cssi/SciSciGPT-SciSciNet huggingface dataset:
Fivebranes from gauge theory

We study theories with 16 supercharges and a discrete energy spectrum. One class of theories has symmetry group $SU(2|4)$. They arise as truncations of $\mathcal{N}=4$ super Yang-Mills theory. They include the plane-wave matrix model, $2+1$ super Yang-Mills theory on $R\ifmmode\times\else\texttimes\fi{}{S}^{2}$ and $\mathcal{N}=4$ super Yang-Mills theory on $R\ifmmode\times\else\texttimes\fi{}{S}^{3}/{Z}_{k}$. We explain how to obtain their gravity duals in a unified way. We explore the regions of the geometry that are relevant for the study of some $1/2$ BPS and near BPS states. This leads to a class of two dimensional (4,4) supersymmetric sigma models with nonzero $H$ flux, including a massive deformed WZW model. We show how to match some features of the string spectrum with the Yang-Mills theory. The other class of theories are also connected to $\mathcal{N}=4$ super Yang-Mills theory and arise by making some of the transverse scalars compact. Their vacua are characterized by a 2D Yang-Mills theory or 3D Chern-Simons theory. These theories realize peculiar super-Poincar\'e symmetry algebras in $2+1$ or $1+1$ dimensions with ``noncentral'' charges. We finally discuss gravity duals of $\mathcal{N}=4$ super Yang-Mills theory on ${\mathrm{AdS}}_{3}\ifmmode\times\else\texttimes\fi{}{S}^{1}$.
Robust vibration control of wind-excited highrise building structures

AbstractA robust filtered sliding mode control (SMC) approach is presented for vibration control of wind-excited highrise building structures. Rather than using a Lyapunov-function based control design, an alternative way is provided to find the control force based on the equivalent control force principle to obtain the control force. A low pass filter is properly selected to remove the high-frequency components of the control force while retaining the structural stability. The performance of the proposed filtered SMC is evaluated by application to a wind-excited 76-story building benchmark problem equipped with an active tuned mass damper (ATMD) on the roof. Due to the elimination of high-frequency part of the control force, the structure, sensors, actuators, and dampers are all less excited, and consequently their response is reduced compared with the unfiltered SMC approach. In addition, the required control forces are reduced which means a reduction in the size of actuators, thus making their implemen...
Determining the Reference Sample Size Needed to Control the Accuracy of the Conditional in‐control ARL of a Normal‐theory CUSUM

The question considered in this paper is how large does an in-control reference sample need to be in order to control the effects of using estimated parameters when using a normal-theory cumulative sum (CUSUM) tracking statistic? Previous research has demonstrated the effect of estimation errors on the conditional in-control average run length of the CUSUM. The contributions of this paper are simple analytical tools that determine the required reference sample size needed to ensure probabilistic control of the relative error of the conditional in-control average run length. The availability of these tools rounds out the design phase of the CUSUM by enabling a practical procedure for determining the needed size of the reference sample. Copyright © 2016 John Wiley & Sons, Ltd.
The Formal and the Foreign: Sarah Orne Jewett’s Garden Fences and the Meaning of Enclosure

Kaye Wierzbicki, “The Formal and the Foreign: Sarah Orne Jewett’s Garden Fences and the Meaning of Enclosure” (pp. 56-91) This essay argues that Sarah Orne Jewett theorizes garden design—particularly the question of whether or not a garden should be fenced—in order to theorize the aesthetic and social implications of her local color genre. Specifically, Jewett’s polemical defense of the garden fence is central to her ability to incorporate foreignness into her fictional landscapes. By placing Jewett’s garden-centric writing into the context of American garden history, this essay counters the prevailing notion that garden fences are transhistorical symbols of rigid protectionism and cultural exclusivity. Instead, Jewett’s garden fences should also be read as theoretically loaded and historically specific sites in the late-nineteenth-century debate between the fence-dismantling garden naturalists and the Colonial Revivalists who sought to preserve or re-erect these fences. As Jewett’s participation in this debate reveals, a garden fence can become a mechanism for defining “the local” as a formal practice that embraces foreignness, in contrast to competing definitions of “the local” that privilege native plants and native persons. Ultimately, Jewett uncovers new theoretical possibilities in the fenced, formal, Colonial Revivalist garden in order to make a case for the cultural expansiveness permitted by local color writing.
Durability of the SLA in High Voltage, High Radiation Environments

A solar array must be able to withstand the hazardous space environment and be able to operate reliably over a long period of time to be considered for space applications. The capability to withstand high voltage operation is another emerging factor required by space solar arrays as power levels continue to increase. The Stretched Lens Array (SLA) uses concentrator technology to offer outstanding measures of performance while at the same time offering protection against radiation, micrometeoroids, and electrostatic discharges common in high voltage operations. Thus it is especially well suited for electric propulsion missions and operation in high radiation environments such as the Van Allen belts or in those found around Jupiter. This paper will describe SLA past testing and flight history along with detailing two future SLA testing opportunities. The SLA is a durable array that can operate in high voltage, high radiation environments.
Analysis and Synthesis of Lighting Atmospheres

