cssi/SciSciGPT-SciSciNet huggingface dataset:
An overview of the vaccinia virus infectome: a survey of the proteins of the poxvirus-infected cell

We have quantitatively profiled the proteins of vaccinia virus-infected HEK293T cells early and late during vaccinia virus infection. Proteins corresponding to 4,326 accessions were identified, the products of 3,798 genes. One hundred thirty-six of the proteins were vaccinia virus-encoded (∼64% of the known vaccinia virus proteome). The remaining accessions were from the host cell. A total of 3,403 of the 4,326 accessions could be confidently quantitated at the precursor peptide level. Although vaccinia virus gene products spanned the entire abundance dynamic range of the cellular proteome, nearly all of the proteome dynamics observed as a result of infection were manifest in the virus gene products with very little plasticity in the host cell proteome. The vaccinia virus gene products could be grouped into four kinetic classes (i.e., four combinations of pre- and postreplicative expression). These protein kinetic classes reflected, almost entirely, the corresponding gene classes within the recently characterized vaccinia virus transcriptome map. The few cellular gene products that showed notable changes in abundance upon vaccinia virus infection were concentrated largely in just a few functional groups. After all of the quantitated cellular gene products were assigned to Gene Ontology (GO)-specific groups, quantitation values for a number of these GO-specific groups were significantly skewed toward over- or underabundance with respect to the global distribution of quantitation values. Quantitative analysis of host cell functions reflected several known facets of virus infection, along with some novel observations.
ELXR: a resource for rapid exon-directed sequence analysis

ELXR (Exon Locator and Extractor for Resequencing) streamlines the process of determining exon/intron boundaries and designing PCR and sequencing primers for high-throughput resequencing of exons. We have pre-computed ELXR primer sets for all exons identified from the human, mouse, and rat mRNA reference sequence (RefSeq) public databases curated by the National Center for Biotechnology Information. The resulting exon-flanking PCR primer pairs have been compiled into a system called ELXRdb, which may be searched by keyword, gene name or RefSeq accession number.
Leakage minimization of nano-scale circuits in the presence of systematic and random variations

This paper presents a novel gate sizing methodology to minimize the leakage power in the presence of process variations. The leakage and delay are modeled as posynomials functions to formulate a geometric programming problem. The existing statistical leakage model of Rao et al. (2004) is extended to include the variations in gate sizes as well as systematic variations. We propose techniques to efficiently evaluate constraints on the /spl alpha/-percentile of the path delays without enumerating the paths in the circuit. The complexity of evaluating the objective function is O(|N|/sup 2/) and that of evaluating the delay constraints is O(|N| + |E|) for a circuit with |N| gates and |E| wires. The optimization problem is then solved using a convex optimization algorithm that gives an exact solution.
Positive surgical margins at radical prostatectomy: importance of intra-operative bladder neck frozen sections.

OBJECTIVE: To determine if intraoperative frozen sections of the bladder neck during radical prostatectomy (RP) could decrease the incidence of final positive surgical margins at the bladder neck. MATERIALS AND METHODS: This prospective cohort study included 51 consecutive men who underwent anatomic RP at University of Florida & Shands Jacksonville. All patients had intraoperative frozen section of bladder neck sent for analysis. Preoperative, operative, and postoperative data were collected and analyzed. Main Outcome Measures: Outcome measures were intraoperative bladder neck margin status, final pathologic bladder neck margin status, and postoperative urinary complications. Median follow-up for the 51 patients was 22 months. RESULTS: The final positive surgical margin rate was 20% (10 patients). An additional three patients had positive surgical margins at the bladder neck intraoperatively. These patients then had a wider resection of the affected bladder neck until the frozen sections were negative for cancer or prostatic tissue. Final pathologic evaluation of bladder neck margin was negative for tumor or persistent prostatic tissue in all 51 men. CONCLUSION: With intra-operative frozen sections, we were able to obtain a negligible positive bladder neck margin rate. Surgeons who are still on the learning curve for RP should consider intra-operative frozen section of the bladder neck.
Running stability is enhanced by a proximo-distal gradient in joint neuromechanical control

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Combined-Modality Therapy for Inoperable non—small-Cell Lung Cancer Using Gemcitabine

Abstract Combined-modality therapy with chemotherapy and radiation appears to be the most efficacious therapeutic modality for patients with locally advanced non—small-cell lung cancer. Most of the trials exploring this approach have utilized older agents such as cisplatin, vinblastine, and etoposide. Recent data suggest that gemcitabine may be superior to these agents therapeutically, with the ability to produce similar or improved outcomes and a milder overall toxicity profile. Moreover, gemcitabine is able to sensitize tumor cells to radiation- induced apoptosis as well as lead to induction of cells in the radioresistant S phase of the cell cycle. These results have suggested that gemcitabine should be tested in concurrent chemoradiotherapy regimens. Significant toxicities seen in the initial trials have led to a number of trials modifying the regimen so that efficacy might be maintained without adverse effects. These modifications have included lowered gemcitabine doses and reduced radiation field sizes. The results of these newer studies suggest that this approach can be highly efficacious, with 1-year survival rates > 50% and response rates as high as 88%.
Party System Polarization and Ideological Congruence: New Data, Causal Mechanisms

