cssi/SciSciGPT-SciSciNet huggingface dataset:
Reactor neutrino spectral distortions play little role in mass hierarchy experiments

The Coulomb enhancement of low energy electrons in nuclear beta decay generates sharp cutoffs in the accompanying antineutrino spectrum at the beta decay endpoint energies. It has been conjectured that these features will interfere with measuring the effect of a neutrino mass hierarchy on an oscillated nuclear reactor antineutrino spectrum. These sawtoothlike features will appear in detailed reactor antineutrino spectra, with characteristic energy scales similar to the oscillation period critical to neutrino mass hierarchy determination near a 53 km baseline. However, these sawtoothlike distortions are found to contribute at a magnitude of only a few percent relative to the mass hierarchy-dependent oscillation pattern in Fourier space. In the Fourier cosine and sine transforms, the features that encode a neutrino mass hierarchy dominate by over sixteen (thirty-three) times in prominence to the maximal contribution of the sawtoothlike distortions from the detailed energy spectrum, given $3.2%/\sqrt{{E}_{\mathrm{vis}}/\mathrm{MeV}}$ (perfect) detector energy resolution. The effect of these distortions is shown to be negligible even when the uncertainties in the reactor spectrum, oscillation parameters, and counting statistics are considered. This result is shown to hold even when the opposite hierarchy oscillation patterns are nearly degenerate in energy space, if energy response nonlinearities are controlled to below 0.5%. Therefore with accurate knowledge of detector energy response, the sawtoothlike features in reactor antineutrino spectra will not significantly impede neutrino mass hierarchy measurements using reactor antineutrinos.
Multidimensional Replica Exchange Simulations for Efficient Constant pH and Redox Potential Molecular Dynamics.

Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, ...
Role of PET imaging for biochemical recurrence following primary treatment for prostate cancer

Prostate cancer is one of the most common cancers in men worldwide, and primary prostate cancer is typically treated with surgery, radiation, androgen deprivation, or a combination of these therapeutic modalities. Despite technical advances, approximately 30% of men will experience biochemical recurrent within 10 years of definitive treatment. Upon detection of a rise in serum prostate specific antigen (PSA), there is great need to accurately stage these patients to help guide further therapy. As a result, there are considerable efforts underway to establish the role of positron emission tomography (PET) in the diagnostic algorithm of biochemically recurrent prostate cancer. This manuscript provides an overview of PET tracers used for the detection and localization of prostate cancer in the setting of biochemical recurrence with a focus on PET tracers that are currently being used in clinical practice in the United States.
Diffusion, mixing, and segregation in confined granular flows

Discrete element method simulations of confined bidisperse granular shear flows elucidate the balance between diffusion and segregation that can lead to either mixed or segregated states, depending on confining pressure. Results indicate that the collisional diffusion is essentially independent of overburden pressure. Because the rate of segregation diminishes with overburden pressure, the tendency for particles to segregate weakens relative to the re-mixing of particles due to collisional diffusion as the overburden pressure increases. Using a continuum approach that includes a pressure dependent segregation velocity and a pressure independent diffusion coefficient, the interplay between diffusion and segregation is accurately predicted for both size and density bidisperse mixtures over a wide range of flow conditions when compared to simulation results. Additional simulations with initially segregated conditions demonstrate that applying a high enough overburden pressure can suppress segregation to the point that collisional diffusion mixes the segregated particles.
Chapter 14 – Applications

The availability of techniques for commonsense reasoning presents an enormous opportunity in that there are many areas that have only begun to be explored that can benefit from the use of commonsense reasoning. Commonsense reasoning provides two important benefits to computer applications: First, commonsense reasoning can be used to give applications a greater degree of understanding about the human world. Users can be freed from having to state everything explicitly because commonsense reasoning can be used to infer what is obvious to a person. Second, commonsense reasoning can be used to give computer programs more flexibility. An application can adapt to an unexpected real-world problem by reasoning about it in order to come up with a solution. We describe several applications that have been built using commonsense reasoning in the event calculus, in business systems, natural language understanding, and vision.
Leaders, States, and Reputations:

Reputational incentives are ubiquitous explanations for war, yet consistent evidence of their effects is elusive for two reasons. First, most work searches for the payment of reputational costs, ye...
A comparison of automated object extraction methods for mound and shell-ring identification in coastal South Carolina

Abstract One persistent archaeological challenge is the generation of systematic documentation for the extant archaeological record at the scale of landscapes. Often our information for landscapes is the result of haphazard and patchy surveys that stem from opportunistic and historic efforts. Consequently, overall knowledge of some regions is the product of ad hoc survey area delineation, degree of accessibility, effective ground visibility, and the fraction of areas that have survived destruction from development. These factors subsequently contribute unknown biases to our understanding of chronology, settlements patterns, interaction, and exchange. Aerial remote sensing offers one potential solution for improving our knowledge of landscapes. With sensors that include LiDAR, remote sensing can identify archaeological features that are otherwise obscured by vegetation. Object-based image analyses (OBIA) of remote sensing data hold particular promise to facilitate regional analyses thorough the automation of archaeological feature recognition. Here, we explore four OBIA algorithms for artificial mound feature detection using LiDAR from Beaufort County, South Carolina: multiresolution segmentation, inverse depression analysis, template matching, and a newly designed algorithm that combines elements of segmentation and template matching. While no single algorithm proved to be consistently superior to the others, a combination of methods is shown to be the most effective for detecting archaeological features.
ETHICAL CONSIDERATIONS FOR STUDENT-BASED REMINISCENCE PROJECTS