(2001). Analysis and Synthesis of Lighting Atmospheres. Journal of the Illuminating Engineering Society: Vol. 30, No. 1, pp. 141-153.
Is sexuality research ‘dirty work’? Institutionalized stigma in the production of sexual knowledge:

Sexuality research has a long history of controversy in the USA. This article examines sexuality research as a form of “dirty work,” an occupation that is simultaneously socially necessary and stig...
Comprehensive Review of Cocaethylene and Cocaine Concentrations in Patients

Cocaethylene (CE) and cocaine (COC) concentrations were reviewed for 41 patients studied by this laboratory and found to have measurable CE in plasma. In 17 instances, urine concentrations of CE and COC were also measured. In 15 cases other drugs in addition to COC and ethanol (ETOH) were detected. Thirty-three cases involved trauma. For the entire series, ages ranged from 19 to 48 years (mean 31 years) with men accounting for 36 cases. Mean concentrations were as follows: plasma CE, 353 nmol/L (range 16.1-1,959); plasma COC, 386 nmol/L (range no measurable amount-1,455); and whole-blood ETOH, 36.5 mmol/L (range no measurable amount-110.9). The ratio CE:COC in plasma ranged 0.1 to 4.7 (mean 1.3). Concentrations of ETOH in whole blood showed significant negative correlation with plasma COC (r = -0.425, P < .01). In addition, plasma CE concentrations showed significant correlation with plasma COC (r = 0.422, P < .01). When available, urine concentrations of CE and COC showed significant correlation with their concentrations in plasma (r = 0.821, P < .01; and r = 0.569, P < .05, respectively). As in plasma, urine concentrations of CE showed significant correlation with urine COC (r = 0.831, P < .01).
Uniform Convergence and Graph Convergence

(1976). Uniform Convergence and Graph Convergence. The American Mathematical Monthly: Vol. 83, No. 8, pp. 641-643.
Assessment of ASCE-7 Ground Motion Scaling Method Using Computer Model of Instrumented High-Rise Building

Performance-based earthquake engineering relies on accurate prediction of seismic demands from structural systems under given hazard conditions. In the pastdecade, numerous approaches in predicting engineering demand parameters (EDPs) from structural systems were established. Some of these methods were implemented into the design guidelines and building codes. Among them, nonlinear static procedures (NSPs) have found a wide usage in practice for checking new designs and evaluating performance of existing structures. Today, there is a paradigm shift towards using nonlinear response history analysis (RHA) in lieu of NSPs to predict EDPs. The pre-requisite to nonlinear RHAs is a set of ground motions to be selected and scaled appropriately so that analyses results would be accurate (unbiased) and efficient (having relatively small dispersion). Considering that ground motions may show significant variability in frequency content and amplitude, small dispersion (variability) of EDPs is desired since it provides a confidence. There are currently many different methods in scaling and selecting records to be used in nonlinear RHAs. Since there are no experimental validation studies available up to date, the effectiveness of these methods can only be assessed using numerical simulations. These simulations require development of realistic computer models. In this respect, structural monitoring plays a key role in providing recorded motions on existing structures which can be used to create their well-calibrated (in terms of modal periods, damping etc.) computer modes. This paper shows how the recorded earthquake data from the 52-story high-rise building located in Los Angeles is utilized to create a realistic three-dimensional computer model. This model is also used to assess the accuracy and efficiency of the ASCE-7 ground motion scaling method in predicting the building’s nonlinear response. It is concluded that the ASCE-7 method results in significantly high dispersion of EDPs despite the fact that median EDPs are well estimated.
Glomerular and tubular interactions between renal adrenergic activity and nitric oxide

Endothelium-dependent nitric oxide (EDNO) exerts control over the processes of glomerular filtration and tubular reabsorption. The importance of the renal nerves to the tonic influence of EDNO in the glomerular microcirculation and proximal tubule was tested by renal micropuncture in euvolemic adult male Munich-Wistar rats. The physical determinants of glomerular filtration and proximal reabsorption were assessed before and during administration of the nitric oxide synthase inhibitor, N G -monomethyl-L-arginine (L-NMMA), in control animals and in animals 5-9 days after either ipsilateral surgical renal denervation (DNX) or after either sham surgery (SEA). L-NMMA caused single-nephron glomerular filtration rate to decline in control and SEA animals but not in DNA rats. L-NMMA caused a reduction in proximal reabsorption in control and SEX rats, which was prevented by prior DNA. DNA did not alter urinary guanosine 3',5'-cyclic monophosphate excretion, and, although DNA upregulates glomerular angiotensin II (ANG II) receptors, prior DNX did not alter intrarenal ANG II content as evaluated by radioimmunoassay. Some component of renal adrenergic activity is required for the full expression of the glomerular and tubular effects of blockade of nitric oxide synthase....(SB)...Renal DA, dopamine receptors in proximal tubule membranes of normotensive Wistar-Kyoto (WKY) and spontaneously hypertensive rats (SHR) were characterized with the novel D, dopamine receptor-selective photoaffinity probe, (±)-7-[ 125 I]iodo-8-hydroxy-3-methyl-1-(4azidophenyl)-2,3,4,5-tetrahydro-1H-3-benzazepine ([ 125 I]MAB). Under nonphotolyzing conditions, saturation studies showed that [ 125 I]MAB bound with similar affinity to DA 1 dopamine receptors in both WKY [dissociation constant (K D ) = 16.3 nM] and SHR (K D = 19.5 nM). At photolysis, [ 125 I]MAB was irreversibly incorporated into a single major protein of 74,000 Da in both WKY and SHR. DA 1 -selective antagonists blocked photolabeling of DA, sites with similar efficiency and specificity in SHR and WKY. However, under identical assay conditions, dopaminergic agonists were unable to block photoincorporation of [ 125 I]MAB in SHR but not in WKY. This pattern of labeling of DA, sites by [ 125 I]MAB may suggest the presence of defective agonist, but not antagonist, binding domains on the receptor in SHR but not in WKY
Probing Single Nanometer-scale Particles with Scanning Tunneling Microscopy and Spectroscopies

