cssi/SciSciGPT-SciSciNet huggingface dataset:
Curriculum Learning for Speech Emotion Recognition From Crowdsourced Labels

This study introduces a method to design a curriculum for machine-learning to maximize the efficiency during the training process of deep neural networks (DNNs) for speech emotion recognition. Previous studies in other machine-learning problems have shown the benefits of training a classifier following a curriculum where samples are gradually presented in increasing level of difficulty. For speech emotion recognition, the challenge is to establish a natural order of difficulty in the training set to create the curriculum. We address this problem by assuming that, ambiguous samples for humans are also ambiguous for computers. Speech samples are often annotated by multiple evaluators to account for differences in emotion perception across individuals. While some sentences with clear emotional content are consistently annotated, sentences with more ambiguous emotional content present important disagreement between individual evaluations. We propose to use the disagreement between evaluators as a measure of difficulty for the classification task. We propose metrics that quantify the inter-evaluation agreement to define the curriculum for regression problems and binary and multi-class classification problems. The experimental results consistently show that relying on a curriculum based on agreement between human judgments leads to statistically significant improvements over baselines trained without a curriculum.
Human progress and its socioeconomic effects in society

Abstract. The goal of this paper is to suggest a definition of human progress given by: an inexhaustible process driven by an ideal of maximum wellbeing of purposeful people which, on attainment of any of its objectives for increasing wellbeing, then seek another consequential objective. The human progress improves the fundamental life-interests of people represented by health, wealth, expansion of knowledge, technology and freedom directed to increase wellbeing throughout the society. These factors support the acquisition by humanity of better and more complex forms of life. However, this study also shows the inconsistency of the equation economic growth= progress because human progress also generates negative effects for human being, environment and society, such as increasing incidence of cancer in advanced countries. Keywords. Human Progress, Economic Growth, Wellbeing, Social Progress, Environmental Degradation, Cancer. JEL. B50, B59, I00, I10, I30, O10, O30, O33, O40.
Compact folded metasurface spectrometer

An optical design space that can highly benefit from the recent developments in metasurfaces is the folded optics architecture where light is confined between reflective surfaces, and the wavefront is controlled at the reflective interfaces. In this manuscript, we introduce the concept of folded metasurface optics by demonstrating a compact spectrometer made from a 1-mm-thick glass slab with a volume of 7 cubic millimeters. The spectrometer has a resolution of ~1.2 nm, resolving more than 80 spectral points from 760 to 860 nm. The device is composed of three reflective dielectric metasurfaces, all fabricated in a single lithographic step on one side of a substrate, which simultaneously acts as the propagation space for light. The folded metasystem design can be applied to many optical systems, such as optical signal processors, interferometers, hyperspectral imagers, and computational optical systems, significantly reducing their sizes and increasing their mechanical robustness and potential for integration.
Extremeness Aversion Is a Cause of Anchoring

When estimating unknown quantities, people insufficiently adjust from values they have previously considered, a phenomenon known as anchoring. We suggest that anchoring is at least partially caused by a desire to avoid making extreme adjustments. In seven studies ( N = 5,279), we found that transparently irrelevant cues of extremeness influenced people's adjustments from anchors. In Studies 1-6, participants were less likely to adjust beyond a particular amount when that amount was closer to the maximum allowable adjustment. For example, in Study 5, participants were less likely to adjust by at least 6 units when they were allowed to adjust by a maximum of 6 units than by a maximum of 15 units. In Study 7, participants adjusted less after considering whether an outcome would be within a smaller distance of the anchor. These results suggest that anchoring effects may reflect a desire to avoid adjustments that feel too extreme.
GEESE: grammatical evolution algorithm for evolution of swarm behaviors

Animals such as bees, ants, birds, fish, and others are able to perform complex coordinated tasks like foraging, nest-selection, flocking and escaping predators efficiently without centralized control or coordination. Conventionally, mimicking these behaviors with robots requires researchers to study actual behaviors, derive mathematical models, and implement these models as algorithms. We propose a distributed algorithm, Grammatical Evolution algorithm for Evolution of Swarm bEhaviors (GEESE), which uses genetic methods to generate collective behaviors for robot swarms. GEESE uses grammatical evolution to evolve a primitive set of human-provided rules into productive individual behaviors. The GEESE algorithm is evaluated in two different ways. First, GEESE is compared to state-of-the-art genetic algorithms on the canonical Santa Fe Trail problem. Results show that GEESE outperforms the state-of-the-art by (a) providing better solution quality given sufficient population size while (b) utilizing fewer evolutionary steps. Second, GEESE outperforms both a hand-coded and a Grammatical Evolution-generated solution on a collective swarm foraging task.
All plug-in electric vehicles are not the same: Predictors of preference for a plug-in hybrid versus a battery-electric vehicle

