cssi/SciSciGPT-SciSciNet huggingface dataset:
Social media mining for birth defects research: A rule-based, bootstrapping approach to collecting data for rare health-related events on Twitter.

Abstract Background Although birth defects are the leading cause of infant mortality in the United States, methods for observing human pregnancies with birth defect outcomes are limited. Objective The primary objectives of this study were (i) to assess whether rare health-related events—in this case, birth defects—are reported on social media, (ii) to design and deploy a natural language processing (NLP) approach for collecting such sparse data from social media, and (iii) to utilize the collected data to discover a cohort of women whose pregnancies with birth defect outcomes could be observed on social media for epidemiological analysis. Methods To assess whether birth defects are mentioned on social media, we mined 432 million tweets posted by 112,647 users who were automatically identified via their public announcements of pregnancy on Twitter. To retrieve tweets that mention birth defects, we developed a rule-based, bootstrapping approach, which relies on a lexicon, lexical variants generated from the lexicon entries, regular expressions, post-processing, and manual analysis guided by distributional properties. To identify users whose pregnancies with birth defect outcomes could be observed for epidemiological analysis, inclusion criteria were (i) tweets indicating that the user’s child has a birth defect, and (ii) accessibility to the user’s tweets during pregnancy. We conducted a semi-automatic evaluation to estimate the recall of the tweet-collection approach, and performed a preliminary assessment of the prevalence of selected birth defects among the pregnancy cohort derived from Twitter. Results We manually annotated 16,822 retrieved tweets, distinguishing tweets indicating that the user’s child has a birth defect (true positives) from tweets that merely mention birth defects (false positives). Inter-annotator agreement was substantial: κ = 0.79 (Cohen’s kappa). Analyzing the timelines of the 646 users whose tweets were true positives resulted in the discovery of 195 users that met the inclusion criteria. Congenital heart defects are the most common type of birth defect reported on Twitter, consistent with findings in the general population. Based on an evaluation of 4169 tweets retrieved using alternative text mining methods, the recall of the tweet-collection approach was 0.95. Conclusions Our contributions include (i) evidence that rare health-related events are indeed reported on Twitter, (ii) a generalizable, systematic NLP approach for collecting sparse tweets, (iii) a semi-automatic method to identify undetected tweets (false negatives), and (iv) a collection of publicly available tweets by pregnant users with birth defect outcomes, which could be used for future epidemiological analysis. In future work, the annotated tweets could be used to train machine learning algorithms to automatically identify users reporting birth defect outcomes, enabling the large-scale use of social media mining as a complementary method for such epidemiological research.
Novel synthesis of graveoline and graveolinine

Cyclization of 2-aryl amides with base lead to quinolone derivatives. Both graveoline and graveolinine were synthesized.GRAPHICAL ABSTRACT
Effects of Fasting on Tissue Amino Acid Concentrations and Urea-Cycle Enzymatic Activities in Young Pigs

Weanling pigs were fed a 30% crude protein (CP) diet for 18 d and then assigned to one of three regimens for either 4 or 8 d: 1) fasting, 2) 3% CP, i.e., maintenance or 3) 30% CP after which they were bled, then sacrificed for tissue assessment. Relative to pigs fasted or fed 30% CP, feeding 3% CP resulted in decreased urea-N and NH3-N excretion in the urine. Arginase and ornithine transcarbamoylase (OTC) activities in liver, and arginase activity in kidney cortex were markedly lower in pigs fed 3% CP compared with those either fasted or fed 30% CP. Hepatic arginase and OTC, however, were higher in fasted pigs than in those fed 30% CP. Pigs fed 3% CP had much lower levels of free threonine, tyrosine, cystathionine, taurine and branched-chain amino acids in plasma, liver, kidney, muscle and brain than fasted pigs or those fed 30% CP. Threonine concentration in brain, liver, muscle and plasma increased as length of the fast increased. Fasted pigs had decreased free alanine levels in plasma, and decreased free serine levels in plasma and liver when compared with fed pigs. Inter-organ comparisons provided evidence that both alanine and serine were important gluconeogenic amino acids during fasting. In general, free amino acid levels in brain were similar between fasted pigs and those fed 30% CP. Fasting for 8 d caused a 10-fold elevation in urinary taurine excretion relative to that observed for 4-d fasted pigs.
The meaning of life

Cet article s'attaque a l'un des problemes majeurs de la philosophie : le sens de la vie. Deplorant le scepticisme philosophique engendre par l'esprit scientifique qui met la culture en danger, l'A. prone un humanisme qui remet la question de la valeur et du sens au centre de l'interrogation philosophique. Nos vies tirent leur sens de leur participation au combat pour la realisation de ce qui doit etre : nous devons etre partenaires de la Creation.
A Modeling Approach that Integrates Individual Behavior, Social Networks, and Cross-Cultural Variation

How do psychological traits shape social networks? How does this relationship influence the spread of behavior? In a recent paper, Muthukrishna and Schaller (Pers. Soc. Psychol. Rev., 2019) use a modeling approach to explore these questions. In doing so, they illustrate the value of using a multilevel approach to study human behavior.
Becoming a Better College Teacher (If You're Lucky)

This contribution is a narrative of how a professor attempted to improve as a teacher over time. The narrator noticed the need for improvement through teaching a new class badly, and learning that ...
Assessment of the effect of communication skills training on communication apprehension in first year pharmacy students - A two-year study.