Scanning tunneling microscopy can be used to isolate single particles on surfaces for further study. Local optical and electronic properties coupled with topographic information collected by the scanning tunneling microscope (STM) give insight into the intrinsic properties of the species under study. Since each spectroscopic measurement is done on a single particle, each sample is ‘monodisperse’, regardless of the degree of heterogeneity of the original preparation. We illustrate this with three example systems – a metal cluster of known atomic structure, metal nanoparticles dispersed from colloid suspensions, and metallocarbohedrenes (Met-Cars) deposited with other reaction products. Au and Ag nanoparticles were imaged using a photon emission STM. The threshold voltage, the lowest bias voltage at which photons are produced, was determined for Au nanoparticles. Electronic spectra of small clusters of Ni atoms on MoS2 were recorded. Preliminary images of Zr-based Met-Car-containing soot were obtained on Au and MoS2 substrates and partial electronic spectra were recorded of these possible Met-Car particles.
Correction for Berla and Pakrasi, Upregulation of Plasmid Genes during Stationary Phase in Synechocystis sp. Strain PCC 6803, a Cyanobacterium.

Volume 78, no. 15, p. 5448–5451, 2012. Page 5449, column 2, lines 5–7: “Copy numbers of pSysA, pCA2.4, and pCC5.2, the plasmids containing the highest-scoring SPPS genes, did not increase at stationary phase under any of the nutritional conditions…” should read “Copy numbers of pSysA,
Data Linkage Strategies to Advance Youth Suicide Prevention: A Systematic Review for a National Institutes of Health Pathways to Prevention Workshop.

Abstract Abstract | Methods | Results | Discussion | References Background: Linking national, state, and community data systems to data from prevention programs could allow for longer-term assessment of outcomes and evaluation of interventions to prevent suicide. Purpose: To identify and describe data systems that can be linked to data from prevention studies to advance youth suicide prevention research. Data Sources: A systematic review, an environmental scan, and a targeted search were conducted to identify prevention studies and potentially linkable external data systems with suicide outcomes from January 1990 through December 2015. Study Selection: Studies and data systems had to be U.S.-based and include persons aged 25 years or younger. Data systems also had to include data on suicide, suicide attempt, or suicidal ideation. Data Extraction: Information about participants, intervention type, suicide outcomes, primary analytic method used for linkage, statistical approach, analyses performed, and characteristics of data systems was abstracted by 2 reviewers. Data Synthesis: Of 47 studies (described in 59 articles) identified in the systematic review, only 6 were already linked to data systems. A total of 153 unique and potentially linkable data systems were identified, but only 66 were classified as “fairly accessible” and had data dictionaries available. Of the data systems identified, 19% were established primarily for research, 11% for clinical care or operations, 29% for administrative services (such as billing), and 52% for surveillance. About one third (37%) provided national data, 12% provided regional data, 63% provided state data, and 41% provided data below the state level (some provided coverage for >1 geographic unit). Limitation: Only U.S.-based studies published in English were included. Conclusion: There is untapped potential to evaluate and enhance suicide prevention efforts by linking suicide prevention data with existing data systems. However, sparse availability of data dictionaries and lack of adherence to standard data elements limit this potential. Primary Funding Source: Agency for Healthcare Research and Quality.
Mesh resolution impacts the accuracy of inverse and forward ECG problems

