cssi/SciSciGPT-SciSciNet huggingface dataset:
Conserved small RNAs govern replication and incompatibility of a diverse new plasmid family from marine bacteria

Plasmids are autonomously replicating extrachromosomal DNA molecules that often impart key phenotypes to their bacterial hosts. Plasmids are abundant in marine bacteria, but there is scant knowledge of the mechanisms that control their replication in these hosts. Here, we identified and characterized the factors governing replication of a new family of plasmids from marine bacteria, typified by the virulence-linked plasmid pB1067 of Vibrio nigripulchritudo. Members of this family are prevalent among, yet restricted to, the Vibrionaceae. Unlike almost all plasmid families characterized to date, the ori regions of these plasmids do not encode a Rep protein to initiate DNA replication; instead, the ori regions encode two partially complementary RNAs. The smaller, termed RNA I, is ∼68-nt long and functions as a negative regulator and the key determinant of plasmid incompatibility. This Marine RNA-based (MRB) plasmid family is the first characterized family of replicons derived from marine bacteria. Only one other plasmid family (the ColE1 family) has previously been reported to rely on RNA-mediated replication initiation. However, since the sequences and structures of MRB RNA I transcripts are not related to those of ColE1 replicons, these two families of RNA-dependent replicons likely arose by convergent evolution.
Genetic basis for multimodal relationship between apolipoprotein (a) size and lipoprotein (a) concentration in Mexican-Americans

The reported general inverse relationship between apolipoprotein (a) (apo(a)) size and plasma lipoprotein (a) (Lp(a)) concentrations was further characterized using 927 samples taken from members of 42 Mexican-American families. When all samples were displayed in a scatter plot of apo(a) size versus natural log of Lp(a) concentration, the expected inverse relationship was observed (r2 = 0.24). However, the scatter plot revealed a multimodal pattern with at least two distinct modes of the inverse relationship between apo(a) size and Lp(a) concentration. Plots of 148 single-banded samples also showed the multimodal pattern, indicating that this pattern did not result from a difference between double- and single-banded samples. Also measured was the Lp(a) concentration associated with each of 508 apo(a) isoforms in samples from 254 double-banded phenotype individuals. These separated isoforms also showed the multimodal pattern. Using pedigree information, 29 different alleles were identified which were found in three or more family members. About 85% of variation in Lp(a) was explained by allele information, suggesting a genetic basis for the multimodal pattern. Thus, the data demonstrate at least two series of apo(a) alleles that have distinct relationships between apo(a) size and Lp(a) concentration.
Periodontal Disease and Recurrent Cardiovascular Events in Survivors of Myocardial Infarction (MI): The Western New York Acute MI Study

Background: Periodontal disease and cardiovascular disease (CVD) have been the focus of much research, but little is known about their roles in the recurrent event risk in patients with CVD. This study investigates whether periodontal disease is related to recurrent CVD events and mortality in survivors of incident myocardial infarction (MI).Methods: Participants (668 males and 216 females; mean age: 54 ± 8.5 years) were recruited (1997 through 2004) from two western New York county hospitals and completed an interviewer-administered questionnaire regarding lifestyle habits, clinical measurements, and a comprehensive dental examination. The periodontal disease status was measured by the mean clinical attachment loss (AL). Follow-up surveys assessed hospitalizations or medical procedures; cardiovascular events were validated by medical records. A National Death Index (NDI) Plus search was conducted. The outcome was recurrent fatal and non-fatal cardiovascular events (International Classification of Disease...
Indications, integration, and technical aspects of local-regional irradiation in the management of advanced breast cancer

This article reviews the indications for radiotherapy in advanced stage disease and discusses the recent prospective trials demonstrating a survival benefit by the addition of radiotherapy. Various treatment plans are reviewed with and without internal mammary node coverage. Although it is not clear whether internal mammary node irradiation can have a favorable impact on survival, it is clear that inadequate treatment planning of the parasternal region can result in excess cardiac morbidity and mortality. Careful planning using computed tomographic systems is required to optimize chest wall planning. With individualized treatment planning, it is hoped that the next generation of trials will show improved survival from further reduction in breast cancer deaths and significantly decreased cardiac toxicity.
Dependence of 5-fluorouracil-mediated radiosensitization on DNA-directed effects

Abstract Purpose : Although 5-fluorouracil (FUra) has been demonstrated to be a radiation sensitizer both in the laboratory and the clinic, it is not known whether radiosensitization results primarily from FUra's DNA or RNA-directed effects. Methods and Materials : We studied the radiosensitizing effects of FUra ± thymidine (dThd)) on HT29 human colon cancer cells, which are relatively sensitive to the DNA-directed action of FUra, in comparison to SW620 and HuTu80 human colon cancer cells, which are relatively resistant to FUra's DNA-directed effects. We hypothesized that if FUra were acting chiefly through DNA dependent mechanisms, HT29 cells would (a) show greater radiosensitization than SW620 and HuTu80 cells under the same conditions of exposure; and (b) demonstrate selective reversal of radiation sensitivity (compared to cytotoxicity) in the presence of FUra + dThd, compared to FUra alone. Results : We found that the enhancement ratio produced by a 24 h exposure to 10 μM FUra was significantly greater in HT29 cells compared to SW620 and HuTu80 cells (enhancement ratios of 2.1 ± 0.1; 1.1 ± 0.1, and 1.3 ± 0.1, respectively). Furthermore, in HT29 cells, dThd blocked FUra-mediated radiosensitization to a greater extent than FUra-mediated cytotoxicity. Thus, our hypotheses were confirmed. Conclusion : These findings support the concept that the manipulation of FUra's DNA-dependent actions, for example, through modulators of thymidylate synthase (TS) activity, may increase radiosensitization in clinical trials in the treatment of gastrointestinal cancers. However, since resistance to the DNA-directed effects of fluoropyrimidines can result from mechanisms unrelated to TS inhibition, additional strategies will be required to potentiate fluoropyrimidine-mediated radiosensitization.
CD28 and ICOS play complementary non-overlapping roles in the development of Th2 immunity in vivo

