cssi/SciSciGPT-SciSciNet huggingface dataset:
Robust architectural support for transactional memory in the power architecture

On the twentieth anniversary of the original publication [10], following ten years of intense activity in the research literature, hardware support for transactional memory (TM) has finally become a commercial reality, with HTM-enabled chips currently or soon-to-be available from many hardware vendors. In this paper we describe architectural support for TM added to a future version of the Power ISA™. Two imperatives drove the development: the desire to complement our weakly-consistent memory model with a more friendly interface to simplify the development and porting of multithreaded applications, and the need for robustness beyond that of some early implementations. In the process of commercializing the feature, we had to resolve some previously unexplored interactions between TM and existing features of the ISA, for example translation shootdown, interrupt handling, atomic read-modify-write primitives, and our weakly consistent memory model. We describe these interactions, the overall architecture, and discuss the motivation and rationale for our choices of architectural semantics, beyond what is typically found in reference manuals.
Brain and liver mitochondrial protein synthesis: potassium dependent chloramphenicol inhibition.

Abstract Protein synthesis in vitro in mitochondrial preparations from mouse brain and mouse liver is sensitive to inhibition by chloramphenicol if potassium is the predominant cation in the incubations, but not when the media are enriched with respect to sodium ion and are potassium ion poor. All preparations of brain mitochondria examined to date also exhibit sensitivity to inhibition by cycloheximide, whereas this is not found with liver mitochondria.
Evaluating the risk of industrial espionage

A methodology for estimating the relative probabilities of different compromise paths for protected information by insider and visitor intelligence collectors has been developed based on an event-tree analysis of the intelligence collection operation. The analyst identifies target information and ultimate users who might attempt to gain that information. The analyst then uses an event tree to develop a set of compromise paths. Probability models are developed for each of the compromise paths that use parameters based on expert judgment or historical data on security violations. The resulting probability estimates indicate the relative likelihood of different compromise paths and provide an input for security resource allocation. Industrial facilities face insider information theft as well as compromise by visitors. The method should be adaptable to most industrial situations with modifications to fit the specific situation and is direct and simple to use. When historical data are not available, expert judgment data can be used as an input. Even in the absence of quantitative data, considerable insight into espionage risk can be gained by developing the compromise paths and their attendant probability models. These qualitative insights may be the greatest benefit gained when applying this methodology.
Diversity as Community and Communions: A Taoist Alternative to Modernity

Contrasts the linear narrative of modernity with the process narrative of the ancient Taoists of China. Written in process narrative, provides a narrative based on the metaphor of the spiral rather than the straight arrow of modernity. Presents a premodern Taoist definition of diversity and applies it to the community literature as an alternative to modernist organizational theory based on process narrative.
Soy protein isolate diet does not prevent increased cortical bone turnover in ovariectomized macaques.

: Forty-one ovariectomized, cynomolgus monkeys were divided into 4 groups and fed a casein and lactalbumin based diet with or without 17β-estradiol, or a soy protein based diet with or without 17β-estradiol for 7 months. Histomorphometry was done on cortical bone from the mid-shaft femur. 17β-estradiol suppressed ovariectomy-induced increases in bone formation rates, regardless of dietary protein source. Soy protein alone did not prevent increased bone turnover and on the endosteal surface, it actually increased bone turnover when compared to casein/lactalbumin fed monkeys.
Uniqueness in some higher order elliptic boundary value problems

The uniqueness of the solution to two boundary value problems for the linear equation Δ3u −a Δ2u +b Δu −cu =F and to two boundary value problems for the quasilinear differential equation Δ2u +ρw(u) =f are proved. The proofs follow as a consequence of maximum principles for a functional which is defined on solutions to the differential equation.
Vagus nerve stimulation (VNS) for major depressive episodes: One year outcomes

Abstract Background: Vagus nerve stimulation has shown promising results in an open, acute phase pilot study of adults in a treatment-resistant major depressive episode. This open, naturalistic follow-up study was conducted to determine whether the initial promising effects were sustained, and whether changes in function would be observed. Methods: Thirty adult outpatients in a treatment-resistant, nonpsychotic major depressive episode received an additional 9 months of vagus nerve stimulation treatment following exit from the 3-month acute study. Changes in psychotropic medications and vagus nerve stimulation stimulus parameters were allowed during this longer-term follow-up study. A priori definitions were used to define response (≥ 50% reduction in baseline Hamilton Rating Scale for Depression total score) and remission (Hamilton Rating Scale for Depression ≤ 10). Results: The response rate was sustained [40% (12/30) to 46% (13/28); p = .317] and the remission rate significantly increased [17% (5/30) to 29% (8/28); p = .045] with an additional 9 months of long-term vagus nerve stimulation treatment after exit from the acute study (1 year total vagus nerve stimulation treatment). Significant improvements in function between acute study exit and the 1-year follow-up assessment as measured by the Medical Outcomes Study Short Form-36 were observed. Conclusions: Longer-term vagus nerve stimulation treatment was associated with sustained symptomatic benefit and sustained or enhanced functional status in this naturalistic follow-up study.
Florida's Medicaid mental health carve-out: lessons from the first years of implementation.