Electrocardiographic imaging (ECGI) has become an important medical diagnosis tool that assists scientists to noninvasively investigate cardiac electric activity. Many previous works have studied the inverse and forward ECG problems to understand how to reconstruct the cardiac electric activity from the body potential distribution. However, the inverse ECG problem is highly ill-conditioned and very sensitive to errors and noises. Thus, there is a need to study the sensitivity of inverse and forward ECG problems. In this paper, we investigated effects of mesh resolution on the accuracy of inverse and forward ECG problems. First, we employed the boundary element method to calculate the relationship between potential distributions on the body and heart surfaces and developed an algorithm to solve inverse and forward ECG problems. Second, we implemented the algorithm to solve the ECG problems in both a concentric spherical geometry and a realistic torso-heart geometry. Third, we evaluated the relative error between our solution and the analytical solution under the condition of different mesh resolutions. Experimental results explicitly show that the relative error in the inverse solution decreased from 30% to 17% when the mesh elements triangulating the two spheres increased from 24 to 400 in the concentric spherical geometry, and that decreased from 26% to 16% when the mesh elements triangulating the heart surface increased from 136 to 546 in the realistic torso-heart geometry.
Chemical Constituents of Sweetpotato Genotypes in Relation to Textural Characteristics of Processed French Fries

Abstract Sweetpotato French fries (SPFF) are growing in popularity, however limited information is available on SPFF textural properties in relation to chemical composition. This study investigated the relationship between chemical components of different sweetpotato varieties and textural characteristics of SPFF. Sixteen sweetpotato genotypes were evaluated for (1) chemical constituents; (2) instrumental and sensory textural properties of SPFF; and (3) the relationship between chemical components, instrumental measurements, and sensory attributes. Dry matter (DM), alcohol-insoluble solids (AIS), starch, sugar, and oil content, and also α- and β-amylase activities were quantified in raw sweetpotatoes and SPFF. Peak force and overall hardness describing instrumental textural properties of SPFF were measured using a texture analyzer. Descriptive sensory analysis was conducted and 10 attributes were evaluated by a trained panel. Results showed that DM, AIS, and starch content in raw sweetpotatoes were significantly correlated (P < 0.05) with instrumental peak force and overall hardness (r = 0.41 to 0.68), and with sensory surface roughness, hardness, fracturability, and crispness (r = 0.63 to 0.90). Total sugar content in raw sweetpotatoes was positively correlated with sensory smoothness and moistness (r = 0.77), and negatively correlated with instrumental peak force and overall hardness (r = –0.62 to –0.69). Instrumental measurements were positively correlated with sensory attributes of hardness, fracturability, and crispness (r = 0.68 to 0.96) and negatively correlated with oiliness, smoothness, moistness, and cohesiveness (r = –0.61 to –0.91). Therefore, DM, AIS, starch, and total sugar contents and instrumental measurements could be used as indicators to evaluate sweetpotato genotypes for SPFF processing. Practical Application In recent years, sweetpotato French fries (SPFF) have grown in popularity, but limited information is available on SPFF textural properties in relation to the differences in chemical constituents among sweetpotato varieties. This study demonstrated that sensory texture attributes of SPFF varied widely and were significantly correlated with chemical components such as dry matter, starch, and total sugar contents of raw sweetpotatoes and instrumental texture measurements of SPFF. The knowledge generated from this study will benefit the food industry and breeding programs with the selection of sweetpotato varieties for improved SPFF quality.
Identifying intraclass correlations necessitating hierarchical modeling

Hierarchical binary outcome data with three levels, such as disease remission for patients nested within physicians, nested within clinics are frequently encountered in practice. One important aspe...
Robust Stability of a Modified Clarke-Gawthrop Self-Tuning Controller

Abstract In the paper, the Clarke-Gawthrop type self-tuning controller is modified and shown to be robust stable with respect to unmodeled plant uncertainties and bounded disturbances. The self-tuning controller is proposed here by the two steps: the first, an optimal control law i5 derived by means of minimizing a quadratic cost function of the Clarke-Gawthrop type; the second, the optimal control law is modified by introducing an estimate of the modeling error as a feedback. The robustness results are derived by neither requiring too much a priori knowledge of the plant parameters, nor using any assumptions on the adaptive signals.
Cognitive strategies in the mental rotation task revealed by EEG spectral power

The classic mental rotation task (MRT; Shepard & Metzler, 1971) is commonly thought to measure mental rotation, a cognitive process involving covert simulation of motor rotation. Yet much research suggests that the MRT recruits both motor simulation and other analytic cognitive strategies that depend on visuospatial representation and visual working memory (WM). In the present study, we investigated cognitive strategies in the MRT using time-frequency analysis of EEG and independent component analysis. We scrutinized sensorimotor mu (µ) power reduction, associated with motor simulation, parietal alpha (pα) power reduction, associated with visuospatial representation, and frontal midline theta (fmθ) power enhancement, associated with WM maintenance and manipulation. µ power increased concomitant with increasing task difficulty, suggesting reduced use of motor simulation, while pα decreased and fmθ power increased, suggesting heightened use of visuospatial representation processing and WM, respectively. These findings suggest that MRT performance involves flexibly trading off between cognitive strategies, namely a motor simulation-based mental rotation strategy and WM-intensive analytic strategies based on task difficulty. Flexible cognitive strategy use may be a domain-general cognitive principle that underlies aptitude and spatial intelligence in a variety of cognitive domains. We close with discussion of the present study's implications as well as future directions.
Impact of a quality-assessment dashboard on the comprehensive review of pharmacist performance

