cssi/SciSciGPT-SciSciNet huggingface dataset:
PLUMED-GUI: An environment for the interactive development of molecular dynamics analysis and biasing scripts

Abstract PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED’s rich syntax to define collective variables (CVs) and VMD’s chemically-aware atom selection language, while working within a natural point-and-click interface. Pre-defined templates and syntax mnemonics facilitate the definition of well-known reaction coordinates. Complex CVs, e.g. involving reference snapshots used for RMSD or native contacts calculations, can be built through dialogs that provide a synoptic view of the available options. Scripts can be either exported for use in simulation programs, or evaluated on the currently loaded molecular trajectories. Script development takes place without leaving VMD, thus enabling an incremental try–see–modify development model for molecular metrics. Program summary Program title: PLUMED-GUI (Collective variable analysis plugin) Catalogue identifier: AERU_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERU_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: 3-clause BSD Open Source No. of lines in distributed program, including test data, etc.: 2651 No. of bytes in distributed program, including test data, etc.: 32359 Distribution format: tar.gz Programming language: TCL/TK. Computer: Workstations, PCs. Operating system: Linux/Unix, OSX, Windows. RAM: Sufficient to run PLUMED [1] and VMD [2]. Classification: 3, 23. Subprograms used: Cat Id Title Reference AEEE_v2_0 PLUMED CPC 185 (2014) 604 Nature of problem: Compute and visualize values of collective variables on molecular dynamics trajectories from within VMD, and interactively develop biasing scripts for the estimation of free-energy surfaces in PLUMED. Solution method: A graphical user interface is integrated in VMD and allows the user to interactively develop and run analysis scripts. Menus and dialogs provide mnemonics and documentation on the syntax to define complex CVs. Restrictions: Tested on systems up to 100,000 atoms. Unusual features: VMD–PLUMED is not a standalone program but a plugin that provides access to PLUMED’s analysis features from within VMD. Additional comments: Distributed with VMD since version 1.9.0. Manual update may be required to access the latest features. Running time: Computations of the values of collective variables, performed by the underlying PLUMED code, depends on the size of the system and the length of the trajectory; it is generally negligible with respect to simulation time. References: [1] G. A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni, G. Bussi, PLUMED 2: New feathers for an old bird, Computer Physics Communications 185 (2014) 604. [2] W. Humphrey, A. Dalke, K. Schulten, VMD: visual molecular dynamics, J Mol Graph 14 (1996) 33–38.
Association between dietary glycemic index and age-related macular degeneration in nondiabetic participants in the Age-Related Eye Disease Study.

Background: Age-related macular degeneration (AMD) is the major cause of irreversible blindness. AMD appears to share several carbohydrate-related mechanisms and risk factors with diabetes-related diseases, including retinopathy and cardiovascular disease (CVD); however, to date, only one small study has addressed this issue. Objective: The objective was to test the hypothesis that dietary glycemic index (dGI), which has been related to the risk of diabetes and CVD, is associated with the risk and severity of AMD in nondiabetic elderly populations. Design: Dietary information was obtained from 4099 participants aged 55-80 y (56% women) in the Age-Related Eye Disease Study (AREDS). A total of 8125 eligible eyes at baseline were classified into 1 of 5 AMD groups according to the size and extent of drusen, the presence of geographic atrophy, and neovascular changes. We used a generalized estimating approach to evaluate the relations between dGI and risk and severity of AMD with eyes as the unit of analysis. Results: Compared with eyes in the first quintile of dGI, eyes in the fourth and fifth quintiles had a significantly or suggestively higher risk of large drusen, geographic atrophy, and neovascularization. The multivariate-adjusted odds ratios (95% CIs) for the highest quintile were 1.42 (1.09, 1.84), 1.78 (0.81, 3.90), and 1.41 (0.95, 2.08), respectively, of which only the odds ratio for large drusen was significant. A significant positive relation between dGI and severity of AMD was also noted (P for trend < 0.001). There was a 49% increase in the risk of advanced AMD (geographic atrophy plus neovascularization) for persons with a dGI higher than the sex median (women: ≥77.9; men: ≥79.3). This result indicated that 20% of prevalent cases of AMD would have been eliminated if the AREDS participants consumed diets with a dGI below the median. Conclusion: The association between dGI and AMD from the AREDS cross-sectional analysis at baseline suggests that a reduction in the dGI, a modifiable risk factor, may provide a means of diminishing the risk of AMD.
Cancer: The Big Questions to Address in Coming Years

Read the anniversary editorial by Editor-in-Chief Timothy R. Rebbeck, [p. 567][1] Molecular epidemiology was introduced in the study of cancer in the early 1980s, with the expectation that it would help overcome some important limitations of epidemiology and facilitate cancer prevention ([1, 2][2
Dysbiosis in Pouchitis: Evidence of Unique Microfloral Patterns in Pouch Inflammation

