cssi/SciSciGPT-SciSciNet huggingface dataset:
Democracy, accountability, and education

Educational standards, assessments, and accountability systems are of immense political moment around the world. But there is no developed theory exploring the role that these systems should play w...
Universal liposomes: preparation and usage for the detection of mRNA

Dye-encapsulating liposomes can serve as signaling reagents in biosensors and biochemical assays in place of enzymes or fluorophores. Detailed here is the use and preparation of streptavidin-coupled liposomes which offer a universal approach to biotinylated target detection. The universal approach provides two advantages, i.e. only one type of liposome is necessary despite varying target and probe sequences and the hybridization event can take place in the absence of potential steric hindrance occurring from liposomes directly conjugated to probes. One objective of this work was to optimize the one-step conjugation of SRB-encapsulating liposomes to streptavidin using EDC. Liposome, EDC, streptavidin concentrations, and reaction times were varied. The optimal coupling conditions were found to be an EDC:carboxylated lipid:streptavidin molar ratio of 600:120:1 and a reaction time of 15 min. The second goal was to utilize these liposomes in sandwich hybridization microtiter plate-based assays using biotinylated reported probes as biorecognition elements. The assay was optimized in terms of probe spacer length, probe concentration, liposome concentration, and streptavidin coverage. Subsequently, the optimized protocol was applied to the detection of DNA and RNA sequences. A detection limit of 1.7 pmol L(-1) and an assay range spanning four orders of magnitude (5 pmol L(-1)-50 nmol L(-1)) with a coefficient of variation </=5.8% was found for synthetic DNA. For synthetic RNA the LOQ was half that of synthetic DNA. A comparison was made to alkaline phosphatase-conjugated streptavidin for detection which yielded a limit of quantitation approximately 80 times higher than that for liposomes in the same system. Thus, liposomes and the optimized sandwich hybridization method are well suited for detecting single-stranded nucleic acid sequences and compares favorably to other sandwich hybridization schemes recently described in the literature. The assay was then used successfully for the clear detection of mRNA amplified by nucleic acid sequence-based amplification (NASBA) isolated from as little as one Cryptosporidium parvum oocyst. The detection of mRNA from oocysts isolated from various water sample types using immunomagnetic separation was also assessed. Finally, to prove the wider applicability and sensitivity of this universal method, RNA amplified from the atxA gene of Bacillus anthracis was detected when the input to the preceding NASBA reaction was as low as 1.2 pg. This highly sensitive liposome-based microtiter plate assay is therefore a platform technology allowing for high throughput and wide availability for routine clinical and environmental laboratory applications.
Endoplasmic Reticulum (ER) Chaperone Regulation and Survival of Cells Compensating for Deficiency in the ER Stress Response Kinase, PERK

The activity of PERK, an endoplasmic reticulum (ER) transmembrane protein kinase, assists in an ER stress response designed to inhibit general protein synthesis while allowing upregulated synthesis of selective proteins such as the ATF4 transcription factor. PERK null mice exhibit phenotypes that especially affect secretory cell types. Although embryonic fibroblasts from these mice are difficult to transfect with high efficiency, we have generated 293 cells stably expressing the PERK-K618A dominant negative mutant. 293/PERK-K618A cells, in response to ER stress: (a) do not properly inhibit general protein synthesis, (b) exhibit defective/delayed induction of ATF4 and BiP, and (c) exhibit exuberant splice activation of XBP1 and robust cleavage activation of ATF6, with abnormal regulation of calreticulin levels. The data suggest compensatory mechanisms allowing for cell survival in the absence of functional PERK. Interestingly, although induction of CHOP (a transcription factor implicated in apoptosis) is notably delayed after onset of ER stress, 293/PERK-K618A cells eventually produce CHOP at normal or even supranormal levels and exhibit increased apoptosis either in response to general ER stress or, more importantly, to specific misfolded secretory proteins.
Quine's Ethical Dilemma