Previous work has shown ICOS can function independently of CD28, but whether either molecule can compensate for the other in vivo is not known. Since ICOS is a potent inducer of Th2 cytokines and linked to allergy and elevated serum IgE in humans, we hypothesized that augmenting ICOS costimulation in murine allergic airway disease may overcome CD28 deficiency. While ICOS was expressed on T cells from CD28(-/-) mice, Th2-mediated airway inflammation was not induced in CD28(-/-) mice by increased ICOS costimulation. Further, we determined if augmenting CD28 costimulation could compensate for ICOS deficiency. ICOS(-/-) mice had a defect in airway eosinophilia that was not overcome by augmenting CD28 costimulation. CD28 costimulation also did not fully compensate for ICOS for antibody responses, germinal center formation or the development of follicular B helper T cells. CD28 and ICOS play complementary non-overlapping roles in the development of Th2 immunity in vivo.
Effects of abstinence from smoking on sleep and daytime sleepiness

This study examined the effect of smoking abstinence on sleep quality, daytime sleepiness, and mood in 18 subjects (10 men and 8 women) aged 35 to 49 years who had smoked at least 20 cigarettes per day for more than 2 years. Subjects were studied on two consecutive weeks following an adaptation night. During week 1 (study nights 1, 2, and 3), the subjects smoked as usual. Smoking abstinence was mandatory during week 2 beginning 3 h prior to night 4 and ending after the final tests on night 6. Complete sleep monitoring each night was followed by multiple sleep latency tests (MSLTs) throughout the day. Psychomotor tests and mood observations were performed throughout the day between the MSLTs. The results of testing when the subjects smoked were compared with those during nonsmoking days and nights. Nights 1 and 4 were considered adaptation nights and not included in the analysis. Overnight studies showed a significant increase in the number of relative arousals (a change in sleep stage to wake, stage 1 sleep, or movement), stage changes, and awakenings during smoking cessation. The MSLT latency to stage 1 sleep decreased during smoking cessation. Also during abstinence, the subjects reported that they felt more irritable, had increased feelings of anxiety, felt greater tension, and had more cravings for cigarettes. We conclude that smoking cessation is associated with increased daytime sleepiness and impaired mood. The daytime sleepiness may be due to the combination of sleep disturbance and withdrawal of the nicotine normally provided through smoking.
Stent graft repair of paraanastomotic aneurysms after open descending thoracic and thoracoabdominal aortic aneurysm repair.

Background After open thoracic and thoracoabdominal aortic aneurysm repair, anastomotic aneurysms can form at or near the suture lines of the graft. Endovascular repair is an alternative to complicated reoperative open surgery. We report on our experience with endovascular treatment of these lesions. Methods A prospectively maintained database of endovascular thoracic aortic aneurysm repairs (TEVARs) performed at Mount Sinai Medical Center was reviewed and the initial procedures, comorbidities, clinical presentation, aneurysm characteristics, type of endograft, adjunctive procedures, and follow-up were analyzed. Results Of the 135 TEVAR procedures performed between June 2001 and December 2008, 9 patients had anastomotic aneurysms after a previous open repair. The mean age was 66.7 (range 41–89) years, 67% of whom were male. Of these 9 patients, 5 had a descending thoracic repair, 3 had a type IV repair, and 1 had a type II thoracoabdominal repair. Aneurysm formation occurred in the following regions: proximal anastomosis ( n = 2); intercostal patch ( n = 1); distal anastomosis ( n = 3); visceral patch ( n = 2); and midgraft ( n = 1). The initial technical success rate was 100%, with 8 patients receiving a thoracic tube graft and 1 a modular bifurcated device. Two patients required an adjunctive carotid–subclavian bypass and 2 required extraanatomic revascularization of the visceral arteries. Mean follow-up was 16.5 months. There was 1 perioperative death secondary to a postoperative myocardial infarction. Three patients developed an endoleak with 1 requiring an intervention. One patient required an open thoracoabdominal repair at 3 months for a penetrating ulcer at the visceral segment and another died from a ruptured thoracic aneurysm proximal to the stent graft at 72 months. Two more died during the follow-up period of non–aneurysm-related causes. Five patients had paraanastomotic shrinkage or no change and 1 had an increase in size, and 3 had no follow-up imaging. Conclusions Stent graft repair of paraanastomotic aneurysms after open descending thoracic and thoracoabdomninal repair is a reasonable option when patients have suitable anatomy. These patients, however, require close follow-up for the development of aneurysmal degeneration adjacent to the stent graft repair.
Benzo[a]pyrene-7,8-dihydrodiol: Selective binding to single stranded DNA and inactivation of ØX174 DNA infectivity