Background & Aims: Pouch inflammation after surgery for ulcerative colitis can significantly alter quality of life and thus ideally should be prevented. Dysbiosis or altered microflora is suspected to be the key pathogenic factor for pouchitis. However, dysbiosis in pouchitis has not been characterized carefully because of a lack of available sensitive microbiological technology suitable for in vivo studies in human beings. Thus, the aims of our study were as follows: (1) to show the use of the length heterogeneity polymerase chain reaction (LH-PCR) technique for studying microflora in human beings, and (2) to use the technique to characterize the microfloral patterns in the ileal pouch of patients with pouchitis. Methods: Microfloral patterns initially were assessed using a 16S ribosomal RNA technique (LH–PCR) to determine the qualitative changes in the luminal and mucosal intestinal flora. We subsequently cloned and sequenced the LH-PCR amplification products from the community 16S ribosomal RNA found in patients with pouchitis and in control pouch to identify the microbial species involved in pouchitis. Results: We have shown unique microfloral patterns in pouchitis. Through cloning and sequencing of the LH-PCR amplicons, we have shown the persistence of Fusobacter and Enteric species associated with the disease state and the absence of specific bacteria such as Streptococcus species in the inflamed pouch. Conclusions: We have shown that the LH-PCR technique is suitable for studying microflora in human beings. By using this technique and the clone sequences, we have shown dysbiosis in the microbial biofilm adherent to the mucosa in pouchitis. Our data provide direct evidence of the role of bacteria in the pathogenesis of pouchitis.
High Efficiency Energy Storage System Design for Hybrid Electric Vehicle with Motor Drive Integration

This paper proposes a new energy storage system (ESS) design including both batteries and ultracapacitors (UC) in hybrid electric vehicle (HEV) and electric vehicle (EV) applications. The conventional designs require a dc-dc converter to interface the UC unit. Herein, the UC can be directly switched across the motor drive dc-link during the peak power demands. The resulting wide voltage variation due to UC power transfer is addressed by the simple modulator introduced in this paper, so that the motor drive performance is not disrupted. Based on this new methodology, the paper further introduces two ESS schemes with different topologies, UC rating and energy flow control. They are applicable to both lightly and heavily hybridized HEVs. Both schemes have the benefits of high efficiency (without a dc-dc link) and low cost. The simulation and experimental results validate the new methodology.
Some dynamical consequences of partial melting in Earth’s deep mantle

We use regional scale numerical models of mantle convection to investigate the simple hypothesis that seismically anomalous thin patches of Earth’s lowermost mantle, termed “ultralow-velocity zones” or ULVZ, are derived from partial melting of ordinary mantle. The models span the lower 500 km of Earth’s mantle, employ both temperature and melting-related contributions to buoyancy, and include a cold randomly moving downwelling introduced from above to maintain a thermal boundary layer. Partial melting of ordinary mantle introduces a ubiquitous partially molten layer above an isothermal core–mantle boundary as a consequence of its isothermal and isobaric conditions, although it naturally develops variations in thickness greater than two orders of magnitude, with the thickest portions occurring at the base of upwelling plumes and a thin layer elsewhere. We find that only a dense partially molten mixture produces partial melt distributions that are compatible with seismic observations of ULVZ; however, if such a melt percolates downward a dense basal liquid layer accumulates above the core–mantle boundary. The apparent requirement of a volumetrically dense and non-percolating melt phase in the lowermost mantle presents serious problems for the hypothesis that ULVZ arise from melting of ordinary mantle, and suggests that such features likely form as a consequence of more complex processes. Furthermore, these considerations suggest that the solidus of ordinary mantle is a reasonable upper bound on the present day temperature of the CMB. © 2007 Published by Elsevier B.V.
Maternal carbohydrate intake and pregnancy outcome.

Experimental evidence indicates that the primary maternal environmental factor that regulates feto-placental growth is substrate delivery to the placental site, which is the product of maternal substrate levels and the rate of placental-bed blood flow. Thus, maternal factors which change either substrate level or flow alter feto-placental growth rate. The best-studied substrate in human pregnancy is glucose, and there is a direct relationship between maternal blood glucose levels and size at birth. Altering the type of carbohydrate eaten (high- v. low-glycaemic sources) changes postprandial glucose and insulin responses in both pregnant and non-pregnant women, and a consistent change in the type of carbohydrate eaten during pregnancy influences both the rate of feto-placental growth and maternal weight gain. Eating primarily high-glycaemic carbohydrate results in feto-placental overgrowth and excessive maternal weight gain, while intake of low-glycaemic carbohydrate produces infants with birth weights between the 25th and the 50th percentile and normal maternal weight gain. The calculated difference in energy retention with similar total energy intakes is of the order of 80,000 kJ. Preliminary information from subsequent metabolic studies indicates that the mechanisms involved include changes in: daily digestible energy requirements (i.e. metabolic efficiency), substrate utilization (glucose oxidation v. lipid oxidation), and insulin resistance and sensitivity. Thus, altering the source of maternal dietary carbohydrate may prove to be a valuable tool in the management of pregnancies at risk for anomalous feto-placental growth and for the prevention and/or treatment of obesity and insulin resistance in the non-pregnant state.
Input power factor compensation for PWM-CSC based high-power synchronous motor drives