The ideological congruence between the median citizen and the government is shaped by various institutional features, especially the party system. The polarization of the party system has large and robust effects on ideological (in)congruence across a variety of political systems. As captured by several approaches to measuring congruence, and across a substantial span of time, more polarization makes it more difficult to form congruent governments in parliamentary democracies. This paper focuses on the process of parliamentary government formation as the causal linkage between polarization and congruence. The analysis supports our expectation that polarization works somewhat differently under the different election rules. In the PR systems we find polarization shaping congruence through its association with greater distances of the plurality or pre-election coalition plurality vote winner, but also through the distances of the legislative median party, the previous government, and even the runner-up plurality party. In the SMD systems the effects are entirely through the plurality (or pre-election coalition plurality) vote winner. New data from CSES Module 3 and from the Manifesto project make it possible to analyze the two data sources in parallel and compare similarities and differences in polarization and its processes.
Position of the Academy of Nutrition and Dietetics: Obesity, Reproduction, and Pregnancy Outcomes

It is the position of the Academy of Nutrition and Dietetics that all women of reproductive age receive education about maternal and fetal risks associated with prepregnancy obesity, excessive gestational weight gain, and significant postpartum weight retention, including potential benefits of lifestyle changes. Behavioral counseling to improve dietary intake and physical activity should be provided to overweight and obese women, beginning in the preconception period and continuing throughout pregnancy, for at least 12 to 18 months postpartum. Weight loss before pregnancy may improve fertility and reduce the risk of poor maternal-fetal outcomes, such as preterm birth, gestational diabetes, gestational hypertension, pre-eclampsia, assisted delivery, and select congenital anomalies. Lifestyle interventions that moderate gestational weight gain may reduce the risk of poor pregnancy outcomes, such as gestational diabetes, gestational hypertension, large for gestational age, and macrosomia, as well as lower the risk for significant postpartum retention. Postpartum interventions that promote healthy diet and physical activity behaviors may reduce postpartum weight retention and decrease obesity-related risks in subsequent pregnancies. Analysis of the evidence suggests that there is good evidence to support the role of diet, physical activity, and behavior changes in promoting optimal weight gain during pregnancy; however, there is currently a relative lack of evidence in other areas related to reproductive outcomes.
Population dynamics of Rhopalosiphum padi (Homoptera : Aphididae) in corn in relation to barley yellow dwarf epidemiology in Southwestern Idaho

Population dynamics of Rhopalosiphum padi (L.) in seed and silage corn were investigated from 1981 through 1985 in southwestern Idaho. Aphid population development was divided into four phases: an immigration period, a lag period, a period of rapid increase where aphid numbers reached several million per hectare, and an emigration period characterized by an increase in alatoid nymphs and alatae. Just before peak aphid densities occurred, prereproductive development time for apterous R. padi was 9.9 ± 0.9 d ($\bar x$ ± SEM) in seed corn and 9.6 ± 0.5 d in silage corn. The reproductive rate of apterae during this same period was 36.6 ± 11.0 nymphs in seed corn and 9.8 ± 2.9 nymphs in silage corn. Flight activity, as indicated by suction trap data, peaked in July and again from September through October or November. These two peaks corresponded with the immigration and emigration of R. padi detected in corn. Residents on corn were assayed for transmission of barley yellow dwarf virus, and the mean frequencies were 36% in 1983, 4% in 1984, and 2% in 1985. Migrant R. padi collected in a modified suction trap in 1985 showed a mean transmission frequency of 6%. Fall migrant R. padi in corn had a mean life span of ≈14 d and a maximum life span of 41 d, which is sufficient time for fall-planted cereals to become infested with these migrants. Monthly maximum and minimum temperatures for epidemic and nonepidemic years differed most in December, January, and February, suggesting a possible temperature–disease relationship.
Looking at the label: White-collar men and the meanings of “metrosexual”:

How do men feel about the “metrosexual” label? How do their views relate to changing norms of masculine self-presentation and increasing acceptance of “out” gay men? We interviewed 30 US white-coll...
Analysis of "Anima" Archetype in Farewell My Concubine

Li Bihua's novel Farewell My Concubine describes the hero Cheng Deiyi being transformed from Xiao Douzi to Cheng Deiyi in the particular context,and eventually becoming Yu Ji with a step-by-step identity recognition process.His psychological journey of transformation is accompanied by a potential unconscious "Anima" archetype.The"Anima" archetype has a profound impact on the Cheng Dieyi's identity construction,self-identity and the ultimate self-destruction.
Analysis of surveillance of men who have sex with men at HIV/AIDS sentinels in Wuxi from 2010 to 2013