Florida, like many other states, has embarked on an experiment with managed mental health care for Medicaid enrollees. Under a 1915(b) waiver, the state's Medicaid agency began a mental health carve-out demonstration in March 1996 in the Tampa Bay area. This qualitative case study seeks to ascertain the impact of the carve-out (and, by comparison, HMO arrangements) on the public mental health sector. Findings suggest that the carve-out demonstration has succeeded in creating a fully integrated mental health delivery system with financial and administrative mechanisms that support a shared clinical model. However, other findings raise concerns about the HMO model in terms of stability, access to care, efficiency, and more generally about the shifting of risk and public responsibility “downstream” to private organizations without sufficient governmental oversight. These findings may offer guidance for other states implementing major managed care policy initiatives for disabled Medicaid enrollees.
A joint test for a unit root and common factor restrictions in the presence of a structural break

Abstract This paper provides evidence that the common factor restrictions (CFR) play an important role in testing for a unit root in the presence of a structural break. We first show that the CFR should not be ignored in the unit root testing procedure when a structural break is allowed for. Then we provide a Wald test statistic for the joint hypothesis of a unit root and the CFR. The empirical finding suggests that the missing common factor restrictions may result in a quite different and perhaps misleading inference.
Inaccurate 25-Hydroxyvitamin D Results from a Common Immunoassay

To the Editor: The great increase in the volume of vitamin D testing over the past several years has created a demand for high-throughput vitamin D testing methods (1). Our laboratory instituted 25-hydroxyvitamin D testing on the DiaSorin LIAISON® platform in October 2009. Soon afterward, some samples were noted not to produce the expected result after dilution with 1 volume of the manufacturer's dilution buffer (i.e., 2-fold dilution). We investigated the frequency of such occurrences, whether the results obtained with diluted or undiluted samples were more consistent with liquid chromatography–tandem mass spectrometry (LC-MS/MS)1 results, and whether the cause of the nonlinear dilution might be due to interfering heterophile antibodies. 25-Hydroxyvitamin D analysis and dilutions were performed on the DiaSorin LIAISON instrument according to the manufacturer's instructions. 25-Hydroxyvitamin D results for diluted (2-fold) and undiluted samples for 928 serum samples (424 consecutive samples in October 2009 and 504 consecutive samples in September 2011). In addition, between October 7, 2009, and August 5, 2011, we repeated the 25-hydroxyvitamin D analyses for 3475 undiluted samples with results >50 μg/L after diluting these samples 2-fold. Results were determined as discrepant if the …
Spin Labeling of Membrane Proteins in Mammalian Brain Synaptic Plasma Membranes: Partial Characterization

Abstract Insight into molecular structure and function of membranes from complex tissue such as brain may be gained by application of sophisticated analytical and physical techniques. Accordingly, the first characterization of the use of electron paramagnetic resonance with a protein-specific spin label to investigate the structure of mammalian synaptosomal membranes is described.
Teaching Communication Skills with Videomodeling and Videofeedback in the University Classroom.

The objective of the study was to examine the use of videotape as a modeling and as a feedback device in skills-based interpersonal communication courses. Videotapes were made of students as they demonstrated self-disclosure and empathic listening skills at the begin ning and at the end of a university family relations course. Students in one section were videotaped during the course, allowed to view their own tapes, and received feedback on their use of the skills. Another section viewed videotapes of other students demonstrating the skills, but were not given an opportunity to view themselves on videotape. A third section served as the control group and did not receive any instruction with videotape. Significant increases in skills performance at post-test were observed in all three groups. The treatment group that viewed modeling of communication skills via videotape had higher performance levels on both empathy and self-disclosure than either the control or videofeed back sections. The findings of the study demonstrated the effectiveness of teaching com munication skills and the effectiveness of video modeling of skills as a teaching technique. Factors that might contribute to higher anxiety among students who receive videofeedback are discussed and future research needs are presented.
Anti-inflammatory Activity of an Orange Peel Polymethoxylated Flavone, 3′,4′,3,5,6,7,8-Heptamethoxyflavone, in the Rat Carrageenan/Paw Edema and Mouse Lipopolysaccharide-Challenge Assays

The anti-inflammatory properties of 3',4',3,5,6,7,8-heptamethoxyflavone (HMF), a citrus polymethoxylated flavone, were studied in the bacterial lipopolysaccharide (LPS)-challenge/tumor necrosis factor-alpha (TNFalpha) response in mice and in the carrageenan/paw edema assay in rats. In each of these trials, HMF administered by intraperitoneal (ip) injection exhibited anti-inflammatory activity, whereas HMF administered orally (po) produced no effects. The inhibition observed in the LPS-challenge/TNFalpha assay correlated with the HMF levels in the blood sera of mice dosed (ip) with either 33 or 100 mg/kg body weight. Low levels of HMF (0.035 +/- 0.024 ppm) were detected in the blood sera of mice dosed orally [100 mg of HMF (suspended in vegetable oil)/kg], whereas ip injection led to higher levels (0.517 +/- 0.051 ppm). This may account for the different levels of anti-inflammatory effects observed in mice following ip vs oral HMF administration. HMF metabolites, including a number of mono- and di-demethylated HMF metabolites and their glucuronic acid conjugates, were also detected, but results of these studies suggest that the glucuronidated metabolites of HMF are inactive in these inflammation models.
A frequency-domain formulation of the Fréchet derivative to exploit the inherent parallelism of the distorted Born iterative method