An input power factor compensation scheme is proposed in this paper for pulse width modulated (PWM) current source converter (CSC) based medium-voltage high-power synchronous motor drives. At high-power levels, the device switching frequency in a PWM-CSC is normally limited to a few hundred hertz. This imposes limitations on the applicable PWM switching schemes and system control schemes. The proposed method can achieve full-range unity power factor control while operating at low switching frequency by combining inverter modulation index control and motor magnetizing current regulation. The modulation index control together with space vector modulation scheme is used in the low-speed range; at high speeds or whenever the converter runs out of modulation index adjustment, the magnetizing current control is enabled. Experimental results obtained from a 480V/42hp drive system verify the proposed scheme.
Gender Differences in the Fagerström Test for Nicotine Dependence in Korean Americans.

INTRODUCTION: This study was conducted to compare gender differences in the psychometric properties of the Fagerstrom Test for Nicotine Dependence (FTND). METHODS: The sample comprised 334 Korean immigrants (97 women and 237 men) who reported daily smoking for the past six months. Item-by-item responses and exploratory factor analyses (EFA) were compared by gender. Promax rotation was selected based on findings from previous studies suggesting correlated factors. RESULTS: Compared with men, women smoked fewer cigarettes per day, were more likely to smoke when ill in bed, and were less likely to smoke frequently in the morning. The entire sample and men within the sample had the same factor loading pattern, where three items (time to first cigarette, the cigarette most hate to give up, and smoke more frequently in the morning) were loaded on Factor 1 (morning smoking) and the remaining three items (difficult to refrain from smoking in public places, number of cigarettes smoked per day, and smoking even when ill in bed) on Factor 2 (daytime smoking). For women, however, neither the 1- nor 2-factor model fit the data well. CONCLUSIONS: For Korean American male smokers, the psychometric properties of the FTND were similar to those seen in other populations, but this was not the case with Korean American women. Clinicians may need to modify their interpretation of nicotine dependence severity if basing only on the FTND with Korean Women. The FTND assesses smoking patterns which has a cultural influence and other measures of nicotine dependence should be considered.
Mesh Optimization for Monte Carlo-Based Optical Tomography

Mesh-based Monte Carlo techniques for optical imaging allow for accurate modeling of light propagation in complex biological tissues. Recently, they have been developed within an efficient computational framework to be used as a forward model in optical tomography. However, commonly employed adaptive mesh discretization techniques have not yet been implemented for Monte Carlo based tomography. Herein, we propose a methodology to optimize the mesh discretization and analytically rescale the associated Jacobian based on the characteristics of the forward model. We demonstrate that this method maintains the accuracy of the forward model even in the case of temporal data sets while allowing for significant coarsening or refinement of the mesh.
Managed Care and Mental Health: Clinical Perspectives and Legal Realities

Managed care is beginning to dominate the delivery of mental health services. The Article reviews limitations on managed care's ability to deal adequately with mental illness. It discusses empirical and other research examining the use of primary care providers as gatekeepers and it explores utilization review mechanisms, focusing particularly on providers' responses to UR. The impact on quality, access and continuity of care on discrete populations is analyzed. The article then surveys a variety of legal issues in the regulation of managed care, particularly as they apply to the provision of mental health services. These include ERISA, parity and liability questions. The emerging role of accreditation in also reviewed. The essential thesis is that the presence of obvious irrationalities in the delivery of quality mental health services suggests that we are in a transitional era. Legislative, judicial and private initiatives are likely to place significantly greater emphasis in the future on issues of quality control.
Stranger Danger, Cell Phones, Traffic, and Active Travel to and from Schools: Perceptions of Parents and Children

This paper summarizes one-on-one interviews with parents and their middle school children to identify similarities and differences in parents' and children's perceptions of the environment that surrounds travel to and from school, how these perceptions form, and how they influence travel mode choice to and from school. Forty-eight interviews were conducted with parent-child pairs in three New Jersey communities. In particular, the interviews examined active travel modes, such as walking and bicycling, to and from school. Direct communication with parents and students allowed for a thick description of perspectives and concerns. Analysis of qualitative data showed differences in adult versus child perceptions and the emergence of several themes related to the environment and children's capacity for independence. Themes included differences in comfort with solo travel, which depended on time of day, parental concern with abductions and sexual offenders, common use of cell phones and GPS technology to address safety fears, and perceptions with respect to the safety of travel modes on the basis of gender. Implications for practice included the support of opportunities for children to walk in groups, such as the designation of meet-up locations, where students could gather without parental accompaniment, and the encouragement of Walk to School and Walk from School days to help parents and students become comfortable with walking trips. To help children attain the benefits of active travel, schools and communities also could provide skills-based education on personal safety and could identify safe areas, where students could go if problems arose. Language: en
Abstract C65: Loss of imprinting of KCNK9 in African American women with triple-negative breast cancer