Objective To investigate the epidemic trend of HIV and syphilis infection among men who have sex with men(MSM)population in Wuxi.Methods MSM subjects were selected by snow ball sampling method in sentinels in Wuxi.Questionnaire-based survey and HIV/syphilis test were conducted.Results A total of 1 020 MSM subjects were investigated from 2010 to 2013,of which 63.3% had homosexual anal intercourse in the last 6months,only 30.2% used condom every time.17.2% of subjects took HIV test in the last year.HIV antibody rate was 12.6%.MSM from other provinces(18.8%)had higher HIV positive rate than that of MSM from Jiangsu(10.3%);the HIV positive rate for MSM who had homosexual anal intercourse in the last 6months(15.6%)was higher than that of who had no homosexual anal intercourse(7.5%);HIV positive rate for MSM who used condom every time in anal sexual intercourse(8.2%)was lower than those of MSM who used condom at times(16.4%)or never(26.9%),all with significant difference(all P0.01).Positive rate of syphilis infection was 14.8%.The positive rate of MSM in comrade bathroom(17.5%)was higher than that in gay bar or KTV(10.8%);MSM ≥40years old had higher positive rate(16.5%)than that of MSM 40years old(14.1%);the positive rate for MSM who used condom every time in anal sexual intercourse(10.3%)was lower than those of MSM who used condom at times(15.3%)or never(22.7%),all with significant difference(all P0.01).Conclusion High risk sexual behaviors were common among MSM in Wuxi,HIV and syphilis infection rate is relatively high.Intervention and surveillance should be strengthened to inhibit the spread of HIV.
Queen Elizabeth’s Leadership Abroad: The Netherlands in the 1570s

In 1576, after Edmund Grindal, archbishop of Canterbury, presumed to lecture Queen Elizabeth on the importance of preaching and on her duty to listen to such lectures, his influence diminished precipitously, and leadership of the established English church fell to Bishop John Aylmer. Grindal’s friends on the Queen’s Privy Council, “forward” Calvinists (or ultra-Protestants), were powerless to save him from the consequences of his indiscretion, which damaged the chances of success of the ultras’ other initiatives. This chapter concerns one of those initiatives: from the late 1560s, they urged their Queen “actively” to intervene in the Dutch wars. They collaborated with Calvinists on the Continent, who befriended Prince William of Orange and who hoped to help him hold together a coalition of religiously reformed and Roman Catholic insurgents in the 17 provinces of the Low Countries. The English ultra-Protestants would have their government send money, munitions, and men in arms to the Netherlands, to tip the balance against viceroys sent by King Philip II of Spain. Grindal’s set-back undermined the English Calvinists’ efforts to form an Anglo-Dutch alliance that, they assumed, would boost the prospects for an international Protestant league.1 Yet Elizabeth did assist the Dutch as they wrestled with decisions forced on them by developments in the Netherlands during the 1570s, and she did so more consistently and more cleverly than many historians of Tudor diplomacy have thought.
Comprehensive study of initial diameter effects and other observations on convection-free droplet combustion in the standard atmosphere for n-heptane, n-octane, and n-decane☆

Abstract This paper reports the results of a comprehensive experimental study on the effect of initial droplet diameter ( D o ) over a very wide range (0.5 mm D o n -heptane, n -octane and n -decane – that are representative of components found in petroleum-based transportation fuels and their surrogates. Spherical symmetry in the burning process was promoted by carrying out the experiments in a reduced convection (stagnant ambience) and buoyancy (low gravity) environment using the facilities of a ground-based drop tower for D o D o > 1.0 mm. The results show that for D o greater than about 2 mm, K decreases with increasing D o in an early period of burning and with the data being correlated in the form K ∼ D o − n based on a scale analysis of an energy balance on the flame. For D o larger than approximately 2 mm the droplet flames often disappeared indicating an extinction mechanism that was speculated to be due to radiative losses from the flame. Concurrently, measurements of wideband radiation dropped significantly and the burning rate gradually approached pure evaporation. In some instances for n -heptane and n -octane radiative extinction was accompanied by droplet evaporation rates that were significantly higher than evaporation in a hot ambience which persisted for a significant fraction of the burning history before decreasing to evaporation in a cold ambience. An energy balance on the drop related the flame temperature to droplet diameter from which it was predicted that flame temperatures after ignition were greater than 1200 K before dropping to under approximately 800 K and remaining constant thereafter until eventually reaching near ambient conditions. This intermediate regime of burning was conjectured to be associated with a low temperature combustion process. The transition to this intermediate regime upon radiative extinction was occasionally accompanied by flame oscillations, the origin of which was uncertain but could have been initiated by motion of the droplet owing to the deployment process.
Preforms in Folsom lithic technology: a view from Blackwater Draw, New Mexico

Conservation of lithic raw materials, multifunctional stone tools, tool curation, and technological efficiency are concepts used in contemporary examinations of Folsom. Along with traditional analy...
Classroom Nutrition Education Combined With Fruit and Vegetable Taste Testing Improves Children's Dietary Intake.

