data analysis included 379 cardiovascular rehabilitation patients. Methods Participants completed measures of depression and potential moderating variables at baseline, 2 months, 6 months, and 12 months and 6-minute work test at baseline and 12 months and wore heart rate monitors to measure exercise for 12 months. Findings Poorer physical functional capacity was predicted by depressed mood score. This relationship was moderated by the percentage of time exercising in target heart rate zone and family support of exercise, but not by perceived benefits and barriers or self-efficacy for exercise. Conclusions Depressive symptoms negatively impact physical functional capacity, and this relationship is moderated by family support and the percentage of time exercising in target heart rate zone. Clinical relevance Improving percentage of time exercising in target heart rate zone may be a mechanism by which patients with depressed mood can optimize physical functional capacity.
Facially Selective and Regioselective Carbometalation of Cyclopropenes by Aryl Grignard Reagents

Described is a Cu-catalyzed methodology for adding aryl Grignard reagents to 3-hydroxymethylcyclopropene derivatives with high regio- and diastereoselectivity. The cyclopropylmetals can be trapped with a variety of electrophiles to generate highly substituted cyclopropanes.
Catalytic enantioselective amination of enolsilanes using C2-symmetric copper(II) complexes as chiral Lewis acids.

[Cu(S,S)-t-Bu-box](OTf)2 (1) catalyzes the enantioselective amination of enolsilanes with azodicarboxylate derivatives. Isomerically pure enolsilanes of aryl ketones, acylpyrroles, and thioesters added to the azo-imide in greater than 95% ee. The use of an alcohol additive was critical to achieving catalyst turnover.
RUPEE: A fast and accurate purely geometric protein structure search

Given the close relationship between protein structure and function, protein structure searches have long played an established role in bioinformatics. Despite their maturity, existing protein structure searches either use simplifying assumptions or compromise between fast response times and quality of results. These limitations can prevent the easy and efficient exploration of relationships between protein structures, which is the norm in other areas of inquiry. To address these limitations we have developed RUPEE, a fast and accurate purely geometric structure search combining techniques from information retrieval and big data with a novel approach to encoding sequences of torsion angles. Comparing our results to the output of mTM, SSM, and the CATHEDRAL structural scan, it is clear that RUPEE has set a new bar for purely geometric big data approaches to protein structure searches. RUPEE in top-aligned mode produces equal or better results than the best available protein structure searches, and RUPEE in fast mode demonstrates the fastest response times coupled with high quality results. The RUPEE protein structure search is available at https://ayoubresearch.com. Code and data are available at https://github.com/rayoub/rupee.
CsTl: A New Example of Tetragonally Compressed Tl66- Octahedra. Electronic Effects and Packing Requirements in the Diverse Structures of ATl (A = Li, Na, K, Cs)

The cesium-richest phase in the Cs−Tl system, CsTl, can be isolated as a pure crystalline phase through slow cooling of cesium-richer compositions in Ta followed by vacuum sublimation of the excess Cs at ∼100 °C. The compound melts incongruently in the neighborhood of 150 °C. The structure was established by single crystal X-ray diffraction at room temperature (orthorhombic Fddd, Z = 48, a = 32.140(3) A, b = 15.136(1) A, and c = 9.2400(7) A. The isolated Tl66- ions in the structure, tetragonally compressed octahedra, exhibit D2 symmetry with ≤0.063(4) A differences in edge lengths from D4h. Extended Huckel calculations confirm the classical nature of the distortion in lowering the cluster electron count and charge. The diamagnetic CsTl differs from KTl, which contains more distorted Tl66- ions (C2h), in a doubled a axis and an additional interpenetrating cluster anion sublattice. The smaller distortion of the clusters in CsTl originates with the lower field of the same number of cation neighbors in a more...
Hemirubin: An Intramolecularly Hydrogen-Bonded Analogue for One-Half Bilirubin.