Abstract This study analyzes data from a survey of drivers (n = 1080) administered in late 2013 to assess factors that influence potential car buyers to consider two different types of plug-in electric vehicles (PEVs) in the United States: plug-in hybrid electric vehicles (PHEVs) and battery electric vehicles (BEVs). The results indicate distinct profiles of respondents preferring PHEVs, which have a gasoline backup engine, versus battery BEVs, which rely solely on a battery for power. Respondents interested in selecting a PHEV consider it more for its economic benefits, such as reduced gasoline and maintenance expenditures. Respondents preferring a BEV are drawn to its environmental and technological appeal. The absence of range anxiety for PHEV is a major factor influencing potential PEV buyers.
Using Program Analysis to Improve API Learnability

Learning from API documentation and tutorials is challenging for many programmers. Improving the learnability of APIs can reduce this barrier, especially for new programmers. We will use the tools of program analysis to extract key concepts and learning dependencies from API source code, API documentation, open source code, and other online sources of information on APIs. With this information we will generate learning maps for any user-provided code snippet, and will take users through each concept used in the code snippet. Users may also navigate through the most commonly used features of an API without providing a code snippet. We also hope to extend this work to help users find the features of an API they need and also help them integrate that into their code.
Vegetation-Rainfall interactions reveal how climate variability and climate change alter spatial patterns of wildland fire probability on Big Island, Hawaii.

Abstract The area burned annually by wildland fire in Hawaii has increased fourfold in recent decades. The archipelago's novel fuel types and climatic heterogeneity pose significant challenges for fire risk assessment and fire management. Probability-based fire occurrence models using historical wildfire records provide a means to assess and attribute fire risk in regions of the world like Hawaii where investment in fire science is limited. This research used generalized additive models to 1) assess the relative contribution of vegetation, climate, and human-caused ignitions to the probability of fire in the northwest quadrant of Hawaii Island and 2) compare how landscape flammability varies due to interannual rainfall variability versus projected changes in mean annual rainfall (MAR) and temperature. Annual fire probability was highest for grasslands and peaked at drier conditions (0.04 at 450 mm MAR) when compared with shrublands (0.03 at 650 mm MAR) and forest (0.015 at 600 mm MAR). Excess rainfall the year prior to fire occurrence increased fire risk across grasslands, and thus overall fire probability, more so than drought the year that fire occurred. Drying and warming trends for the region under projected climate change increased maximum values of fire probability by as much as 375% and shifted areas of peak landscape flammability to higher elevation. Model predictions under future climate also indicate the largest changes in landscape flammability will happen by mid-Century. The influence of antecedent wet years on fire risk can improve near-term predictions of fire risk in Hawaii while climate projections indicate that fire management will need to be prioritized at upper elevations where high value natural resources are concentrated.
Secure Outsourced Matrix Computation and Application to Neural Networks

Homomorphic Encryption (HE) is a powerful cryptographic primitive to address privacy and security issues in outsourcing computation on sensitive data to an untrusted computation environment. Comparing to secure Multi-Party Computation (MPC), HE has advantages in supporting non-interactive operations and saving on communication costs. However, it has not come up with an optimal solution for modern learning frameworks, partially due to a lack of efficient matrix computation mechanisms. In this work, we present a practical solution to encrypt a matrix homomorphically and perform arithmetic operations on encrypted matrices. Our solution includes a novel matrix encoding method and an efficient evaluation strategy for basic matrix operations such as addition, multiplication, and transposition. We also explain how to encrypt more than one matrix in a single ciphertext, yielding better amortized performance. Our solution is generic in the sense that it can be applied to most of the existing HE schemes. It also achieves reasonable performance for practical use; for example, our implementation takes 9.21 seconds to multiply two encrypted square matrices of order 64 and 2.56 seconds to transpose a square matrix of order 64. Our secure matrix computation mechanism has a wide applicability to our new framework EDM, which stands for encrypted data and encrypted model. To the best of our knowledge, this is the first work that supports secure evaluation of the prediction phase based on both encrypted data and encrypted model, whereas previous work only supported applying a plain model to encrypted data. As a benchmark, we report an experimental result to classify handwritten images using convolutional neural networks (CNN). Our implementation on the MNIST dataset takes 28.59 seconds to compute ten likelihoods of 64 input images simultaneously, yielding an amortized rate of 0.45 seconds per image.
RF-pick: comparing order picking using a HUD with wearable RFID verification to traditional pick methods

Order picking accounts for 55% of the annual $60 billion spent on warehouse operations in the United States. Reducing human-induced errors in the order fulfillment process can save warehouses and distributors significant costs. We investigate a radio-frequency identification (RFID)-based verification method wherein wearable RFID scanners, worn on the wrists, scan passive RFID tags mounted on an item's bin as the item is picked; this method is used in conjunction with a head-up display (HUD) to guide the user to the correct item. We compare this RFID verification method to pick-to-light with button verification, pick-to-paper with barcode verification, and pick-to-paper with no verification. We find that pick-to-HUD with RFID verification enables significantly faster picking, provides the lowest error rate, and provides the lowest task workload.
The Evolution of Data Science: A New Mode of Knowledge Production