Background: It has been long suspected that prenatal nutrition and environmental toxins play a role in promoting breast cancer. Genomic imprinting is an inherited form of parent-of-origin-specific epigenetic gene regulation that is dysregulated by poor prenatal nutrition and environmental toxins. Recent studies show that exposure to the environmental plastic bis-phenol A and vitamin D deficiencies promote loss of normal imprinting. African American (AA) women are known to have vitamin D deficiency at a significantly higher frequency than women of Northern European descent. Here we investigated a mechanism that may explain the higher rate of aggressive triple-negative breast cancers (TNBC) in AA women. Methods and Results: KCNK9 encodes TASK3, a pH-regulated potassium channel membrane protein that is overexpressed in 40% of breast cancer. Our studies have identified a differentially methylated region (DMR) for KCNK9 and shown monoallelic expression of KCNK9 in breast tissue. Using patient samples, we show loss of imprinted expression in tumor cells, loss of KCNK9 regulatory methylation in 75% of TNBC samples, and loss of methylation in non-cancerous tissue from high-risk AA women. In live TNBC cells and non-cancerous mammary epithelial cells from high-risk women, loss of KCNK9 DMR methylation correlates with increased mitochondrial membrane potential. Significance: This is the first identification of the KCNK9 DMR and demonstration that loss of methylation and overexpression of TASK3 increases mitochondrial membrane potential and promotes apoptosis resistance. These novel findings regarding KCNK9 loss of methylation and its disruption in a subset of tumors may lead to new approaches in diagnosis and targeted therapy of breast cancer. Citation Format: Shraddha Desai, David Skaar, Eric Dietze, Adrian Ambrose, Randy Jirtle, Victoria Seewaldt. Loss of imprinting of KCNK9 in African American women with triple-negative breast cancer. [abstract]. In: Proceedings of the Sixth AACR Conference: The Science of Cancer Health Disparities; Dec 6–9, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2014;23(11 Suppl):Abstract nr C65. doi:10.1158/1538-7755.DISP13-C65
Inland Desalination and Brine Management: Salt Recovery and Beneficial Uses of Brine

Concentrate stream control is of the most prevalent problems with brackish water desalination. Aside from a few communities located next to the ocean, the rest of country does not have direct access to the ocean for disposal of the concentrate stream. Thus conventional methods for concentrate management of inland water desalination are commonly designed to dispose of the concentrate. However recent research has shown that it is possible to precipitate and recover metals and nutrients (salts) from concentrate using chemical and biological processes. The recovery of salts could provide a substantial increase in revenue, offsetting the cost of inland desalination, ideal for small developing communities. This paper focuses on developing a suggested protocol for addressing the issue of salt recovery from concentrate stream for inland desalination and find appropriate uses through the application of emerging technologies.
Selected Socioeconomic and Demographic Characteristics Associated with Purchasing Involvement

This research develops a Likert-type scale to measure final consumers' involvement with the purchasing activity. The scale is employed to test hypotheses concerning relationships between market cha...
Abstract ED05-03: Social media use, communication inequalities, and public health: Where we are and where we need to go

Social media are emerging as an important platform for communication and health information exchange. Yet, despite the increase in popularity and use, only a limited number of empirical studies document which segments of the adult population are and are not using social media and with what, if any, affect on health. Preliminary studies highlight that while there are still significant inequalities by race and socioeconomic status in Internet access, once access is gained, use of social media such as social networking sites is equally prolific across socio-demographic groups. This ubiquity of use presents both significant opportunities and challenges for cancer communication efforts. With the new communication channel emerges a real need for refined measurement that adequately reflects the innate dynamism of the platform and a nuanced understanding of the links between computer/technology-mediated communication and health across populations to ensure that existing digital divides and health disparities are not exacerbated but rather narrowed. Citation Information: Cancer Prev Res 2011;4(10 Suppl):ED05-03.
Defects in Quasi-One Dimensional Oxide Conductors: K0.3MoO3

The electronic structure of the prototypical quasi-one dimensional (1D) conductor K03MoO3 has been studied using high resolution photoemission spectroscopy. In particular, the electronic structure of defects was investigated in order to understand the mechanism for charge density wave pinning and destruction of the Peierls transition. Defects were found to radically alter the electronic structure close to the Fermi level (EF), thus strongly modifying the structure of the Fermi surface. While a low emission intensity at EF has been interpreted as evidence for a Luttinger liquid ground state in a ID metal, we show that non-stoichiometric surfaces lead to similar effects. The nature of the ground state is discussed in the context of these results.
POPULATION STUDIES IN PREDOMINANTLY SELF‐POLLINATED SPECIES. II. ANALYSIS OF QUANTITATIVE GENETIC CHANGES IN A BULK‐HYBRID POPULATION OF BARLEY