BACKGROUND We tested the effectiveness of the Go Wild With Fruits and Veggies! (GWWFV) Extension curriculum on increasing fruit and vegetable (FV) intake of third graders. METHODS An intervention study was used testing self-reported FV intake pre/post GWWFV. Recruited schools were randomized to control (12 schools, N = 369, third grade children) or intervention (14 schools, N = 378, third grade children). Measures included items from a validated FV food frequency survey. Access to the federal Fresh Fruit and Vegetable Snack Program (FFVSP), and taste testing within GWWFV were also measured. Between-group differences in FV intake were evaluated using 1-way ANOVA for unadjusted models and 1-way ANCOVA for baseline adjusted models. The Tukey-Kramer test was employed for post hoc comparisons. RESULTS Students with access to the FFVSP consumed more fruits (p < .01) and vegetables (p < .0001). Students who participated in the FFVSP and GWWFV with taste testing consumed more fruits and vegetables (p < .05) compared with students who participated in the FFVSP and GWWFV without taste testing, along with the control group. CONCLUSIONS The FFVSP and GWWFV with taste testing demonstrated a positive influence on FV intake in third grade children. Leveraging environmental approaches with interactive learning experiences create desired outcomes.
Inhibition of Wnt Signaling Pathways Impairs Chlamydia trachomatis Infection in Endometrial Epithelial Cells

Chlamydia trachomatis infections represent the predominant cause of bacterial sexually transmitted infections. As an obligate intracellular bacterium, C. trachomatis is dependent on the host cell for survival, propagation, and transmission. Thus, factors that affect the host cell, including nutrition, cell cycle, and environmental signals, have the potential to impact chlamydial development. Previous studies have demonstrated that activation of Wnt/β-catenin signaling benefits C. trachomatis infections in fallopian tube epithelia. In cervical epithelial cells chlamydiae sequester β-catenin within the inclusion. These data indicate that chlamydiae interact with the Wnt signaling pathway in both the upper and lower female genital tract (FGT). However, hormonal activation of canonical and non-canonical Wnt signaling pathways is an essential component of cyclic remodeling in another prominent area of the FGT, the endometrium. Given this information, we hypothesized that Wnt signaling would impact chlamydial infection in endometrial epithelial cells. To investigate this hypothesis, we analyzed the effect of Wnt inhibition on chlamydial inclusion development and elementary body (EB) production in two endometrial cell lines, Ishikawa (IK) and Hec-1B, in nonpolarized cell culture and in a polarized endometrial epithelial (IK)/stromal (SHT-290) cell co-culture model. Inhibition of Wnt by the small molecule inhibitor (IWP2) significantly decreased inclusion size in IK and IK/SHT-290 cultures (p < 0.005) and chlamydial infectivity (p ≤ 0.01) in both IK and Hec-1B cells. Confocal and electron microscopy analysis of chlamydial inclusions revealed that Wnt inhibition caused chlamydiae to become aberrant in morphology. EB formation was also impaired in IK, Hec-1B and IK/SHT-290 cultures regardless of whether Wnt inhibition occurred throughout, in the middle (24 hpi) or late (36 hpi) during the development cycle. Overall, these data lead us to conclude that Wnt signaling in the endometrium is a key host pathway for the proper development of C. trachomatis.
Detecting the scales at which birds respond to structure in urban landscapes

Little empirical information exists about how birds respond to urban landscape structure across multiple scales. We explored how the variation in percent tree canopy cover, at four different scales, affected the abundance of bird species across various urban sites in North America. Bird counts were derived from previous studies, and tree patches were measured from aerial photographs that represented areas of 0.2 km2, 1.5 km2, 25.0 km2, and 85.0 km2. At each of the four areas, we conducted regressions between bird counts and percent cover of various tree patch sizes. From these analyses, we determined the area (called the best prediction area—BPA) and the patch size (called the best patch size—BPS) that accounted for a significant amount of the variation in bird counts, beyond the variation accounted for by these parameters measured at other scales. BPA and BPS were calculated primarily to take into account the high degree of collinearity that existed among the amount of tree canopy cover measured across the four scales.
Case study: patient-derived clear cell adenocarcinoma xenograft model longitudinally predicts treatment response