Abstract Introduction The purpose of the study is to assess the impact of a communication skills course on communication apprehension (CA) in two cohorts of first-year (P1), first quarter pharmacy students over a consecutive two-year span. Methods The personal report of CA (PCRA-24) was administered at the beginning and completion (pre-post) of a skills-centered communication course to two cohorts of P1, first quarter pharmacy students over a consecutive two-year period. The delivery of the communications course was redesigned during this timeframe based on post-course analysis data and student feedback to incorporate opportunities for students to engage in active learning activities throughout the course. Results Results of the study revealed a statistically significant reduction of total CA in both cohorts. Cohort 1 had significant reduction of CA in all four measured domains: group discussion meetings, interpersonal communication, and public speaking. Cohort 2 had significant reduction in two of the domains (group and meeting). Conclusions Overall, this study indicated that the format of this P1, first quarter communications course had a positive effect on student CA. In addition to the data collected for this research project, post-course evaluations and student comments indicated an overall positive reaction to the design and delivery of the course material, active learning assignments, and assessments.
A step towards equitable clinical trial recruitment: a protocol for the development and preliminary testing of an online prostate cancer health information and clinical trial matching tool

Recruitment of a diverse participant pool to cancer clinical trials is an essential component of clinical research as it improves the generalizability of findings. Investigating and piloting novel recruitment strategies that take advantage of ubiquitous digital technologies has become an important component of facilitating broad recruitment and addressing inequities in clinical trial participation. Equitable and inclusive recruitment improves generalizability of clinical trial outcomes, benefiting patients, clinicians, and the research community. The increasing prevalence of online connectivity in the USA and use of the Internet as a resource for medical information provides an opportunity for digital recruitment strategies in cancer clinical trials. This study aims to measure the acceptability, preliminary estimates of efficacy, and feasibility of the Trial Library intervention, an Internet-based cancer clinical trial matching tool. This study will also examine the extent to which the Trial Library website, designed to address the linguistic and literacy needs of broader patient populations, influences patient-initiated conversations with physicians about clinical trial participation. This is a study protocol for a non-randomized, single-arm pilot study. This is a mixed methods study design that utilizes the statistical analysis of quantitative survey data and the qualitative analysis of interview data to assess the participant experience with the Trial Library intervention. This study will examine (1) acceptability as a measure of participant satisfaction with this intervention, (2) preliminary measure of efficacy as a measure of proportion of participants with documented clinical trial discussion in the electronic medical record, and (3) feasibility of the intervention as a measure of duration of clinical visit. The principles that informed the design of the Trial Library intervention aim to be generalizable to clinical trials across many disease contexts. From the ground up, this intervention is built to be inclusive of the linguistic, literacy, and technological needs of underrepresented patient populations. This study will collect essential preliminary data prior to a multi-site randomized clinical trial of the Trial Library intervention. This study has received institutional approval from the Committee of Human Subjects Research at the University of California, San Francisco.
Combining omics technologies with CRISPR-based genome editing to study food microbes

The implementation of omics technologies such as genomics, proteomics and transcriptomics has revolutionized our understanding of microbiomes, and shed light on the functional attributes and mechanisms of action underlying the ability of probiotics to impact host health and starter cultures to drive food fermentation. Recently, molecular machines from CRISPR-Cas systems have redefined the gene editing toolbox and democritized our ability to alter the genome of food microorganisms. An integrated approach in which CRISPR-based genome editing is informed by omics studies is poised to enable the engineering of microorganisms and the formulation of microbiomes impacting the food supply chain. Here, we highlight the current applications of omics technologies in food microorganisms and CRISPR-based genome editing technologies in bacteria, and discuss how this integrated approach enables effective engineering of food microbes to generate enhanced probiotic strains, develop novel biotherapeutics and alter microbial communities in food matrices.
Patient Characteristics of VA Telehealth Users During Hurricane Harvey

Introduction: Research on patient characteristics of telehealth users is relatively new. More studies are needed to understand the characteristics of telehealth users during disasters. This study attempts to bridge this gap and examines patient characteristics of telehealth users compared with nontelehealth users at the Houston VA Medical Center (VAMC) immediately before and after Hurricane Harvey (2017). Methods: Since use of telehealth services reached its peak and gradually declined within 2 weeks after the landfall, the data analyses focused on 14 days before/14 days after Harvey. Two sets of analyses were conducted using chi-square, t test, and one-way analysis of variance: (1) Patient characteristics of telehealth users were compared with nontelehealth users. (2) Patient characteristics were compared between 3 subgroups of telehealth users. Results: Compared with nontelehealth users, telehealth users were older (mean age: 60.8 vs 58.5 years, P < .001) and had a higher mean Nosos health risk score (1.9 vs 1.4, P < .001). They also had a higher mean number of outpatient visits (28.0 vs 19.8, P < .001), higher emergency room use (37% vs 29%, P < .001), and higher rates of hospitalizations (21% vs 13%, P < .001) during the 12 months before Harvey. When compared to less frequent telehealth users, the most frequent telehealth users were the oldest and most medically complex patients. Conclusions: As the largest integrated health care system in the United States, the VA has many advantages favoring successful implementation of telehealth services during disasters. However, more research is needed to better understand how VA telehealth could meet the varying needs of veterans to lower risk of harm during differing types of disasters.
Constraints on narrow exotic states from K + p and K L 0 p scattering data