Intergenerational reminiscence projects have a variety of benefits for both student interviewers and older participants. At the same time, work of this type is not without risk. The purpose of this presentation is to provide instructors in the planning stage of a student-based reminiscence project with a suggested framework for managing the ethical issues they are most likely to encounter. We first describe three basic ethical principles developed within the context of research with human subjects: respect for persons, beneficence, and justice (Belmont Report, 1979). We then discuss how these principles can be adapted for student-based reminiscence projects. Specific issues addressed include informed consent, confidentiality, and fairness in selecting participants.
Self-assembled nematic colloidal motors powered by light

Biological motors are marvels of nature that inspire creation of their synthetic counterparts with comparable nanoscale dimensions, high efficiency and diverse functions. Molecular motors have been synthesized, but obtaining nanomotors through self-assembly remains challenging. Here we describe a self-assembled colloidal motor with a repetitive light-driven rotation of transparent micro-particles immersed in a liquid crystal and powered by a continuous exposure to unstructured ~1 nW light. A monolayer of azobenzene molecules defines how the liquid crystal’s optical axis mechanically couples to the particle’s surface, as well as how they jointly rotate as the light’s polarization changes. The rotating particle twists the liquid crystal, which changes polarization of traversing light. The resulting feedback mechanism yields a continuous opto-mechanical cycle and drives the unidirectional particle spinning, with handedness and frequency robustly controlled by polarization and intensity of light. Our findings may lead to opto-mechanical devices and colloidal machines compatible with liquid crystal display technology. Biological motors which convert energy into mechanical work inspire the fabrication of synthetic motors. Here the authors demonstrate self-assembled colloidal motors which are driven to a range of responses controlled by the feedback between light polarization and deformation of a liquid crystal.
Impact of dataset uncertainties on machine learning model predictions: the example of polymer glass transition temperatures

Over the past decade, there has been a resurgence in the importance of data-driven techniques in material science and engineering. The utilization of state-of-the art algorithms, coupled with the increased availability of experimental and computational data, has led to the development of surrogate models offering the promise of rapid and accurate predictions of materials properties based solely on their structure or composition. Such machine learning models are trained on available past data and are thus susceptible to the intrinsic uncertainties/errors associate with these past measurements. The glass transition temperature (Tlsubggl/subg) of polymers, a property of paramount interest in polymer science, is one strong example of a material property that can show widespread variation in the final reported value as a result of a variety of intrinsic and extrinsic factors that occur during the experimental measurement process. In the current work, we curate a large database of Tlsubggl/subg measurements from a variety of data sources and proceed to investigate the statistical nature of the inherent uncertainties in the database. Through the partitioning of the dataset using statistically relevant measures, we investigate the effect of variations in the dataset on the performance of the final machine learning model. We demonstrate that measures of central tendency (such as mean and median) are valid approximations when dealing with multiple reported values of Tlsubggl/subg for the same polymeric material. Moreover, the Bayesian model noise/uncertainty that emerges from our machine-learning pipeline is able to represent quantitatively the underlying noise/uncertainties in the experimental measurement of Tlsubggl/subg.
Strength and cohesive behavior of thermoset polymers at the microscale: A size-effect study

Abstract This study investigated, experimentally and numerically, the fracturing behavior of thermoset polymer structures featuring cracks and sharp u-notches. It is shown that, even for cases in which the sharpness of the notch would suggest otherwise, the failure behavior of cracked and pre-notched specimens is substantially different, the failure loads of the former configuration being about three times lower than the latter one. To capture this interesting behavior a two-scale cohesive model is proposed. The model is in excellent agreement with the experimental data and its predictions allow to conclude that (a) residual plastic stresses cannot explain the very high failure loads of notched structures; (b) the strength of the polymer at the microscale can be from six to ten times larger than the values measured from conventional tests whereas the fracture energy at the microscale can be about forty times lower; (c) the pre-notched specimens investigated in this work failed when the stress at the tip reached the microscale strength whereas the cracked specimens failed when the energy release rate reached the total fracture energy of the material. The foregoing considerations are of utmost importance for the design of microelectronic devices or polymer matrix composites for which the main damage mechanisms are governed by the strength and cohesive behavior at the microscale.
The Weight of Essentials in Economic Activity

The paper develops a measure for the weight of essential goods and services in different spheres of economic activity. The first measure is concerned with the sphere of production, which makes use ...
Adolescents’ Personality Traits and Positive Psychological Orientations: Relations with Emotional Distress and Life Satisfaction Mediated by School Connectedness