Purpose The impact of a quality-assessment dashboard and individualized pharmacist performance feedback on the adherence of order verification was evaluated. Methods A before-and-after study was conducted at a 1,440-bed academic medical center. Adherence of order verification was defined as orders verified according to institution-derived, medication-related guidelines and policies. Formulas were developed to assess the adherence of verified orders to dosing guidelines using patient-specific height, weight, and serum creatinine clearance values from the electronic medical record at the time of pharmacist verification. A total of 5 medications were assessed by the formulas for adherence and displayed on the dashboard: ampicillin–sulbactam, ciprofloxacin, piperacillin–tazobactam, acyclovir, and enoxaparin. Adherence of order verification was assessed before (May 1–July 31, 2015) and after (November 1, 2015–January 31, 2016) individualized performance feedback was given based on trends identified by the quality-assessment dashboard. Results There was a significant increase in the overall adherence rate postintervention (90.1% versus 91.9%, p = 0.040). Among the 34 pharmacists who participated, the percentage of pharmacists with at least 90% overall adherence increased postintervention (52.9% versus 70.6%, p = 0.103). Time to verification was similar before and after the study intervention (median, 6.0 minutes; interquartile range, 3–13 minutes). The rate of documentation for nonadherent orders increased significantly postintervention (57.1% versus 68.5%, p = 0.019). Conclusion The implementation of the quality-assessment dashboard, educational sessions, and individualized performance feedback significantly improved pharmacist order-verification adherence to institution-derived, medication-related guidelines and policies and the documentation rate of nonadherent orders.
Socrates and Early Socratic Philosophers of Law

Socrates is arguably the most important and elusive figure in the history of moral philosophy. The few known facts about his life are easily told. He was an Athenian citizen, born in 469 B.C., and worked as a sculptor. He served his city bravely in the Peloponnesian War, but did not seek an active role in politics. Nevertheless, he was briefly forced into prominence after the battle of Arginusae when, as one of the presidents of the Assembly, he resisted the clamor to try the generals en masse, which he saw as illegal. During the rule of the Thirty Tyrants (404–403 B.C.) he refused an order to take part in arresting Leon of Salamis. After the restoration of democracy, he was put on trial in 399 for introducing strange gods and corrupting the young.2 He refused to save himself by opting for exile or by using any of the devices by which defendants usually sought to arouse the sympathy of Athenian juries. As a result, he was condemned and put to death by poisoning.
DeepPET: A deep encoder–decoder network for directly solving the PET image reconstruction inverse problem

Abstract The purpose of this research was to implement a deep learning network to overcome two of the major bottlenecks in improved image reconstruction for clinical positron emission tomography (PET). These are the lack of an automated means for the optimization of advanced image reconstruction algorithms, and the computational expense associated with these state-of-the art methods. We thus present a novel end-to-end PET image reconstruction technique, called DeepPET, based on a deep convolutional encoder–decoder network, which takes PET sinogram data as input and directly and quickly outputs high quality, quantitative PET images. Using simulated data derived from a whole-body digital phantom, we randomly sampled the configurable parameters to generate realistic images, which were each augmented to a total of more than 291,000 reference images. Realistic PET acquisitions of these images were simulated, resulting in noisy sinogram data, used for training, validation, and testing the DeepPET network. We demonstrated that DeepPET generates higher quality images compared to conventional techniques, in terms of relative root mean squared error (11%/53% lower than ordered subset expectation maximization (OSEM)/filtered back-projection (FBP), structural similarity index (1%/11% higher than OSEM/FBP), and peak signal-to-noise ratio (1.1/3.8 dB higher than OSEM/FBP). In addition, we show that DeepPET reconstructs images 108 and 3 times faster than OSEM and FBP, respectively. Finally, DeepPET was successfully applied to real clinical data. This study shows that an end-to-end encoder–decoder network can produce high quality PET images at a fraction of the time compared to conventional methods.
Imprinting Errors and IVF

Imprinting disorders have been reported in children conceived by IVF. There is concern that procedures of IVF may interfere with epigenetic processes responsible for setting imprint marks during gametogenesis. This possibility seems plausible in light of the rarity of these conditions and results of experiments examining imprint marks in model organisms subjected to in vitro manipulations. We quantitatively summarized published human data on this question by meta-analysis, relating IVF to the risk of four model imprinting disorders. Estimates of summary relative risk were 3.7 (95% confidence interval (CI) = 1.7–7.8) for Angelman syndrome, 6.1 (95% CI = 3.8–11) for Beckwith-Wiedemann syndrome, and 5.7 (95% CI = 1.4–22) for Prader-Willi syndrome. Published data were insufficient to conduct meaningful analyses of risk of Silver-Russel syndrome. These results are consistent with the elevated risk of imprinting disorders following IVF, although absolute risk of these outcomes remains low. Elevated risk could in theory arise from either detrimental effects of IVF procedures or increased occurrence of aberrant methylation of imprinted genes in gametes of subfertile parents.
Use of Acute Toxicity Data in the Design and Interpretation of Subchronic and Chronic Toxicity Studies