With its consideration for nonlinear scattering phenomena, the distorted Born iterative method (DBIM) is known to provide images superior to those of linear tomographic methods. However, the complexity involved with the production of superior images has prevented DBIM from overtaking simpler imaging schemes in commercial applications. The iterative process and need to solve the forward-scattering problem multiple times make DBIM a slow algorithm compared to diffraction tomography. Fortunately, as computer prices continue to decline, it is becoming easier to assemble large, distributed computer clusters from low-cost personal computer systems. These are well-suited to DBIM inversions, and offer great promise in accelerating the method. Traditional frequency-domain DBIM formulations produce an image by inverting the Frechet derivative. If the derivative is treated as a matrix, it is costly to construct and awkward to invert on distributed computer systems. This paper presents an interpretation of the Freche...
A descriptive study of behavioral responses of sexual harassment targets: Implications for control theory

The problem of sexual harassment in the workplace can be viewed within the framework of personal control. In particular, sexual harassment can be viewed as an infringement upon employees' rights to control the conditions under which they work. Targets of harassment must tolerate sexual harassment to avoid negative consequences such as termination, demotion, distasteful remarks or jokes, and so forth. Previous research (Wortman & Brehm, 1975; Greenberger & Strasser, 1986) into personal control has drawn upon two theories—reactance theory and learned helplessness theory—to explain behavioral responses to infringement upon personal control. The purpose of this study is to investigate the efficacy of personal control theories in explaining responses of targets who file discrimination suits.
Evaluation of a high accuracy reflectometer for specular materials

A high accuracy method for measuring the spectral reflectivity of specular materials over the 0.300-15.0-microm wavelength range is described. The performance of the reflectometer has been evaluated, and results for an evaporated aluminum film are compared with those obtained by the Bennett-Koehler instrument upon which our design is based. For highly reflecting materials, like those of current interest for laser mirror coatings, it is possible to achieve accuracies, based upon evaluated systematic errors, of the order of 1 part in 10(3). Discussion of the effects of sample tilt, detector linearity optical configuration, and bandwidth on the measurements is presented.
Corticosteroids alter G protein inwardly rectifying potassium channels protein levels in hippocampal subfields

Corticosterone or cortisol, stress hormones in rat and human, respectively, alter neurotransmitter receptor-mediated responses in the brain. Corticosterone could alter these responses by modifying any component of the receptor-effector pathway. Many of these receptors are linked to guanine nucleotide regulatory proteins (G proteins) which, in turn, can activate second messenger systems and/or ion channels, such as G protein inwardly rectifying potassium channels (GIRK). The aim of these experiments was to determine whether corticosterone treatment altered the levels of GIRK proteins in rat hippocampus. Corticosterone treatment selectively altered the levels of GIRK1 and GIRK2 (measured on immunoblots) depending on the subfield of the hippocampus examined. These data lend credence to the hypothesis that corticosterone differentially alters neurotransmitter receptor-mediated responses dependent on the brain area.
Hydrazine sulfate and cancer cachexia

Abstract Hydrazine sulfate, a gluconeogenic blocking agent designed to inhibit cancer cachexia, has produced significant subjective response in late‐stage cancer patients as well as a degree of accompanying “objective”; response, while at the same time inducing little or no important clinical side effects. In addition the drug has been demonstrated to inhibit tumor growth and potentiate the action of cytostatics in a variety of experimental animal tumors. The mechanism of action for these latter responses is indicated to be indirect and not a function of tumor cytotoxicity. It is suggested that new indices of subjective response replace standard cytotoxic criteria in the evaluation of a non‐cytotoxic drug.
The genetic and cellular basis of antigen and receptor stimulated regulation.

The genetic restrictions controlling the activation of cells imposed by activating cells with ligand, idiotype or anti-idiotype have been examined. Anti-idiotype can induce idiotype-bearing effector or suppressor T cells in strains of different H-2 types which have similar VH genes. Antigens (ligand) can be used to generate idiotype-positive T, in A/J or C.AL-20 mice and at least certain antigens (hapten-carrier conjugates) may, under special circumstances, induce apparently idiotype bearing effector cells as deduced from functional studies. Idiotype coupled to cell surfaces can be used to induce anti-idiotypic effector or suppressor cells. The ability to induce such Ts is limited, however, to mice with the appropriate VH genes, irrespective of their H-2 type. Moreover, in mice which elaborate idiotype-positive suppressor molecules, I-J encoded determinants were also found to be present on the same molecular complex. Thus, the H-2 complex may play a constitutive role in assembly of certain idiotypic cell surface products important in the immune response.
Manganese, copper and zinc concentrations in human skin lesions.