Abstract When single-stranded OX174 DNA is exposed to certain dihydrodiol derivatives of benzo[a]pyrene and benz[a]anthracene, inhibition of viral DNA infectivity is observed. Binding studies with labeled trans -7,8-dihydrodiol of benzo[a]pyrene and anti -benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide indicate that the diol preferentially reacts with single-stranded DNA, whereas the diolepoxide reacts equally well with both single- and double-stranded DNA, as well as with RNA. Also, the diol and diolepoxide derivatives show a marked difference in their capacity to complex with specific deoxyhomopolymers, i.e., Poly dI. These observations suggest that the diol and diolepoxide derivatives recognize different binding sites in nucleic acids, and that the diol derivative may play an important role in mutagenesis and carcinogenesis induced by polycyclic aromatic hydrocarbons.
Parallelization of reordering algorithms for bandwidth and wavefront reduction

Many sparse matrix computations can be speeded up if the matrix is first reordered. Reordering was originally developed for direct methods but it has recently become popular for improving the cache locality of parallel iterative solvers since reordering the matrix to reduce bandwidth and wave front can improve the locality of reference of sparse matrix-vector multiplication (SpMV), the key kernel in iterative solvers. In this paper, we present the first parallel implementations of two widely used reordering algorithms: Reverse Cut hill-McKee (RCM) and Sloan. On 16 cores of the Stampede supercomputer, our parallel RCM is 5.56 times faster on the average than a state-of-the-art sequential implementation of RCM in the HSL library. Sloan is significantly more constrained than RCM, but our parallel implementation achieves a speedup of 2.88X on the average over sequential HSL-Sloan. Reordering the matrix using our parallel RCM and then performing 100 SpMV iterations is twice as fast as using HSL-RCM and then performing the SpMV iterations, it is also 1.5 times faster than performing the SpMV iterations without reordering the matrix.
Self-consistent electronic structure of lithium clusters.

The electronic structure of lithium clusters with 15, 27, and 59 atoms has been calculated self-consistently with use of the linear combination of atomic orbitals method. The results suggest that the conduction electrons in these clusters behave much like electrons in the spherical jellium-background model in that a similar shell-like structure is seen, albeit split by the crystal field. Friedel oscillations that appear in the conduction electron density are also much like those of jellium-sphere calculations. The crystal field removes the high degeneracy of the spherical symmetry, distributing the energy levels over the conduction band without destroying the shell-like structure. For clusters in the size range we have investigated, large energy gaps between shells should strongly influence cluster stability. Stability may also depend on crystal-field splitting to a lesser degree. In larger clusters the energy gaps between shells will become comparable to the crystal-field splitting and the shell-like structure will disappear. Mulliken population analysis and conduction-band widths indicate a trend towards bulk with increasing cluster size, although the electron density in the center of the largest cluster may not be entirely bulklike because of the penetration of Friedel oscillations.
On the induced phase shift of dynamically forced optical fibers: theory and numerical simulation

In this paper, we present a formulation and numerical simulation for the phase shift of light as it is passed through dynamically forced optical fibers. A generalized representation for the induced phase shift, as well as a finite element model appropriate for an isotropic, arbitrarily oriented fiber is developed. These general expressions are then specialized to the particular case of a straight, finite length of fiber, which is forced normally along its entire length. Calculations are carried out for three quite different fiber configurations over a spectrum of frequencies, and the resulting phase and strain responses are presented and discussed.
Platelet Gene Expression as a Biomarker Risk Stratification Tool in Acute Myocardial Infarction: A Pilot Investigation

Platelets play a major role in the pathophysiology of acute myocardial infarction (AMI). Recent evidence reveals megakaryocyte-derived platelet pre-mRNA is spliced to mRNA and then translated into functional proteins in response to external stimulation. An exon microarray analyzes pre-mRNA alternative splicing and is thus applicable for studying gene expression in the anucleate platelet. We hypothesized a subset of megakaryocyte/platelet genes exists that are significantly over or underexpressed in AMI compared with stable coronary artery disease (CAD), yielding a gene expression profile for further study. Microarray analysis employing platelet mRNA was used to generate gene expression data in the above two patient groups. Unsupervised hierarchical clustering has revealed an expression profile that includes 95 over- or under-expressed genes depicted in a heat map where separation of both sets takes place. This preliminary study reveals a platelet-based gene expression signature that differentiates between AMI and stable CAD, and further study may yield a prognostic tool for a future AMI event in atherosclerosis risk factor-based subsets of CAD patients.
An image algebra for pictorial data manipulation

Abstract Manipulation and transformation of symbolic images requires, in order to become efficient, various high-level data structures and procedures. This is especially true for applications of heuristic type. This paper introduces an image algebra which is based on symbolic projections and includes three fundamental aspects, i.e., a set of powerful relational operators, a generalized representation of "empty space" objects, and multilevel data representation for hierarchical data. Application to spatial reasoning is discussed.
Acoustic characteristics and dynamic structural loading of an ASTOVL aircraft in hover