This contribution shows that the relative toxic potency of 4 chlorinated dibenzo-pdioxins (CDDs) is similar in 2 species with different sensitivities (guinea pig, rat). More importantly, it also demonstrates that the relative toxic potencies of these homologues and their mixture is essentially identical for acute, subchronic and chronic dosing in the same species (rat). The importance and usefulness of careful considerations of toxicokinetic and toxicodynamic data obtained in acute experiments for the design of subchronic and chronic toxicity studies is discussed.
Squiggle: a user-friendly two-dimensional DNA sequence visualization tool

SUMMARY Squiggle is a software tool that automatically generates interactive web-based two-dimensional graphical representations of raw DNA sequences. Built with ease of use in mind, Squiggle implements several prior sequence visualization algorithms and introduces novel visualization methods designed to maximize human usability. AVAILABILITY AND IMPLEMENTATION Squiggle is written in Python 3 and freely available under the permissive MIT license. The open-source code can be downloaded from github.com/Lab41/squiggle as well as the Python Package Index. The installation instructions and user guide are available at squiggle.readthedocs.org.
Does residential sorting explain geographic polarization

Political preferences in the United States are highly correlated with population density, at national, state, and metropolitan-area scales. Using new data from voter registration records, we assess the extent to which this pattern can be explained by geographic mobility. We find that the revealed preferences of voters who move from one residence to another correlate with partisan affiliation, though voters appear to be sorting on non-political neighborhood attributes that covary with partisan preferences rather than explicitly seeking politically congruent neighbors. But, critically, we demonstrate through a simulation study that the estimated partisan bias in moving choices is on the order of five times too small to sustain the current geographic polarization of preferences. We conclude that location must have some influence on political preference, rather than the other way around, and provide evidence in support of this theory.
The Psychosocial Evaluation of Live Donors

Live organ donation is an essential and thriving part of organ transplantation. The transplant community allows live donors to express their autonomy by taking risk to themselves to benefit the recipient and to help ease the ever-increasing waitlist. Medical and psychosocial outcomes for the first post-donation decade have been encouraging for kidney and liver donors. Lung, pancreas, small intestine, and uterine donations have also been studied, but to a lesser extent. Kidney donation remains the most common type of live organ donation with altruistic or non-directed donation from strangers growing. At present non-directed donation of other solid organs is controversial given the increased medical and surgical risk. This chapter will review the procedures to evaluate these unique candidates as well as the risks and outcomes of live organ donation. The psychosocial team is important in this process to ensure a careful selection of organ donors and positive donor outcomes.
The Effect of Financial Conflict of Interest, Disclosure Status, and Relevance on Medical Research from the United States.

Financial interactions between industry and healthcare providers are reportable. Substantial discrepancies have been detected between industry and self-report of these conflicts of interest (COIs). Our aim was to determine if authors who fail to disclose reportable COI are more likely to publish findings that are favorable to industry than authors with no COI. In this blinded, observational study of medical and surgical primary research articles in PubMed, 590 articles were reviewed. Reportable financial relationships between authors and industry were evaluated. COIs were considered to have relevance if they were associated with the product(s) mentioned by an article. Primary outcome was favorability, defined as an impression favorable to the product(s) discussed by an article and determined by 3 independent, blinded clinicians for each article. Primary analysis compared Incomplete Self-Disclosure to No COI. Two-level multivariable mixed-effects ordered logistic regression was used to assess factors associated with favorability. A 69% discordance rate existed between industry and self-report in COI disclosure. When authors failed to disclose COI, their conclusions were more likely to favor industry partners than authors without COI (favorable ratings 73% versus 62%, RR 1.18, p = < 0.001). On univariate (any COI 74% versus no COI 62%, RR 1.11, p = < 0.001) and multivariable analyses, any COI was associated with favorability. All financial COIs (disclosed or undisclosed, relevant or not relevant, research or non-research) influence whether studies report findings favorable to industry sponsors.
Inference for Income Mobility Measures in the Presence of Spatial Dependence

Income mobility measures provide convenient and concise ways to reveal the dynamic nature of regional income distributions. Statistical inference about these measures is important especially when i...
The Cognitive Bases for Deciding When Policies Are Just

It has long been recognized that, psychologically, we experience ought, a moral demand, when we relate a choice before us to our conception of an ideal self. Based on this reality, ideal observer theories have been promulgated for centuries. I draw on Roderick Firth’s most precise version. What is right is defined by the approval of an Ideal Observer who is omniscient with respect to factual knowledge, omni-percipient in imagining how everyone is affected by one’s decision, and is impartial. Drawing on neuro-ethical research and other psychological studies, I support these criteria for moral decision-making and argue for changing how impartiality is understood. Impartiality is not attained by being disinterested and dispassionate but rather by having equal empathy for everyone, including oneself, as in the Golden Rule.
A systematic review of the methodology used to study weight change among young adults attending college.