Abstract Trace element analysis by neutron activation was performed on biopsies from normal skin, benign and malignant lesions. Particular attention was focused on Cu, Zn and Mn contents since good “baseline” values are available for normal skin biopsies. The most important results were obtained for Cu and Mn where significant concentration differences were associated with malignancy or benignity. Average values of Mn in normal skin, in benign nevi and in malignant lesions were 0.1 ± 0.1, 1.1 ± 0.6 and 4.7 ± 1.9 μg/g (dry weight), respectively. For Zn our values for normal skin were substantially lower than those reported by others. For malignant biopsies, half the samples showed, elevated Zn levels while half showed depressed levels. Cu concentrations in five of six malignant samples averaged 308 μg/g compared to a value of 4.3 μg/g for normal skin.
Domain switching criteria for piezoelectric materials

Experimental results reported by many researchers showed that the coercive electric field for ferroelectric switching depends on mechanical stresses present in the material. Similarly, the coercive stress for ferroelastic switching depends on the electric field. To model these dependences, several domain switching criteria based on different considerations have been proposed in earlier studies. In this paper, these domain switching criteria are briefly reviewed and the predictions based on these domain switching criteria are compared with the available experimental data for 180 degree(s) domain switching in PZT. It is found that the predictions do not match the experimental results. Motivated by this observation, a new domain switching criterion based on internal energy density is proposed. This new criterion is found to yield very good predictions compared with the existing experimental results for 180 degree(s) domain switching in PZT. To verify the new domain switching criterion for 90 degree(s) switching, experiments were conducted using PZT-5H. The new experimental result indicates that the new domain switching criterion gives a much better prediction than other existing criteria.
Electrophilic aromatic nitrosation. Isolation and X-ray crystallography of the metastable NO+ complex with nitrosoarene

Isolation of the unstable 1∶1 complex of 4-nitrosoanisole with NO+PF6− allows its precise X-ray structural characterization. The charge-transfer crystal is formed via strong N⋯N coordination [the distance of 1.938(5) A corresponding to a σ-bond order of ≈0.2] in the mean plane of the planar 4-nitrosoanisole donor. Thorough analysis of its molecular geometry in terms of valence resonance and MO schemes reveals a strong charge polarization with a local negative charge localized on the nitroso group and a local positive charge distributed over the adjacent p-methoxybenzyl moiety. Such a charge distribution accommodates the well-known passivation of nitrosoarenes to multiple nitrosation and explains the ease of demethylation of the complex. Comparison of a variety of nitroso- and nitroarene structures has shown that the nitrosoarene experiences a much stronger quinoidal distortion of the aromatic ring as compared with the latter. This indicates a stronger electron-withdrawing effect of the nitroso group relative to that of the nitro group. The weakened aromatic resonance in the nitrosoarenes could be responsible for the observed slower rate and the measurable isotope effect in electrophilic nitrosation as opposed to nitration.
An analysis of bicycle route choice preferences in Texas, US

In the US, the rise in motorized vehicle travel has contributed to serious societal, environmental, economic, and public health problems. These problems have increased the interest in encouraging non-motorized modes of travel (walking and bicycling). The current study contributes toward this objective by identifying and evaluating the importance of attributes influencing bicyclists’ route choice preferences. Specifically, the paper examines a comprehensive set of attributes that influence bicycle route choice, including: (1) bicyclists’ characteristics, (2) on-street parking, (3) bicycle facility type and amenities, (4) roadway physical characteristics, (5) roadway functional characteristics, and (6) roadway operational characteristics. The data used in the analysis is drawn from a web-based stated preference survey of Texas bicyclists. The results of the study emphasize the importance of a comprehensive evaluation of both route-related attributes and bicyclists’ demographics in bicycle route choice decisions. The empirical results indicate that travel time (for commuters) and motorized traffic volume are the most important attributes in bicycle route choice. Other route attributes with a high impact include number of stop signs, red light, and cross-streets, speed limits, on-street parking characteristics, and whether there exists a continuous bicycle facility on the route.
Fibroblast growth factor receptor 3 and the human chondrodysplasias.

Heterozygous mutations of the gene encoding the fibroblast growth factor receptor 3 (FGFR3) have been found in persons with achondroplasia, thanatophoric dysplasia, and hypochondroplasia. They exhibit considerable genetic homogeneity, and specific mutations strongly correlate with the clinical sever
Behavior Modification in the Treatment of Hypertension

This study examines the use of a behavior modification program as an adjunct to the medical treatment of essential hypertension. The subjects, outpatients with medically treated, but uncontrolled, essential hypertension, were exposed to group interaction (including such processes as peer reinforcement, peer competition, and cognitive dissonance), individual blood pressure monitoring, stimulus control, and direct social influence. The control subjects received only routine medical treatment for their hypertension. Results indicated that the experimental subjects significantly decreased their diastolic blood pressures between pre- and post-treatment measures (spanning a period of four weeks), whereas the control subjects showed no such change. Thus it appears possible to use behavior modification to help in the treatment of essential hypertension.
Pensions and fertility: in search of a link

In overlapping generations models with endogenous fertility wherein the retired partake of consumption but do not contribute to production (through their labor), fertility has a positive and a negative externality. These can be internalized through a child allowance (or tax) or a linkage between pension benefits and the number of children. The prescription rest crucially on the assumption that no parents are better than others in raising their children and that fertility can be perfectly controlled. When either of these two assumptions are violated, the case for such policy recommendations are greatly weakened.
Effect of augmented plantarflexion power on preferred walking speed and economy in young and older adults.