Measurements of surface dynamic loading and freestream acoustics were made for an ASTOVL model in hover, to quantify the effects of elevated temperature on the acoustic field and surface loading. Data were acquired for a many combinations of operating parameters: model height above the ground plane, nozzle pressure ratio, and jet exit stagnation temperature. For many conditions, strong tones were observed, with amplitudes up to 150 dB. The frequencies of the strongest tones were well predicted by a model assuming feedback between the nozzle exit and the ground plane. The model also accounts for many of the variations in frequency observed with changes in model height, nozzle pressure ratio, and jet temperature. Broadband sound pressure levels up to 170 dB were also recorded. The maximum levels occurred at approximately 3 equivalent jet diameters above the ground plane. For the majority of the cases, the increase in noise due to temperature was less than expected based on free jet correlations.
The Preterm Prediction Study: Effect of gestational age and cause of preterm birth on subsequent obstetric outcome

Abstract Objective: We sought to evaluate the association between prior spontaneous preterm delivery and subsequent pregnancy outcome. Study Design: A total of 1711 multiparous women with singleton gestations were prospectively evaluated at 23 to 24 weeks' gestation. Prior pregnancies were coded for the presence or absence of a prior spontaneous preterm delivery. If a prior spontaneous preterm delivery had occurred, the gestation of the earliest prior delivery (13-22, 23-27, 28-34, and 35-36 weeks' gestation) was recorded. Current gestations were categorized as spontaneous preterm delivery at Results: The incidences of spontaneous preterm delivery before 28, 30, 32, 35, and 37 weeks' gestation were 0.8%, 1.1%, 1.9%, 5.1%, and 11.9%, respectively. Those with a prior spontaneous preterm delivery carried a 2.5-fold increase in the risk of spontaneous preterm delivery in the current gestation over those with no prior spontaneous preterm delivery (21.7% vs 8.8%; P ≤ .001). Gravid women with an early prior spontaneous preterm delivery (23-27 weeks' gestation) had a higher risk of recurrent spontaneous preterm delivery (27.1% vs 8.8%; P ≤ .001). Prior spontaneous preterm delivery was more closely associated with subsequent early spontaneous preterm delivery at P Conclusion: Prior spontaneous preterm delivery is highly associated with recurrence in the current gestation. An early prior spontaneous preterm delivery is more predictive of recurrence and is most highly associated with subsequent early spontaneous preterm delivery. (Am J Obstet Gynecol 1999;181:1216-21.)
Endovascular repair of thoracic aortic lesions with the Zenith TX1 and TX2 thoracic grafts: Intermediate-term results

Purpose This prospective study was designed to assess the technical success and outcome after patients with thoracic aortic pathology at high risk for conventional therapy were treated with the Zenith TX1 and TX2 endovascular graft. Methods Between 2001 and 2004, patients at high risk for conventional surgical therapy presenting with chronic aortic dissections, thoracic aneurysms, or aortobronchial or aortoesophageal fistulas were treated with a single- or multiple-piece endovascular grafts. Surgical modification of proximal or distal fixation sites was performed when necessary to establish adequate regions for device landing zones. Follow-up studies included radiographic evaluation before discharge and at 1, 6, 12, and 24 months. Aortic morphologic characteristics were determined by using three-dimensional imaging studies and centerline of flow measurements. Statistical analyses were performed with Kaplan Meier analysis to assess survival, factors predictive of poor outcome, and morphologic changes, including sac shrinkage. Results A total of 100 patients (42% women) were treated, including 81 aneurysms, 15 aortic dissections (with aneurysms), 2 patients with fistulous connections (1 aortobronchial and 1 aortoesophageal), 1 subclavian artery aneurysm, and 1 aortic rupture. Mean follow-up and aneurysm size were 14 months and 62 mm, respectively. Most patients (55%) had undergone prior aortic aneurysm repair. Surgical modifications were required to create adequate implantation sites in 29% patients, including 14 elephant trunk/arch reconstructions, 18 carotid-subclavian bypasses, and 4 visceral vessel bypasses. Iliac conduits were required in 19 patients. Overall mortality was 17%, and aneurysm-related mortality was 14% at 1 year. Sac regression (>5 mm maximum diameter decrease) was observed in 52% and 56% at 12 and 24 months. Growth was noted in one patient (1.6%) at 12 months. Endoleaks were detected in eight patients (8.5%) at 30 days and three patients (6%) at 12 months. Secondary interventions were required in 15 patients. Migration (>10 mm) of the proximal or distal stent was noted in three patients (6%) (two proximal and one distal), none of which required treatment or resulted in an adverse event. Conclusions Acceptable intermediate-term outcomes have been achieved in the treatment of high-risk patients in the setting of both favorable and challenging anatomic situations with these devices. The complexity of the patient population, in contrast to endovascular infrarenal repair, attests to the differences in the pathophysiology aortic disease in the anatomic beds.
Determination of stability constants of Cu(I), Cd(II) & Zn(II) complexes with thiols using fluorescent probes