Contemporary models emphasize linkages between malleable positive psychological orientations and enhanced quality of life. As such, it is important to consider if these positive orientations provide unique explanatory power beyond the long-established relations between quality of life and within-person, less malleable personality traits. This study contributed to the literature by examining the relations among adolescents’ personality traits, positive psychology orientations, and self-reported quality of life indicators. These relations were further examined by considering the mediating effects of the important contextual influences of school connectedness. Self-report responses of 1867 California high school students to an 88-item schoolwide online survey that included the Big Five Inventory-10 (Neuroticism, Extraversion, Openness to Experience, Agreeableness, and Conscientiousness), the Social Emotional Health Survey-Secondary (Belief in Self, Belief in Others, Emotional Competence, and Engaged Living), the School Connectedness Scale, the Brief Multidimensional Life Satisfaction Scale, and the Social Emotional Distress Scale-Secondary were used to examine relations. Stepwise multiple regression analyses showed that after controlling for demographic variables (Block 1: sex, grade, and ethnicity) the personality traits (Block 2) were, as expected, significantly associated with life satisfaction and emotional distress. Supporting study hypotheses, the inclusion of positive psychological orientations (Block 3) explained significantly more variance of students’ life satisfaction (△R2 = 26%) and emotional distress (△R2 = 5%). Mediation analyses using Structural Equation Modeling (SEM) found that only positive psychological orientations had significant indirect relations with quality of life through school connectedness. Implications and future research and practice are discussed.
Soil microbial restoration strategies for promoting climate-ready prairie ecosystems

Tractable practices for soil microbial restoration in tallgrass prairies reclaimed from agriculture are a critical gap in traditional ecological restoration. Long-term fertilization and tilling permanently alter soil bacterial and fungal communities, requiring microbe-targeted restoration methods to improve belowground ecosystem services and carbon storage in newly restored prairies. These techniques are particularly important when restoring for climate-ready ecosystems, adapted to altered temperature regimes. To approach these issues, we conducted a multi-factorial greenhouse experiment to test the effects of plant species richness, soil amendment and elevated temperature on soil microbial diversity, growth, and function. Treatments consisted of three seedlings of one plant species (Andropogon gerardii) or one seedling each of three plant species (A. gerardii, Echinacea pallida, Coreopsis lanceolata). Soil amendments included cellulose addition, inoculation with a microbial community collected from an undisturbed remnant prairie, and a control. We assessed microbial communities using extracellular enzyme assays, Illumina sequencing of the bacterial 16S rRNA gene, predicted bacterial metabolic pathways from sequence data and phospholipid fatty acid analysis (PLFA), which includes both bacterial and fungal lipid abundances. Our results indicate that addition of cellulose selects for slow-growing bacterial taxa (Verrucomicrobia) and fungi at ambient temperature. However, at elevated temperature, selection for slow-growing bacterial taxa is enhanced, while selection for fungi is lost, indicating temperature sensitivity among fungi. Cellulose addition was a more effective means of altering soil community composition than addition of microbial communities harvested from a remnant prairie. Soil water content was typically higher in the A. gerardii treatment alone, regardless of temperature, but at ambient temperature only, predicted metagenomics pathways for bacterial carbon metabolism were more abundant with A. gerardii. In summary, these results from a mesocosm test case indicate that adding cellulose to newly restored soil and increasing the abundance of C4 grasses, such as A. gerardii, can select for microbial communities adapted for slow growth and carbon storage. Further testing is required to determine if these approaches yield the same results in a field-level experiment.
Urticaria and Angioedema

Involving the superficial skin layers, urticaria may be intensely pmritic, with serpiginous raised edges and blanched centers. Angioedema involves the deeper skin layers and is usually not pmritic. Either may be associated with incapacitating gastrointestinal colic, life-threatening upper respiratory obstruction, or hypotension.
Online Scan Diagnosis : A Novel Approach to Volume Diagnosis

In this paper, we present a novel approach to run scan diagnosis in a high volume manufacturing (HVM) environment. Our methodology enables two usage modes during scan diagnosis; we can perform diagnosis on all failing partitions on all units (a) on production testers directly or (b) on a few compute machines. Diagnosis or fault dictionary based methods are employed to pre-generate a suspect database (DB) for each design partition. Computationally efficient capture and chain diagnosis algorithms are developed to query the DB to form a suspect universe that explains the fail signature. Only certain pages of the DB are loaded in memory at any given time, requiring no more than a few megabytes of RAM. The technique has been successfully demonstrated on two Intel products with significant cost savings realized over the traditional approach. Diagnosis results have been validated by comparing against the output of a commercial diagnosis tool on thousands of wafers; more importantly, 97% of actual defects confirmed by physical failure analysis (FA) are successfully identified by the proposed approach.
Teaching Statistics to Psychologists

The introduction of computerized statistical packages over the past three decades has dramatically altered graduate education in psychology for better and for worse. Students now are more broadly trained in technique but this improvement has occurred at the expense of training in design. The availability of statistical packages in the hands of those without professional training has implications for psychology as a profession. Keywords: statistics; graduate training; computer
Unsupervised Learning Reveals Geography of Global Ocean Dynamical Regions