Abstract With age, loss of skeletal muscle mass (sarcopenia) results in decreased muscle strength and power. Decreased strength and power, in turn, are closely linked with declines in physical function. Preferred walking speed, a marker of physical function, is slower in older adults compared to young adults. Research suggests that older adults may walk slower as a consequence of decreased plantarflexor power at push-off. In this study, we hypothesized that providing additional plantarflexion (PF) power during push-off would (1) increase preferred walking speed, and (2) reduce metabolic cost of transport (MCOT), in young and older adults. PF power was augmented using powered ankle-foot orthoses (PAFOs). The PAFOs, which use pneumatic actuators to provide an additional PF moment, were based on a design by Ferris et al. [Ferris DP, Czerniecki JM, Hannaford B. An ankle-foot orthosis powered by artificial pneumatic muscles. J Appl Biomech 2005;21:189–97.]. Nine young (23.3 ± 1.6 years) and seven older (74.6 ± 6.6 years) adults participated. For the young adults, eight out of nine increased their preferred walking speed when push-off power was augmented (1.18 ± 0.16 to 1.25 ± 0.16 m/s, p = 0.03). A similar, but non-significant, trend in preferred walking speed was observed for the older adults. With augmented push-off power, MCOT for young adults decreased from 0.395 ± 0.057 to 0.343 ± 0.047 (p = 0.008); indicating that the neuromuscular system was able to adapt to use external energy to reduce metabolic cost. Only three older adults were tested but MCOT values showed a similar trend. Augmenting PF power increases gait speed and reduces MCOT in young adults. Older adults may need a longer period to take advantage of additional push-off power.
Solubility of ZrO2 in Cryolite-Based Molten Salt System

Electrolysis of cryolite-based molten salt is an important method for Al-Zr alloy production. The dissolution of ZrO2 in the melts effects current efficiency and energy consumption of the production process of Al-Zr alloy, so it is most importance to study the solubility of ZrO2 in the melts. In this paper, the solubility of ZrO2 in the cryolite-based molten salt of different composition at different temperatures was measured by isothermal saturation method. It was found that ZrO2 content increased rapidly in the initial stage, but the increase rate was very slow after two hours, so it was thought that ZrO2 was nearly saturation after two hour-after dissolution. The solubility of ZrO2 in cryolite-based molten salt increased markedly when increased the temperature and addition of CaF2. The solubility of ZrO2 in 2.2NaF·AlF3-Al2O3-CaF2 molten salt is similar with solubility of ZrO2 in the 2.2NaF·AlF3-CaF2, it is reach 5.5wt%.
Grain Boundaries in NiO

Defocus-imaging and high-resolution electron microscopy (HREM) are used to study tilt grain boundaries (GB) in NiO near the axis over the whole range of possible misorientation. Faceting and structural periodicities within facets are observed in high- and low-angle GBs. A reduced atomic density at high-angle GBs is suggested by the defocus behavior.
BIFURCATIONS DUE TO AN AUTO-CATALYTIC REACTION IN A CSTR

Abstract Steady state bifurcation in an isothermal CSTR, with the reactions A→B, B→l (the first one being auto-catalytic) taking place in it, has been studied recently using the singularity theory based formulation of Golubitsky and Schaeffer. With the residence time as the bifurcation parameter, this approach indicates that the model is unstable to small perturbations. In this work, we introduce a perturbation through a third reaction and demonstrate that additional behaviors are possible. An analysis of the original model with the feed concentrations of A and B as the bifurcation parameters does not indicate any instability. Furthermore, when the model is analyzed using Mather's formalism, no instability is seen An instance of degenerate Hopf bifurcation is identified for the specific case of no B in the feed. Again, an approach based on singularity theory is used
On the Submission and Processing of Division 8 Program Presentations for the APA Convention

An analysis of the 278 Division 8postersubmissionsfor the 1983 APA convention examined characteristics of poster submitters, what was submitted, and how posters were evaluated by reviewers. The results provided a profile of first authors in terms of APA and Division 8 membership, gender, seniority, work setting, and geographic location. Gender distributions were examined for the total of 553 authors. Submissions were categorized into four topic areas: group processes and interaction, cognitive processing, intraindividual, and subcultures and ethnicity. The program review process did not reveal biases by seniority or topic area. Among three criteria used to evaluate poster submissions, reviewers appeared to emphasize the importance of the topic in deciding whether to accept or reject.
Effect of humidity on stiction and friction of the head/disk interface

The effect of humidity on the frictional behavior of the head/disk interface is investigated. Experimental results show that stiction and friction are strongly affected by humidity, surface roughness, the presence of a lubricant film on the disk surface, and dwell time. Ellipsometric measurements indicate that the adsorbed water film on a disk surface grows nonlinearly with humidity, suggesting that the films are a major factor in causing stiction at high humidity. >
Natural Competence in the Hyperthermophilic Archaeon Pyrococcus furiosus Facilitates Genetic Manipulation: Construction of Markerless Deletions of Genes Encoding the Two Cytoplasmic Hydrogenases

In attempts to develop a method of introducing DNA into Pyrococcus furiosus, we discovered a variant within the wild-type population that is naturally and efficiently competent for DNA uptake. A pyrF gene deletion mutant was constructed in the genome, and the combined transformation and recombination frequencies of this strain allowed marker replacement by direct selection using linear DNA. We have demonstrated the use of this strain, designated COM1, for genetic manipulation. Using genetic selections and counterselections based on uracil biosynthesis, we generated single- and double-deletion mutants of the two gene clusters that encode the two cytoplasmic hydrogenases. The COM1 strain will provide the basis for the development of more sophisticated genetic tools allowing the study and metabolic engineering of this important hyperthermophile.
Variation in Age at ESRD in Autosomal Dominant Polycystic Kidney Disease

Background Heterogeneity manifest as more severe disease in successive generations has been attributed to genetic anticipation in patients with autosomal dominant polycystic kidney disease (ADPKD). We evaluated variation in age at end-stage renal disease (ESRD) in ADPKD families for evidence of anticipation. Study Design Retrospective. Setting & Participants 413 families with ADPKD seen at our single center between 1985 and 2004 (including 95 families with documented polycystic disease type 1 [PKD1] and 213 ADPKD families with parents born before 1930). Predictor Generational status. Outcome Age at ESRD onset. Measurements Time to ESRD was evaluated by using survival analysis, Cox regression, and descriptive statistics. Unstable trinucleotide repeat expansion was evaluated by means of genotyping in 6 PKD1 families. Results We analyzed 413 ADPKD families (1,391 parent-offspring pairs) with known age at ESRD or last known age without ESRD (informative pairs). There was no difference in age at ESRD between parents and offspring by means of Cox regression after adjusting for correlations among family members and sex (hazard ratio, 1.019; 95% confidence interval, 0.919 to 1.13; P = 0.7). Similar analysis of PKD1 informative pairs and those with parents born before 1930 showed no differences in age at ESRD. Male ADPKD patients were 42% more likely to reach ESRD ( P P = 0.01) than female patients. Limitations Hypertension treatment unknown. Conclusions We found no evidence for anticipation of ESRD in patients with ADPKD; thus, the observed variation in age at ESRD may result from other genetic, sex, or environmental causes.
Guest editorial how to avoid the reviewer's axe: one editor's view

Editor’s Note: Stephen D. Senturia has been a member of the Board of Editors for IEEE/ASME JMEMS since the journal’s first issue in 1992 and was named a Senior Editor in 1998. This experience, coupled with his service from 1985–1995 as the Solid-State Sensors Editor for the IEEE Transactions on Electron Devices, adds up to 17 years in an editor’s chair. Over the years, Steve has kept mental notes on the myriad of problems that authors have with reviewers and has been inspired to compile the following “advice to the author” about ways to keep reviewers satisfied; hence, to keep them “at bay.”
Mutation Rates, Spectra, and Genome-Wide Distribution of Spontaneous Mutations in Mismatch Repair Deficient Yeast

DNA mismatch repair is a highly conserved DNA repair pathway. In humans, germline mutations in hMSH2 or hMLH1, key components of mismatch repair, have been associated with Lynch syndrome, a leading cause of inherited cancer mortality. Current estimates of the mutation rate and the mutational spectra in mismatch repair defective cells are primarily limited to a small number of individual reporter loci. Here we use the yeast Saccharomyces cerevisiae to generate a genome-wide view of the rates, spectra, and distribution of mutation in the absence of mismatch repair. We performed mutation accumulation assays and next generation sequencing on 19 strains, including 16 msh2 missense variants implicated in Lynch cancer syndrome. The mutation rate for DNA mismatch repair null strains was approximately 1 mutation per genome per generation, 225-fold greater than the wild-type rate. The mutations were distributed randomly throughout the genome, independent of replication timing. The mutation spectra included insertions/deletions at homopolymeric runs (87.7%) and at larger microsatellites (5.9%), as well as transitions (4.5%) and transversions (1.9%). Additionally, repeat regions with proximal repeats are more likely to be mutated. A bias toward deletions at homopolymers and insertions at (AT)n microsatellites suggests a different mechanism for mismatch generation at these sites. Interestingly, 5% of the single base pair substitutions might represent double-slippage events that occurred at the junction of immediately adjacent repeats, resulting in a shift in the repeat boundary. These data suggest a closer scrutiny of tumor suppressors with homopolymeric runs with proximal repeats as the potential drivers of oncogenesis in mismatch repair defective cells.
Compensatory Evolution in RNA Secondary Structures Increases Substitution Rate Variation among Sites