Is data science a new field of study or simply an extension or specialization of a discipline that already exists, such as statistics, computer science, or mathematics? This article explores the evolution of data science as a potentially new academic discipline, which has evolved as a function of new problem sets that established disciplines have been ill-prepared to address. The authors find that this newly-evolved discipline can be viewed through the lens of a new mode of knowledge production and is characterized by transdisciplinarity collaboration with the private sector and increased accountability. Lessons from this evolution can inform knowledge production in other traditional academic disciplines as well as inform established knowledge management practices grappling with the emerging challenges of Big Data.
Lower Bounds for Differentially Private RAMs

In this work, we study privacy-preserving storage primitives that are suitable for use in data analysis on outsourced databases within the differential privacy framework. The goal in differentially private data analysis is to disclose global properties of a group without compromising any individual’s privacy. Typically, differentially private adversaries only ever learn global properties. For the case of outsourced databases, the adversary also views the patterns of access to data. Oblivious RAM (ORAM) can be used to hide access patterns but ORAM might be excessive as in some settings it could be sufficient to be compatible with differential privacy and only protect the privacy of individual accesses.
HELIX: holistic optimization for accelerating iterative machine learning

Machine learning workflow development is a process of trial-and-error: developers iterate on workflows by testing out small modifications until the desired accuracy is achieved. Unfortunately, existing machine learning systems focus narrowly on model training---a small fraction of the overall development time---and neglect to address iterative development. We propose Helix, a machine learning system that optimizes the execution across iterations---intelligently caching and reusing, or recomputing intermediates as appropriate. Helix captures a wide variety of application needs within its Scala DSL, with succinct syntax defining unified processes for data preprocessing, model specification, and learning. We demonstrate that the reuse problem can be cast as a Max-Flow problem, while the caching problem is NP-Hard. We develop effective lightweight heuristics for the latter. Empirical evaluation shows that Helix is not only able to handle a wide variety of use cases in one unified workflow but also much faster, providing run time reductions of up to 19x over state-of-the-art systems, such as DeepDive or KeystoneML, on four real-world applications in natural language processing, computer vision, social and natural sciences.
E-RNN: Design Optimization for Efficient Recurrent Neural Networks in FPGAs

Recurrent Neural Networks (RNNs) are becoming increasingly important for time series-related applications which require efficient and real-time implementations. The two major types are Long Short-Term Memory (LSTM) and Gated Recurrent Unit (GRU) networks. It is a challenging task to have real-time, efficient, and accurate hardware RNN implementations because of the high sensitivity to imprecision accumulation and the requirement of special activation function implementations. A key limitation of the prior works is the lack of a systematic design optimization framework of RNN model and hardware implementations, especially when the block size (or compression ratio) should be jointly optimized with RNN type, layer size, etc. In this paper, we adopt the block-circulant matrix-based framework, and present the Efficient RNN (E-RNN) framework for FPGA implementations of the Automatic Speech Recognition (ASR) application. The overall goal is to improve performance/energy efficiency under accuracy requirement. We use the alternating direction method of multipliers (ADMM) technique for more accurate block-circulant training, and present two design explorations providing guidance on block size and reducing RNN training trials. Based on the two observations, we decompose E-RNN in two phases: Phase I on determining RNN model to reduce computation and storage subject to accuracy requirement, and Phase II on hardware implementations given RNN model, including processing element design/optimization, quantization, activation implementation, etc. Experimental results on actual FPGA deployments show that E-RNN achieves a maximum energy efficiency improvement of 37.4$\times$ compared with ESE, and more than 2$\times$ compared with C-LSTM, under the same accuracy.
A Framework to Analyze Interactions between Transmission and Distribution Systems

Analyzing the interactions between transmission and distribution (T&D) systems is becoming imperative with the increased penetrations of distributed energy resources (DERs) on electric power distribution networks. An assessment of the impacts of DERs connected to distribution system on the transmission system operations is required especially for the conditions leading to increased level of system unbalance. In this paper, a coupled T&D analysis framework is developed through co-simulation approach. The framework separately solves the decoupled T&D models. The T&D interactions are captured by exchanging the power flow solutions at the point of common coupling (PCC). The proposed co-simulation framework adopts an iterative coupling approach that results in a co-simulation model close to the stand-alone T&D system model. The proposed framework is tested using IEEE-9 bus transmission system model and EPRI’s Ckt-24 test distribution feeder model. A case study in which the IEEE-9 bus model interfaced with three ckt24 models is also presented to demonstrate the scalability of the approach. The conditions of convergence by exchanging the boundary variables at the PCC are examined in detail using several case studies with varying levels of load unbalance.
Machine Learning Classical Interatomic Potentials for Molecular Dynamics from First-Principles Training Data

The ever-increasing power of modern supercomputers, along with the availability of highly scalable atomistic simulation codes, has begun to revolutionize predictive modeling of materials. In partic...
Defecation by the ctenophore Mnemiopsis leidyi occurs with an ultradian rhythm through a single transient anal pore