Dynamically similar regions of the global ocean are identified using a barotropic vorticity (BV) framework from a 20-year mean of the Estimating the Circulation and Climate of the Ocean state estimate at 1° resolution. An unsupervised machine learning algorithm, K-means, objectively clusters the standardized BV equation, identifying five unambiguous regimes. Cluster 1 covers 43 ± 3.3% of the ocean area. Surface and bottom stress torque are balanced by the bottom pressure torque and the nonlinear torque. Cluster 2 covers 24.8 ± 1.2%, where the beta effect balances the bottom pressure torque. Cluster 3 covers 14.6 ± 1.0%, characterized by a "Quasi-Sverdrupian" regime where the beta effect is balanced by the wind and bottom stress term. The small region of Cluster 4 has baroclinic dynamics covering 6.9 ± 2.9% of the ocean. Cluster 5 occurs primarily in the Southern Ocean. Residual "dominantly nonlinear" regions highlight where the BV approach is inadequate, found in areas of rough topography in the Southern Ocean and along western boundaries.
Insulin-like growth factor I, binding proteins -1 and -3, risk of type 2 diabetes and macronutrient intakes in men

The insulin-like growth factor (IGF) axis may be involved in the development of type 2 diabetes. We examined the associations of IGF-I and IGF binding proteins (IGFBP)-1 and -3 with diabetes risk and evaluated macronutrient intakes related to the observed associations. In a nested case–control study of the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study of Finnish male smokers aged 50–69 years, the IGF variables were measured from baseline serum samples for a random sample of 310 men with diabetes diagnosed during a 12-year follow-up and for 310 controls matched by age, recruitment day and intervention group. Diet at baseline was assessed using a validated FFQ. The associations of IGF proteins with diabetes risk were estimated using conditional logistic regression and the associations with macronutrient intakes using linear regression. IGF-I and IGFBP-3 were not associated with the incidence of diabetes. Higher IGFBP-1 was associated with lower diabetes risk in an unadjusted crude model (OR 0·25; 95 % CI 0·15, 0·42 in the highest quartile compared with the lowest), but not after adjustment for BMI (corresponding OR 0·76; 95 % CI 0·41, 1·40). Intakes of carbohydrates, plant protein and milk protein associated positively and intake of meat protein and fat negatively with IGFBP-1 (P<0·005). IGFBP-1 was inversely associated with diabetes risk, but the association was substantially dependent on BMI. The associations between macronutrient intakes and IGFBP-1 may reflect influences of nutrients or foods on insulin concentrations.
Government venture capital research: fake science and bad public policy

We review statistical methods used to estimate the impact of crowding out of private venture capital (VC) by government VC. We review three types of failures that have plagued the VC literature and...
Candidate traits in elections: when good news for selection is bad news for accountability

We analyze a two-election political agency model with moral hazard and adverse selection in which candidates have observable traits such as job qualifications that help voters to imperfectly predict politicians' types. Candidate's traits can help voters select good types of politicians. However, selecting candidates with good traits can reduce accountability because the voter cannot commit to throw out politicians with good traits who produce bad outcomes. This result explains when and why voters may sometimes select candidates who they believe are less likely to be competent.
Modeling the determinants of meet-or-just-beat behavior in distribution discontinuity tests

Abstract We develop new distribution discontinuity tests conditional on multiple explanatory variables for analyzing meet-or-just-beat behavior around benchmarks. These tests combine Burgstahler and Dichev's (1997) meet-or-just-beat intuition with a flexible statistical model that addresses important limitations of the existing tests. Our method considerably outperforms logit-based tests of distribution discontinuity determinants and changes the interpretation of a major finding in the earnings discontinuity literature. As a secondary benefit, it also has slightly higher statistical power than histogram-based tests of distribution discontinuity existence. Our method is robust, easy to implement using our publicly available Stata command, and could benefit researchers in many fields.
The evolving 5G case study in spectrum management and industrial policy

Abstract Even before the International Telecommunication Union (“ITU”) reaches consensus on spectrum allocations for fifth generation wireless technologies (“5G”), commercial ventures scramble to offer new equipment and services. Expediting 5G wireless service can benefit consumers and businesses at the risk of stressing the traditional process of spectrum planning that combines study, dialogue and consensus building at ITU conferences. This paper explains why most nations refused to endorse key United States 5G spectrum allocation proposals at the ITU’s, 2015 World Radio Conference. U.S. representatives underestimated the time needed for consensus building, despite increasing demand for wireless video and the evolving Internet of Things. Other contributing factors include U.S. support for treating spectrum like property, use of “incentive auctions” to clear broadcast television spectrum with unprecedented speed and enough existing wireless spectrum allocations in most nations. The paper concludes that the U.S. cannot expect faster frequency reallocations, particularly when it and other nations pursue matters having little to do with spectrum optimization. The paper offers recommendations on best practices for improving the consensus building process.
CFO Gender and Financial Statement Irregularities

The increasing presence of women in upper echelon positions draws attention to the possible effects of executive gender on corporate decisions and actions. In this study, we formulate theory about ...
Untargeted metabolomic analysis in naturally occurring canine diabetes mellitus identifies similarities to human Type 1 Diabetes