There is growing evidence that interactions between biological molecules (e.g., RNA-RNA, protein-protein, RNA-protein) place limits on the rate and trajectory of molecular evolution. Here, by extending Kimura's model of compensatory evolution at interacting sites, we show that the ratio of transition to transversion substitutions (kappa) at interacting sites should be equal to the square of the ratio at independent sites. Because transition mutations generally occur at a higher rate than transversions, the model predicts that kappa should be higher at interacting sites than at independent sites. We tested this prediction in 10 RNA secondary structures by comparing phylogenetically derived estimates of kappa in paired sites within stems (kappa(p)) and unpaired sites within loops (kappa(u)). Eight of the 10 structures showed an excellent match to the quantitative predictions of the model, and 9 of the 10 structures matched the qualitative prediction kappa(p) > kappa(u). Only the Rev response element from the human immunovirus (HIV) genome showed the reverse pattern, with kappa(p) < kappa(u). Although a variety of evolutionary forces could produce quantitative deviations from the model predictions, the reversal in magnitude of kappa(p) and kappa(u) could be achieved only by violating the model assumption that the underlying transition (or transversion) mutation rates were identical in paired and unpaired regions of the molecule. We explore the ability of the APOBEC3 enzymes, host defense mechanisms against retroviruses, which induce transition mutations preferentially in single-stranded regions of the HIV genome, to explain this exception to the rule. Taken as a whole, our findings suggest that kappa may have utility as a simple diagnostic to evaluate proposed secondary structures.
Attention-getting skills of deaf children using American Sign Language in a preschool classroom

Visual attention is a necessary prerequisite to successful communication in sign language. The current study investigated the development of attention-getting skills in deaf native-signing children during interactions with peers and teachers. Seven deaf children (aged 21-39 months) and five adults were videotaped during classroom activities for approximately 30 hr. Interactions were analyzed in depth to determine how children obtained and maintained attention. Contrary to previous reports, children were found to possess a high level of communicative competence from an early age. Analysis of peer interactions revealed that children used a range of behaviors to obtain attention with peers, including taps, waves, objects, and signs. Initiations were successful approximately 65% of the time. Children followed up failed initiation attempts by repeating the initiation, using a new initiation, or terminating the interaction. Older children engaged in longer and more complex interactions than younger children. Children's early exposure to and proficiency in American Sign Language is proposed as a likely mechanism that facilitated their communicative competence.
Gain and power of CO2 gasdynamic lasers.

This paper presents experimental and theoretical studies of the small signal gain and the radiant power for one configuration of CO2 gasdynamic lasers to define the optimum-gas temperature, pressure and gas compositions for the gain and the laser power. The laser was operated with two gas mixtures (CO2-N2-He and CO2-N2-H2O) at temperatures of 800-2200 deg K, pressures of 2-16 atm, and a wide range of gas compositions. For this laser optimum gas temperatures were roughly 1500-1600 deg K for gain and more than 2200 deg K for power. It was found that the gasdynamic laser would not oscillate for He or H2O concentrations of less than 10% and 1%, respectively. The various kinetic processes for establishing gain and the various laser cavity parameters that determine laser power were examined. The theories were assessed for their ability to predict gain and power. In most cases, the gain theory gave excellent quantitative results whereas the power theory gave only qualitative results. Laser power of nearly 2 kw was obtained.
Isolation and characterization of microsatellite loci from the endangered highlands scrub hypericum (Hypericum cumulicola)

We report the isolation of 19 primer pairs for amplification of polymorphic microsatellite loci for Hypericum cumulicola. These markers were evaluated in 24 individuals from one population; two to four alleles were detected per locus, and observed heterozygosity ranged from 0 to 0.5. Two loci demonstrated significant heterozygote deficiencies, possibly due to null alleles, and significant linkage disequilibrium was found between six pairs of loci. The remaining microsatellite loci will help determine if genetic differentiation is responsible for life-history differences between natural and anthropogenically disturbed populations of H. cumulicola.
Nash Equilibrium Problems With Scaled Congestion Costs and Shared Constraints

We consider a class of convex Nash games where strategy sets are coupled across agents through a common constraint and payoff functions are linked via a scaled congestion cost metric. A solution to a related variational inequality problem provides a set of Nash equilibria characterized by common Lagrange multipliers for shared constraints. While this variational problem may be characterized by a non-monotone map, it is shown to admit solutions, even in the absence of restrictive compactness assumptions on strategy sets. Additionally, we show that the equilibrium is locally unique both in the primal space as well as in the larger primal-dual space. The existence statements can be generalized to accommodate a piecewise-smooth congestion metric while affine restrictions, surprisingly, lead to both existence and global uniqueness guarantees. In the second part of the technical note, we discuss distributed computation of such equilibria in monotone regimes via a distributed iterative Tikhonov regularization (ITR) scheme. Application to a class of networked rate allocation games suggests that the ITR schemes perform better than their two-timescale counterparts.
Fast two-level-dynamic-programming algorithm for speech recognition

A three-stage architecture for speech recognition is presented; it includes preprocessing, phoneme recognition, and natural language postprocessor. Within this context of phoneme-based utterance recognition, the paper focuses on the often problematic speed of the second stage and reengineers a standard two-level-dynamic-programming (TLDP) approach to achieve an increase in speed of 75%. Our fast two-level-dynamic-programming algorithm (FTLDP) uses a phoneme clustering technique to reduce the reference search space and silence detection to reduce the length of the utterance to recognize. An overview of the FTLDP algorithm is presented as well as some results.
US Household Food Shopping Patterns: Dynamic Shifts Since 2000 And Socioeconomic Predictors.