Abstract Defecation in the ctenophore Mnemiopsis leidyi is a stereotyped sequence of effector responses that occur with a regular ultradian rhythm. Time intervals between repeated defecations of individual animals depend on body size, ranging from ~10 min in small larvae to ~1 hr in large adults. New features and corrections of previous reports of the gastrovascular system during and between defecations are described in detail by video microscopy. Contrary to the scientific literature, the defecating organ of the excretory complex is just one of the two anal canals which possesses the animal’s only anal pore. The anal pore is not visible as a permanent structure as depicted in textbooks, but appears at defecation and disappears afterward. DIC microscopy reveals that opening and closing of the anal pore resemble a reversible ring of tissue fusion between apposed endodermal and ectodermal layers at the aboral end. Mnemiopsis thus appears to have an intermittent anus and therefore an intermittent through-gut that reoccur at regular intervals. The temporality of a visible anal pore in Mnemiopsis is novel, and may shed light on the evolution of a permanent anus and through-gut in animals. In addition, mirror image dimorphism of the diagonal anal complex occurs in larval ctenophores but not in adults, indicating developmental flexibility in diagonal symmetry of the anal complex.
A Penalized Likelihood Method for Balancing Accuracy and Fairness in Predictive Policing

Racial bias of predictive policing algorithms has been the focus of recent research and, in the case of Hawkes processes, feedback loops are possible where biased arrests are amplified through self-excitation, leading to hotspot formation and further arrests of minority populations. In this article we develop a penalized likelihood approach for introducing fairness into point process models of crime. In particular, we add a penalty term to the likelihood function that encourages the amount of police patrol received by each of several demographic groups to be proportional to the representation of that group in the total population. We apply our model to historical crime incident data in Indianapolis and measure the fairness and accuracy of the two approaches across several crime categories. We show that fairness can be introduced into point process models of crime so that patrol levels proportionally match demographics, though at a cost of reduced accuracy of the algorithms.
Constraint Programming

Constraint programming is a remarkable success story. It quickly moved from research laboratories to industrial applications in the late 1980s and is in daily use to solve complex optimization throughout the world. At the same time, constraint programming has continued to evolve, addressing new needs and opportunities. This talk reviews some recent progress in constraint programming. The first part of the talk starts with its fundamental contribution, the ability to express and exploit combinatorial substructures to prune infeasible solutions and find feasible solutions. It also reviews some of the benefits of its architecture on a variety of applications in scheduling, rostering, and combinatorial matching, emphasizing the underlying modeling and computation techniques. The second part of the talk argues that constraint programming is an integration technology and reviews some hybridizations of constraint programming, including local search, mathematical programming, and global optimization. The final part of the talk gives a brief overview of some promising, novel applications of constraint programming.
Development and Testing of a Modular Upper Extremity Exoskeleton for Infants

A passive upper extremity exoskeleton has been developed for people with neuromuscular weakness. The WREX (Wilmington Robotic EXoskeleton) has been used successfully for a number of years by people with disabilities such as muscular dystrophy and arthrogryposis. This paper describes the modification of the WREX to be fitted with infants. The Pediatric WREX Plus (P-WREX+) can selectively assist or resist antigravity arm movements based on the needs of each individual. It consists of a 3-D printed device that can be mounted to a jacket or a chair and allows infants more access to their environment by augmenting anti-gravity arm movement. The target population is infants born with brain injuries and at high risk for significant neuro-motor impairments. The paper describes the development of the device and testing with an infant with arthrogryposis over a 6-month period.
Knowledge, Perceptions, and Patterns of Fish Oil Use in Cardiac Patients.

Background:Fish oils are the most widely used nonvitamin, nonmineral dietary supplements in the United States. They are not over-the-counter medications and are neither approved nor indicated for t...
The lost dimension: pruned plants in Roman gardens

This paper focuses on evidence for the pruning and dwarfing of plants represented in Roman garden paintings. In two particularly fine examples of this type, from the Villa of Livia at Prima Porta near Rome, and the House of the Golden Bracelet at Pompeii, the artists have carefully portrayed pruning marks and other horticultural practices that alter the size and natural habit of plants. This evidence complements archaeobotanical findings by showing the above-ground appearance of garden plants attested in the archaeological record. The remains of a garden that may be linked to garden paintings were found in 2007 in the Great Peristyle at the Villa Arianna at Stabiae, near Pompeii. Seeking evidence for the interpretation of this garden, paintings and texts have been critically examined. The results reveal a wealth of evidence for plant pruning management in the paintings linked to nemora tonsilia or silva tonsilia—the art of pruning groups of trees and shrubs for ornamental presentation, initiated by C. Matius during the reign of Augustus in the 1st century bc. This art of pruning woody plants may be a virtuoso display of the horticultural skills involved in the management of the broader cultivated landscape of Rome and Pompeii.
Long-Term Oncologic Outcomes after Primary Retroperitoneal Lymph Node Dissection: Minimizing the Need for Adjuvant Chemotherapy.