There has been little progress in the use of patient-derived xenografts (PDX) to guide individual therapeutic strategies. In part, this can be attributed to the operational challenges of effecting successful engraftment and testing multiple candidate drugs in a clinically workable timeframe. It also remains unclear whether the ancestral tumor will evolve along similar evolutionary trajectories in its human and rodent hosts in response to similar selective pressures (i.e., drugs). Herein, we combine a metastatic clear cell adenocarcinoma PDX with a timely 3 mouse x 1 drug experimental design, followed by a co-clinical trial to longitudinally guide a patient's care. Using this approach, we accurately predict response to first- and second-line therapies in so far as tumor response in mice correlated with the patient's clinical response to first-line therapy (gemcitabine/nivolumab), development of resistance and response to second-line therapy (paclitaxel/neratinib) before these events were observed in the patient. Treatment resistance to first-line therapy in the PDX is coincident with biologically relevant changes in gene and gene set expression, including upregulation of phase I/II drug metabolism (CYP2C18, UGT2A, and ATP2A1) and DNA interstrand cross-link repair (i.e., XPA, FANCE, FANCG, and FANCL) genes. A total of 5.3% of our engrafted PDX collection is established within 2 weeks of implantation, suggesting our experimental designs can be broadened to other cancers. These findings could have significant implications for PDX-based avatars of aggressive human cancers.
Theory of Workarounds

Although mentioned frequently in the organization, management, public administration, and technology literatures, workarounds are understudied and undertheorized. This article provides an integrated theory of workarounds that describes how and why workarounds are created. The theory covers most types of workarounds and most situations in which workarounds occur in operational systems. This theory is based on a broad but useful definition of workaround that clarifies the preconditions for the occurrence of a workaround. The literature review is organized around a diagram that combines the five “voices” in the literature of workarounds. That diagram is modeled after the diagram summarizing Orton and Weick’s [1990] loose coupling theory, which identified and combined five similar voices in the literature about loose coupling. Building on that basis, the theory of workarounds is a process theory driven by the interaction of key factors that determine whether possible workarounds are considered and how they are executed. This theory is useful for classifying workarounds and analyzing how they occur, for understanding compliance and noncompliance to methods and management mandates, for incorporating consideration of possible workarounds into systems analysis and design, and for studying how workarounds and other adaptations sometimes lead to larger planned changes in systems.
What makes a good scientific question?: supporting independent student-driven inquiry

Students rarely have the opportunity to pose scientific questions or participate in research design. In this study, we identify the criteria that scientists used to guide a group of seven undergraduate students during an extended phase of project articulation. We categorize the criteria according to epistemic and social dimensions and describe the ways in which the students were able to reason with these criteria as they developed their question and research plan.
Machine Learning Aided Efficient Tools for Risk Evaluation and Operational Planning of Multiple Contingencies

In power system reliability assessment, the system security limits and adequacy indices depend on the set of contingencies analyzed. Consequently the final solution strategies for short term operational and long term investment planning studies also depend on the set of contingencies considered for planning. Generally, planning is done for the most critical contingency, with the assumption that the solution strategy for the most constraining contingency will also perform well on the contingencies that have lower severity. But this is not always true. In reality, under highly stressed and uncertain nature of power system conditions, the operational rules for the most constraining contingency may not be effective for all other contingencies. In fact some contingencies, which are generally less severe, may have more pronounced ill-effect during certain other operating conditions. Therefore, it is important to perform a comprehensive contingency analysis of many contingencies under several operating conditions (a computationally burdensome task), screen the most important ones among them that may violate the probabilistic reliability criteria, and devise effective solution strategies. Thus, the focus of this chapter is to devise a computationally efficient operational planning strategy against voltage stability phenomena for many critical contingencies. The chapter accomplishes this with the help of a hybrid approach that combines the strength of model-based analytical indicators and data driven techniques to design two important aspects of planning for multiple contingencies, namely: risk based contingency ranking and contingency grouping. Utilizing realistic probability distributions of operating conditions together with machine learning techniques makes the risk assessment process of multiple contingencies credible and computationally tractable. In order to group the contingencies efficiently for devising a common solution strategy, the chapter introduces a novel graphical index, termed as progressive entropy that captures the degree of overlap among post-contingency performances of various contingencies. The objective of the proposed contingency grouping method is to strike a balance between producing simple and accurate operational guidelines for multiple contingencies, while reducing the operational complexity in terms of the total number of guidelines that operators handle.
Empirical analysis of the general utility problem in machine learning

The overfit problem in inductive learning and the utility problem in speedup learning both describe a common behavior of machine learning methods: the eventual degradation of performance due to increasing amounts of learned knowledge. Plotting the performance of the changing knowledge during execution of a learning method (the performance response) reveals similar curves for several methods. The performance response generally indicates an increase to a single peak followed by a more gradual decrease in performance. The similarity in performance responses suggests a model relating performance to the amount of learned knowledge. This paper provides empirical evidence for the existence of a general model by plotting the performance responses of several learning programs. Formal models of the performance response are also discussed. These models can be used to control the amount of learning and avoid degradation of performance.
Breeding for oil and protein content in maize

Three newly-developed maize hybrids, Illinois 6021, Illinois 6052, and Illinois 6001 yield about 30% more oil, and 10% more protein than present commercial hybrids. In addition they are similar to standard hybrids in other agronomic traits.
Shock and awe? Fiscal consequences of terrorism