Under the assumption that differential food access might underlie nutritional disparities, programs and policies have focused on the need to build supermarkets in underserved areas, in an effort to...
Dynamic Programming Algorithms for Haplotype Block Partition and Applications to Association Studies

We develop a dynamic programming algorithm for haplotype block partitioning to minimize the number of representative single nucleotide polymorphisms (SNPs) required to account for most of the haplotype quality in each block. The block quality is a function of the haplotypes defined by the SNPs in the block. Any measure of haplotype quality can be used in the algorithm and of course the measure should depend on the specific application. The dynamic programming algorithm is applied to analyze the haplotype data on chromosome 21 of Patil et al. Using the same criteria as in Patil et al. (6), we identify a total of 3,582 representative SNPs and 2,575 blocks which are 21.5% and 37.7%, respectively, smaller than those identified using a greedy algorithm of Patil et al. We also compare the power of association studies using all SNPs, tag SNPs and the same number of randomly chosen SNPs.
Laparoscopic treatment of endometrial cancer: A cost-effectiveness analysis

6127 Background: Endometrial cancer has traditionally been staged using an open abdominal incision. Laparoscopic staging offers the benefits of a minimally invasive approach and may also be economi...
Connecting Replication and Repair: YoaA, a Helicase-Related Protein, Promotes Azidothymidine Tolerance through Association with Chi, an Accessory Clamp Loader Protein

Elongating DNA polymerases frequently encounter lesions or structures that impede progress and require repair before DNA replication can be completed. Therefore, directing repair factors to a blocked fork, without interfering with normal replication, is important for proper cell function, and it is a process that is not well understood. To study this process, we have employed the chain-terminating nucleoside analog, 3’ azidothymidine (AZT) and the E. coli genetic system, for which replication and repair factors have been well-defined. By using high-expression suppressor screens, we identified yoaA, encoding a putative helicase, and holC, encoding the Chi component of the replication clamp loader, as genes that promoted tolerance to AZT. YoaA is a putative Fe-S helicase in the XPD/RAD3 family for which orthologs can be found in most bacterial genomes; E. coli has a paralog to YoaA, DinG, which possesses 5’ to 3’ helicase activity and an Fe-S cluster essential to its activity. Mutants in yoaA are sensitive to AZT exposure; dinG mutations cause mild sensitivity to AZT and exacerbate the sensitivity of yoaA mutant strains. Suppression of AZT sensitivity by holC or yoaA was mutually codependent and we provide evidence here that YoaA and Chi physically interact. Interactions of Chi with single-strand DNA binding protein (SSB) and with Psi were required to aid AZT tolerance, as was the proofreading 3’ exonuclease, DnaQ. Our studies suggest that repair is coupled to blocked replication through these interactions. We hypothesize that SSB, through Chi, recruits the YoaA helicase to replication gaps and that unwinding of the nascent strand promotes repair and AZT excision. This recruitment prevents the toxicity of helicase activity and aids the handoff of repair with replication factors, ensuring timely repair and resumption of replication.
Cross-species transmission of CWD prions

Prions cause fatal neurodegenerative diseases in humans and animals and can be transmitted zoonotically. Chronic wasting disease (CWD) is a highly transmissible prion disease of wild deer and elk that affects cervids over extensive regions of the United States and Canada. The risk of cross-species CWD transmission has been experimentally evaluated in a wide array of mammals, including non-human primates and mouse models expressing human cellular prion protein. Here we review the determinants of cross-species CWD transmission, and propose a model that may explain a structural barrier for CWD transmission to humans.
Hydration of the Fluoride Anion: Structures and Absolute Hydration Free Energy from First-Principles Electronic Structure Calculations

A series of first-principles electronic structure calculations have been performed to determine the most stable structures of F-(H2O)n clusters (n = 4, 8, 12, and 16) and the hydration free energy of fluoride anion (F-). The calculated results show that a new, tetrahedrally coordinated fluoride anion hydration structure F-(H2O)4 cluster is lower in Gibbs free energy than the previously considered most stable structure of F-(H2O)4. The first ab initio prediction of potential stable hydration structures for F-(H2O)n clusters (n = 8, 12, and 16) are given. The energetic results show that the tetrahedrally coordinated fluoride anion hydration structure becomes more stable as compared to the other hydration structures with a pyramidal coordination, i.e., a surface ion cluster state, as the cluster size increases from n = 8 to n = 12 to n = 16. This suggests that, with increasing n, the fluoride anion will be internally solvated in large enough F-(H2O)n clusters. These results provide insight into the transitio...