Fluorometric competing-ligand titrations were used to measure stability constants of Zn(II), Cd(II) and Cu(I) complexes of cysteine and glutathione (GSH). Cu(I)-stability constants were also determined for the dipeptides Arg-Cys and Gln-Cys which are produced by a marine alga under copper stress. The fluorescent ion indicators FluoZin-1 and BTC (Invitrogen) were used as competing ligands in titrations involving Zn(II) and Cd(II). Phen Green SK (Invitrogen) was likewise used in Cu(I) titrations. Conditional and cumulative general stability constants were determined using a least squares fit of the titration data to speciation models. The measured stability constants of Cd(II) and Zn(II) complexes were consistent with previous work, validating our method and assumptions. Our results also include the first general stability constants for Cu(I)-cysteine complexes and an alternative set for Cu(I)-GSH complexes. While these stability constants indicate that Cu(I) forms strong complexes with thiols, they are not strong enough to effectively buffer Cu(I) in seawater.
Epitaxially grown graphene field-effect transistors with electron mobility exceeding 1500 cm 2 /Vs and hole mobility exceeding 3400 cm 2 /Vs

In this paper, we report, for the first time, the observation of n-type and p-type transition on epitaxially grown graphene films by top-gate bias. More importantly, the measured electron and hole mobility on fabricated top-gate graphene field-effect transistors exceeds 1500 cm2/Vs and 3400 cm2/Vs, respectively.
NONSIMILAR SOLUTIONS FOR HEAT TRANSFER IN WALL JET FLOWS

An analysis is presented to investigate the flow and heat transfer characteristics of a laminar plane wall jet with non-isothermal wall as well as uniform suction and blowing at the surface and a laminar cylindrical wall jet. The approach used is local nonsimilarity method, wherein, the nonsimilanty terms appearing in the momentum and energy equations are retained and simplifications are introduced only in the auxiliary system of equations. To insure the accuracy of the results, solutions are obtained for three levels of truncation of the governing equations. For the case of plane wall jet problem, both a series solution as well as local nonsimilarity solution have been given and the agreement between the two is found to be very good. For the cylindrical wall jet problem, the results obtained by the local nonsimilarity approach in the present paper have been compared with the series solution results. Numerical results for the wall shear stress, velocity distribution, wall heat transfer rate and temperatur...
A simple technic for making dental porcelain jacket crowns.

6. A rubber impression in a compound lined tray must be poured within three hours; if compound is not used to line the tray, the impression may be poured days later. 7. Sufficient setting time for the rub­ ber material should be allowed to achieve resiliency. At least ten minutes from start of mixing is recommended as being sufficient. 8. The enamel portion of the proxi­ mal buccal and lingual walls of the cav­ ity preparation should be flared well into the buccal and lingual embrasures, wherever compatible with esthetics. 9. The tray method of impression taking is recommended. 10. Salivation must be controlled by profound local anesthesia for the tray impression technic. 11. The rubber material is remark­ ably stable. 12. The surface of dies from the rub­ ber impression is superior to that of dies from reversible hydrocolloid. 13. A rubber impression of the tray type permits a second pouring. 14. It is not recommended that an attempt be made to correct a rubber impression by adding newly mixed rub­ ber and reseating. 15. An impression technic is recom­ mended which revolves around the simul­ taneous use of two rubber materials of different viscosities, and a newly designed plastic tube or plastic tipped syringe.
Insights into activity-dependent map formation from the retinotectal system: a middle-of-the-brain perspective

The development of orderly topographic maps in the central nervous system (CNS) results from a collaboration of chemoaffinity cues that establish the coarse organization of the projection and activity-dependent mechanisms that fine-tune the map. Using the retinotectal projection as a model system, we describe evidence that biochemical tags and patterned neural activity work in parallel to produce topographically ordered axonal projections. Finally, we review recent experiments in other CNS projections that support the proposition that cooperation between molecular guidance cues and activity-dependent processes constitutes a general paradigm for CNS map formation.
2-halogenoethylamines as potential folic acid antagonists I. Synthesis and biological activity of ethyl-N-[1-(2-amino-4-hydroxy-6-methyl-5-pyrimidyl)-3-(2-chloro)- propyl]-p-aminobenzoate

The synthesis of the title compound (VII) is described. The key intermediate in this synthesis was prepared from 1-chloro-2,3-epoxypropane and ethyl- p -aminobenzoate. Preliminary biological data, including toxicity, and antitumor and folic reductase inhibitory actions, are presented.
Manipulated flow reduces downstream defensiveness

Flow is a psychological state people experience when performing highly challenging tasks with a high degree of skill. It is related to happiness, creativity, and productivity. In three experiments, we developed a manipulation of flow and assessed its effects on subsequent defensive behavior. In all three experiments, participants who played a game with more features of flow (e.g. engagement, match of challenge and skill, performance feedback) reported more feelings of flow (e.g. enjoyment, concentration and interest) and less downstream defensiveness. The results suggest that we developed a flexible, reliable manipulation of flow, and that inducing people to experience flow may reduce their subsequent defensive behavior.
Performance Modeling and Optimization of Deadline-Driven Pig Programs