A model for one-half bilirubin, the neurotoxic yellow-orange pigment of jaundice, 9-[2-(2-carboxyethyl)benzyl]-2,3,7,8-tetramethyl-1,10-dihydrodipyrrin (1, hemirubin) was synthesized following SnCl(4)-catalyzed Friedel-Crafts acylation at C(9) of 2,3,7,8-1-oxo-1,10-dihydrodipyrrin (7) with methyl o-(chlorocarbonyl)hydrocinnamate. Unlike earlier bilirubin model compounds, hemirubin is predicted and found to engage in intramolecular hydrogen bonding. Like bilirubin, the propionic acid carboxyl group of hemirubin is linked to the opposing dipyrrinone by intramolecular hydrogen bonds, and thus, 1 shares in some of the solution properties of its parent bilirubin, e.g., an acid that is less polar than its methyl ester.
Fast P(RMNE): Fast forensic DNA probability of random man not excluded calculation

High throughput sequencing (HTS) of DNA forensic samples is expanding from the sizing of short tandem repeats (STRs) to massively parallel sequencing (MPS). HTS panels are expanding from the FBI 20 core Combined DNA Index System (CODIS) loci to include SNPs. The calculation of random man not excluded, P(RMNE), is used in DNA mixture analysis to estimate the probability that a person is present in a DNA mixture. This calculation encounters calculation artifacts with expansion to larger panel sizes. Increasing the floating-point precision of the calculations allows for increased panel sizes but with a corresponding increase in computation time. The Taylor series higher precision libraries used fail on some input data sets leading to algorithm unreliability. Herein, a new formula is introduced for calculating P(RMNE) that scales to larger SNP panel sizes while being computationally efficient (patent pending).
Synthesis of the pentacyclic xestobergsterol skeleton

Abstract An approach to the synthesis of the histamine release inhibitor xestobergsterol is described. The intramolecular Pauson-Khand reaction was used to generate the D and E rings of the steroid.
Identification of Novel Protein Lysine Acetyltransferases in Escherichia coli

ABSTRACT Posttranslational modifications, such as Ne-lysine acetylation, regulate protein function. Ne-lysine acetylation can occur either nonenzymatically or enzymatically. The nonenzymatic mechanism uses acetyl phosphate (AcP) or acetyl coenzyme A (AcCoA) as acetyl donor to modify an Ne-lysine residue of a protein. The enzymatic mechanism uses Ne-lysine acetyltransferases (KATs) to specifically transfer an acetyl group from AcCoA to Ne-lysine residues on proteins. To date, only one KAT (YfiQ, also known as Pka and PatZ) has been identified in Escherichia coli. Here, we demonstrate the existence of 4 additional E. coli KATs: RimI, YiaC, YjaB, and PhnO. In a genetic background devoid of all known acetylation mechanisms (most notably AcP and YfiQ) and one deacetylase (CobB), overexpression of these putative KATs elicited unique patterns of protein acetylation. We mutated key active site residues and found that most of them eliminated enzymatic acetylation activity. We used mass spectrometry to identify and quantify the specificity of YfiQ and the four novel KATs. Surprisingly, our analysis revealed a high degree of substrate specificity. The overlap between KAT-dependent and AcP-dependent acetylation was extremely limited, supporting the hypothesis that these two acetylation mechanisms play distinct roles in the posttranslational modification of bacterial proteins. We further showed that these novel KATs are conserved across broad swaths of bacterial phylogeny. Finally, we determined that one of the novel KATs (YiaC) and the known KAT (YfiQ) can negatively regulate bacterial migration. Together, these results emphasize distinct and specific nonenzymatic and enzymatic protein acetylation mechanisms present in bacteria. IMPORTANCENe-Lysine acetylation is one of the most abundant and important posttranslational modifications across all domains of life. One of the best-studied effects of acetylation occurs in eukaryotes, where acetylation of histone tails activates gene transcription. Although bacteria do not have true histones, Ne-lysine acetylation is prevalent; however, the role of these modifications is mostly unknown. We constructed an E. coli strain that lacked both known acetylation mechanisms to identify four new Ne-lysine acetyltransferases (RimI, YiaC, YjaB, and PhnO). We used mass spectrometry to determine the substrate specificity of these acetyltransferases. Structural analysis of selected substrate proteins revealed site-specific preferences for enzymatic acetylation that had little overlap with the preferences of the previously reported acetyl-phosphate nonenzymatic acetylation mechanism. Finally, YiaC and YfiQ appear to regulate flagellum-based motility, a phenotype critical for pathogenesis of many organisms. These acetyltransferases are highly conserved and reveal deeper and more complex roles for bacterial posttranslational modification.
HOMOLYTIC LIQUID‐PHASE REACTIONS OF 1,3‐DIOXACYCLANES (REVIEW)