Purpose:We analyzed the oncologic outcomes of men undergoing primary retroperitoneal lymph node dissection and characterized the use of adjuvant chemotherapy and template dissections.Materials and ...
Defensive Investment in Municipal Water Hardness Reduction

We produce estimates of household's willingness to pay (WTP) for reduction in water hardness using a defensive investment framework. Using total dissolved solids (TDS) data observed in municipal water supplies in combination with product-by-store level point-of-sale scanner data on consumable water softening product sales, we provide among the first revealed preference estimates of WTP for water hardness reduction and quality control. Using instrumental variable regressions, we find that household's marginal WTP increases as the observed TDS in municipal water increases. Aggregating these estimated WTP at county level, we show how total WTP varies geographically, after controlling for income and fixed effects. Our estimations provide evidence that households have a non-negligible WTP for water hardness reduction, which has important policy implications for optimal water hardness management by municipal water authorities, and those policies aimed to target salinity management within surface and subsurface water supplies.
The Energetics of Cyclopropene, 1,4-Cyclohexadiene, and Some of Their Hetero- and/or Exocyclic Derivatives

The recently defined concept of “ultradiagonal” strain energy is applied to cyclopropene, cyclopropenone, and methylenecyclopropene and their respective diaza and diphospha derivatives using ab initio (DFT) calculations. In the relatively few cases where comparisons could be made between theory and either experiment or earlier calculational studies, very good agreement for both energies and structures were found. This gives us confidence for the remaining species. The results were also qualitatively explained, and the concept of ultradiagonal strain gibbs energy is briefly discussed.
Higher classification sensitivity of short metagenomic reads with CLARK-S

The growing number of metagenomic studies in medicine and environmental sciences is creating increasing demands on the computational infrastructure designed to analyze these very large datasets. Often, the construction of ultra-fast and precise taxonomic classifiers can compromise on their sensitivity (i.e. the number of reads correctly classified). Here we introduce CLARK-S, a new software tool that can classify short reads with high precision, high sensitivity and high speed. AVAILABILITY AND IMPLEMENTATION CLARK-S is freely available at http://clark.cs.ucr.edu/ CONTACT: stelo@cs.ucr.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Synthesis of lanopylin B1.

Phase-transfer alkylation of diethyl 2-oxopropylphosphonate (9) with 2-iodoalkyl azide afforded 40% of azido phosphonate 6, which underwent a phase-transfer Horner−Emmons Wittig reaction with heptadecanal to provide 80% of azido enone 5. An intramolecular aza-Wittig reaction with polymer-bound Ph3P in toluene at reflux completed the first synthesis of lanopylin B1 in 76% yield.
Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape

Summary Large-scale single-cell RNA sequencing (scRNA-seq) studies that profile hundreds of thousands of cells are becoming increasingly common, overwhelming existing analysis pipelines. Here, we describe how to enhance and accelerate single-cell data analysis by summarizing the transcriptomic heterogeneity within a dataset using a small subset of cells, which we refer to as a geometric sketch. Our sketches provide more comprehensive visualization of transcriptional diversity, capture rare cell types with high sensitivity, and reveal biological cell types via clustering. Our sketch of umbilical cord blood cells uncovers a rare subpopulation of inflammatory macrophages, which we experimentally validated. The construction of our sketches is extremely fast, which enabled us to accelerate other crucial resource-intensive tasks, such as scRNA-seq data integration, while maintaining accuracy. We anticipate our algorithm will become an increasingly essential step when sharing and analyzing the rapidly growing volume of scRNA-seq data and help enable the democratization of single-cell omics.
Synthesis, structure, and characterization of a new two-dimensional lead(II) vanadate, Ba3PbV4O14

Abstract A new two-dimensional lead(II) vanadate, Ba 3 PbV 4 O 14 has been synthesized by standard solid state techniques using BaCO 3 , PbO, and V 2 O 5 as reagents. The structure of Ba 3 PbV 4 O 14 was determined by single-crystal X-ray diffraction. Ba 3 PbV 4 O 14 crystallizes in the triclinic space group P -1 (no. 2), with a = 7.2997(15) (A), b = 7.2932(15) (A), c = 13.379(3) (A), α = 93.68(3)°, β = 99.68(3)°, γ = 91.49(3)°, V = 700.2(2) (A 3 ) and Z = 2. Ba 3 PbV 4 O 14 exhibits a novel two-dimensional layered structure consisting of corner shared VO 4 tetrahedra that are linked by edge shared PbO 7 polyhedra, in which the Ba 2+ cations occupy the interlayer region. The Pb 2+ cations are in asymmetric coordination environments attributable to its lone pair. Infrared, Raman, and UV–vis diffuse reflectance spectroscopy, thermogravimetric analysis, and dipole moment calculations are also presented.
Specialization of a polyphenism switch gene following serial duplications in Pristionchus nematodes