Many applications associated with live business intelligence are written as complex data analysis programs defined by directed acyclic graphs of MapReduce jobs, for example, using Pig, Hive, or Scope frameworks. An increasing number of these applications have additional requirements for completion time guarantees. In this article, we consider the popular Pig framework that provides a high-level SQL-like abstraction on top of MapReduce engine for processing large data sets. There is a lack of performance models and analysis tools for automated performance management of such MapReduce jobs. We offer a performance modeling environment for Pig programs that automatically profiles jobs from the past runs and aims to solve the following inter-related problems: (i) estimating the completion time of a Pig program as a function of allocated resources; (ii) estimating the amount of resources (a number of map and reduce slots) required for completing a Pig program with a given (soft) deadline. First, we design a basic performance model that accurately predicts completion time and required resource allocation for a Pig program that is defined as a sequence of MapReduce jobs: predicted completion times are within 10p of the measured ones. Second, we optimize a Pig program execution by enforcing the optimal schedule of its concurrent jobs. For DAGs with concurrent jobs, this optimization helps reducing the program completion time: 10p--27p in our experiments. Moreover, it eliminates possible nondeterminism of concurrent jobs’ execution in the Pig program, and therefore, enables a more accurate performance model for Pig programs. Third, based on these optimizations, we propose a refined performance model for Pig programs with concurrent jobs. The proposed approach leads to significant resource savings (20p--60p in our experiments) compared with the original, unoptimized solution. We validate our solution using a 66-node Hadoop cluster and a diverse set of workloads: PigMix benchmark, TPC-H queries, and customized queries mining a collection of HP Labs’ web proxy logs.
A Multi-Agent System for Modular Platform Design in a Dynamic Electronic Market Environment

Electronic markets and web-based supply chain management have improved traditional product development processes by increasing the participation of customers and applying various trading processes between companies and suppliers in a dynamic electronic market environment. A multi-agent system is an appropriate tool to implement a product development system in a distributed environment because of its flexibility, scalability, and adaptability. This paper introduces a multi-agent system (MAS) based on market mechanisms to support modular platform design. The agent architecture for the proposed MAS is described, including specific agent roles, knowledge, and strategies. In particular, a reputation mechanism is used to select stable and reputable modules for the platform by detecting and dismissing volatile modules in a dynamic electronic market environment. We demonstrate the implementation of the proposed MAS using a multi-agent development framework and how to use module reputation for selecting a module for the platform. Through experiments, we illustrate that the MAS can be used to design modules in a product platform using the proposed market mechanisms.Copyright © 2006 by ASME
Depth-Dependent Dissociation of Nitric Acid at an Aqueous Surface: Car−Parrinello Molecular Dynamics

The acid dissociation of a nitric acid HNO3 molecule located at various depths in a water slab is investigated via Car−Parrinello molecular dynamics simulations. HNO3 is found to remain molecular when it is adsorbed on top of the surface with two hydrogen-bonds, and to dissociate—although not always—by transferring a proton to a water molecule within a few picoseconds when embedded at various depths within the aqueous layer. The acid dissociation events are analyzed and discussed in terms of the proton donor−acceptor O−O hydrogen bonding distance and the configurations of the nearest-neighbor solvent waters of an HNO3·H2O pair. Four key structural features for the HNO3 acid dissociation are identified and employed to analyze the trajectory results. Key solvent motions for the dissociation include the decrease of the proton donor−acceptor O−O hydrogen bonding distance and a 4 to 3 coordination number change for the proton-accepting water. The Eigen cation (H3O+), rather than the Zundel cation (H5O2+), is f...
Detecting low-frequency functional connectivity in fMRI using unsupervised clustering algorithms

Recent research in functional magnetic resonance imaging (fMRI) revealed slowly varying temporally correlated fluctuations between functionally related areas. These low-frequency oscillations of less than 0.08 Hz appear to be a property of symmetric cortices, and they are known to be present in the motor cortex among others. These low-frequency data are difficult to detect and quantify in fMRI. Traditionally, user-based regions of interests (ROI) or "seed clusters" have been the primary analysis method. We propose in this paper to employ unsupervised clustering algorithms employing arbitrary distance measures to detect the resting state of functional connectivity. There are two main benefits using unsupervised algorithms instead of traditional techniques: (1) the scan time is reduced by finding directly the activation data set, and (2) the whole data set is considered and not a relative correlation map. The achieved results are evaluated for different distance metrics. The Euclidian metric implemented by the standard unsupervised clustering approaches is compared with a more general topographic mapping of proximities based on the correlation and the prediction error between time courses. Thus, we are able to detect functional connectivity based on model-free analysis methods implementing arbitrary distance metrics.
Semiconductor nanostructures in biological applications

Semiconductor nanostructures in biological applications are discussed. Results are presented on the use of colloidal semiconductor quantum dots both as biological tags and as structures that interact with and influence biomolecules. Results are presented on the use of semiconducting carbon nanotubes in biological applications.
An Interview with Ilan Stavans.