The literature data on the liquid-phase homolytic isomerization, addition, substitution, and oxidation reactions of 1,3-dioxacyclanes are examined. The problems involved in the formation, stabilities, kinetics, and mechanisms of the transformations of free radicals in a series of cyclic acetals are discussed. Possibilities for the application of the homolytic transformations of 1,3-dioxacyclanes in organic synthesis are demonstrated.
Asymmetric Total Synthesis of (+)-Apovincamine and a Formal Synthesis of (+)-Vincamine. Demonstration of a Practical “Asymmetric Linkage” between Aromatic Carboxylic Acids and Chiral Acyclic Substrates

Asymmetric syntheses of (+)-apovincamine (1a) and (+)-vincamine (2) are described. Construction of the pentacyclic diene lactam 14, a pivotal intermediate for synthesis of the cis-fused vincane-type alkaloids, began by Birch reduction−alkylation of the chiral benzamide 3 to give the 6-ethyl-1-methoxy-4-methyl-1,4-cyclohexadiene 4. Conversion of 4 to 2,5-cyclohexadienone 5 (92% overall yield from 3) and HPLC analysis of 5 demonstrated the diastereomeric purity resulting from the Birch reduction−alkylation to be >100:1. Dienone 5 was converted to butyrolactone 9 (47% overall yield from 3), and 9 was coupled with tryptamine (10) to give the amide 11a. Amido keto aldehyde 13 was obtained from 11a, and acid-catalyzed tricyclization and subsequent base-induced elimination of MeOH provided the desired cis-fused pentacyclic diene lactam 14. Examination of the two-step process 13 → 14 revealed a novel base-induced epimerization at C(21) which served to interconvert 14 and 17, possibly by the involvement of a homoe...
Regioselective synthesis of benzimidazole thiophene inhibitors of polo-like kinase 1

Abstract A regioselective synthesis of novel 1-(2-thienyl)-benzimidazole inhibitors of polo-like kinase 1 is described. Amination of substituted 2-iodo or -bromo nitrobenzenes with a 2-aminothiophene derivative catalyzed by Pd2dba3 and XANTPHOS in the presence of excess Cs2CO3 afforded good yields of the coupled products. Subsequent reduction and cyclization of these intermediates provided the desired benzimidazole compounds.
Gaussian fluctuations from the 2D KPZ equation

We prove the two dimensional KPZ equation with a logarithmically tuned nonlinearity and a small coupling constant, scales to the Edwards–Wilkinson equation with an effective variance.
A protocol to accomplish ‘homo-Robinson’ annulation: application to the guanacastepene problem

A sequence which accomplishes the preparation of cycloheptadienones by ring-expansion of fused cyclohexenones has been developed and applied to the improved synthesis of a key intermediate in the total synthesis of guanacastepene A.
General Approaches to Phosphinidenes Via Retroadditions

Abstract Retroadditions – thermal and photochemical decomposition of phosphiranes and 3-phospholenes – offer general routes to free phosphinidenes.
Powerful Water Masers in Active Galactic Nuclei

Luminous water maser emission in the 616–523 line at 22GHz has been detected from two dozen galaxies. In all cases the emission is confined to the nucleus and has been found only in AGN, in particular, in Type 2 Seyferts and LINERs. I argue that most of the observed megamaser sources are powered by X-ray irradiation of dense gas by the central engine. After briefly reviewing the physics of these X-Ray Dissociation Regions, I discuss in detail the observations of the maser disk in NGC 4258, its implications, and compare alternative models for the maser emission. I then discuss the observations of the other sources that have been imaged with VLBI to date, and how they do or do not fit into the framework of a thin, rotating disk, as in NGC 4258. Finally, I briefly discuss future prospects, especially the possibility of detecting other water maser transitions.
RiboTag translatomic profiling of Drosophila oenocytes under aging and induced oxidative stress.