Polyphenism is an extreme manifestation of developmental plasticity, requiring distinct developmental programs and the addition of a switch mechanism. Because the genetic basis of polyphenism switches has only begun to be understood, how their mechanisms arise is unclear. In the nematode Pristionchus pacificus, which has a mouthpart polyphenism specialized for alternative diets, a gene (eud-1) executing the polyphenism switch was recently identified as the product of lineage-specific duplications. Here, we infer the role of gene duplications in producing a switch gene. Using reverse genetics and population genetic analyses, we examine evidence for competing scenarios of degeneration and complementation, neutral evolution, and functional specialization. Of the daughter genes, eud-1 alone has assumed switch-like regulation of the mouth polyphenism. Measurements of life-history traits in single, double, and triple sulfatase mutants did not, given a benign environment, identify alternative or complementary roles for eud-1 paralogs. Although possible roles are still unknown, selection analyses of the sister species and 104 natural isolates of P. pacificus detected purifying selection on the genes, suggesting their functionality by their fixation and evolutionary maintenance. Our approach shows the tractability of reverse genetics in a nontraditional model system to study evolution by gene duplication.
Scheduling Beyond CPUs for HPC

High performance computing (HPC) is undergoing significant changes. The emerging HPC applications comprise both compute- and data-intensive applications. To meet the intense I/O demand from emerging data-intensive applications, burst buffers are deployed in production systems. Existing HPC schedulers are mainly CPU-centric. The extreme heterogeneity of hardware devices, combined with workload changes, forces the schedulers to consider multiple resources (e.g., burst buffers) beyond CPUs, in decision making. In this study, we present a multi-resource scheduling scheme named BBSched that schedules user jobs based on not only their CPU requirements, but also other schedulable resources such as burst buffer. BBSched formulates the scheduling problem into a multi-objective optimization (MOO) problem and rapidly solves the problem using a multi-objective genetic algorithm. The multiple solutions generated by BBSched enables system managers to explore potential tradeoffs among various resources, and therefore obtains better utilization of all the resources. The trace-driven simulations with real system workloads demonstrate that BBSched improves scheduling performance by up to 41% compared to existing methods, indicating that explicitly optimizing multiple resources beyond CPUs is essential for HPC scheduling.
Application of the intramolecular Yamamoto vinylogous aldol reaction to the synthesis of macrolides.

An intramolecular version of the Yamamoto vinylogous aldol reaction, a method that employs the bulky Lewis acid ATPH to control the site of aldolization, is described. This macrocyclization process is effective for the construction of 10-, 12-, and 14-membered macrolides. The yields are high (70−90%), and the reaction can proceed with excellent remote stereocontrol (dr ≥ 20:1) with chiral substrates.
Ytterbium(III) triflate-catalyzed asymmetric nucleophilic addition of functionalized lithium (α-carbalkoxyvinyl)cuprates to chiral p-toluenesulfinimines (thiooxime S-oxides)

Ytterbium(III) triflate has been found to catalyze anionic additions of functionalized lithium (α-carbalkoxyvinyl)cuprates to chiral p-toluenesulfinimines (thiooxime S-oxides) in a cosolvent system (Et2OCH2Cl2). This new system has made it possible to utilize those p-toluenesulfinimines of low solubility in Et2O as the electrophiles to react with anionic (α-carbalkoxyvinyl)cuprates for the asymmetric synthesis of the corresponding β-mono and β,β-disubstituted Baylis-Hillman adducts. Modest yields (51.0–64.4% yield) and good to excellent diastereoselectivities (> 90% de) were obtained.
Prevotella copri, a potential indicator for high feed efficiency in western steers.

There has been a great interest to identify a microbial marker that can be used to predict feed efficiency of beef cattle. Such a marker, specifically one that would allow an early identification of animals with high feed efficiency for future breeding efforts, would facilitate increasing the profitability of cattle operations and simultaneously render them more sustainable by reducing their methane footprint. The work presented here suggests that Prevotella copri might be an ideal microbial marker for identifying beef cattle with high feed efficiency early in their life span and in the production cycle. Developing more refined quantification techniques that allow correlation of P. copri to feed efficiency of beef cattle that can be applied by lay people in the field holds great promise to improve the economy of cattle operations while simultaneously reducing their environmental impact by mitigating methane production from enteric fermentation.
Effects of thermal stress on amount, composition, and antibacterial properties of coral mucus.