Abstract This interview with Ilan Stavans addresses central experiences tied to the educational and immigrant experiences of Latinos in the United States. Culture, immigration, assimilation, and language are the prisms through which this experience is understood. Ilan Stavans responds to questions concerning cultural heterogeneity and cultural homogeneity. For instance, to what extent might any degree of homogeneity or heterogeneity among Latinos factor into their incorporation in the U. S. social order generally and the educational establishment in particular? Thus, the reader is invited to question commonsense assumptions regarding language, culture, and assimilation.
Surface-constrained 3D reconstruction in cryo-EM

Random spherically-constrained (RSC) reconstruction is a new form of single particle reconstruction (SPR) using cryo-EM images of membrane proteins embedded in spherical lipid vesicles to generate a 3D protein structure. The method has many advantages over conventional SPR, including a more native environment for protein particles and an initial estimate of the particle's angular orientation. These advances allow us to determine structures of membrane proteins such as ion channels and derive more reliable structure estimates. We present an algorithm that relates conventional SPR to the RSC model, and generally, to projection images of particles embedded with an axis parallel to the local normal of a general 2D manifold. We illustrate the performance of this algorithm in the spherical system using synthetic data.
The correlation of running ability and physiological variables in Thoroughbred racehorses

Summary The running abilities of 25 Thoroughbred racehorses were measured at distances of 1200, 1600 and 20000 m. Various physiological variables were measured subsequently on the treadmill and correlated with running speed. There was a negative correlation for running speed with the velocity (VLa4) and work rate (WLa4) at which blood lactate reaches a steady-state concentration of 4 mmol/litre and a positive correlation with peak plasma lactate, suggesting that plasma lactate concentrations of faster horses rise more rapidly and to higher levels than do those of slower horses. The correlation between running speeds and heart rates (HR) was stronger for unfit than fit horses, suggesting that cardiovascular effects of training are more beneficial to slower horses. The significant correlation between running speeds and V200 suggests that the HR of faster horses increases more rapidly than in slower horses performing similar exercise. The correlation of running speeds and O2max suggests that the HR of faster horses increases more rapidly than in slower horses performing similar exercise. The correlation of running speeds and VO2max suggests that faster horses utilise more oxygen during maximal intensity exercise. The correlation of running speeds with minimum pH and minimum HCO3− suggests that faster horses maintain speed at higher hydrogen ion (H+) concentrations. Correlations between running speeds and the measured variables were consistently stronger for the longer distance runs. Because VLa4 and WLa4 were obtained during sub-maximal exercise, these variables were determined to be the best correlates of running performance.
Ellipsometric determination of universal critical adsorption scaling functions

In this paper we determine and compare a number of theoretical models which describe the universal scaling functions for critical adsorption in the strong surface field limit. The $P1$ and $P3$ models, which are continuous up to and including the first and third derivatives, respectively, provide excellent descriptions of the ellipsometric data for four different critical binary liquid mixtures. The exponential-Pad\'e model, initially proposed by Liu and Fisher [Phys. Rev. A 40, 7202 (1989)], provides a reasonable but less accurate description of the one-phase experimental data. This later model has the advantage, however, that it is continuous in all derivatives.
A homology transfer for a class of simplicial maps

We construct a homology transfer τ*∶H*(B)→ H*(E) for a certain class of proper simplicial maps p∶E →B. Roughly, the important hypothesis is that there is a compact space F, so that all fibres Fx>=p−1(x), xɛB, are quotient spaces of F, in a certain locally controlled manner. The composition p*τ*∶ H*(B)→H*(E)→H*(B) is multiplication by the Euler characteristic of F.
Resuscitation-induced gut edema and intestinal dysfunction

Background:Mesenteric venous hypertension and subsequent gut edema play a pivotal role in the development of intra-abdominal hypertension. Although gut edema is one cause of intra-abdominal hypertension, its impact on gut function is unknown. The purpose of this study was to create a model of acute
Cognitive neuroscience and freedom: healing the disciplinary divide

Nao e nada facil admitir, por exemplo, que a vida moral, juridica instaurada e estruturada com a aceitacao, quase que dogmatica, da pressuposicao de que agimos livremente e por isso mesmo somos responsaveis por nossos atos, resultaria da nossa ignorância do que nos move a agir. Talvez seja mais dificil ainda compreender e admitir que no mundo das experiencias afetivas cotidianas seja indispensavel para constituicao de sujeitos morais responsaveis que se proceda ate certo ponto, “como se” um livrearbitrio definisse as acoes individuais. Em seu esforco de conciliar determinismo e liberdade, observamos que o pensamento de Atlan se desenvolve na fronteira dos lugares epistemologicos da ciencia e da filosofia. E tambem sua preocupacao, o que fica muito claro no texto de Ana Maria e Cecilia, que e indispensavel uma aproximacao das ciencias naturais com as ciencias humanas, sem que elas percam sua identidade epistemologica definida por seus lugares de atuacao e por seus diferentes objetivos. Compreender o mundo em que vivemos e a nos mesmos como parte dele nao sera possivel com uma ciencia que se isola das demais formas de saber e que recusa as contribuicoes que elas podem nos oferecer. E quanto a liberdade?! Se nao e facil demonstrar que somos livres, nao deixa de ser tambem dificil admitir que devamos compreender a natureza humana unicamente nos limites das determinacoes que as ciencias naturais apontam em suas manifestacoes. Vem-me a mente um texto do sociologo Peter Berger que expressa, de uma forma metaforica mas elucidativa, esta questao: localizamonos na sociedade e assim reconhecemos nossa propria posicao, determinada por fios sutis. Por um momento, vemo-nos realmente como fantoches. De repente, porem, percebemos uma diferenca decisiva entre o teatro de bonecos e nosso proprio drama. Ao contrario dos bonecos, temos a possibilidade de interromper nossos movimentos, olhando para o alto e divisando o mecanismo que nos moveu. Este ato constitui o primeiro passo para a liberdade (Berger, 2004). Apos todas estas reflexoes fica minha interrogacao: a biologia, as neurociencias, as ciencias cognitivas podem sim apontar-nos os fios que nos prendem e que nos levam de la para ca. Mas sera que, sozinhas, sao suficientes para explicar por que somos capazes de interromper os movimentos e olharmos para cima reconhecendo o que nos movia? Referencia bibliografica
Law and psychiatry: Liability for forensic evaluations: a word of caution