Populations of predominantly self-fertilized species are generally considered to be highly uniform and to lack the genetic flexibility necessary to respond to long-term changes in environment. Yet a large proportion of flowering plants practice mixed selfing and outcrossing, and among these species many are both highly successful and versatile. Apparently, therefore, adopting self-fertilization need not place undue restrictions on the genetic system and some evidence is available that populations of inbreeders are not as uniform as has often been imagined. This is perhaps because selfing is rarely if ever complete and when regular or sporadic failures of the selfing mechanism occur, gene exchange can take place among members of the different partially isolated families that constitute the population. In fact, a theoretical case can be made that the mating system of mixed selfing and random outcrossing is only one of many possible variants of the model described by Wright (1931 and later) as optimum for evolution, namely, division of the population into a series of sub-groups among which isolation and intercommunication are kept in proper balance. It is only recently that detailed studies of variability have been undertaken in populations of self-pollinated species and that experimental evidence has been presented on selection and sub-speciation, reproductive method and colonization, and other aspects of evolution in these species (reviews in Stebbins 1950, 1957; Baker 1953, 1959; Grant 1958; Morley 1959). Theoretical work (Hayman 1953; Reeve
Late Devonian (Famennian) rugose coral fauna of the Percha Shale of southwestern New Mexico

Solitary rugose corals (Cnidaria, Rugosa) are common to abundant in the calcareous Box Member of the late Famennian Percha Shale (Lower expansa Zone) of southwestern New Mexico; the Box is best developed in the western part of the Percha outcrop belt. The corals include a number of forms characteristic of Strunian faunas throughout the world. Recognized here are Gorizdronia sp. cf. G. tenuis Rozkowska, Campophyllum? ursinum n. sp., Caninia cooperi n. sp., Siphonophyllia? folia n. sp., S.? corbicula n. sp., “Bothrophyllum” argenteum n. sp., “B.” argenteum argenteum n. subsp., “B.” argenteum bilateralis n. subsp., “B.” argenteum dibunophylloides n. subsp., Arachnolasmella elytra n. sp., and Cyathoclisia sp. A. This fauna is clearly ancestral to Carboniferous genera and species. Percha species, where represented by large populations, are seen to be remarkably variable, especially in axial structure.
Effects of Irrigation and Fertilization on the Growth and Root Environment of Hybrid Rice

A field experiment was conducted to investigate the effects of irrigation and fertilization on the growth and root environment of hybrid rice.The results showed: The yield of rice grain was increased by 10.5%~11.3% under aerobic irrigation than under flooding irrigation,relying on more grain number per panicle mainly.Aerobic irrigation promoted dry matter and LAI at every growth stage as compared with traditional irrigation under different management of N Fertilizer.Both Eh and actinomyces of the soil under aerobic irrigation were more than aerobic irrigation.Organic fertilizer decreases Eh value and increases actinomyces of the soil.Under aerobic irrigation and input of the same N rate,the actinomyces of the soil in organic fertilizer plots were more than in chemical fertilizer plots.
Epidemiological characteristics of Age Distribution of Measles Incidence in Baoding City During 2005-2009

[Objective]To analyze the epidemiological characteristics of age distribution of measles incidence in Baoding City during 2005-2009,and provide scientific evidence for specific strategies and measures of measles elimination..[Methods]Descriptive epidemiology was adopted to analyze the constituent ratio of age and age incidence of measles cases.[Results]The constituent ratio of measles cases during 2005-2007 and 2009-2009∶ for 8 months age group,that was 12.67% and 15.60%,respectively;for ≤2 years age group,that was 40.3% and 58.01%,respectively,showing upward tendency;for 3～7 years age group,that was 14.3% and 12.3%,respectively,showing downward tendency;patients ≥15 years occupied 36.71% and 26.40% of total cases.The measles incidences among each age group between 0～8 years old during 2005-2009 were all above 11.37/100 000,the peak appeared in ≤1 year age group.[Conclusion]Most of measles cases were found among children,especially among children ≤2 years old.The constituent ratio of measles cases of 8 month increased annually,and measles cases ≥15 years occupies higher proportion.It is suggested to improve the coverage rates of 2 doses and timely coverage rate of measles vaccine among infants aged 8 months,to conduct measles supplementary immunization activities(SIAs) at suit time,and strengthen adult measles surveillance and the population immunity level monitoring.
Dynamic Structure of Neural Variability in the Cortical Representation of Speech Sounds.