The surface mucus layer of reef-building corals supports feeding, sediment clearing, and protection from pathogenic invaders. As much as half of the fixed carbon supplied by the corals' photosynthetic symbionts is incorporated into expelled mucus. It is therefore reasonable to expect that coral bleaching (disruption of the coral-algal symbiosis) would affect mucus production. Since coral mucus serves as an important nutrient source for the entire reef community, this could have substantial ecosystem-wide consequences. In this study, we examined the effects of heat stress-induced coral bleaching on the composition and antibacterial properties of coral mucus. In a controlled laboratory thermal challenge, stressed corals produced mucus with higher protein (β = 2.1, p < 0.001) and lipid content (β = 15.7, p = 0.02) and increased antibacterial activity (likelihood ratio = 100, p < 0.001) relative to clonal controls. These results are likely explained by the expelled symbionts in the mucus of bleached individuals. Our study suggests that coral bleaching could immediately impact the nutrient flux in the coral reef ecosystem via its effect on coral mucus.
Synthesis of cationic lipids from 1,2,4-butanetriol

Abstract Starting from 1,2,4-butanetriol, a series of quaternary ammonium lipids with diether, ether/ester, and diester bonds as linkage between the hydrocarbon chains and butane backbone were synthesized for gene delivery.
New homochiral cyclic diol ligands for titanium alkoxide catalyzed phosphonylation of aldehydes

Abstract An investigation of the structural effects of chiral diol ligands on the enantioselectivity of phosphonylation was performed. Cyclic diols, and cyclohexanediol in particular, were identified as effective ligands for titanium alkoxide catalyzed asymmetric phosphonylation.
Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions

Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological function of many PTMs remains unknown. This is especially true for prokaryotic PTM systems, many of which have only recently been recognized and studied in depth. It is increasingly apparent that a deep sampling of abundance across a wide range of environmental stresses, growth conditions, and PTM types, rather than simply cataloging targets for a handful of modifications, is critical to understanding the complex pathways that govern PTM deposition and downstream effects. We utilized a deeply-sampled dataset of MS/MS proteomic analysis covering 9 timepoints spanning the Escherichia coli growth cycle and an unbiased PTM search strategy to construct a temporal map of abundance for all PTMs within a 400 Da window of mass shifts. Using this map, we are able to identify novel targets and temporal patterns for N-terminal N α acetylation, C-terminal glutamylation, and asparagine deamidation. Furthermore, we identify a possible relationship between N-terminal N α acetylation and regulation of protein degradation in stationary phase, pointing to a previously unrecognized biological function for this poorly-understood PTM. Unbiased detection of PTM in MS/MS proteomics data facilitates the discovery of novel modification types and previously unobserved dynamic changes in modification across growth timepoints.
Whence Lotka-Volterra?: Conservation laws and integrable systems in ecology

Competition in ecology is often modeled in terms of direct, negative effects of one individual on another. An example is logistic growth, modeling the effects of intraspecific competition, while the Lotka-Volterra equations for competition extend this to systems of multiple species, with varying strengths of intra- and interspecific competition. These equations are a classic and well-used staple of quantitative ecology, providing a framework to understand species interactions, species coexistence, and community assembly. They can be derived from an assumption of random mixing of organisms, and an outcome of each interaction that removes one or more individuals. However, this framing is somewhat unsatisfactory, and ecologists may prefer to think of phenomenological equations for competition as deriving from competition for a set of resources required for growth, which in turn may undergo their own complex dynamics. While it is intuitive that these frameworks are connected, and the connection is well-understood near to equilibria, here, we ask the question: when can consumer dynamics alone become an exact description of a full system of consumers and resources? We identify that consumer-resource systems with this property must have some kind of redundancy in the original description, or equivalently there is one or more conservation laws for quantities that do not change with time. Such systems are known in mathematics as integrable systems. We suggest that integrability in consumer-resource dynamics can only arise in cases where each species in an assemblage requires a distinct and unique combination of resources, and even in these cases, it is not clear that the resulting dynamics will lead to Lotka-Volterra competition.
RERconverge: an R package for associating evolutionary rates with convergent traits.

Motivation When different lineages of organisms independently adapt to similar environments, selection often acts repeatedly upon the same genes, leading to signatures of convergent evolutionary rate shifts at these genes. With the increasing availability of genome sequences for organisms displaying a variety of convergent traits, the ability to identify genes with such convergent rate signatures would enable new insights into the molecular basis of these traits. Results Here we present the R package RERconverge, which tests for association between relative evolutionary rates of genes and the evolution of traits across a phylogeny. RERconverge can perform associations with binary and continuous traits, and it contains tools for visualization and enrichment analyses of association results. Availability and implementation RERconverge source code, documentation and a detailed usage walk-through are freely available at https://github.com/nclark-lab/RERconverge. Datasets for mammals, Drosophila and yeast are available at https://bit.ly/2J2QBnj. Supplementary information Supplementary data are available at Bioinformatics online.
Total synthesis of (+/-)-cytisine via the intramolecular heck cyclization of activated N-alkyl glutarimides.

A synthesis of racemic cytisine 1 has been developed utilizing an intramolecular Heck cyclization to prepare the bridged tricyclic intermediate 2. The cyclization employs activated glutarimide-derived ketene aminals 3 (X = P(O)OEt2 or SO2CF3) and represents the first use of such intermediates in metal-catalyzed processes.
Stereoselective synthesis of epoxides by reaction of donor/acceptor-substituted carbenoids with α,β-unsaturated aldehydes

Abstract The reaction of donor/acceptor-substituted carbenoids with α,β-unsaturated aldehydes results in the highly diastereoselective synthesis of epoxides.
Reactions of Alkali‐Halide Clusters

This article reviews recent experimental work on reactive processes involving alkali-halide clusters (AHC). The processes discussed include: adsorption of molecules on AHCs [1]; reactive collisions of alkali-fluoride clusters with silicon surfaces [2]; and the primary photochemistry of alkali-bromide and -iodide clusters [3,4]. Earlier work on evaporation and cleavage processes, and experiments on clusters with excess electrons, are not reviewed.
o-Nitrobenzyl as a photocleavable nitrogen protecting group for indoles, benzimidazole, and 6-chlorouracil

Abstract The potential for the o-nitrobenzyl group as an alternative nitrogen protecting group for various indoles, benzimidazole, and 6-chlorouracil was determined. Treatment of the appropriate NH containing substrate with LiH or NaH in DMF followed by o-nitrobenzyl bromide afforded reasonable yields of N-alkylated products. To effect removal of this group, simple photolysis with 300 nm light afforded good yields of starting substrate.
Synthesis and complexation properties of a water-soluble optically active cyclophane incorporating a 4-naphthyl-1,2,3,4-tetrahydroisoquinoline unit as a chiral spacer

The unnatural alkaloid 6-methoxy-4-[2-(6-methoxynaphthalenyl)]-1,2,3,4-tetrahydroisoquinoline (5) was prepared as a chiral spacer for optically active cyclophane receptors. Optical resolution of the building block was accomplished through diastereomeric salt formation with dibenzoytartaric acid. The S configuration was assigned by X-ray crystallographic methods to the hydrochloride salt of (−)-5. Starting from enantiomerically pure 5, the optically active cyclophanes (R)- (S)-4 were prepared. These cyclophanes, in which the chiral alkaloid spacer is bridged to an chiral diphenylmethane unit, are efficient binders of naphthalene derivatives in D 2 O/CD 3 OD (60:40, v/v and show a modest degree of chiral recognition in the inclusion complexation of naproxen derivatives
A new general synthesis of isomeric nucleosides

Abstract An efficient new method for the synthesis of isonucleosides is described. The key step in the synthesis was the direct coupling of purine and pyrimidine bases with the cyclic sulfate of a carbohydrate intermediate. This reaction proceeded with high regiospecificity and stereospecificity.
Precipiton strategies applied to the isolation of α-substituted β-ketoesters

Abstract Diaryl alkene 1 Z is a ‘precipiton’, a protecting group that allows reaction products to be isolated by simple filtration. Here we illustrate the use of this protecting group for the preparation and isolation, without distillation or chromatography, of pure α-substituted β-ketoesters. The precipiton 1 Z was prepared in 43% overall yield. It is anticipated that development of precipiton-based syntheses will provide a new alternative for automated reaction product isolation that may be useful for bench-scale and process-scale chemical preparations.
Horizontal Gene Transfer of Functional Type VI Killing Genes by Natural Transformation.

Horizontal gene transfer (HGT) can have profound effects on bacterial evolution by allowing individuals to rapidly acquire adaptive traits that shape their strategies for competition. One strategy for intermicrobial antagonism often used by Proteobacteria is the genetically encoded contact-dependent type VI secretion system (T6SS), a weapon used to kill heteroclonal neighbors by direct injection of toxic effectors. Here, we experimentally demonstrate that Vibrio cholerae can acquire new T6SS effector genes via horizontal transfer and utilize them to kill neighboring cells. Replacement of one or more parental alleles with novel effectors allows the recombinant strain to dramatically outcompete its parent. Using spatially explicit modeling, we examine how this process could affect the ecology and evolution of surface-attached microbial populations. HGT of T6SS effector-immunity pairs is risky: transformation brings a cell into conflict with its former clone mates but can be adaptive when superior T6SS alleles are acquired. More generally, we find that these costs and benefits are not symmetric and that high rates of HGT can act as a hedge against competitors with unpredictable T6SS efficacy. We conclude that antagonism and horizontal transfer drive successive rounds of weapon optimization and selective sweeps, dynamically shaping the composition of microbial communities.IMPORTANCE The contact-dependent type VI secretion system (T6SS) is frequently used by Proteobacteria to kill adjacent competitors. While DNA released by T6 killing can be horizontally acquired, it remains untested whether T6 genes themselves can be horizontally acquired and then utilized to compete with neighboring cells. Using naturally transformable Vibrio cholerae, we provide the first direct empirical support for the hypothesis that T6 genes are exchanged horizontally (e.g., from dead competitors) and functionally deployed to compete with neighboring cells. Using computational simulations, we also demonstrate that high rates of HGT can be adaptive, allowing V. cholerae to improve upon existing T6 weaponry and survive direct encounters with otherwise superior competitors. We anticipate that our evolutionary results are of broad microbiological relevance, applying to many bacteria capable of HGT that utilize the T6SS or similar antagonistic systems, and highlight the profound impact of HGT in shaping microbial community structure.