We consider the effect of exotic S = + 1 resonances Θ+ and Θ++ on K+p elastic scattering data (total cross section) and the process KL0p → KS0p. Data near the observed Θ+ (1540) are examined for evidence of additional states. The width limit for a Θ++ state is reconsidered.
Hearing Screening Failure Among Students With Reading Impairment: Rate and Relation to Specific Reading Deficits

Background The purpose of this preliminary study was to explore one potential underlying factor that may contribute to poor reading outcomes: minimal hearing loss. Additionally, we compared decodin...
Training Physician Assistants to Use Medical Interpreters Effectively.

PURPOSE To examine the internal consistency of a validated instrument for physician assistant (PA) communication skills with interpreters and evaluate a training activity focused on effectively working with interpreters during a standardized patient assessment. METHODS Six cohorts of PA students completed training on how to communicate with patients who required an interpreter. Students then completed an assessment with a limited English-proficient patient and interpreter. Student competency was assessed using a previously validated measure. Data were analyzed using a multivariable Poisson regression model. RESULTS There were usable data on 439 PA students. The median number of areas that students performed/partially performed was 10 out of 12 (inter-quartile range: 3). The Poisson regression model revealed significant differences between cohorts. Areas for further training include using Teach-Back (n = 203) and thanking the interpreter (n = 170). CONCLUSIONS Although the PA students performed well, there is considerable room for improvement in certain communication techniques.
Existence and structure of P-area minimizing surfaces in the Heisenberg group

We study existence and structure of $P-$area minimizing surfaces in the Heisenberg group under Dirichlet and Neumann boundary conditions. We show that there exists an underlying vector field $N$ that characterized existence and structure of $P$-area minimizing surfaces. This vector field exists even if there is no $P$-area minimizing surface satisfying the prescribed boundary conditions. We prove that if $\partial \Omega$ satisfies a so called Barrier condition, it is sufficient to guarantee existence of such surfaces. Our approach is completely different from previous methods in the literature and makes major progress in understanding existence of $P$-area minimizing surfaces.
HIV May Accelerate Coronary Artery Disease Progression Through Promoting the Adverse Effects of Conventional Cardiovascular Risk Factors and Illicit Drugs

Background: Only the independent effect of human immunodeficiency virus (HIV)-infection on coronary artery disease (CAD) has been investigated in cross-section studies, while rather than directly, HIV-infection may accelerate CAD through promoting the effects of risk factors. Furthermore, there is no information on the potential effects of HIV-infection on coronary plaque volumes. Therefore, we investigated whether HIV-infection directly or indirectly promotes clinical and volumetric characteristics of CAD in a observational longitudinal study. Methods: 300 individuals without cardiovascular symptoms (210 male; age: 48·0±7·2 years; 226 HIV-infected) underwent coronary CT angiography at two time points (mean follow-up: 4·0±2·3 years). We quantified Agatston-score, number of coronary plaques, segment stenosis score, and also segmented the coronary plaques to enumerate total, noncalcified (-100–350HU) and calcified (≥351HU) plaque volumes. Linear mixed models were used to assess the effects of HIV-infection, atherosclerotic cardiovascular disease (ASCVD) risk, years of cocaine use and high-sensitivity C-reactive protein on CT markers of CAD. Findings: There was no significant difference in annual progression rates between HIV-infected and -uninfected (p>0·05 for all). Multivariately, HIV-infection was not associated with any CAD parameter (p>0·05 for all). However, among HIV-infected individuals, each year of cocaine use significantly increased all CAD parameters (p<0·05 for all), while ASCVD risk score was significantly associated with CAD parameters except for Agatston-score (p<0·05). However, these associations were only apparent among HIV-infected individuals. Importantly, none of the HIV-medications were associated with any of the CAD outcomes. Interpretation: HIV-infection is not directly associated with CAD and therefore HIV-infected are not destined to have worse CAD profiles as compared to uninfected individuals. However, more aggressive management of conventional cardiovascular risk factors and abstinence from illicit drugs may be needed to achieve similar CAD status. Funding Statement: Procedures and tests were funded by the National Institute on Drug Abuse, and the National Institutes of Health (NIH R01DA12777, R01DA15020, R01DA25524, R21DA048780 and U01DA040325). Declaration of Interests: None. Ethics Approval Statement: The Committee on Human Research at the Johns Hopkins School of Medicine (Baltimore, MD) approved the study protocol, and all study participants provided written informed consent. All procedures used in this study were in accordance with HIPAA, local and federal regulations, and the Declaration of Helsinki.
The Use of the Net Promoter Score (NPS) in an Outpatient Allergy and Pulmonary Clinic: An Innovative Look into Using Tablet-Based Tool vs Traditional Survey Method.