Accurate sensory discrimination is commonly believed to require precise representations in the nervous system; however, neural stimulus responses can be highly variable, even to identical stimuli. Recent studies suggest that cortical response variability decreases during stimulus processing, but the implications of such effects on stimulus discrimination are unclear. To address this, we examined electrocorticographic cortical field potential recordings from the human nonprimary auditory cortex (superior temporal gyrus) while subjects listened to speech syllables. Compared with a prestimulus baseline, activation variability decreased upon stimulus onset, similar to findings from microelectrode recordings in animal studies. We found that this decrease was simultaneous with encoding and spatially specific for those electrodes that most strongly discriminated speech sounds. We also found that variability was predominantly reduced in a correlated subspace across electrodes. We then compared signal and variability (noise) correlations and found that noise correlations reduce more for electrodes with strong signal correlations. Furthermore, we found that this decrease in variability is strongest in the high gamma band, which correlates with firing rate response. Together, these findings indicate that the structure of single-trial response variability is shaped to enhance discriminability despite non–stimulus-related noise. SIGNIFICANCE STATEMENT Cortical responses can be highly variable to auditory speech sounds. Despite this, sensory perception can be remarkably stable. Here, we recorded from the human superior temporal gyrus, a high-order auditory cortex, and studied the changes in the cortical representation of speech stimuli across multiple repetitions. We found that neural variability is reduced upon stimulus onset across electrodes that encode speech sounds.
MITIGATION COST AND CLIMATE DAMAGE VERSUS INCENTIVE SHIFTS OF CLIMATE COALITION

Climate damage and greenhouse gas (GHG) mitigation cost plays important roles in a region’s willingness and incentives to join the global climate coalition. Negotiation of climate treaty can be modeled as a cooperative bargaining game of externality provision. The core of this game is a good representation of incentives of the participants. In this paper, we examine the relationship between the shocks of mitigation cost/climate damage and the shifts of the core of cooperative bargaining game of climate negotiation within the framework of RICE [Nordhaus and Yang, 1996. A regional dynamic general equilibrium model of alternative climate change strategies. American Economic Review, 86, 741–765], a widely used integrated assessment model (IAM) of climate change. Constructing a method that maps the core allocations onto a convex hull on the simplex of social welfare weights, we describe the scope of the core in simple metrics and capture the shifts of the core representation on the simplex in response to the shocks of mitigation cost and climate damage. A series of simulations are conducted in RICE to demonstrate the usefulness of the approach explored here. In addition, policy implications of methodological results are indicated.
A SQUID NDE Measurement Model Using BEM

As the commercial and military aircraft fleets age, additional resources are required to ensure their airworthiness. As the aircraft become older, the more likely they are to develop structural damage that may lead to unscheduled repairs or, in the worst case, accidents. Fatigue and corrosion are the two main causes of structural damage in aging aircraft and this research examines the use of a Superconducting QUantum Interference Device (SQUID) as a tool for Nondestructive Evaluation (NDE) to detect and characterize these aging aircraft problems. The primary advantage of using SQUIDs in NDE over other techniques is the ability to detect second layer cracks and corrosion commonly found in aircraft structures.
Inhibition of p38 MAPK Reduces Ionizing Radiation-Induced Hematopoietic Cell Injury.

Our previous studies demonstrated that exposure to ionizing radiation (IR) causes long-term bone marrow (BM) damage by induction cellular senescence in hematopoietic cells. The senescent hematopoietic cells exhibited an elevated activity of the senescence associated β-galactosidase (SA-β-gal), a biomaker for senescent cells, and expressed increased levels of p16 Ink4a (p16), whose expression has been implicated in the establishment and maintenance of cellular senescence. Activation of the p38 MAPK pathway has been implicated in the induction of cell cycle arrest and senescence in response to a variety of stressors in part by up-regulating the expression of p16. Therefore, in the present study we examined the role of the p38 MAPK pathway in IR-induced hematopoietic cell senescence. The results showed that exposure of male C57BL/6 mice to a sublethal dose (6.5 Gy) of total body irradiation (TBI) caused a sustained activation (>4 weeks) of p38 in Lin − c-kit + Sca-1 + (LKS + ) hematopoietic stem cells (HSCs). This activation was associated with a persistent up-regulation of p16 and quantitative and qualitative reduction of LKS + HSCs. Inhibition of p38 activity with SB202190 (a specific p38 inhibitor) attenuated IR-induced inhibition of the hematopoietic function of BM hematopoietic cells in an in vitro colony forming cell (CFC) assay. Moreover, the production of hematopoietic progenitor cells (HPCs) in SB202190-treated BM cells was 7.5 fold higher than that of irradiated cells without SB202190 treatment after five weeks of long-term BM cell culture (LTBMC); and the cells treated with SB202190 after IR retained their clonogenic function while the control irradiated cells lose their ability to form colonies. These findings suggest that p38 may play an important role in mediating IR-induced suppression of hematopoietic cell function and pharmacological inhibition of the p38 pathway may potentially be developed as novel therapeutic strategy to ameliorate IR- and chemotherapy-induced BM toxicity.
Clinical outcomes of helical conformal versus nonconformal palliative radiation therapy for axial skeletal metastases