This article investigates how the frequency and severity of terrorism affect government finances in a large sample of 156 developed and developing countries over the period 1970–2016. The empirical results indicate that terrorism has a negative effect on tax revenue performance, especially in countries where terrorism has become endemic with frequent attacks and large numbers of fatalities relative to population, and that this effect becomes more pronounced in dynamic models accounting for potential endogeneity. Similarly, controlling for a plethora of economic, demographic and institutional factors, we find compelling evidence that terrorism is associated with a significant increase in military spending as a share of national income. These effects of terrorism on government operations and finance appear to be greater in countries where attacks are frequent and result in large numbers of fatalities. Our empirical findings also confirm that the state of public finances in developing countries is more vulnerable to acts of terrorism than those in countries that are richer and more diversified.
Efficient Location Sensing in Longitudinal Cohort Studies

A longitudinal cohort study is a popular research method to observe a group of people over a prolonged period of time, e.g., to learn about their health, wellness, and social habits. Smartphones have become a very popular tool to perform such studies at a large scale. Location is an essential form of sensor data that can not only be used to monitor users’ mobility and social interaction patterns, but also to identify places of personal significance, i.e., places where a user spends a significant amount of time, such as a user’s home, workplace, and preferred social gathering places. However, continuously tracking a user’s location can have significant impacts on the battery lifetime of a smartphone. Therefore, instead of frequent period location sensing, this paper identifies smartphone events that can be used to trigger location sensing at a much lower rate (and therefore more energy-efficiently), while still providing accurate location data. In this work, we demonstrate that this approach allows us to determine a user’s significant places with an accuracy of 85%, while saving over 60% in computational and energy overheads.
A Locality-Aware, Energy-Efficient Cache Design for Large-Scale Multi-Core Systems

Energy efficiency has become the first priority when designing high-performance computing systems, and caches play a key role in improving the performance. However, as caches represent a dominant proportion of the total area in a processor, they dissipate a significant amount of the total energy consumption. A non-unified data cache architecture is suggested to tackle this issue without sacrificing performance. This architecture is based on the principle of providing a smaller cache for a group of frequently used references, which does not require a large cache to provide a high hit rate. Thus, the non-unified design reduces the number of accesses to a relatively large L1 data cache, thereby saving energy and enabling efficient performance. This paper examines the energy consumption of a non-unified data cache design as compared to that of a conventional unified data cache. As a powerful system requires allocation of a significant number of cores on a single die, minimizing the L1 caches in each core helps to incorporate more cores in one chip. Therefore, we conduct experiments for different sizes of L1 data caches, ranging from quite large to small. The experimental results show that compared to a conventional L1 data cache, the non-unified design reduces data cache dynamic energy consumption, on average, by up to 22% for a small data cache (such as a 4KB cache), and by up to 82% for a relatively large (such as a 32KB) cache.
Semi-discrete Green's function for solution of anisotropic thermal/electrostatic Boussinesq and Mindlin problems: Application to two-dimensional material systems

Abstract Green's function (GF) for steady state Laplace/Poisson equation is derived for an anisotropic, finite two-dimensional (2D) composite material by solving a combined Boussinesq–Mindlin problem. A semi-discrete model of the material is developed in which only one Cartesian coordinate axis is discretized, while the other is treated as a continuous variable. The Fourier integral for the continuous coordinate is obtained analytically. Thus, a 2D problem needs only a 1D discretization. An approximate analytical estimate shows that the numerical convergence of our model is at least an order of magnitude better than fully discretized models. Numerical results are reported for the GF for a phosphorene composite containing an array of metallic inclusions. The GF is useful as a starting solution in boundary element calculations. It can be used for deriving the full solution of the Laplace/Poisson equation for an arbitrary distribution of sources and boundary values, used for modeling heat flow and electrostatic potential distribution in a 2D composite. These material systems are of strong topical interest because of their potential application in revolutionary new solid-state devices for energy conversion and quantum computing. This paper is another step towards developing GF based characterization techniques for modern 2D materials.
A Comparison of Changes in Median Nerve Cross-sectional Area Between Endoscopic and Mini-Open Carpal Tunnel Release