Introduction Patient satisfaction has become an essential metric in addition to the type of care they receive. Phone calls, emails, and text to patients after their healthcare visit are the typical way of obtaining the data reflecting patient satisfaction. The purpose of this retrospective quality improvement study is to compare the traditional post-outpatient clinic survey method with an onsite concise two-question survey using a tablet method immediately after the patient visit using Net Promoter Score (NPS) questions. Methods Data were collected retrospectively from February to August 2018 from an outpatient subspecialty clinic in southern California using an existing database from two different sources: the traditional method (TM) and the tablet-based tool (TBT), using NPS. The TM data were obtained from a third﻿-party company using two questions via phone, email, and text collected 2-4 weeks after the patient's visit. The TBT has only two questions that were given to patients upon their visit check-out. These two questions assessed both provider and clinic's performance using the NPS method. Results In total, there were 1708 patients seen from February to August 2018. In the TM, the total outgoing messages during this period were 580 (34.0%) with 156 responses (27%). In the TBT, 648 out of 1708 (37.9%) surveys were collected with a 100% response rate. The NPS score showed that 99.2% of the providers were promoters. The NPS score for the clinic was 96% which reflects a promoter score. Conclusion Our results indicate that when using the TBT immediately after their visit to the clinic, a higher response rate was noted. In addition, both methods had similar outcomes in terms of patient satisfaction NPS scores. Future prospective studies with a larger sample size are warranted to evaluate the effectiveness of the TBT tool in assessing patient satisfaction.
Quantum Chemistry for Physicists

The laws of quantum mechanics completely determine the wave function of any given molecule, and, in principle, we can calculate the eigenfunctions and energy eigenvalues by solving Schrodinger’s equation. In practice, however, only the simplest systems, such as the hydrogen atom, have an explicit, exact solution, and for the more interesting complex systems we have to resort to approximations. It is an art to develop appropriate approximations. Depending on the purpose, many different schemes have been used, ranging from ab-initio calculations to semiempirical methods. Here we start from atomic orbitals and then show how they can be combined with molecular orbitals molecular orbital. Although we keep the discussion elementary, we will be able to understand the stability of chemical bonds, the type of wave functions involved, and the approximate energies of the various electronic states. Starting from our simple results we can get more realistic approximations by adding correction terms.
Introduction to information-based complexity

Information-based complexity is based on three assumptions: information is partial, contaminated, and it costs. Its goal is to create a general theory about problems with such information, and to apply the results to solving specific problems in varied disciplines. Some of the questions asked in information- based complexity are listed and some results are indicated. Information-based complexity is contrasted with combinatorial complexity which studies problems such as the traveling salesman problem and linear programming. In combinatorial complexity, information is assumed to be complete, exact, and free. The relation between information theory and information-based complexity is briefly discussed.
Regulation of open complex formation at the Escherichia coli galactose operon promoters. Simultaneous interaction of RNA polymerase, gal repressor and CAP/cAMP.

The regulation of open complex formation at the Escherichia coli galactose operon promoters by galactose repressor and catabolite activator protein/cyclic AMP (CAP/cAMP) was investigated in DNA-binding and kinetic experiments performed in vitro. We found that gal repressor and CAP/cAMP bind to the gal regulatory region independently, resulting in simultaneous occupancy of the two gal operators and the CAP/cAMP binding site. Both CAP/cAMP and gal repressor altered the partitioning of RNA polymerase between the two overlapping gal promoters. Open complexes formed in the absence of added regulatory proteins were partitioned between gal P1 and P2 with occupancies of 25% and 75%, respectively. CAP/cAMP caused open complexes to be formed nearly exclusively at P1 (98% occupancy), gal repressor caused a co-ordinated, but incomplete, switch in promoter partitioning from P1 to P2 in both the absence and presence of . We measured the kinetic constants governing open complex formation and decay at the gal promoters in the absence and presence of gal repressor and CAP/cAMP. had the largest effect on the kinetics of open complex formation, resulting in a 30-fold increase in the apparent binding constant. We conclude that the regulation of open complex formation at the gal promoters does not result from competition between gal repressor, and RNA polymerase for binding at the gal operon regulatory region, but instead results from the interactions of the three proteins during the formation of a nucleoprotein complex on the gal DNA fragment. Finally, we present a kinetic model for the regulation of open complex formation at the gal operon.
Orientation and temperature dependence of some mechanical properties of the single-crystal nickel-base superalloy René N4: Part II. Low cycle fatigue behavior