Abstract Purpose Palliative radiation therapy (RT) for bone metastases has traditionally been delivered with conventional, nonconformal RT (NCRT). Conformal RT (CRT) is potentially more complex and expensive than NCRT, but may reduce normal tissue dose and subsequently toxicity. In this retrospective analysis, we compared CRT with NCRT to investigate the association between conformality and toxicity. Methods and materials A retrospective analysis of patients receiving palliative RT for axial skeletal bone metastases from 2012 to 2014 was conducted. Patient and treatment characteristics were obtained including dosimetric variables, acute toxicity, and subjective pain during treatment and in the acute posttreatment period (≤60 days after completion). Statistical analyses included t tests, χ 2 tests, and multivariate logistic regression. Results A total of 179 patients and 254 bone metastases were identified (142 CRT, 112 NCRT) . The CRT and NCRT groups were well matched for baseline characteristics (number of fractions, field size, treatment sites, and concurrent chemotherapy). In multivariate logistic regression models, technique (CRT vs NCRT) was not associated with development of acute toxicity. Regarding toxicity, Eastern Cooperative Oncology Group performance status and total dose were significantly associated with a higher rate of acute toxicity during RT (odds ratios, 0.649 and 1.129 and P = .027 and .044, respectively), and only a higher number of vertebral bodies in the treatment field was significantly associated with acute toxicity post-treatment (odds ratios, 1.219, P = .028). CRT was associated with improvement in bone pain during and posttreatment ( P = .049 and .045, respectively). Conclusions Our results demonstrate no difference in acute toxicity following palliative RT with CRT compared with NCRT for painful bone metastases; however, treatment volume did predict for increased toxicity. Larger studies may further elucidate the value of CRT including the impact of dose escalation for bone metastases and differences in patient reported outcomes between RT techniques.
Refining forelimb asymmetry analysis: Correlation with Montoya staircase contralateral function post-stroke.

Abstract Background Forelimb Asymmetry Test is a simple test of motor function, using exploration behavior of a rat in a novel environment and counting the number of times that a rat touches the wall with either forepaw. Our lab has noticed, however, that there appears to be an increased number of fingertip touches to the wall following a stroke in the impaired forelimb. New method We counted the number of times that the animal either laid its palm flat against the wall of the chamber or touched the wall with only its fingertips, for both the left and right forepaws. We also separated bouts of exploration, so we could clearly determine if fingertip touches normally were associated with a transition from resting state to exploration state. Results and comparison with existing methods Fishers exact test indicated that there were significant differences in the way that the animals touched the wall pre-stroke compared to post-stroke, with more fingertip touches occurring post-stroke. Counting palm touches as normal and fingertip touches as abnormal increases the sensitivity of the Forelimb Asymmetry analysis and gives a good correlation with the contralateral functional deficits determined by Montoya Staircase post-stroke. If we counted every wall touch as normal (palm touches and fingertip touches), we see a loss of sensitivity and a poor correlation with contralateral function as determined by Montoya Staircase. Conclusions This refinement of the Forelimb Asymmetry analysis improves correlation with Montoya Staircase contralateral function after stroke.
Communication and Production in Indonesian History

It is a well-known fact that the world significance of Indonesia, or the Dutch East Indies as it was formerly called, is based mainly on two factors: its geographical location and its natural resources. These factors are of vital importance today, but they have existed all along and have had a profound influence on the shaping of the Indonesian past. Naturally, their relative importance did not remain constant throughout the centuries, and it is the very interplay between these two controlling elements which helps to explain or clarify some of the actual events, crises, and changes in the history of the archipelago. In fact, a careful study of that interplay might lead to a new periodization of Indonesian history, which would serve to supplement the traditional division according to the dominant cultural influence.
Risk of Postoperative Complications in Patients with Obstructive Sleep Apnea following Skull Base Surgery.

Objectives Obstructive sleep apnea (OSA) presents several challenges in skull base surgery, including increased intracranial pressure, worsened OSA with nasal packing, and avoidance of positive airway pressure (PAP) therapy postoperatively. The objective of this study was to examine the risk of postoperative complications in a skull base population with OSA in which PAP therapy is withheld. Study Design Retrospective cohort study. Setting Tertiary care hospital. Subjects and Methods Medical records of 414 adult patients undergoing anterior skull base procedures between January 1, 2014, and January 7, 2017, were retrospectively reviewed. Revision surgeries, skull base infections, sinus surgery, and orbital cases were excluded. Results Fifty-four (13.0%) patients with a diagnosis of OSA were identified. While the known patients with OSA were more likely to require postoperative supplemental oxygen (odds ratio [OR], 4.29; 95% confidence interval [CI], 2.38-7.75; P 30 kg/m2 and hypertension) and demonstrated an increased risk of serious respiratory events (OR, 4.41; 95% CI, 1.24-15.7; P = .034) and CSF leak (13.6% vs 4.7%; P = .018). Conclusions Skull base patients with known OSA can be successfully managed with diligent care in the perioperative period when PAP therapy is withheld. However, OSA is likely underdiagnosed in the skull base population, and patients at high risk for undiagnosed OSA may be at the greatest risk for respiratory complications and CSF leak. Increased presurgical awareness and implementation of a perioperative management algorithm is needed.
Critical behavior in Ni2MnGa and Ni2Mn0.85Cu0.15Ga