Abstract Introduction Young adulthood is a sensitive developmental period that is high-risk for weight gain. Ample research has focused on weight gain among college students; however meta-analyses report 2 kg or ≥3%); 2) weight measurement protocols; and 3) including weight/BMI in analyses of predictors of weight change. Methods Three databases were systematically searched. Studies were included in the review if the primary goal was to determine magnitude of weight change and/or test predictors of weight change during the academic year, and they reported weight at 2+ time points. Results A total of 81 studies were included in the review. Most studies (90%; 73/81) did not use an evidence-supported definition of weight gain. Studies that used an evidence-supported definition reported estimates of gain among students who gained weight to be beyond the range of normal weight fluctuation (4.0–7.5 kg), and occurred in a subset ( 50% of students. Most studies that measured height and weight (71%; 42/59) did not use a fasting protocol and the majority (63%; 37/59) did not conduct measurements at the same time of day. A higher percentage of studies that used a standardized measurement protocol reported weight change >2 kg (44% vs 20%). A lower percentage of studies that used a standardized measurement protocol had substantial variability in weight change estimates (50% vs 69%). The majority of studies that tested predictors of weight gain (74%; 42/57) included weight/BMI as a covariate in analyses. Conclusions The body of literature examining weight change among college students suffers from limitations that may have contributed to overestimations in the percent of students who gain weight, and simultaneous underestimations of the magnitude of weight gain among those who gain weight. Weight gain may be limited to approximately 30% of students in a sample, and weight gain among this subset of students may be substantial (>4 kg). Going forward, use of both an evidence-supported weight gain definition and fasting measurement protocol will likely enhance accuracy in characterizing weight gain among college students, as well as improve researchers' ability to detect important predictors of weight gain.
Hox binding specificity is directed by DNA sequence preferences and differential abilities to engage inaccessible chromatin

While Hox genes encode for conserved transcription factors (TFs), they are further divided into anterior, central, and posterior groups based on their DNA-binding domain similarity. The posterior group expanded in the deuterostome clade and patterns caudal and distal vertebrate structures such as the spinal neuronal diversity required for motor function. Our data revealed that limb-level patterning central Hoxc6, Hoxc8 and posterior Hoxc10 have a reduced ability to access occluded sites compared to other tested Hox TFs. Thus, their genomic binding relies more on cell-specific chromatin accessibility. Although posterior Hoxc9, Hoxc10 and Hoxc13 induce different fates, they share motif preference. However, Hoxc9 and Hoxc13 have a unique ability to access sites occluded by chromatin, resulting in divergent genomic binding patterns. From these results, we propose that the differential abilities of posterior Hox TFs to bind to previously inaccessible chromatin is the predominant force driving their patterning diversification.
Causal Clustering for 1-Factor Measurement Models on Data with Various Types.

The tetrad constraint is a condition of which the satisfaction signals a rank reduction of a covariance submatrix and is used to design causal discovery algorithms that detects the existence of latent (unmeasured) variables, such as FOFC. Initially such algorithms only work for cases where the measured and latent variables are all Gaussian and have linear relations (Gaussian-Gaussian Case). It has been shown that a unidimentional latent variable model implies tetrad constraints when the measured and latent variables are all binary (Binary-Binary case). This paper proves that the tetrad constraint can also be entailed when the measured variables are of mixed data types and when the measured variables are discrete and the latent common causes are continuous, which implies that any clustering algorithm relying on this constraint can work on those cases. Each case is shown with an example and a proof. The performance of FOFC on mixed data is shown by simulation studies and is compared with some algorithms with similar functions.
Three-Electrode Device for Applying Two-Dimensional Vector Electric Fields to Single In As Quantum Dots

Electric field tuning of single $\mathrm{In}\mathrm{As}$ quantum dots (QDs) provides an important tool for physics experiments and for the development of scalable and in situ--tunable devices. Control of a single QD with either a growth direction or an in-plane electric field is well established, but a device that can apply the two-dimensional (2D) vector electric fields necessary to simultaneously and independently tune more than one parameter has not yet been demonstrated. We use comsol multiphysics simulations to illustrate the device-design challenges in applying a uniform 2D electric field in a $\mathrm{Ga}\mathrm{As}$ solid-state system and to systematically explore the effects of electrode coverage, mesa size, and doping on the device performance. We develop and present a design that can apply 2D electric fields to a single QD while remaining compatible with optical experiments. We then fabricate and characterize a proof-of-concept device that validates the design presented here. We discuss the applications for this device and the potential for full 2D-electric-field control of a single QD or a quantum-dot molecule.
Manifold learning for knowledge discovery and design in nanophotonics

The systematic realization of the nature of the optical functionalities requires significant knowledge about the influence of nanostructure features on the propagation of electromagnetic waves. Due to the lack of such valuable information, cumbersome numerical calculations are currently the prevalent approach in designing nanostructures. In this talk, we introduce a novel technique based on manifold learning to reduce the complexity of the design problems. The developed algorithms provide valuable insights about the feasibility of a desired optical response and the roles of design parameters in forming the response through low-dimensional visualization. This extracted underlying information can be employed in different settings to accelerate the design of electromagnetic nanostructures for a wide range of applications.
Managing the Release of Consumable Digital Goods in Freemium Games