undergo a psychiatric evaluation by an expert, Dr. Miller, who had been retained by the insurer. After performing the examination that was ordered by the court, Dr. Miller drafted a report for the insurer and later testified in a videotaped deposition prepared for use at trial. Before the trial could be held, Ms. Dalton and the insurance company reached a settlement, and Dr. Miller’s testimony was never heard. However, Ms. Dalton then filed another suit, this time against Dr. Miller, alleging irregularities in his conduct of the psychiatric examination and discrepancies between his written report for the insurance company and the testimony he provided in his deposition. Among her many claims, Ms. Dalton alleged misrepresentation and deceit, invasion of privacy, intentional infliction of emotional distress, abuse of process, and civil conspiracy, all of which allegedly compromised her legal case and caused her significant distress. The trial court that was assigned to hear these claims granted Dr. Miller’s motion to dismiss the case on the grounds that he was entitled to “quasi-judicial immunity” for his actions in connection with the psychiatric evaluation. Quasi-judicial immunity derives from the common law, which, as the U.S. Supreme Court noted, “provided absolute immunity from subsequent damages liability for all persons—governmental or otherwise—
Laser processing of polymer thin films for chemical sensor applications

Contemporary and next-generation commercial and defense-related platforms offer countless applications for thin-film polymer coatings, including the areas of microelectronics, optoelectronics, and miniature chemical and biological sensors. In many cases, the compositional and structural complexity, and the anisotropy of the material properties preclude the processing of many of these polymers by conventional physical or chemical vapor deposition methods. The Naval Research Laboratory has developed several advanced laser-based processing techniques for depositing polymer thin films for a variety of structures and devices. The two techniques detailed in this work, matrix-assisted pulsed laser evaporation (MAPLE) and MAPLE direct-write (MAPLE DW), are based on the concept of laser absorption by a matrix solution consisting of a solvent and the desired polymer. MAPLE is a physical vapor deposition process that takes place inside a vacuum chamber, while MAPLE DW is a laser forward-transfer process that is carried out under atmospheric conditions. Both processes have been successfully used in the fabrication of thin films and structures of a range of organic materials and systems. Examples of their use in the fabrication of two types of chemical sensors, together with a comparison of the performance of these laser-processed sensors and that of similar sensors made by traditional techniques are provided.
Coherent acousto-optic mode coupling in dispersion- compensating fiber by two acoustic gratings with orthogonal vibration directions

The acousto-optic mode coupling from core to LP11cl mode of a dispersion-compensating fiber excited by two acoustic waves with orthogonal perturbations is studied by use of a novel composite piezoelectric transducer. Highly polarization-dependent mode-selective spectra are observed that are due to coherent acousto-optic coupling between the core and various constituent cladding modes. Potential applications for implementing an all-fiber wavelength-tunable polarization analyzer are also discussed.
To clone or not to clone: method analysis for retrieving consensus sequences in ancient DNA samples.

2011 Winters M, Barta JL, Monroe C, and Kemp BM. To clone or not to clone: Method analysis for retrieving consensus sequences in ancient DNA samples. PLoS One 6(6): e21247. DOI: 10.1371/journal.pone.0021247.
Alterations in hemostasis associated with hyperthermia in a canine model.

Use of hyperthermia in the treatment of cancer and viral infection has received renewed interest. However, the in vivo relationship between hyperthermia and direct versus indirect effects upon hemostasis are incompletely defined, although we do know that disseminated intravascular coagulation (DIC) is a common sequel to heat stroke. The purpose of the present study was to more precisely define the relationship between hyperthermia and derangements of hemostasis, thereby providing a guideline for the development of safe hyperthermia treatment regimens. The present investigation examined the in vivo effects of high-grade whole-body hyperthermia (WBH) (42.5 degrees C, 90 min) on hemostasis in a canine model. Induction of hyperthermia via extracorporeal circulation of heated blood (ECC-WBH) caused thrombocytopenia, increased plasma fibrin degradation products (FDPs), prolonged clotting times, increased serum liver enzymes, and evidence of spontaneous bleeding. However, when WBH was induced by peritoneal lavage (PL-WBH), transient thrombocytopenia was the only significant alteration. Temporal correlation between hemostatic alterations and elevations in serum alanine aminotransferase (ALT) levels in the ECC-WBH treatment group suggested that liver injury is responsible, at least in part, for the coagulopathy associated with high-grade hyperthermia and that in the absence of liver injury, identical degrees of hyperthermia cause only incidental decreases in platelet numbers.