Purpose The purpose of this study was to determine whether there is a difference in the change in cross-sectional area (CSA) of the median nerve in patients undergoing carpal tunnel release (CTR) based on surgical technique and whether this change is associated with changes in patient-reported outcomes evaluated using the Carpal Tunnel Syndrome Assessment Questionnaire. Methods Individuals with carpal tunnel syndrome were evaluated with ultrasound and the CTSAQ before and 6 weeks after surgery. Patients were eligible for inclusion if they underwent either a mini-open CTR (MOCTR) or endoscopic CTR (ECTR). A single surgeon performed all surgeries. Changes in median nerve CSA, Carpal Tunnel Syndrome Assessment Questionnaire scores, and their associated surgical technique (MOCTR vs ECTR) were analyzed. Results A total of 77 patients were enrolled, 13 of whom were lost to follow-up, which left 64 for analysis. Of those, 42 patients underwent ECTR and 22 MOCTR. Mean age was 55 years; there were 52 women and 12 men. Mean changes in CSA for endoscopic and mini-open techniques from before to 6 weeks after surgery were –1.9 mm2 (95% confidence interval [CI], –1.1 to –2.7) and +0.6 mm2 (95% CI, –1.6 to 0.4), respectively. Mean Symptom Severity Scores improved after endoscopic and mini-open release by 1.7 (95% CI, 1.4–2.1) and 1.5 (95% CI, 1.2–1.9), respectively. Mean Functional Status Scores improved after endoscopic and mini-open release by 1.2 (95% CI, 0.9–1.9) and 0.7 (95% CI, 0.03–1.3), respectively. Conclusions Patients undergoing ECTR demonstrated decreased median nerve CSA, whereas those undergoing MOCTR demonstrated increased median nerve CSA at 6 weeks. All patients undergoing surgical intervention demonstrated improvement in both Symptom Severity Scores and Functional Status Scores after surgery. Whereas both techniques successfully improve patient outcome scores, an increase in CSA after MOCTR may be seen in the initial postoperative period, potentially contributing to a slower short-term improvement in outcome in functional scores compared with ECTR. Type of study/level of evidence Therapeutic IV.
Implementing an e-commerce curriculum in a CIS program

In this paper we describe the development of an e-commerce curriculum in the CIS program at Southern Oregon University. The e-commerce curriculum is incorporated through a set of two courses. The first is a client-server programming course that introduces the structure of the web along with client and server side scripting techniques. The second is a corporate web development course, which builds on the earlier course by introducing elements of e-commerce technology such as security and encryption, electronic payment systems, agents and XML.
Corpus Mysticum: A Response to Vanhoozer, Horton, and Allen:

This article examines Augustine’s theology of the totus Christus, outlined in the article “Totus Christus: A Proposal for Protestant Christology and Ecclesiology”, in greater detail. It refines the...
Effect of Concomitant Tricuspid Valve Surgery With Left Ventricular Assist Device Implantation.

Background Tricuspid regurgitation (TR) is common in advanced heart failure (HF) patients. However, the effect of concomitant tricuspid valve repair or replacement (tricuspid valve intervention [TVI]) with left ventricular assist device (LVAD) implantation is controversial. The aim of this study was to investigate the longitudinal trend of TR after LVAD implantation and the effect of TVI on the TR trend and clinical outcomes. Methods We retrospectively reviewed patients at our institution who underwent LVAD implantation between April 2014 and August 2018. We evaluated the grade of TR by echocardiography before and after LVAD implantation. Moderate or greater TR was defined as significant. Results Among 199 consecutive patients, 194 had at least 2 echocardiographic TR assessments before and after LVAD implantation. Of these patients, 108 were included in the TVI-positive (TVI+) group and 86 in the TVI-negative (TVI–) group. In the TVI+ group, the prevalence of significant TR decreased from 52% to about 20% in the first 6 months after implantation (P Conclusions Concomitant TVI with LVAD implantation improved TR in most patients but did not have an impact on clinical outcomes. Significant postoperative TR after LVAD implantation, in patients with and without TVI, was associated with worse HF-free outcomes.
Safety, Tolerability and Efficacy of Dietary Supplementation with Concord Grape Juice in Gulf War Veterans with Gulf War Illness: A Phase I/IIA, Randomized, Double-Blind, Placebo-Controlled Trial.

Approximately 30 percent of U.S. veterans deployed during the Gulf War (1990–1991) have been diagnosed with Gulf War Illness (GWI), a chronic multi-symptom disorder without widely available specific treatments. We investigated whether the consumption of Concord grape juice (CGJ), rich in anti-inflammatory flavonoids, would be tolerated and safe in individuals with GWI and explored improvement in cognitive function and fatigue. Thirty-six veterans with GWI enrolled in a 24-week randomized, double-blind, Phase I/IIA clinical trial to explore safety, tolerability, and feasibility of 16 ounces daily of commercially available CGJ compared to placebo. Participants completed neurocognitive tests and self-reported surveys at baseline, 12 and 24 weeks. Thirty-one participants (86%) completed the study; no dropouts were related to side effects. Thirty participants (83%) documented ≥80% adherence. There were no statistically significant unadjusted differences between CGJ and placebo groups in change in efficacy measures from baseline to endpoint. We employed general linear regression models controlling for baseline differences between groups which indicated statistically significant improvement in the Halstead Category Test–Russell Revised Version (RCAT) at endpoint in the CGJ group compared to placebo (8.4 points, p = 0.04). Other measures of cognitive functioning did not indicate significant improvements in the adjusted analyses (p-values: 0.09–0.32), nor did the fatigue variable (p = 0.67). CGJ was safe and well-tolerated by veterans with GWI. Our data suggest high tolerability and potential benefit from CGJ in veterans with GWI and can be used to inform future studies of efficacy.
Towards a stabilized Kerr optical frequency comb with spatial interference