The critical behaviors of polycrystalline Ni2MnGa and Ni2Mn0.85Cu0.15Ga have been examined through high-resolution bulk magnetization measurements. The critical exponents, β and γ, were derived from modified Arrott plots using the Kouvel-Fisher method. The values of the extracted critical exponents satisfied the scaling equation of state and associated exponent relations, indicating self-consistency of the extracted values. In Ni2MnGa, the critical exponents (β = 0.401 ± 0.003, γ = 1.27 ± 0.02) indicate a deviation from the 3D-Heisenberg values toward the mean-field values, likely due to the presence of long-range Ruderman-Kittel-Kasuya-Yosida interactions. However, the critical exponents of Ni2Mn0.85Cu0.15Ga (β = 0.389 ± 0.004, γ = 1.39 ± 0.02) are closer to the 3D-Heisenberg values. This indicates a weakening of the long-range exchange interactions due to the substitution of Cu in the Mn site.
Emergence of Item Response Modeling in Instrument Development and Data Analysis

In summary, readers are encouraged to read carefully the IRT articles in this special issue. They provide theoretical as well as practical arguments in favor of using IRT models in the health outcomes measurement field. At the same time, readers should be aware that the IRT field is complex and software is limited and, in my judgment, not very user friendly (although some packages are better than others). In addition, sample sizes will often need to be larger than in classical measurement, at least with the more general IRT models, and applications are rarely straightforward. Considerable practical experience is needed to ensure successful applications of IRT in the development and validation of instruments for health outcomes measurement.
Effects of Monoterpenes and Mevinolin on Murine Colon Tumor CT-26 in Vitro and its Hepatic “Metastases” in Vitro

d-Limonene is a monocyclic monoterpene which has been used for many years as a flavoring, perfuming, or degreasing agent. Recently, this product and its biologic metabolites have been highlighted for their chemotherapeutic potential in the management of certain common malignant diseases. Some of its metabolic actions interfere with certain aspects of cholesterol metabolism which are vital to the malignant cell and hopefully less critical to the normal cell. The mammalian cell has, as a major component of its plasma membrane, cholesterol which helps to maintain the integrity of the cell, and modulates the fluidity of the cellular lipid membrane. It thus serves as a major regulatory agent for chemical signals sent from other cells, transport of critical metabolites in and out of the cell, and for the membrane association of receptors, enzymes, and a wide variety of proteins which serve to regulate the intracellular processes of the cell.1
Beyond Topology: A Lagrangian Metaphor to Visualize the Structure of 3D Tensor Fields

Topology was introduced in the visualization literature some 15 years ago as a mathematical language to describe and capture the salient structures of symmetric second-order tensor fields. Yet, despite significant theoretical and algorithmic advances, this approach has failed to gain wide acceptance in visualization practice over the last decade. In fact, the very idea of a versatile visualization methodology for tensor fields that could transcend application domains has been virtually abandoned in favor of problem-specific feature definitions and visual representations. We propose to revisit the basic idea underlying topology from a different perspective. To do so, we introduce a Lagrangian metaphor that transposes to the structural analysis of eigenvector fields a perspective that is commonly used in the study of fluid flows. Indeed, one can view eigenvector fields as the local superimposition of two vector fields, from which a bidirectional flow field can be defined. This allows us to analyze the structure of a tensor field through the behavior of fictitious particles advected by this flow. Specifically, we show that the separatrices of 3D tensor field topology can in fact be captured in a fuzzy and numerically more robust setting as ridges of a trajectory coherence measure. As a result, we propose an alternative structure characterization strategy for the visual analysis of practical 3D tensor fields, which we demonstrate on several synthetic and computational datasets.
Cellular Damage and the Neuropathology of Status Epilepticus

The neuropathology of status epilepticus (SE) is well established. This chapter will review the histopathology and pathophysiology of cellular damage associated with SE based on observations from human cases and experimentally induced SE. The mechanisms of hyperexcitability leading to excitotoxic cell death will be discussed. This chapter concentrates on human generalized convulsive status epilepticus (GCSE) because it is most relevant, but the complementary nature of experimental findings from animal research will be emphasized.
Brazil's Case Against Private-Sponsored Events for Judges: A Not-Yet-Perfect Attempt at Fighting Institutional Corruption

The paper first reviews some definitions of institutional corruption. Then, it argues that there might be an example of institutional corruption based on the Brazilian legal practice: that of private sponsoring of seminars and professional events aimed at judges. This practice has been recently restricted by a regulation which limits private sponsorship to thirty percent of all expenses. The paper suggests that, legal technicalities aside, restricting private sponsoring to thirty percent of expenses might legitimize the practice, and that, given professional characteristics of judges, a complete ban on private sponsoring would be desirable.