While predominant as a disease entity, knowledge voids exist regarding the pathogenesis of canine diabetes. To test the hypothesis that diabetic dogs have similar metabolomic perturbations to humans with type 1 diabetes (T1D), we analyzed serum metabolomic profiles of breed- and body weight-matched, diabetic (n = 6) and healthy (n = 6) dogs by liquid chromatography-mass spectrometry (LC-MS) profiling. We report distinct clustering of diabetic and control groups based on heat map analysis of known and unknown metabolites. Random forest classification identified 5/6 dogs per group correctly with overall out of bag error rate = 16.7%. Diabetic dogs demonstrated significant upregulation of glycolysis/gluconeogenesis intermediates (e.g., glucose/fructose, C6H12O6, keto-hexose, deoxy-hexose, (P < 0.01)), with significant downregulation of tryptophan metabolism metabolites (e.g., picolinic acid, indoxyl sulfate, anthranilate, (P < 0.01)). Multiple amino acids (AA), AA metabolites, and bile acids were also significantly lower in diabetic versus healthy dogs (P < 0.05) with the exception of the branched chain AA valine, which was elevated in diabetic animals (P < 0.05). Metabolomic profiles in diabetic versus healthy dogs shared similarities with those reported in human T1D (e.g., alterations in glycolysis/gluconeogensis metabolites, bile acids, and elevated branched chain AA). Further studies are warranted to evaluate the utility of canine diabetes to provide novel mechanistic insights to the human disorder.
Isolation, Development, and Genomic Analysis of Bacillus megaterium SR7 for Growth and Metabolite Production Under Supercritical Carbon Dioxide

Supercritical carbon dioxide (scCO2) is an attractive substitute for conventional organic solvents due to its unique transport and thermodynamic properties, its renewability and labile nature, and its high solubility for compounds such as alcohols, ketones, and aldehydes. However, biological systems that use scCO2 are mainly limited to in vitro processes due to its strong inhibition of cell viability and growth. To solve this problem, we used a bioprospecting approach to isolate a microbial strain with the natural ability to grow while exposed to scCO2. Enrichment culture and serial passaging of deep subsurface fluids from the McElmo Dome scCO2 reservoir in aqueous media under scCO2 headspace enabled the isolation of spore-forming strain Bacillus megaterium SR7. Sequencing and analysis of the complete 5.51 Mbp genome and physiological characterization revealed the capacity for facultative anaerobic metabolism, including fermentative growth on a diverse range of organic substrates. Supplementation of growth medium with L-alanine for chemical induction of spore germination significantly improved growth frequencies and biomass accumulation under scCO2 headspace. Detection of endogenous fermentative compounds in cultures grown under scCO2 represents the first observation of bioproduct generation and accumulation under this condition. Culturing development and metabolic characterization of B. megaterium SR7 represent initial advancements in the effort toward enabling exploitation of scCO2 as a sustainable solvent for in vivo bioprocessing.
Efficient synthesis of 4-O- and C-substituted-7-azaindoles

6-Chloro-4-nitro- and 4,6-dichloro-1H-pyrrolo[2,3-b]pyridine are versatile building blocks that allow the synthesis of 4-substituted 7-azaindole derivatives by simple nucleophilic displacement of the 4-substituent. Herein, we report on their reaction with phenolates and activated methylene nucleophiles.
Synthesis and Characterization of a New Layered Ethylene-Diammonium Manganese(II) Phosphate, (C2N2H10)Mn2(PO4)2·2H2O

A new ethylene-diammonium manganese(II) phosphate, (C2H10N2)Mn2(PO4)2·2H2O, has been synthesized hydrothermally and characterized by thermogravimetric analysis, infrared spectroscopy, and magnetic susceptibility measurements. Its crystal structure was determined by single-crystal X-ray diffraction. The compound crystallizes in the triclinic system with the noncentrosymmetric space group P1 and cell parameters a = 4.910(1) A, b = 5.762(1) A, c = 9.832(2) A, α = 78.11(1)°, β = 87.75(1)°, and γ = 85.63(1)°. The manganese(II) ions form approximately square-planar layers of corner-sharing octahedra, with the layers bound by hydrogen bonds with the ammonium. The dc magnetization and ac susceptibility studies show that the compound is a 2D Heisenberg-like antiferromagnet with small additional interplanar and canting interactions. It undergoes a magnetic phase transition at 17.5(1) K; canted antiferromagnetic order is proposed for the low-temperature phase. A crossover in the critical exponent of magnetization is...
Polymeric potassium diaquahexa-μ-cyano-holmium(III)ruthenium(II) dihydrate

The crystal structure of the title bimetallic cyanide-bridged complex, {K[HoRu(CN)6(H2O)2]·2H2O}n, was determined by means of single-crystal X-ray diffraction techniques. The coordination about the central holmium(III) ion is eightfold in a square-antiprismatic arrangement, while the ruthenium(II) ion is octahedrally coordinated. Channels permeating the crystal lattice contain the potassium cations and two zeolitic water mol­ecules. The HoIII and K atoms lie at sites with mm symmetry and the Ru atom is at a site with 2/m symmetry.
Long-term surveillance defines spatial and temporal patterns implicating Culex tarsalis as the primary vector of West Nile virus.