We measured a soliton’s carrier frequency created by a silicon nitride Kerr comb from an interference pattern created by a spatial interferometer. The optical frequencies were determined from the interference pattern by simultaneously calibrating against an interference pattern from the pump optical frequency. Results were compared to real-time measurements by an optical spectrum analyzer (OSA). The spatial interferometer and the OSA results tracked each other, and the resulting RMS error is presented.
Pan-Cancer Analysis Reveals Technical Artifacts in TCGA Germline Variant Calls

Abstract The degree to which germline variation drives cancer development and shapes tumor phenotypes remains largely unexplored, possibly due to a lack of large scale publicly available germline data for a cancer cohort. Here we called germline variants on 9,618 cases from The Cancer Genome Atlas (TCGA) database representing 31 cancer types. We identified batch effects affecting loss of function (LOF) variant calls that can be traced back to differences in the way the sequence data were generated both within and across cancer types. Overall, LOF indel calls were more sensitive to technical artifacts than LOF Single Nucleotide Variant (SNV) calls. In particular, whole genome amplification of DNA prior to sequencing led to an artificially increased burden of LOF indel calls, which confounded association analyses relating germline variants to tumor type despite stringent indel filtering strategies. Due to the inherent noise we chose to remove all 614 amplified DNA samples, including all acute myeloid leukemia and virtually all ovarian cancer samples, from the final dataset. This study demonstrates how insufficient quality control can lead to false positive germline-tumor type associations and draws attention to the need to be sensitive to problems associated with a lack of uniformity in data generation in TCGA data. Author Summary Cancer research to date has largely focused on genetic aberrations specific to tumor tissue. In contrast, the degree to which germline, or inherited, variation contributes to tumorigenesis remains unclear, possibly due to a lack of accessible germline variant data. In this study we identify germline variants in 9,618 samples using raw germline exome data from The Cancer Genome Atlas (TCGA). There are substantial differences in the way exome sequence data was generated both across and within cancer types in TCGA. We observe that differences in sequence data generation introduced batch effects, or variation that is due to technical factors not true biological variation, in our variant data. Most notably, we observe that amplification of DNA prior to sequencing resulted in an excess of predicted damaging indel variants. We show how these batch effects can confound germline association analyses if not properly addressed. Our study highlights the difficulties of working with large public genomic datasets like TCGA where samples are collected over time and across data centers, and particularly cautions the use of amplified DNA samples for genetic association analyses.
Detection and Classification of Defects in Organic Photovoltaic Devices Using Thermoreflectance Imaging

Thermoreflectance imaging is a high resolution, non-contact thermal imaging technique, which can be used to identify and characterize different types of defects in organic solar cells.
Introduction to our Special Issue on Salted Paper Prints

It is fitting that our first photography special issue focuses on one of the first photographic processes: the salted paper print. Announced in 1839 by British polymath William Henry Fox Talbot (18...
Treatment Delay in Melanoma: A Risk Factor Analysis of an Impending Crisis

Risk factors associated with melanoma treatment delay (MTD) have been inadequately studied. To elucidate MTD associations based on patient and tumor characteristics, a retrospective cohort study was performed for cutaneous melanoma cases reported to the National Cancer Database (NCDB) between 2004 and 2015. We evaluated the number of days from diagnosis to treatment initiation, analyzing postponements more than 45 days as moderate MTD (mMTD) and postponements more than 90 days as severe MTD (sMTD). Greater MTD rates were independently associated with patients who are older than 50 years, female, nonwhite, not privately insured, and treated at an academic facility and who have more advanced tumor stage and head/neck primaries.
Does Ontology Matter

In this paper, I argue that various disputes in ontology have important ramifications and so are worth taking seriously. I employ a criterion according to which whether a dispute matters depends on how integrated it is with the rest of our theoretical projects. Disputes that arise from previous tensions in our theorizing and have additional implications for other issues matter, while insular disputes do not. I apply this criterion in arguing that certain ontological disputes matter; specifically, the disputes over concrete possible worlds and coincident material objects. Finally, I consider how one could show that some ontological disputes do not matter, using a Platonism/nominalism dispute as an example.
Rethinking the Role of the Dormant Commerce Clause in State Tax Jurisdiction

Perhaps the biggest controversy in state and local taxation today concerns the constitutional authority of the states to impose taxes on goods purchased over the Internet. Some argue that the current, bright-line rule of "physical presence" is the appropriate standard for determining a state's jurisdiction under the dormant Commerce Clause. Others contend that jurisdiction should instead be resolved on the more pragmatic basis of a firm's "economic presence" in the taxing state. Regardless, commentators seem to agree that the dormant Commerce Clause imposes jurisdictional limits on state taxation; the dispute concerns the content of those standards. This article contends that the debate thus far has ignored a more fundamental question: whether the Commerce Clause even speaks to the question of state tax jurisdiction. My thesis is that the attribution of a nexus requirement to the dormant Commerce Clause is, at least in part, analytically confused, and that it is premised on some questionable empirical assumptions.