The low cycle fatigue (LCF) properties of a single-crystal nickel-base superalloy, Rene* N4, have been examined at 760 and 980 °C in air. Specimens having crystallographic orientations near [001], [01l], [111], [023], [236], and [145] were tested in fully reversed, total-strain-controlled LCF tests at a frequency of 0.1 Hz. At 760 °C, this alloy exhibited orientation dependent tension-compression anisotropies of yielding which continued to failure. Also at 760 °C, orientations exhibiting predominately single slip exhibited serrated yielding for many cycles. At 980 °C, orientation dependencies of yielding behavior were smaller. In spite of the tension-compression anisotropies, cyclic stress range-strain range behavior was not strongly orientation dependent for either test temperature. Fatigue life on a total strain range basis was highly orientation dependent at both 760 and 980 °C and was related chiefly to elastic modulus, low modulus orientations having longer lives. Stage I crack growth on (111) planes was dominant at 760 °C, while Stage II crack growth occurred at 980 °C. Crack initiation generally occurred at near-surface micropores, but occasionally at oxidation spikes in the 980 °C tests.
INDUCTION OF α-AMYLASE OF BACILLUS STEAROTHERMOPHILUS BY MALTODEXTRINS

Welker, N. E. (Western Reserve University, Cleveland, Ohio) and L. Leon Campbell. Induction of α-amylase of Bacillus stearothermophilus by maltodextrins. J. Bacteriol. 86:687–691. 1963.—Technical-grade maltose contained 3.5% glucose, 0.5% maltotriose, and 2.5% of the higher molecular weight maltodextrins. The first five homologues (maltose being the first in the series) of the maltodextrin series were isolated and purified. Each member of the series was found to be chromatographically pure. The physical and chemical properties were determined. It was shown that the contaminating maltodextrins found in technical grade maltose were linear (1–4 linked) polymers of glucose, ranging from maltotriose to maltohexaose. The addition of maltose, maltotriose, maltohexaose, maltopentaose, and maltotetraose (all at 10−4m) to cultures growing in a chemically defined medium resulted in a stimulation in the differential rate of α-amylase synthesis by 1.2, 1.6, 1.9, 2.3, and 3.0 times that of the sucrose control, while glucose had no effect. The induction data indicate that Bacillus stearothermophilus 1503–4 is a partial constitutive strain with respect to α-amylase synthesis.
Cathepsin E: A Novel Target for Regulation by Class II Transactivator

The aspartic proteinase cathepsin E (CatE) has been implicated in Ag processing. In this study we report that CatE expression is negatively regulated by the MHC class II transactivator (CIITA). CIITA-deficient murine and human B cells expressed greater CatE than wild-type B cells, whereas overexpression of CIITA in a human gastric carcinoma cell line, AGS, resulted in decreased CatE mRNA and protein. AGS cells expressing CIITA also exhibited decreased processing of OVA Ag. Inhibition of CatE expression is specific to the type III CIITA isoform and maps to the acidic and proline/serine/threonine-rich (PST) protein domains of CIITA. We found that CatE expression is inducible by PU.1 and p300, and that this induction can be reversed by CIITA. These findings demonstrate a novel phenomenon: regulation of CatE Ag processing by CIITA in an isoform-dependent manner.
Qualidade do ar interno em ambientes hospitalares

Este trabalho tem o objetivo de tracar uma revisao sobre a qualidade do ar em ambientes internos, dando enfase aos hospitalares. Em unidades de saude, a qualidade do ar pode exercer uma influencia direta e de grande significância na velocidade de recuperacao dos pacientes e na ocorrencia de infeccoes hospitalares. Embora haja inumeros contaminantes do ar, estes podem ser facilmente distinguiveis quanto a sua natureza, sendo classificados como sendo de natureza biologica e nao-biologica. Similarmente ao que ja vem se observando internacionalmente, a expectativa e de que, tambem no Brasil, ocorra um aumento no controle da qualidade do ar de ambientes internos, com a adocao de medidas mais rigorosas especificas para fontes de diferentes naturezas e a inclusao de um programa de medida e controle/abatimento desses contaminantes.
Severity of arthritis is predicted by antibody response to gp135 in chronic infection with caprine arthritis-encephalitis virus.

Antibody titers to caprine arthritis-encephalitis virus surface glycoprotein gp135 and core protein p28 in synovial fluid and serum from 35 goats infected for 3 years were compared with the histologic severity of arthritis in these animals. Anti-gp135 antibody titers in synovial fluid and serum directly reflect the severity of carpal arthritis in chronically infected goats. Images
Molecular Basis of Hypokalemia-Induced Ventricular Fibrillation

Background—Hypokalemia is known to promote ventricular arrhythmias, especially in combination with class III antiarrhythmic drugs like dofetilide. Here, we evaluated the underlying molecular mechanisms. Methods and Results—Arrhythmias were recorded in isolated rabbit and rat hearts or patch-clamped ventricular myocytes exposed to hypokalemia (1.0–3.5 mmol/L) in the absence or presence of dofetilide (1 μmol/L). Spontaneous early afterdepolarizations (EADs) and ventricular tachycardia/fibrillation occurred in 50% of hearts at 2.7 mmol/L [K] in the absence of dofetilide and 3.3 mmol/L [K] in its presence. Pretreatment with the Ca-calmodulin kinase II (CaMKII) inhibitor KN-93, but not its inactive analogue KN-92, abolished EADs and hypokalemia-induced ventricular tachycardia/fibrillation, as did the selective late Na current (INa) blocker GS-967. In intact hearts, moderate hypokalemia (2.7 mmol/L) significantly increased tissue CaMKII activity. Computer modeling revealed that EAD generation by hypokalemia (wi...
Sparse matrix computations on an FFP machine

The authors describe and analyze an algorithm for performing Gaussian elimination on sparse linear systems with a FFP machine, a small-grain parallel computer. Given an equation Ax=b, where A is an n*n matrix, the algorithm yields a permuted upper-triangular system, from which the authors obtain x by back-substitution. If A has e nonzero entries and if f fill-ins are created during elimination, then the algorithm solves the system in O(h*(e+f)) time, using O(e+f) processing elements. The parameter h is the height of the FFP machine's connection network, which is O(log(e+f)). The algorithm makes no assumptions about the structure of A and requires no preprocessing. The pivot order can be given in advance, or it can be chosen at run-time by the Markowitz heuristic with only a linear increase in cost. Also presented are results of simulation on sample problems, both randomly generated and from the Boeing-Harwell set. The results of the simulations, in operation counts, are used to estimate the performance of an FFP machine hardware prototype. >
Post-Modern Man: Psychocultural Responses to Social Trends

The most important social trends of the contemporary period are interpreted as giving rise to a polarization between two types of culture and personality: the “modernistic” and the “underground.” Evidence for the two types is drawn from cultural products (mainly literature and the visual arts), psychiatric observations, and accounts of emerging modes of behavior among the youth. A psychological mechanism for this dualistic impact of social trends on culture and personality is hypothetically identified. “Post-modern” man is conceptualized by his recognition of the tension between “modernistic” and “underground” tendencies in his own mind. Theories of psychological modernization are criticized in the light of the foregoing.
8-(Hydroxymethyl)-3,N4-etheno-C, a potential carcinogenic glycidaldehyde product, miscodes in vitro using mammalian DNA polymerases

8-(Hydroxymethyl)-3,N(4)-etheno-C (8-HM-epsilonC) is an exocyclic adduct resulting from the reaction of dC with glycidaldehyde, a mutagen and animal carcinogen. This compound has now been synthesized and its phosphoramidite incorporated site-specifically into a defined 25-mer oligonucleotide. In this study, the mutagenic potential of this adduct in the 25-mer oligonucleotide was investigated in an in vitro primer-template extension assay using four mammalian DNA polymerases. The miscoding potentials were also compared to those of an analogous derivative, 3,N(4)-etheno C (epsilonC), in the same sequence. Both adducts primarily blocked replication by calf thymus DNA polymerase alpha at the modified base, while human polymerase beta catalyzed measurable replication synthesis through both adducts. Nucleotide insertion experiments showed that dA and dC were incorporated by pol beta opposite either adduct, which would result in a C --> T transition or C --> G transversion. Human polymerase eta, a product of the xeroderma pigmentosum variant (XP-V) gene, catalyzed the most efficient bypass of the two lesions with 25% and 32% for 8-HM-epsilonC and epsilonC bypassed after 15 min. Varying amounts of all four bases opposite the modified bases resulted with pol eta. Human polymerase kappa primarily blocked synthesis at the base prior to the adduct. However, some specific misincorporation of dT resulted, forming an epsilonC.T or 8-HM-epsilonC.T pair. From these data, we conclude that the newly synthesized glycidaldehyde-derived adduct, 8-HM-epsilonC, is a miscoding lesion. The bypass efficiency and insertion specificity of 8-HM-epsilonC and epsilonC were similar for all four polymerases tested, which could be attributed to the similar planarity and sugar conformations for these two derivatives as demonstrated by molecular modeling studies.
Relationship Between Parasitic and Saprophytic Fitness in Cochliobolus Heterostrophus, Cause of Southern Leaf Blight of Maize

In hemibiotrophic plant pathogens such as Cochliobolus heterostrophus (anamorph=Bipolaris maydis), selection can occur during both the parasitic and saprophytic phases of its life cycle. The importance of selection for parasitic fitness in populations of plant pathogens is well recognized, but the role of selection during the saprophytic (or overwintering) phase on the composition of pathogen populations is largely unstudied.
Protein segment finder: an online search engine for segment motifs in the PDB

Finding related conformations in the Protein Data Bank (PDB) is essential in many areas of bioscience. To assist this task, we designed a search engine that uses a compact database to quickly identify protein segments obeying a set of primary, secondary and tertiary structure constraints. The database contains information such as amino acid sequence, secondary structure, disulfide bonds, hydrogen bonds and atoms in contact as calculated from all protein structures in the PDB. The search engine parses the database and returns hits that match the queried parameters. The conformation search engine, which is notable for its high speed and interactive feedback, is expected to assist scientists in discovering conformation homologs and predicting protein structure. The engine is publicly available at http://ari.stanford.edu/psf and it will also be used in-house in an automatic mode aimed at discovering new protein motifs.
The promise of expertise: Walter Lippmann and the policy sciences

Walter Lippman addressed over his lifetime many of the questions raised still in the policy sciences about the proper role for the social scientist in the policy process, the potential contributions of various disciplines to an understanding of the issues, the kinds of circumstances most likely to nurture excellent policy analysis and the means whereby both a narrow elite and a wider public can be well informed about critical subjects and policy options. This article examines Lippmann's intellectual formation to deal with these questions and his reflections on institutions designed to foster policy analysis as well as the proper training of a policy expert. The article concludes with an examination of Lippmann's career as a practitioner in the policy world, and especially as a bridge between different communities.
3-D-conformal radiation therapy for pediatric giant cell tumors of the skull base.

Giant cell tumors (GCT) of the base of skull are rare neoplasms. This report reviews the treatment of four pediatric patients presenting with aggressive giant cell tumor, using fractionated and combined, conformal proton and photon radiation therapy at Massachusetts General Hospital and Harvard Cyclotron Laboratory.
Identifying Depression in the Old Old

The Zung Self-Rating Depression Scale (SDS) was used as one measure of dysphoria in a cohort of 349 community-residing elderly. The earlier findings of Zung were replicated, both in terms of higher mean scores than in younger populations and with regard to the rank ordering of SDS items in the age group 75 and above. The five most frequently reported symptoms in Zung's study were repeated in this study, as were low-frequency symptoms. At a one-year follow-up visit, a significant test-retest correlation of 0.607 (p
Identifying dynamic interactors of protein complexes by quantitative mass spectrometry

Dynamically interacting proteins associate and dissociate with their binding partners at high on/off rates. Although their identification is of great significance to proteomics research, lack of an efficient strategy to distinguish stable and dynamic interactors has hampered the efforts toward this goal. In this work, we developed a new method, MAP (mixing after purification)-SILAC (stable isotope labeling of amino acids in cell culture), to quantitatively investigate the interactions of protein complexes by mass spectrometry. In combination with the original SILAC approach, stable and dynamic components were effectively distinguished by the differences in their relative abundance ratio changes. We applied the newly developed strategies to decipher the dynamics of the human 26 S proteasome-interacting proteins. A total of 67 putative human proteasome-interacting proteins were identified by the MAP-SILAC method among which 14 proteins would have been misidentified as background proteins due to low relative abundance ratios in standard SILAC experiments and 57 proteins have not been reported previously. In addition, 35 of the 67 proteins were classified as stable interactors of the proteasome complex, whereas 16 of them were identified as dynamic interactors. The methods reported here provide a valuable expansion of proteomics technologies for identification of important but previously unidentifiable interacting proteins.
Isolation and Identification of the Major Heparan Sulfate Proteoglycans in the Developing Bovine Rib Growth Plate

Heparan sulfate proteoglycans are thought to mediate the action of growth factors. The heparan sulfate-containing proteoglycans in extracts of the bovine fetal rib growth plate were detected using the monoclonal antibody 3G10, which recognizes a neoepitope generated by heparitinase digestion (David, G., Bai, X. M., Van der Schueren, B., Cassiman, J. J., and Van den Berghe, H. (1992) J. Cell Biol. 119, 961–975). The heparan sulfate proteoglycans that react with this antibody were identified using antisera to known proteoglycans; purified using CsCl density gradient centrifugation, molecular sieve, and ion exchange chromatography; and then characterized. The major heparan sulfate proteoglycans in the growth plate had core proteins of 200 kDa and larger and were identified as perlecan and aggrecan. These two heparan sulfate proteoglycans could be effectively separated from each other by CsCl density gradient centrifugation alone. Perlecan contained 25% heparan sulfate and 75% chondroitin sulfate. The heparan sulfate chains on growth plate perlecan were considerably smaller than the chondroitin sulfate chains, and the heparan sulfate disaccharide content was different than that found for heparan sulfate from either kidney, tumor tissue, or growth plate aggrecan. Aggrecan contained only 0.1% heparan sulfate, which was localized to the CS-1 domain of aggrecan. These results indicate that perlecan and aggrecan would be the principal candidate proteoglycans involved in the action of heparan sulfate-binding proteins in the developing growth plate.
Supervisor self-disclosure: balancing the uncontrollable narcissist with the indomitable altruist.

The purpose of this article is to provide supervisors with a framework to determine the effectiveness of self-disclosure in supervision. We posit how self-disclosures can be both memorable to the trainee and facilitative of supervision process and outcome, specifically the supervisory working alliance, trainee disclosure, and trainee edification. Case examples based on the literature and our own personal experiences are offered to illustrate the models' applicability.
Effect of the surface on ion-beam damage build-up in ZnO

Lattice disorder in ZnO irradiated with heavy ions is anomalous, exhibiting an intermediate peak (IP) between the surface and bulk. Bombarding (0 0 0 1) ZnO single crystals with 500 keV Xe ions at two angles shows that the formation and propagation of the IP are independent of the displacement generation profile. The ZnO surface plays the dominant role in IP formation and propagation. The IP likely traps and annihilates mobile point defects, as evidenced by a step in Rutherford backscattering/channeling spectra.
Isospin mixing in 12C

Abstract We observe a yield to the 1+ T = 1 level in 12C at 15.11 MeV in the isospin forbidden 12C(d, d') and 10B(α, d) reactions at about 1 % of the yield to the 1+ T = 0 level at 12.71 MeV. Observed yields to the T = 12+ level at 16.11 MeV in both reactions at about half the yield to the 15.11 MeV level preclude attributing this observed isospin violation entirely to final state mixing. From the ratios of the spectroscopic factors for the 12.71 and 15.11 MeV levels in 12C and the ground state of 12B from the 13C(d, t) and 13C(d, 3He) reactions, we find a charge dependent matrix element between the 1+ states in 12C of 179 ± 75 keV.
Overview of hybrid subspace methods for uncertainty quantification, sensitivity analysis

Abstract The role of modeling and simulation has been heavily promoted in recent years to improve understanding of complex engineering systems. To realize the benefits of modeling and simulation, concerted efforts in the areas of uncertainty quantification and sensitivity analysis are required. The manuscript intends to serve as a pedagogical presentation of the material to young researchers and practitioners with little background on the subjects. We believe this is important as the role of these subjects is expected to be integral to the design, safety, and operation of existing as well as next generation reactors. In addition to covering the basics, an overview of the current state-of-the-art will be given with particular emphasis on the challenges pertaining to nuclear reactor modeling. The second objective will focus on presenting our own development of hybrid subspace methods intended to address the explosion in the computational overhead required when handling real-world complex engineering systems.
GPS-Tracked Buoy for Water Level Measurements

With the advancement of differential, kinematic GPS techniques, water level measurements with the accuracy of centimeter- or decimeter-level is possible when buoys are placed close to a coastal base station or at distances of thousands of kilometers from shore, respectively. Applications of these techniques to observe tides and waves and to detect tsunamis have been demonstrated. This paper will first briefly review existing water level measurement methods, the needs for coastal and open ocean water level measurements, previous GPS buoy experiments, and GPS measurement uncertainties and precision positioning techniques. These will then be followed by a brief description of the application of GPS buoys in hydrographic surveying and the development of a real-time water level reporting GPS buoy to support US National Oceanic and Atmospheric Administration (NOAA) National Ocean Service (NOS) nautical charting mission. The present measurement system consists of a portable spherical buoy and a shore base station. Utilizing Real-Time Kinematic (RTK) differential GPS technique, accurate water level data were collected and reported in real-time at six- minute intervals in complying with NOS water level measurement standards. The buoy’s motion sensors provide automated corrections for wave-induced buoy motions. Several field tests conducted near NOAA water level stations have shown that the root-mean-square (rms) of differences between the two measurement systems is on the order of 2 cm. The buoy also provides surface wave information. The portability and the accuracy of the system offer possibilities for other applications in coastal waters. Future enhancements include satellite data telemetry and monitoring, option for post processing, and solar power supplementation.Copyright © 2006 by ASME
Coupling to Trapped Atoms with a Magnetic Cantilever

We are interested in using a magnetic microfabricated cantilever to both magnetically trap and drive transitions in laser-cooled Rb atoms. We ascertain the feasibility and show a possible scenario for such an experiment.
Transmission modes and the evolution of virulence : With special reference to cholera, influenza, and AIDS.

Application of evolutionary principles to epidemiological problems indicates that cultural characteristics influence the evolution of parasite virulence by influencing the success of disease transmission from immobilized, infected hosts. This hypothesis is supported by positive correlations between virulence and transmission by biological vectors, water, and institutional attendants. The general evolutionary argument is then applied to the causes and consequences of increased virulence for three diseases: cholera, influenza and AIDS.
Congestive heart failure in elderly patients: controlled study of delapril versus captopril.

In this controlled trial, 30 elderly patients with congestive heart failure, New York Heart Association (NYHA) classes II and III, were randomly assigned to treatment with captopril 25 mg three times daily or delapril 15 mg twice daily. At the end of an 8-week treatment period, clinical symptoms of heart failure were significantly relieved by both drugs, with a consistent and statistically significant improvement in patients' quality of life evaluated using a symptoms/activity scale (p
A Comparison of Phase Organization of Model Segmented Polyurethanes with Different Intersegment Compatibilities

Three series of chemically well-defined polyurethanes were synthesized with the same hard segments but different soft-segment chemistries of interest in biomedical applications. The multiblock polyurethanes have soft segments composed of either an aliphatic polycarbonate [poly(1,6-hexyl 1,2-ethyl carbonate)], polytetramethylenoxide, or a mixed macrodiol of polyhexamethylenoxide and hydroxyl-terminated poly(dimethylsiloxane) and the same hard-segment chemistry [4,4′-methylenediphenyl diisocyanate and 1,4-butanediol]. Analysis using small-angle X-ray scattering and other methods demonstrates that demixing of the hard and soft segments varies greatly between the three series of copolymers. For example, the PDMS/PHMO-based copolymers exhibit a three-phase, core−shell morphology, while the other two series exhibit a typical two-phase structure. In addition to quantitative measurements of hard/soft-segment demixing for the two-phase copolymers, FTIR spectroscopy was used to assess inter- and intracomponent hydr...