Aging is accompanied with loss of tissue homeostasis and accumulation of cellular damages. As one of the important metabolic centers, liver shows age-related dysregulation of lipid metabolism, impaired detoxification pathway, increased inflammation and oxidative stress response. However, the mechanisms for these age-related changes still remain unclear. In the fruit fly, Drosophila melanogaster, liver-like functions are controlled by two distinct tissues, fat body and oenocytes. Compared to fat body, little is known about how oenocytes age and what are their roles in aging regulation. To characterize age- and stress-regulated gene expression in oenocytes, we performed cell-type-specific ribosome profiling (RiboTag) to examine the impacts of aging and oxidative stress on oenocyte translatome in Drosophila. We show that aging and oxidant paraquat significantly increased the levels of reactive oxygen species (ROS) in adult oenocytes of Drosophila, and aged oenocytes exhibited reduced sensitivity to paraquat treatment. Through RiboTag sequencing, we identified 3324 and 949 differentially expressed genes in oenocytes under aging and paraquat treatment, respectively. Aging and paraquat exhibit both shared and distinct regulations on oenocyte translatome. Among all age-regulated genes, oxidative phosphorylation, ribosome, proteasome, fatty acid metabolism, and cytochrome P450 pathways were down-regulated, whereas DNA replication and immune response pathways were up-regulated. In addition, most of the peroxisomal genes were down-regulated in aged oenocytes, including genes involved in peroxisomal biogenesis factors and fatty acid beta-oxidation. Many age-related mRNA translational changes in oenocytes are similar to aged mammalian liver, such as up-regulation of innate immune response and Ras/MAPK signaling pathway and down-regulation of peroxisome and fatty acid metabolism. Furthermore, oenocytes highly expressed genes involving in liver-like processes (e.g., ketogenesis). Our oenocyte-specific translatome analysis identified many genes and pathways that are shared between Drosophila oenocytes and mammalian liver, highlighting the molecular and functional similarities between the two tissues. Many of these genes were altered in both oenocytes and liver during aging. Thus, our translatome analysis provide important genomic resource for future dissection of oenocyte function and its role in lipid metabolism, stress response and aging regulation.
RNA Polymerase Clamp Movement Aids Dissociation from DNA but Is Not Required for RNA Release at Intrinsic Terminators

In bacteria, disassembly of elongating transcription complexes (ECs) can occur at intrinsic terminators in a 2- to 3-nucleotide window after transcription of multiple kilobase pairs of DNA. Intrinsic terminators trigger pausing on weak RNA-DNA hybrids followed by formation of a strong, GC-rich stem-loop in the RNA exit channel of RNA polymerase (RNAP), inactivating nucleotide addition and inducing dissociation of RNA and RNAP from DNA. Although the movements of RNA and DNA during intrinsic termination have been studied extensively leading to multiple models, the effects of RNAP conformational changes remain less well defined. RNAP contains a clamp domain that closes around the nucleic acid scaffold during transcription initiation and can be displaced by either swiveling or opening motions. Clamp opening is proposed to promote termination by releasing RNAP-nucleic acid contacts. We developed a cysteine crosslinking assay to constrain clamp movements and study effects on intrinsic termination. We found that biasing the clamp into different conformations perturbed termination efficiency, but that perturbations were due primarily to changes in elongation rate, not the competing rate at which ECs commit to termination. After commitment, however, inhibiting clamp movements slowed release of DNA but not of RNA from the EC. We also found that restricting trigger-loop movements with the RNAP inhibitor microcin J25 prior to commitment inhibits termination, in agreement with a recently proposed multistate-multipath model of intrinsic termination. Together our results support views that termination commitment and DNA release are separate steps and that RNAP may remain associated with DNA after termination.
Liquid‐phase autoxidation of organic compounds at elevated temperatures. Absolute rate constant for intermolecular hydrogen abstraction in hexadecane autoxidation at 120–190°C

The absolute rate constants for the intermolecular hydrogen abstraction reactions of secondary hydrogens by secondary alkylperoxy radicals in hexadecane autoxidation, k3, have been determined in the temperature range of 120–190°C using the stirred flow reactor technique. Absolute rate constants determined in this study for hexadecane are in good agreement with those determined for other hydrocarbons in liquid phase, on a per hydrogen basis, at lower temperatures. Arrhenius parameters for k3/H derived from this study are A = 108.6 M−1 s−1 and Ea = 16.0 kcal/mol. The values of these parameters provide experimental confirmation for previous estimates made from both lower temperature reactions in the liquid phase and higher temperature reactions in the gas phase. © 1994 John Wiley & Sons, Inc.
Stereoselective cyclopropanation of homoallylic alcohols. Formal attachment of a cyclopropane to a preexisting ring

Abstract Complementary methods for the formal attachment of a cyclopropane to a preexisting ring system that lead to the exclusive formation of either of two possible relative stereochemical relationships are described.
Partitioning the Effects of Eco-Evolutionary Feedbacks on Community Stability*

AbstractA fundamental challenge in ecology continues to be identifying mechanisms that stabilize community dynamics. By altering the interactions within a community, eco-evolutionary feedbacks may play a role in community stability. Indeed, recent empirical and theoretical studies demonstrate that these feedbacks can stabilize or destabilize communities and, moreover, that this sometimes depends on the relative rate of ecological to evolutionary processes. So far, theory on how eco-evolutionary feedbacks impact stability exists only for a few special cases. In our work, we develop a general theory for determining the effects of eco-evolutionary feedbacks on stability in communities with an arbitrary number of interacting species and evolving traits for when evolution is slow and fast. We characterize how eco-evolutionary feedbacks lead to stable communities that would otherwise be unstable, and vice versa. Additionally, we show how one can identify the roles of direct and indirect feedbacks between ecolog...
Improved synthetic route to n-B18H22.

Simple iodine oxidation of the B9H12- anion in toluene at room temperature reliably gives excellent yields (∼80%) of n-B18H22 (anti-B18H22) and thus provides a convenient, large-scale, safe route to this important polyborane cluster.
Palladium-catalyzed heteroannulation of internal alkynes by vinylic halides

Abstract A number of heterocycles have been synthesized regioselectively in good yields by treating appropriate functionally-substituted vinylic halides with internal alkynes in the presence of a palladium catalyst.
A new polytype of orthoboric acid, H3BO3-3T

The crystal structure of H3BO3-3T, a new trigonal polytype of orthoboric acid, consists of sheets of hydrogen-bonded B(OH)3 mol­ecules similar to those found in the triclinic structure of orthoboric acid, H3BO3-2A. In each case, van der Waals forces connect the sheets. However, the stacking sequences of the sheets differ between the two polymorphs. In H3BO3-3T (space group P32), the sheets are stacked in the repeating sequence ABC…, whereas in H3BO3-2A (space group P \overline 1), the sheets are stacked in the repeating sequence AB….
Biomimetic Cyclization of Enamide-Containing Polyenes as a New Route to Azapolycycles†

Enamide 4 was studied for its effectiveness as a polyene precursor in biomimetic cyclizations. While most conventional Lewis acids were poor cyclization promoters, FeCl(3).6H(2)O initiated the conversion of 4 into tricycles 6 and 7 in excellent yield. The two isomeric products result from the cyclization of intermediate aldehyde 5 by either a chair or boat B-ring transition state. These results suggest that enamides may be incorporated into polyene precursors for the construction of larger azapolycycles such as azasteroids.
N-difluoromethylation of phenylazoles

Abstract In the presence of one equivalent of NaH, 2- and 4-phenylimidazole and 3-phenyl-1,2,4-triazole can be N-difluoromethylated with ClCF 2 H. The difluoromethylation of 5-phenyltetrazole requires two equivalents of NaH. A mechanism is proposed to account for these differences.
MOLECULAR DESIGN OF HETEROGENEOUS CATALYSTS

A discussion on the molecular design of solid catalysts is presented. Rather than reviewing the many definitions of design principles and methodologies for synthesis of classes of catalysts, a specific case study is provided. Salient features of protein-based (enzyme, antibody) catalysts are enumerated and used to guide the creation of two new types of solid catalytic materials, namely, organic functionalized molecular sieves and amorphous imprinted organosilicates. The solid catalysts are compared to an antibody catalyst and their behaviors contrasted.
Synthesis of N-aryl-aza-crown ethers via Pd-catalyzed amination reactions of aryl chlorides with aza-crown ethers

Abstract The Pd2(dba)3/P(i-BuNCH2CH2)3N ( 1 ) catalyst system effectively catalyzes the coupling of aza-crown ethers with electronically diverse aryl chlorides, affording N-aryl-aza-crown ethers in good yields. The Pd2(dba)3/P(i-BuNCH2)3CMe ( 2 ) catalyst system containing the more constrained bicyclic triaminophosphine is useful for aryl chlorides possessing base-sensitive ester, nitro, and nitrile functional groups.
Metathesis approach to the synthesis of polyheterocyclic structures from oxanorbornenes.

The synthesis of stereochemically defined tri- and penta-heterocyclic ring systems 9 and 28, respectively, via the metathesis reaction of substituted oxanorbornanes derived from 3 is described.
Comparative Studies on the Synthesis of an anti,syn Stereotriad with Chiral Allenylstannane and Allenylindium Reagents

Addition of the chloroallenylstannane derived from the Bu3Sn allene (S)-2 and SnCl4 to nonracemic α-methyl-β-oxygenated aldehyde 1a afforded mixtures of anti,syn and anti,anti adducts 3a and 3b. Wh...