A common practice for freemium games is to launch with a simple and intuitive design and release premium features over time in the form of in-app purchases (IAPs) to monetize players.We propose an optimal control model that yields insights into the optimality and economic justification of such an approach. Through analytically characterizing the game life cycle and optimal release pattern of IAP for certain structured instances, we characterize when games optimally launch with an initial period free of IAPs in order to maximize the growth of its player-base and later exploit this player-base for generating revenue by releasing IAPs. This strategy balances the tradeoff between the effects of IAP release on acquiring and retaining players with the revenuegenerating potential of selling IAPs. Our model also admits comparative statics results on how exogenous factors, such as the social nature of the game, influence the optimal time of initial IAP release. In a numerical study, we show that a game can be permanently free if it generates revenues outside of player purchases, say through advertising revenue. We also consider the possibility of an operating loss during the free period due to per-player operating costs. We show the length of the loss period (while the game is totally free) and the magnitude of loss depends on exogenous factors, including the strength of word-of-mouth.
Teaching Reform for the Non-electric Class Professional Electrician Experiments Based on BB Platform

Aiming at the existing problems of non-electric class professional electrics experiments teaching,this paper puts forward a new experiment teaching mode based on the BB platform. The teaching platform,experiment contents,experiment report form and the assessment way have been reformed. Practices indicate that this teaching reformation can improve the students' learning efficiency,strengthen the connection of professional teachers and experiment teachers,and improve the teaching quality of non-electric professional electrician experiment.
Toward the use of neural networks for influenza prediction at multiple spatial resolutions

Mitigating the effects of disease outbreaks with timely and effective interventions requires accurate real-time surveillance and forecasting of disease activity, but traditional health care–based surveillance systems are limited by inherent reporting delays. Machine learning methods have the potential to fill this temporal “data gap,” but work to date in this area has focused on relatively simple methods and coarse geographic resolutions (state level and above). We evaluate the predictive performance of a gated recurrent unit neural network approach in comparison with baseline machine learning methods for estimating influenza activity in the United States at the state and city levels and experiment with the inclusion of real-time Internet search data. We find that the neural network approach improves upon baseline models for long time horizons of prediction but is not improved by real-time internet search data. We conduct a thorough analysis of feature importances in all considered models for interpretability purposes.
The Role of PERK in Understanding Development of Neurodegenerative Diseases

Neurodegenerative diseases are an ever-increasing problem for the rapidly aging population. Despite this, our understanding of how these neurodegenerative diseases develop and progress, is in most cases, rudimentary. Protein kinase RNA (PKR)-like ER kinase (PERK) comprises one of three unfolded protein response pathways in which cells attempt to manage cellular stress. However, because of its role in the cellular stress response and the far-reaching implications of this pathway, error within the PERK pathway has been shown to lead to a variety of pathologies. Genetic and clinical studies show a correlation between failure of the PERK pathway in neural cells and the development of neurodegeneration, but the wide array of methodology of these studies is presenting conflicting narratives about the role of PERK in these affected systems. Because of the connection between PERK and pathology, PERK has become a high value target of study for understanding neurodegenerative diseases and potentially how to treat them. Here, we present a review of the literature indexed in PubMed of the PERK pathway and some of the complexities involved in investigating the protein’s role in the development of neurodegenerative diseases as well as how it may act as a target for therapeutics.
Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury Severity

Lipids play many biological roles including membrane formation, protection, insulation, energy storage, and cell division. These functions have brought great interest to lipidomic studies for understanding their dysregulation in toxic exposure, inflammation, and diseases. However, lipids have shown to be analytically challenging due to their highly isomeric nature and vast concentration ranges in biological matrices. Therefore, powerful multidimensional techniques such as those integrating liquid chromatography, ion mobility spectrometry, collision induced dissociation, and mass spectrometry (LC-IMS-CID-MS) have recently been implemented to separate lipid isomers as well as provide structural information and increased feature identification confidence. These multidimensional datasets are however extremely large and highly complex, resulting in challenges in data processing and annotation. Here, we have overcome these challenges by developing sample-specific multidimensional libraries using the freely available software Skyline. Specifically, the human plasma library developed for this work contains over 500 unique, experimentally validated lipids, which is combined with adapted Skyline functions for highly confident lipid annotations such as indexed retention time (iRT) for retention time prediction and IMS drift time filtering for increased sensitivity and selectivity. For broad comparison with other lipidomic studies, this human plasma database was initially used to annotate LC-IMS-CID-MS data from a NIST SRM 1950 extract, giving comparable results to previous studies. This workflow was then utilized to assess matched plasma and bronchoalveolar lavage fluid (BALF) samples from patients with varying degrees of smoke inhalation injury to identify potential lipid-based patient prognostic and diagnostic markers. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY