cssi/SciSciGPT-SciSciNet huggingface dataset:
SNP Genotyping using Sequenom MassARRAY 7K Platform

Many high-throughput single-nucleotide polymorphism (SNP) genotyping technologies are currently available. The method for SNP genotyping described in this unit is based on the commercially available Sequenom MassARRAY platform which offers several attractive features for users desiring an accurate SNP genotyping assay. The assay described is based on primer extension and offers two levels of specificity. First a locus-specific PCR reaction takes place, followed by a locus-specific primer extension reaction (homogeneous Mass Extend, or hME assay) in which an oligonucleotide primer anneals immediately upstream of the polymorphic site being genotyped. The extension of the primer is according to the sequence of the variant site and can be a single complementary base or a series of complementary bases. Through the use of MALDI-TOF mass spectrometry, the mass of the extended primer is determined. The preparation of probe and genomic DNA is also described in this unit. Keywords: genotyping; SNP; MassARRAY; high-throughput; PCR
Detecting and Studying Higgs Bosons at a Photon-Photon Collider

We examine the potential for detecting and studying Higgs bosons at a photon-photon collider facility associated with a future linear collider. Our study incorporates realistic $\gam\gam$ luminosity spectra based on the most probable available laser technology. Results include detector simulations. We study the cases of: a) a SM-like Higgs boson; b) the heavy MSSM Higgs bosons; c) a Higgs boson with no $WW/ZZ$ couplings from a general two Higgs doublet model.
The ORCHESTRA Collaborative Data Sharing System

Sharing structured data today requires standardizing upon a single schema, then mapping and cleaning all of the data. This results in a single queriable mediated data instance. However, for settings in which structured data is being collaboratively authored by a large community, e.g., in the sciences, there is often a lack of consensus about how it should be represented, what is correct, and which sources are authoritative. Moreover, such data is seldom static: it is frequently updated, cleaned, and annotated. The ORCHESTRA collaborative data sharing system develops a new architecture and consistency model for such settings, based on the needs of data sharing in the life sciences. In this paper we describe the basic architecture and implementation of the ORCHESTRA system, and summarize some of the open challenges that arise in this setting.
Early lapses in a cessation attempt: lapse contexts, cessation success, and predictors of early lapse.

Introduction The great majority of smokers relapse when they make quit attempts. Therefore, understanding the process of relapse may guide the development of more effective smoking cessation or relapse prevention treatments. The goal of this research is to extend our understanding of the context of initial lapses that occur within 8 weeks of quitting by using more comprehensive assessments of context, a contemporary sample, and sophisticated analytic techniques. Methods Participants from a randomized controlled smoking cessation trial completed baseline assessments of demographics and tobacco dependence, a daily smoking calendar to determine latency to lapse and relapse (7 consecutive days of smoking), and an assessment of initial lapse context (affect, location, activity, interpersonal, smoke exposure, and cigarette availability). Latent class analysis (LCA) was used to analyze the 6 early lapse (within the first 8 weeks; N = 551) context dimensions; logistic regression and Cox regression were used to relate context to cessation outcomes. Results LCA revealed 5 distinct initial lapse context classes (talking, with friends, angry; social; alone; with spouse, angry; and with smoking spouse) that were differentially related to cessation outcome. The easy availability of cigarettes characterized almost 75% of lapses, but being with friends, drinking, and not being at home were associated with a lower likelihood of progression to relapse. Conclusions Early lapsing is highly related to ultimate relapse, and lapsing in frequently experienced contexts seemed most strongly linked with progression to full relapse.
Horizontal gauge symmetry and a new picture for the b quark

We attempt to use a horizontal gauge symmetry in addition to SU(2)/sub L/ x U(1) to understand Cabibbo universality and the fermion masses. We compute the mixing angle between the light (u,d,s,c) and the heavy (t,b,g,h) quarks and show that it is small. The Cabibbo angle remains undetermined. In this scheme flavor-changing neutral currents exist between the heavy and the light fermions. Owing to this the picture of the decay of the b quark differs from the currently held view. The masses of all the predicted fermions are predicted.
Motion-Verb Generalizations in English and Spanish: Influences of Language and Syntax

English and Spanish speakers differ in the ways they talk about motion events, but how have these different modes of expression become instantiated as differing generalizations—as syntactic rules, lexical patterns, or both? In two studies, we asked English- and Spanish-speaking adults to interpret novel motion verbs presented in three types of sentence frames. Overall, English speakers expected novel verbs to encode the manner of motion, whereas Spanish speakers expected the verbs to encode the path of motion. The sentence frames also significantly affected how the speakers interpreted the novel verbs. We conclude that speakers of different languages represent their different generalizations about the composition of motion verbs both lexically and syntactically, and discuss how these generalizations might be important for issues of language acquisition and linguistic relativity.
Linear Radon-Nikodym Theorems for States on a von Neumann Algebra

Several linear Radon-Nikodym theorems for states on a von Neumann algebra are obtained in the context of a one parameter family of positive cones introduced by H. Araki. Among other results, we determine when a normal state </) admits a linear Radon-Nikodym derivative with respect to a distinguished normal faithful state 90 in the sen.se of Sakai, that is, $=hpQ-\-$0h with a positive h in the algebra.
Entrepreneurial human capital and the long-run survival of firms in India

Abstract This paper analyses the characteristics of entrepreneurs that contribute to firms' survival in less-developed countries (LDCs). The study, which relies on data collected in a 1971 survey of entrepreneurs in South India and a follow-up survey of surviving firms in 1993, finds that entrepreneurial human capital greatly influences firm survival. The results indicate that firms founded by older entrepreneurs in higher castes are most likely to survive, but that increased education of the founding entrepreneur reduces survival. These results provide evidence that opportunities of entrepreneurs outside the firm, ignored in most theories, are important in firm survival.
The role of religiosity in dietary beliefs and behaviors among urban African American women.

The relationship between religiosity and health has been investigated in many studies, with most finding positive associations. However, little is known about the role of religiosity in dietary factors, particularly among African American women. We used a self-administered questionnaire to examine the association between religiosity and dietary beliefs and behaviors among African American women. Women with strong religious beliefs and behaviors reported more interest in eating more fruits and vegetables, perceived their consumption as being more important, and consumed more fruits and vegetables than women low in religious beliefs and behaviors. These findings highlight the role of both religious beliefs and behaviors as they relate to diet-related beliefs and behaviors in this population. Women with strong religious beliefs consume more fruits and vegetables than those with weaker beliefs and behaviors.
Loss of leucine-rich repeat kinase 2 causes age-dependent bi-phasic alterations of the autophagy pathway

Dominantly inherited missense mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common genetic cause of Parkinson's disease, but its normal physiological function remains unclear. We previously reported that loss of LRRK2 causes impairment of protein degradation pathways as well as increases of apoptotic cell death and inflammatory responses in the kidney of aged mice. Our analysis of LRRK2-/- kidneys at multiple ages, such as 1, 4, 7, and 20 months, revealed unique age-dependent development of a variety of molecular, cellular, and ultrastructural changes. Gross morphological abnormalities of the kidney, including altered size, weight, texture, and color, are evident in LRRK2-/- mice at 3-4 months of age, along with increased accumulation of autofluorescent granules in proximal renal tubules. The ratio of kidney/body weight in LRRK2-/- mice is increased at 1, 4, and 7 months of age (~10% at 1 month, and ~20% at 4 and 7 months), whereas the ratio is drastically decreased at 20 months of age (~50%). While kidney filtration function evaluated by levels of blood urea nitrogen and serum creatinine is not significantly affected in LRRK2-/- mice at 12-14 months of age, expression of kidney injury molecule-1, a sensitive and specific biomarker for epithelial cell injury of proximal renal tubules, is up-regulated (~10-fold). Surprisingly, loss of LRRK2 causes age-dependent bi-phasic alterations of the autophagic activity in LRRK2-/- kidneys, which is unchanged at 1 month of age, enhanced at 7 months but reduced at 20 months, as evidenced by corresponding changes in the levels of LC3-I/II, a reliable autophagy marker, and p62, an autophagy substrate. Levels of α-synuclein and protein carbonyls, a general oxidative damage marker, are also decreased in LRRK2-/- kidneys at 7 months of age but increased at 20 months. Interestingly, the age-dependent bi-phasic alterations in autophagic activity in LRRK2-/- kidneys is accompanied by increased levels of lysosomal proteins and proteases at 1, 7, and 20 months of age as well as progressive accumulation of autolysosomes and lipofuscin granules at 4, 7-10, and 20 months of age. LRRK2 is important for the dynamic regulation of autophagy function in vivo.
Approach to addressing missing data for electronic medical records and pharmacy claims data research.

Author(s): Bounthavong, Mark; Watanabe, Jonathan H; Sullivan, Kevin M | Abstract: ObjectiveThe complete capture of all values for each variable of interest in pharmacy research studies remains aspirational. The absence of these possibly influential values is a common problem for pharmacist investigators. Failure to account for missing data may translate to biased study findings and conclusions. Our goal in this analysis was to apply validated statistical methods for missing data to a previously analyzed data set and compare results when missing data methods were implemented versus standard analytics that ignore missing data effects.DesignUsing data from a retrospective cohort study, the statistical method of multiple imputation was used to provide regression-based estimates of the missing values to improve available data usable for study outcomes measurement. These findings were then contrasted with a complete-case analysis that restricted estimation to subjects in the cohort that had no missing values. Odds ratios were compared to assess differences in findings of the analyses. A nonadjusted regression analysis ("crude analysis") was also performed as a reference for potential bias.SettingVeterans Integrated Systems Network that includes VA facilities in the Southern California and Nevada regions.PatientsNew statin users between November 30, 2006, and December 2, 2007, with a diagnosis of dyslipidemia.Main outcome measureWe compared the odds ratios (ORs) and 95% confidence intervals (CIs) for the crude, complete-case, and multiple imputation analyses for the end points of a 25% or greater reduction in atherogenic lipids.ResultsData were missing for 21.5% of identified patients (1665 subjects of 7739). Regression model results were similar for the crude, complete-case, and multiple imputation analyses with overlap of 95% confidence limits at each end point. The crude, complete-case, and multiple imputation ORs (95% CIs) for a 25% or greater reduction in low-density lipoprotein cholesterol were 3.5 (95% CI 3.1-3.9), 4.3 (95% CI 3.8-4.9), and 4.1 (95% CI 3.7-4.6), respectively. The crude, complete-case, and multiple imputation ORs (95% CIs) for a 25% or greater reduction in non-high-density lipoprotein cholesterol were 3.5 (95% CI 3.1-3.9), 4.5 (95% CI 4.0-5.2), and 4.4 (95% CI 3.9-4.9), respectively. The crude, complete-case, and multiple imputation ORs (95% CIs) for 25% or greater reduction in TGs were 3.1 (95% CI 2.8-3.6), 4.0 (95% CI 3.5-4.6), and 4.1 (95% CI 3.6-4.6), respectively.ConclusionThe use of the multiple imputation method to account for missing data did not alter conclusions based on a complete-case analysis. Given the frequency of missing data in research using electronic health records and pharmacy claims data, multiple imputation may play an important role in the validation of study findings.
The interrelation of glutathione reductase, catalase, glutathione peroxidase, superoxide dismutase, and glucose-6-phosphate in the pathogenesis of rheumatoid arthritis.

Rheumatoid arthritis (RA) is the most common form of inflammatory arthritis, a systemic autoimmune disease characterized by chronic inflammation of the synovial joints, ultimately leading to joint destruction and permanent disability, affecting 1% of the world population. Oxidative stress in rheumatoid inflammation, due to the fact that antioxidant systems are impaired in RA and caused by fee radicals, might have an essential role in etiology of RA. This review includes the interrelation of antioxidants against free radicals in RA patients. There is much evidence that antioxidant team that covers glutathione reductase, catalase, glutathione peroxidase, superoxide dismutase, and glucose-6-phopshate destroy reactive oxygen species and other free radicals through enzymatic as well as nonenzymatic means. The change in relative levels of antioxidants vis-a-vis free radical formation and level could be used as indicators for effective and earlier diagnosis of RA.
Driving Evaluation in Older Adults

Individuals increasingly maintain active driver status later into life. The prevalence of age-related medical conditions (e.g., dementia) negatively affects the cognitive, visual, and physical abilities deemed necessary for safe driving. Thus, clinicians are increasingly called upon to comment on an older patient’s ability to remain an active driver. The current chapter aims to provide the clinician with a practical understanding of the literature on driving research that has been conducted in older drivers. We ­introduce concepts and challenges inherent in conducting driving research, and provide a review of the literature on the effects of healthy aging and neurological disease on driving performance. Special focus on cognition and driving is meant to help translate empirical studies into clinical applications. Finally, guidelines are provided for the clinician faced with evaluating driving capacity of an older adult.
Improving photon detector efficiency using a high-fidelity optical controlled-not gate

A significant problem for optical quantum computing is inefficient or inaccurate photodetectors. It is possible to use controlled-not (cnot) gates to improve a detector by making a large cat state, then measuring every qubit in that state. In this paper we develop a code that compares five different schemes for making multiple measurements, some of which are capable of detecting loss and some of which are not. We explore how each of these schemes performs in the presence of different errors, and derive a formula to find at what probability of qubit loss it is worth detecting loss, and at what probability does this just lead to further errors than the loss introduces.
Parity and time reversal in J/Ψ decay

With the prospect of large numbers of J/Ψ decay events becoming available in the near future, it is interesting to search for symmetry violating effects as probes of new physics and tests of the standard model. J/Ψ decay events could provide the first observation of weak effects in otherwise strongly decaying particles. We calculate a T-odd asymmetry in the J/Ψ decay into photon plus lepton pair due to Z boson exchange. Extensions to hadronic final states are also discussed.
Organizational Code: A Complexity Theory Perspective on Technology and Intellectual Property Regulation

This foreword notes the importance of considering emerging aggregate patterns of strategic legal and business behavior as a form of regulation that differs from computer code as a method of regulation, on one hand, and law, on the other.
Growth of Epitaxial IrSi3 Layers on Si(111)

Epitaxial IrSi3 films have been grown on Si (111) by molecular beam epitaxy (MBE) at temperatures ranging from 630 to 800 °C and by solid phase epitaxy (SPE) at 500 °C. Good surface morphology was observed for IrSi3 layers grown by MBE at temperatures below 680 °C, and an increasing tendency to form islands is noted in samples grown at higher temperatures. Transmission electron microscopy (TEM) analysis reveals that the IrSi3 layers grow epitaxially on Si(111) with three epitaxial modes depending on the growth conditions. For IrSi3 layers grown by MBE at 630 °C, two epitaxial modes were observed with ~ 50% area coverage for each mode. Single mode epitaxial growth was achieved at a higher MBE growth temperature, but with island formation in the IrSi3 layer. A template technique was used with MBE to improve the IrSi3 surface morphology at higher growth temperatures. Furthermore, single-crystal IrSi3 was grown on Si(111) at 500 °C by SPE, with annealing performed in-situ in a TEM chamber.
Biologic effects of Mycoplasma pneumoniae and other mycoplasmas from man on hamster tracheal organ culture.

SummaryThe applicability of organ culture systems to the study of mycoplasma infections is illustrated by the experiments described. Tracheal organ culture provided a controllable environment for analysis of the interaction between M. pneumoniae and the natural target cell of this pathogen, the ciliated respiratory epithelium. Mycoplasma pneumoniae produced distinct cytopathology in this system that was not seen with other human mycoplasmas tested. In addition, virulent M. pneumoniae produced tissue damage more effectively than did an attenuated strain. The observations suggest that this experimental model may be useful for the analysis of factors contributing to organism pathogenicity.
Excited-State Behavior of ortho-Phenylenes

The excited-state properties of unsubstituted ortho-phenylene oligomers have been studied using TD-DFT. Calculations of vertical transitions at the helical ground-state geometries are in good qualitative agreement with the experimental UV–vis spectra. In the excited state, the spring-like compounds compress; for the longer oligomers, this compression is localized at one end of the oligomer. This behavior explains the unusual experimentally observed hypsochromic shifts in fluorescence spectra with increasing oligomer length.
Rapidly Scaling Dialog Systems with Interactive Learning

In personal assistant dialog systems, intent models are classifiers that identify the intent of a user utterance, such as to add a meeting to a calendar or get the director of a stated movie. Rapidly adding intents is one of the main bottlenecks to scaling—adding functionality to—personal assistants. In this paper we show how interactive learning can be applied to the creation of statistical intent models. Interactive learning (Simard, ICE: enabling non-experts to build models interactively for large-scale lopsided problems, 2014) combines model definition, labeling, model building, active learning, model evaluation, and feature engineering in a way that allows a domain expert—who need not be a machine learning expert—to build classifiers. We apply interactive learning to build a handful of intent models in three different domains. In controlled lab experiments, we show that intent detectors can be built using interactive learning and then improved in a novel end-to-end visualization tool. We then applied this method to a publicly deployed personal assistant—Microsoft Cortana—where a non-machine learning expert built an intent model in just over 2 h, yielding excellent performance in the commercial service.
Study of Preprocessing Electronic Map in Oracle Spatial before Searching a Shortest Path

Due to the electronic map is unable to applied to search a shortest path originally,some algorithms for processing(electronic) map are given before searching it.First,a virtual point-layer is created based on road-layer in electronic map,then some roads in road-layer matching the criteria of being decomposed and being merged are decomposed and merged respectively.After that a road network is built according to the preprocessed road-layer and virtual point-layer.At last,the actual(star-)(ting-point) and ending-point given by user are mapped to the virtual point-layer according to all layers in electronic map.In this paper,some algorithms for decomposing road-layer,merging road-layer, building road network,mapping starting-point and ending-point are designed in detail based on oracle spatial.Simulation and applications to search a shortest path based on(Xi'an) electronic map show that these algorithms correct for preprocessing electronic map.
Exercise-induced endothelial progenitor cell mobilization is attenuated in impaired glucose tolerance and type 2 diabetes

Circulating endothelial progenitor cells (EPCs) contribute to vascular homeostasis and are fewer in those with type 2 diabetes mellitus (T2DM) compared with normal glucose tolerance (NGT), suggesting a link between EPCs and T2DM-associated vasculopathies. The purpose of this study was to assess EPC number and mobilization by acute submaximal exercise in older adults with NGT, impaired glucose tolerance (IGT) or T2DM. We tested the hypothesis that EPC mobilization is lower in IGT compared with NGT and further reduced in older adults with T2DM. Forty-five older (50-75 yr of age) men and women with NGT (n = 18), IGT (n = 10), or T2DM (n = 17) were characterized and underwent submaximal aerobic exercise tests with blood sampling for enumeration of vascular endothelial growth factor receptor 2+ (VEGFR2+) cells, CD34+ hematopoetic progenitor cells, and CD34+/VEGFR2+ EPCs by flow cytometry before and after exercise. Basal EPC number was 65 and 61% lower in the IGT and T2DM groups, respectively, compared with the NGT group (P < 0.05). EPC number increased 23% after acute exercise in the NGT group (P < 0.01), but did not change in the IGT or T2DM groups. Before and after exercise, VEGFR2+ cell number was lower in a stepwise manner across the NGT, IGT, and T2DM groups (P < 0.05). Basal CD34+ cell number was lower in the IGT group compared with NGT (P < 0.05), but did not change after exercise in any group. These findings suggest a CD34+/VEGFR2+ EPC mobilization defect in IGT and T2DM that could play a role in the cardiovascular diseases and capillary rarefaction associated with insulin resistance.
Monetary Rewards and Job Satisfaction: A Comparison between the United States and China

In the US, literature in management field assuming a strong positive link between monetary rewards and job satisfaction in theoretical studies, however, empirical studies show weak, even non-related, link between the two variables. Very limited studies have provided evidences outside the US. The purpose of the present study is to examine similarity and difference of the relation between monetary rewards and job satisfaction in two counties, the US and China. It answers two basic questions: Does money improve job satisfaction? And, does money works in the same way in the US and China? Survey based data are analyzed using partial least square (PLS) based structural equation modeling (SEM). The result shows Money does not improve job satisfaction in the US. In China, similarly, money only marginally increases satisfaction. In both countries, intrinsic motivation is the main contributor to job satisfaction.
Rightness = Right-Maker: Reduction or Reductio?

I have recently argued that if the causal theory of reference is true, then, on pain of absurdity, no normative ethical theory is true. In this journal, Michael Byron has objected to my reductio by appealing to Frank Jackson’s moral reductionism. The present essay defends my reductio while also casting doubt upon Jackson’s moral reductionism.
Accessibility Evaluation: Manual Development and Tool Selection for Evaluating Accessibility of E-Textbooks

The growing availability of digital learning materials and their integration in many facets of the education system have created a need for evaluating the accessibility and usability of e-learning materials. In some cases, these digital resources are simple conversions of the original, printed materials into electronic formats. In other cases, the digital versions of the materials take advantage of the interactive abilities of the online and electronic media to enhance students’ learning experiences. Regardless of format, however, the content needs to be accessible. Although accessibility guidelines and accessibility evaluations tools are available to users, there is no comprehensive accessibility evaluation technique to help guide users in selecting the most accessible learning materials. In this study, we surveyed existing accessibility tools, selected a recommended tool set, and created a manual for post-secondary educators, students, and other stakeholders to use for evaluating the accessibility of e-textbooks.
Basic Principles of Consuming Academic Literature

Situation: As clinicians we are responsible to drive our practice based on evidence published in academic literature (Dawes M, Summerskill W, Glasziou P, et al. BMC Med Educ. 2005;5:1). Background: Evidence-based medicine is currently taught as part of medical school curriculum (Bloch RM, Swanson MS, Hannis MD. Acad Med. 1997;72:431–2). Assessment: Few clinicians, and even fewer medical students, are skilled in analyzing, understanding and implementing medical evidence into practice. Recommendation: Since a large part of medical safety and quality improvement work is based on aligning medical practice with current evidence, it is of utmost importance to develop at least a rudimentary systematic approach to understanding academic literature.
Spatial downscaling of SMAP passive microwave radiometer soil moisture using vegetation index and surface temperature

Soil moisture derived from the SMAP passive microwave radiometers has a spatial resolution of 36km. In the case of applications of weather, catchment hydrology and agriculture there is a requirement of high spatial resolution. In this paper we present an innovative method to downscale passive soil moisture retrievals using vegetation index and surface temperature.
Vegetation development on pumice at Mount St. Helens, USA

This study explores early vegetation development on pumice at Mount St.Helens. We monitored species annually in a grid of 200 contiguous100-m2 plots between 1989 and 1999. Of interestwere how vegetation changed and if it became more homogeneous over time.Speciesrichness and cover increased annually. Diversity(H′) stabilized by 1996 and began to decline aslong-livedstress-tolerant species such as Agrostis pallens, Carexmertensii and Penstemon cardwellii began todominate. Protected sites had more species and higher cover than did exposedones. Plots next to relict vegetation had more species and cover than diddistant plots. The vegetation initially was dominated by species with gooddispersal, but subsequently those with poor dispersal became dominant. Wecompared species expansion patterns to a model based on random colonization.Theresults implied that populations with poor dispersal derived from a fewcolonists that then produced seeds for local expansion. Detrendedcorrespondenceanalysis showed a pronounced shift in species composition. This analysis alsoshowed that species composition was becoming more homogeneous over time.However, significant heterogeneity remained and some plots are diverging fromothers. As yet, this vegetation is not developing towards a regional vegetationtype. Rather, an unusual community with Agrostis spp.,Carex spp., Penstemon cardwellii, Lupinuslepidus, Anaphalis margaritacea and Salixcommutata has developed. The accumulation phase of primarysuccessionis nearly complete. The next phase, in which vertical structure develops asSalix and conifers mature, has scarcely begun. It shouldbemarked by the invasion of forest understory species and loss of subalpinemeadowspecies. Assembly rules based on biotic interactions may then become evident.
A Novel Uropathogenic Escherichia Coli Genome (strain D3) and Comparative Analysis with Other Uropathogenic and Nonpathogenic Strains

Background: Bacterial urinary tract infections are extremely prevalent, with half of women having at least one infection at some point in their lives. Most often the causative pathogen the common gut microbe Escherichia coli. One such E. coli, strain D3, caused a bladder infection in a male adult, and was resistant to multiple antibiotics. We sequenced and assembled the genome of D3, and present it along with a comparative analysis against other pathogenic and nonpathogenic E. Coli strains. Results: By comparing the predicted proteins of D3 with those from 5 uropathogenic and 7 nonpathogenic E. Coli strains, we generated a list of 38 genes present in most (4-5) pathogenic strains, but absent in all nonpathogenic strains. Among these were 9 proteins of the Pap fimbrial operon, which has previously been associated with cell adherence and the formation of biofilms. Lastly, we analyzed the list of predicted genes uniquely present in D3 compared to all other strains, and identified multiple transposable elements. Conclusions: The presence of fimbria in most pathogenic E. coli strains, and their absence in nonpathogenic ones, suggests that they play a role in pathogenicity, a notion supported by previous work. We also found that D3-specific genes are strongly enriched with transposases, recombinases, and integrase, suggesting that these mobile elements have been inserted or expanded in D3, relative to other strains in the study.
Olfactory dysfunction and cognition among older adults in the United States.

BACKGROUND In this work we assess the association between olfactory dysfunction and cognition in a nationally representative sample of older adults in the United States. METHODS Participants aged ≥60 years (n = 1236) from the 2013-2014 National Health and Nutritional Examination Survey underwent both olfactory and cognitive testing. Olfaction was assessed by both objective test (8-odor Pocket Smell Test: smell impairment defined as score ≤2) and self-report. Cognitive assessment consisted of the Digit Symbol Substitution Test (DSST), the Animal Fluency Test, and the Consortium to Establish a Registry for Alzheimer's Disease (CERAD). Regression models were used to examine the association between olfaction and cognition while adjusting for demographics, cardiovascular factors, and associated medical history. RESULTS The prevalence of smell impairment in US older adults was 18.0% (95% confidence interval [CI], 14.0-22.0%) and 22.0% (95% CI, 18.5-25.6%) based on objective smell test and self-report, respectively. In a multivariate model adjusted for relevant factors, low smell test scores were consistently associated with low scores on cognitive assessments, with a DSST score difference of -1.5 (95% CI, -2.2 to -0.8), Animal Fluency Test score difference of -0.4 (95% CI, -0.7 to -0.1), and CERAD Word List score difference of -0.4 (95% CI, -0.6 to -0.2) per 1-point decrease in smell test score. There was no association between self-reported smell impairment and cognition. CONCLUSION Objectively measured olfactory dysfunction is independently associated with cognitive impairment. These findings are consistent with previous studies and suggest the utility of objective olfactory tests as an indicator for cognitive impairment as compared with self-reported olfactory dysfunction, which is an uncertain indicator.
Scalable Construction of Clock Trees With Useful Skew and High Timing Quality

Clock trees can be constructed based on static arrival time constraints or dynamic implied skew constraints. Dynamic implied skew constraints allow the full timing margins to be utilized. However, the dynamic skew constraints require a high run-time complexity to be evaluated. In contrast, static arrival time constraints are more restrictive but can be evaluated in constant time. Consequently, there is a tradeoff between timing margin utilization and run-time. In this paper, a scalable clock tree synthesis (CTS) framework is proposed for the construction of low-cost useful skew trees (USTs) with high timing quality. The scalability is based on combining the use of arrival time constraints with virtual minimum and maximum delay offsets, which facilitates that a pair of smaller subtrees can be joined into a larger subtree in constant time. The ability to quickly join subtrees is leveraged to perform a high degree of solution space exploration, which translates into the construction of USTs with low-cost. In particular, clock trees with various routing tree topologies, buffer tree topologies, buffer sizes, and stem wire lengths are explored. Moreover, the arrival time constraints are specified with the objective of being the least restrictive to reduce cost. Furthermore, the constraints are respecified throughout the tree construction process using a slack graph (SG) to expose additional timing margins. The high timing quality is obtained by seamlessly integrating arbitrary timing models using the SG. Finally, the proposed CTS framework is integrated with a clock tree optimization framework to demonstrate that the constructed USTs are capable of meeting timing constraints under the influence of on-chip variations.
Modeling, assignment and scheduling of tasks in distributed real-time systems

This thesis presents an integrated approach to the modeling, assignment and scheduling of tasks in distributed real-time systems. It is important to rigorously analyze and design such a system because any incorrect operation may lead to a serious consequence, such as loss of human lives. A new performance measure, called the system hazard, or the maximum normalized task response time, is used. The system hazard is a better measure than simply meeting task deadlines because it also indicates how early tasks can be completed before their deadlines. For a single processor with only independent periodic tasks, optimal scheduling algorithms with respect to the system hazard are derived for both static and dynamic cases. Two best bounds of processor utilization for these optimal algorithms are also computed. The scheduling of dependent periodic tasks in a distributed system is treated as a Multi-Project scheduling problem (MPSP). The MPSP is solved by a branch-and-bound (B&B) algorithm where dominance properties and lower-bound costs are derived for an optimal scheduling. Demonstrative examples and computational experiences are given. Based on the exact system hazard of a complete assignment, an optimal solution to the problem of allocating (or assigning and scheduling) periodic tasks to the processing nodes (PNs) of a distributed real-time system is carried out. The solution approach used is another B&B algorithm. Following the allocation of tasks, a continuous-time Markov Chain (CTMC) model is constructed for the concurrent execution of the assigned tasks. Tasks in each PN are first decomposed into activities. The activities and precedence constraints among them are then modeled by a Generalized Stochastic Petri Net (GSPN), from which a sequence of homogeneous CTMCs is built. The CTMC model is useful for the study of various design and analysis issues in distributed real-time systems, such as a combined task and message scheduling problem (TMSP). Using the CTMC model, the TMSP is formulated as a Semi-Markov Decision Process to minimize the expected number of tasks missing deadlines. Optimal centralized and sub-optimal decentralized solutions to the TMSP are derived using the dynamic programming technique.
The Double Helix and Double-Edged Sword: How the Public Thinks about Genes.