West Nile virus (WNV) has become the most epidemiologically important mosquito-borne disease in the United States, causing ~50,000 cases since its introduction in 1999. Transmitted primarily by Culex species, WNV transmission requires the complex interplay between bird reservoirs and mosquito vectors, with human cases the result of epizootic spillover. To better understand the intrinsic factors that drive these interactions, we have compiled infection data from sentinel chickens, mosquito vectors, and human cases in Iowa over a 15 year period (2002–2016) to better understand the spatial and temporal components that drive WNV transmission. Supplementing these findings with mosquito abundance, distribution, and host preferences data, we provide strong support that Culex tarsalis is the most important vector of human WNV infections in the region. Together, our analysis provides new insights into WNV infection patterns in multiple hosts and highlights the importance of long-term surveillance to understand the dynamics of mosquito-borne-disease transmission.
Catalytic reactions of samarium (II) iodide

Abstract A system for in situ regeneration of SmI2 from SmI3 is described which allows the annulation of ketones to γ-lactones, the deoxygenation of oxiranes to olefins and radical π-cyclization to be conducted with 10 mole % SmI2.
Synthesis of Carbacephems from Serine

Carbacephems have been synthesized from d-serine by two routes involving construction first of the six-membered ring followed by cyclization to give the bicyclic β-lactam. In one route, alkylation of a lactim ether was accomplished with Ni(Acac)2 as a catalyst. The desired R stereochemistry at the carbon corresponding to C-6 of the cephem was obtained by stereospecific hydrogenation of a vinylogous carbamate. The second route involved a stereospecific Michael cyclization to give the same C-6 stereochemistry. Closure of a piperidyl β-amino acid intermediate common to both routes was accomplished using a modified Mukaiyama reagent found to be superior in our system to the traditional reagent. The resulting carbacephem core was stereospecifically substituted at C-7 with an ethyl or amino functionality. The ethylated intermediate was transformed into a stable enol triflate useful for the further elaboration of biologically important carbacephems.
Evolutionary design of regulatory control. I. A robust control theory analysis of tradeoffs.

Abstract The evolutionary design of regulatory control balances various tradeoffs in performance. Fast reaction to environmental change tends to favor plastic responsiveness at the expense of greater sensitivity to perturbations that degrade homeostatic control. Greater homeostatic stability against unpredictable disturbances tends to reduce performance in tracking environmental change. This article applies the classic principles of engineering control theory to the evolutionary design of regulatory systems. The engineering theory clarifies the conceptual aspects of evolutionary tradeoffs and provides analytic methods for developing specific predictions. On the conceptual side, this article clarifies the meanings of integral control, feedback, and design, concepts that have been discussed in a confusing way within the biological literature. On the analytic side, this article presents extensive methods and examples to study error-correcting feedback, which is perhaps the single greatest principle of design in both human-engineered and naturally designed systems. The broad framework and associated software code provide a comprehensive how-to guide for making models that focus on functional aspects of regulatory control and for making comparative predictions about regulatory design in response to various kinds of environmental challenge. The second article in this series analyzes how alternative regulatory designs influence the relative levels of genetic variability, stochasticity of trait expression, and heritability of disease.
Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways.

Background: A recent study of the gene expression patterns of Zika virus (ZIKV) infected human neural progenitor cells (hNPCs) revealed transcriptional dysregulation and identified cell cycle-related pathways that are affected by infection. However deeper exploration of the information present in the RNA-Seq data can be used to further elucidate the manner in which Zika infection of hNPCs affects the transcriptome, refining pathway predictions and revealing isoform-specific dynamics. Methodology/Principal findings: We analyzed data published by Tang et al. using state-of-the-art tools for transcriptome analysis. By accounting for the experimental design and estimation of technical and inferential variance we were able to pinpoint Zika infection affected pathways that highlight Zika’s neural tropism. The examination of differential genes reveals cases of isoform divergence. Conclusions: Transcriptome analysis of Zika infected hNPCs has the potential to identify the molecular signatures of Zika infected neural cells. These signatures may be useful for diagnostics and for the resolution of infection pathways that can be used to harvest specific targets for further study.
Contact, Travel, and Transmission: The Impact of Winter Holidays on Influenza Dynamics in the United States.

Background The seasonality of influenza is thought to vary according to environmental factors and human behavior. During winter holidays, potential disease-causing contact and travel deviate from typical patterns. We aim to understand these changes on age-specific and spatial influenza transmission. Methods We characterized the changes to transmission and epidemic trajectories among children and adults in a spatial context before, during, and after the winter holidays among aggregated physician medical claims in the United States from 2001 to 2009 and among synthetic data simulated from a deterministic, age-specific spatial metapopulation model. Results Winter holidays reduced influenza transmission and delayed the trajectory of influenza season epidemics. The holiday period was marked by a shift in the relative risk of disease from children toward adults. Model results indicated that holidays delayed epidemic peaks and synchronized incidence across locations, and that contact reductions from school closures, rather than age-specific mixing and travel, produced these observed holiday influenza dynamics. Conclusions Winter holidays delay seasonal influenza epidemic peaks and shift disease risk toward adults because of changes in contact patterns. These findings may inform targeted influenza information and vaccination campaigns during holiday periods.
Design, Synthesis, and Conformational Analysis of a Proposed Type I β-Turn Mimic

In an effort to design a dipeptide structural mimic of protein and peptide β-turns, we have prepared and evaluated the conformation of derivatives of the novel, highly constrained ten-membered lactam, (3S,10S)-(6E)-2-azacyclodec-6-enone (1). A synthetic route utilizing ring-closing olefin metathesis (RCM) has been used to prepare this novel ten-membered ring in high yield. X-ray crystallography and 1H NMR analysis have established that ring closure proceeds to give the trans-olefin and that 1 exists in two conformations, that of a chair−chair and chair−boat. Monte Carlo-molecular mechanics conformational searching has indicated that this ring system would be a good mimic of a type I β-turn. The synthesis of model tri- and tetrapeptide analogues based on 1 is reported. NMR studies indicate that the tetrapeptide derivatives constrain the i+1 and i+2 torsion angles to within 30° of those predicted for an ideal type I β-turn (φ1 = −82°, ψ1 = −20°, φ2 = −107°, ψ2 = −18°) and that this conformation was shown to...
Asymptotically optimal minimizers schemes.

Motivation The minimizers technique is a method to sample k-mers that is used in many bioinformatics software to reduce computation, memory usage and run time. The number of applications using minimizers keeps on growing steadily. Despite its many uses, the theoretical understanding of minimizers is still very limited. In many applications, selecting as few k-mers as possible (i.e. having a low density) is beneficial. The density is highly dependent on the choice of the order on the k-mers. Different applications use different orders, but none of these orders are optimal. A better understanding of minimizers schemes, and the related local and forward schemes, will allow designing schemes with lower density and thereby making existing and future bioinformatics tools even more efficient. Results From the analysis of the asymptotic behavior of minimizers, forward and local schemes, we show that the previously believed lower bound on minimizers schemes does not hold, and that schemes with density lower than thought possible actually exist. The proof is constructive and leads to an efficient algorithm to compare k-mers. These orders are the first known orders that are asymptotically optimal. Additionally, we give improved bounds on the density achievable by the three type of schemes.
A Self-Correcting Variable-Metric Algorithm Framework for Nonsmooth Optimization

An algorithm framework is proposed for minimizing nonsmooth functions. The framework is variable-metric in that, in each iteration, a step is computed using a symmetric positive definite matrix whose value is updated as in a quasi-Newton scheme. However, unlike previously proposed variable-metric algorithms for minimizing nonsmooth functions, the framework exploits self-correcting properties made possible through BFGS-type updating. In so doing, the framework does not overly restrict the manner in which the step computation matrices are updated, yet the scheme is controlled well enough that global convergence guarantees can be established. The results of numerical experiments for a few algorithms are presented to demonstrate the self-correcting behaviors that are guaranteed by the framework.
Formal intermolecular 4 + 4 approach to cyclooctanoids: 4 + 3 capture of the Nazarov oxyallyl intermediate with simple 1,3-dienes.

Simple 1,4-dien-3-ones and 1,3-dienes react in the presence of BF3·OEt2 via a domino Nazarov electrocyclization/intermolecular [4 + 3]-cycloaddition sequence to furnish keto-bridged cyclooctenes in good yield. Most cases showed high diastereofacial selectivity and/or endo/exo selectivity, and surprising levels of regioselectivity were observed when isoprene was used as the diene partner.
Synthesis of pyrrolo[2,3-d]pyrimidines via cyclocondensation of β-alkoxy- and β-amino-α-bromoaldehydes

Abstract A series of β-alkoxy- and β-amino-α-bromoaldehydes was synthesized. The cyclocondensation of these intermediates with 2,4-diamino-6-hydroxypyrimidine yielded a series of pyrrolo[2,3- d ]pyrimidines containing heteroatoms in the side chain. Choice of protecting group proved critical to the success of the bromination and cyclocondensation reactions. A number of oxygen and nitrogen protecting groups were examined and the results are described herein.
Vanadyl Oxalatophosphate Compounds (C2H10N2)[VO(HPO4)]2(C2O4) and (CH6N3)2[[VO(HPO4)]2(C2O4) and Their Thermal Transformation to (VO)2P2O7 via VOHPO4

The vanadyl oxalatophosphates (C2H10N2)[VO(HPO4)]2(C2O4), 1, and (CH6N3)2[VO(HPO4)]2(C2O4), 2, have been synthesized hydrothermally and characterized by a combination of techniques including infrared spectroscopy, single-crystal/powder X-ray diffraction, scanning/transmission electron microscopy, thermogravimetric analysis, and magnetic susceptibility measurements. The structures of 1 and 2 contain the same type of {[VO(HPO4)]2(C2O4)}2- layer, including both oxalate and phosphate anions coordinated to vanadium cations, as found in the previously reported (NH4)2[VO(HPO4)]2(C2O4)·H2O. Above ∼550 °C, 1 and 2 transform to (VO)2P2O7, the catalyst for the oxidation of butane to maleic anhydride. An intermediate phase with the composition VOHPO4 is observed in the decomposition reactions. Crystal data: (1) triclinic, space group P1 (no. 2); a = 6.3595(7) A, b = 6.6236(7) A, c = 9.224(1) A, α = 98.216(2)o, β = 108.128(2)o, γ = 100.672(2)o, V = 354.42(7) A3, Z = 1; (2) triclinic, space group P1 (no. 2); a = 6.3...
Germline silencing of UASt depends on the piRNA pathway.

Abstract One of the most extensively used techniques in Drosophila is the Gal4/UAS binary system, which allows tissue-specific misexpression or knockdown of specific genes of interest. The original UAS vector, UASt, can only be activated for transgene expression in somatic tissues but not in the germline cells (Brand and Perrimon, 1993). Here, we find that the piwi-interacting RNA (piRNA) pathway is involved in suppressing UASt expression in ovarian germline cells. Individually knocking down or mutating components of the piRNA biogenesis pathway (e.g., Piwi, AGO3, Aub, Spn-E, Su(var)2–10, Hsp83, and Vasa) resulted in the expression of the UASt-reporter (GFP or RFP) in the germline. An RNA-seq analysis of small RNAs revealed that the hsp70 promoter of UASt is targeted by piRNAs, and in the aub mutant ovary, the amount of piRNAs targeting the hsp70 promoter is reduced by around 40 folds. In contrast, the SV40 3′UTR of the UASt, which happens to be targeted by the nonsense-mediated RNA decay (NMD) pathway, is not responsible for germline UASt suppression, as UASt-reporters with NMD-insensitive 3′UTR fail to show germline expression. Taken together, our studies reveal a crucial role of the piRNA pathway, potentially via the suppression of the hsp70 promoter, in germline UASt silencing in Drosophila ovaries.
Catalytic, Nucleophilic Allylation of Aldehydes with 2-Substituted Allylic Acetates: Carbon–Carbon Bond Formation Driven by the Water–Gas Shift Reaction

The ruthenium-catalyzed allylation of aldehydes with allylic acetates has been expanded to incorporate substituents at the 2-position of the allylic components. Allylic acetates bearing a variety of substituents (CO2-t-Bu, COMe, Ph, CH(OEt)2, and Me) undergo high-yielding additions with aromatic, α,β-unsaturated, and aliphatic aldehydes. The conditions of the reaction were found to be mild (75 °C, 24–48 h) and only required the use of 2–3 mol % of the triruthenium dodecacarbonyl catalyst under 40–80 psi of CO. The stoichiometries of water and allylic acetate employed were found to be critical to reaction efficiency.
Pyruvate carboxylase supports the pulmonary tropism of metastatic breast cancer

Overcoming systemic dormancy and initiating secondary tumor grow under unique microenvironmental conditions is a major rate-limiting step in metastatic progression. Disseminated tumor cells encounter major changes in nutrient supplies and oxidative stresses compared to the primary tumor and must demonstrate significant metabolic plasticity to adapt to specific metastatic sites. Recent studies suggest that differential utilization of pyruvate sits as a critical node in determining the organotropism of metastatic breast cancer. Pyruvate carboxylase (PC) is key enzyme that converts pyruvate into oxaloacetate for utilization in gluconeogenesis and replenishment of the TCA cycle. Patient survival was analyzed with respect to gene copy number alterations and differential mRNA expression levels of PC. Expression of PC was analyzed in the MCF-10A, D2-HAN and the 4 T1 breast cancer progression series under in vitro and in vivo growth conditions. PC expression was depleted via shRNAs and the impact on in vitro cell growth, mammary fat pad tumor growth, and pulmonary and non-pulmonary metastasis was assessed by bioluminescent imaging. Changes in glycolytic capacity, oxygen consumption, and response to oxidative stress were quantified upon PC depletion. Genomic copy number increases in PC were observed in 16–30% of metastatic breast cancer patients. High expression of PC mRNA was associated with decreased patient survival in the MCTI and METABRIC patient datasets. Enhanced expression of PC was not recapitulated in breast cancer progression models when analyzed under glucose-rich in vitro culture conditions. In contrast, PC expression was dramatically enhanced upon glucose deprivation and in vivo in pulmonary metastases. Depletion of PC led to a dramatic decrease in 4 T1 pulmonary metastasis, but did not affect orthotopic primary tumor growth. Tail vein inoculations confirmed the role of PC in facilitating pulmonary, but not extrapulmonary tumor initiation. PC-depleted cells demonstrated a decrease in glycolytic capacity and oxygen consumption rates and an enhanced sensitivity to oxidative stress. Our studies indicate that PC is specifically required for the growth of breast cancer that has disseminated to the lungs. Overall, these findings point to the potential of targeting PC for the treatment of pulmonary metastatic breast cancer.
Rh2(S-PTAD)4-catalyzed asymmetric cyclopropenation of aryl alkynes

Abstract Rh2(S-PTAD)4 is an effective catalyst for the asymmetric cyclopropenation of aryl alkynes using a siloxyvinyldiazoacetate as the carbenoid precursor. Upon deprotection of the silyl protecting group, highly enantioenriched cyclopropenes bearing geminal acceptor groups can be accessed. These cyclopropenes undergo regioselective rhodium(II)-catalyzed ring expansion to furans.