The implications of genetic explanations for behavioral traits such as violence and the public’s interpretations of them. Virtual Mentor is a monthly bioethics journal published by the American Medical Association.
The Nature of Entropy

Entropy is different from conserved energies and system variables like T and V that can be measured in the laboratory. However, the product TS has units of energy which suggests that entropy produced in an irreversible process also produces energy. Both the entropy S and the product TS are related to the randomness of the system. The connection between randomness and both entropy and energy is one of the more interesting concepts in thermodynamics. Its physical meaning can be approached probabilistically
Mineral Induction by Immobilized Polyanions

I shall briefly trace the developments leading to the hypothesis that polyanionic proteins from molluscan shell and dentin play a predominate role in initial mineral formation and present our recent experiments that support this hypothesis. I shall concentrate on the developments related to the role of the soluble matrix from molluscan shell because more progress has been made with the system.
Even-odd effect of a spin- S impurity coupled to a quantum critical system

We discuss an even-odd effect for an impurity with $N$-fold-degenerate internal states immersed in a two-dimensional superfluid--Mott-insulator quantum critical bath which is described by a spin-$S$ XY Bose-Kondo impurity model with $N=2S+1$. Using a dimensional- and momentum-cutoff regularized renormalization group and unbiased large-scale Monte Carlo numerical simulations, we establish the phase diagram for the $S=1$ impurity with all relevant terms included. We show that a threefold-degenerate $S=1$ impurity coupled to a critical bath has a nondegenerate ground state with a quantized charge, in qualitative contrast to the spin-1/2 case where the impurity is partially screened. We then argue that all impurities with odd-$2S$ degeneracy share the same universal physics as the spin-1/2 case and all impurities with even-$2S$ degeneracy are the same as the spin-1 case. We validate our conjecture with unbiased Monte Carlo simulations up to $S=2$. A physical consequence of this even-odd effect is that two spin-$1/2$ impurities in the critical bath form a long-range entangled state at a low temperature, which can be realized in ultracold atoms in an optical lattice.
Plants in changing environmental conditions of the anthropocene

The Anthropocene is the period of Earth history since the Industrial Revolution and is defined by the impact of mankind on the environment. Greenhouse gas concentrations, temperatures, precipitation, and atmospheric pollutants have changed significantly from 1750 to today. Climatic and environmental change will accelerate in the twenty-first century. Plants act as pivot points in global biogeochemical cycles. Plants provide many important ecosystem services including food production. Elevated carbon dioxide (CO2) concentration enhances plant productivity. Rising temperature stimulates plant productivity at high latitudes but impairs plant productivity at many temperate and tropical latitudes. Greater drought impairs plant productivity. Elevated ozone (O3) concentration impairs plant productivity. Crop plants can be adapted to future environmental change. Future environmental change can be mitigated by appropriate management of plants in agricultural and natural ecosystems.
Therapeutic Role of Fat Injection in the Treatment of Recalcitrant Migraine Headaches.

Background:This study was designed to assess the safety and efficacy of site-specific fat injection for the treatment of refractory migraine headaches following medical or surgical treatment.Methods:A prospective cohort study was performed on consecutive patients who had migraine headaches with pers
The parallel trajectories and increasing integration of landscape ecology and land system science

ABSTRACTLandscape Ecology and Land Systems Science share a common concern for the dynamics of landscapes, their environmental and human drivers and consequences, and the sustainability of land as a...
Assessing IMF's Crisis Prevention and Management Record

According to Robert Litan, the IMF is in the crisis prevention and management business. 1 He does not, however, say anything about whether it has in fact prevented any activity or practice of its clients that would otherwise end in a crisis. And when it comes to crisis management, Litan does not dispute the IMF’s warts that critics have noted, including moral hazard and unwise macro and microeconomic conditions that it has imposed. Nevertheless, he argues that presence of mistakes does not warrant dismantling the fund. He draws an analogy with the Federal Reserve, which was not abolished, despite its big mistakes in the 1930s. The Federal Reserve may not have been eliminated after 1933, but it was subsequently stripped of policymaking power (even allowing for the 1937-38 increase in reserve requirements—the one break in system passivity) by the two-decade predominance of the Treasury in monetary matters. What happened to the Federal Reserve between 1933 and the 1950s may be a good example to follow were the IMF to be shorn of its delusions of global indispensability, given its sorry record of crisis prevention and management.
Training patients to review scientific reports for the Patient-Centered Outcomes Research Institute: an observational study.

OBJECTIVE The peer review of completed Patient-Centered Outcomes Research Institute (PCORI) funded research includes reviews from patient reviewers (patients, caregivers, and patient advocates). Very little is known about how best to support these reviewers in writing helpful comments from a patient-centred perspective. This study aimed to evaluate the effect of a new training in peer review for patient reviewers. DESIGN Observational study. SETTING Online. PARTICIPANTS Adults registered in the PCORI Reviewer Database as a patient stakeholder. INTERVENTION A new online training in peer review. MAIN OUTCOME MEASURES Changes in reviewers' knowledge and skills; change in self-efficacy and attitudes, satisfaction with the training and perceived benefits and relevance of the training. RESULTS Before-after training survey data were analysed for 37 (29.4% of 126) patient reviewers invited to participate in an online training as part of a quality improvement effort or as part of a PCORI peer review. The reviewers improved their answers to the knowledge questions (p<0.001, median number of answers improved 4 (95% CI 3 to 5), large effect size (ES) Cohen's w=0.94) after the training, particularly in the questions targeting the specifics of PCORI peer review. Reviewers improved their skills in recognising helpful review comments, but those without peer-review background improved proportionally more (p=0.008, median number of answers improved 2 (95% CI 1 to 3), medium ES w=0.60). The use of training modestly increased reviewers' confidence in completing a high-quality peer review (p=0.005, mean increase in 5-point Likert rating 0.51 (95% CI 0.17 to 0.86), small-to-medium ES Cliff's delta=0.32) and their excitement about providing a review slightly increased (p=0.019, mean increase in 5-point Likert rating 0.35 (95% CI 0.03 to 0.68), small ES delta=0.19). All reviewers were satisfied with the training and would recommend it to other reviewers. CONCLUSIONS Training improved knowledge, skills and self-efficacy and slightly increased enthusiasm for completing a PCORI peer review.
Predictive value of neutrophil-lymphocyte ratio (NLR) and platelet-lymphocyte ratio (PLR) In hepatocellular carcinoma (HCC) patients treated with nivolumab (N)

Abstract Background Currently there are no recognized or validated biomarkers to identify HCC patients(pts) likely to benefit from N. Several studies have established the inverse relationship between inflammation-based scores such as NLR, PLR and survival in other solid tumours treated with immunotherapy. We evaluated the relationship between NLR and PLR and survival outcomes in HCC pts treated with N at Mount Sinai Hospital. Methods One hundred and four HCC pts treated between June 2016 and July 2018 were identified. NLR=Absolute neutrophil count/ Absolute lymphocyte count (ALC) and was calculated pretreatment and at 6-8 weeks after 3 doses (Posttreatment) of N. PLR=Platelet count/ALC. Kaplan-Meier analysis and the log-rank test were used to calculate and compare Overall and Progression free survival (OS, PFS) between NLR Results Median age was 66 (29-89) years. Median treatment duration was 26 (2-149) weeks. Child Pugh score (CPS, N = 96) was A in 64 (66%) and B in 32 (33%) pts. Barcelona Clinic Liver Cancer (BCLC) stage was B in 21 (20%) and C in 83 (80%) pts. Median follow-up time was 17 months (95% CI (15.7, 20.7). NLR was Table . 744P Pretreatment PLR group N(%) OS (months) 36(36) 35 P = 0.0495 > = 119 & 32(31) 10 > = 224 33(33) 15 Post treatment PLR group 35(35) Not Reached P = 0.0126 > = 126 & 31(31) 19 > = 229 33(33) 10 Conclusions This study suggests that lower NLR and PLR levels may predict better survival outcomes in HCC patients treated with N. The potential role of NLR and PLR as early predictors of immunotherapy outcomes in HCC pts warrants further evaluation. Legal entity responsible for the study Mount Sinai Hospital. Funding Has not received any funding. Disclosure All authors have declared no conflicts of interest.
Addressing the Disease Burden of Vertically Acquired Hepatitis C Virus Infection Among Opioid-Exposed Infants.

Background This study aims to estimate the disease burden of vertically acquired hepatitis C virus (HCV) in a large Midwestern hospital and to identify factors associated with HCV diagnostic testing among high-risk infants. Methods This is a retrospective analysis of an infant cohort (n = 58 427) born from 2014 to 2016 in the Greater Cincinnati region, where universal maternal urine testing is conducted at delivery to assess for intrauterine drug exposure (IUDE). Demographics and birth characteristics were analyzed among high-risk infants to identify factors associated with receiving HCV testing. A nested, matched, case-control analysis examined the association of pediatric HCV infection and IUDE. Results The HCV prevalence rate among high-risk infants who received testing was 3.6%-5.2% of births. Approximately 66.7% of maternally acquired HCV infections may be missed using current testing recommendations. Prenatal care had no significant effect (adjusted odds ratio [aOR], 1.2; 95% confidence interval [CI], 0.4-3.5) on the odds of a high-risk infant receiving HCV testing. Opioid-exposed cases had a more than 6-fold increase in the odds of HCV infection (aOR, 6.2; 95% CI, 2.3-16.6]) compared with nonopioid exposed infants. Conclusions The IUDE was significantly associated with increased odds of pediatric HCV infection in this population. The gaps in pediatric HCV testing identified in this study, despite known risk level and maternal infection, suggest the need for increased focus on HCV identification in the pediatric population.