While Quine clearly states his position regarding the difference between the methodology of ethics and that of science, he is less clear on the nature of ethical language. Variously, he treats ethical sentences as cognitive and noncognitive. If ethical “sentences” are noncognitive, they do not admit of truth or falsity and therefore have no claim to be occasion sentences or observation sentences. And moral theory is thereby clearly demarcated from science. If ethical sentences are cognitive, however, we could have ethical occasion sentences. It would be easier, on this interpretation, to make sense of Quine's insistence that ethics is subject to a coherency theory of truth, and that we may have real derivative and ultimate moral conflicts. I argue that, as Quine's system now stands, there are good reasons to take either interpretation. I do not demonstrate that one of these two positions is incorrect, but rather that Quine has yet to clearly state his position on the matter. I then consider some of the ramifications of taking a cognitivist interpretation of Quine's system by sketching a role empathy, newly emphasized in Quine's work, might play with respect to the cognitive status of ethical sentences. If we accept that ethical sentences are cognitive, empathy may allow us to learn moral occasion sentences from our fellow language users and justify or modify those moral occasion sentences through the use of social evidence.
Selecting subsidy strategies for housing allowance programs

Abstract The market effects of alternative housing payment formulas are analyzed and compared for a metropolitan housing market using measures of efficiency and distributional equity. The effects of “earmarking” allowance payments are considered. Estimated market effects are based on a model of housing market behavior over a 10-year period. The results differ significantly from what one might anticipate based on demand analyses of individual behavior. “Housing gap” formulas perform better than percent-of-rent formulas. Certain characteristics of the housing market together with particular income redistribution effects of the allowances appear to explain the market behavior.
Analysis of time-dose factors in squamous cell carcinoma of the oral tongue and floor of mouth treated with radiation therapy alone

Abstract This is a retrospective analysis of 147 patients with squamous cell carcinoma of the oral tongue and floor of mouth who were treated with radical radiation therapy at the University of Florida between October 1964 and December 1977. Control of the primary lesion was analyzed in respect to total dose, time, treatment modality, and split vs. continuous course therapy. There is an increase in local control of T2 lesions of the oral tongue with treatment by radium alone or radium and less than 3000 rad external beam irradiation as compared to radium and 3000 rad or more external beam (p = 0.02) and in T3 lesions of the floor of mouth with treatment by radium and 3000 rad or more external beam as compared to external beam alone (p = 0.11). Analysis of time-dose factors reveals an increase in local control with increasing dose over shorter periods of time in T3 lesions of the floor of mouth and T2–3 lesions of the oral tongue. Whereas dose appears to be important in all of these groups, overall treatment time appears to influence local control more in oral tongue lesions than in floor of mouth lesions.
Tests of correlation between immediate postoperative gastroduodenal transit times and weight loss after laparoscopic sleeve gastrectomy

Background Previous studies have shown accelerated gastric emptying after sleeve gastrectomy. This study aimed to determine whether a correlation exists between immediate postoperative gastroduodenal transit time and weight loss after laparoscopic sleeve gastrectomy (LSG). Specifically, correlation tests were conducted to determine whether more rapid transit after LSG correlated with increased weight loss.
Scene masking is affected by trial blank-screen luminance

The current study investigated the role of the inter-screen luminance contrast (ISLC) of trial blank screens between target and mask screens in visually masking scenes. Participants performed a scene gist recognition task in which we varied mask strength, blank screen luminance, and stimulus onset asynchrony (SOA). Results showed that the more luminant white, and less luminant black, blank screens produced greater masking than intermediate luminance gray blank screens adjusted to the mean luminance of the target screens, specifically for black screens at SOAs<36ms and for white screens at all SOAs. Our findings suggest that researchers interested in controlling for 'extraneous factors' should use gray blank screens as they eliminate any contribution of the ISLC component of masking. However, researchers interested in creating and examining differences in processing at early SOAs (<36ms) should use black blank screens as these were shown to increase variation in the SOA function. We examine the impact of blank screen luminance on masking.Blank screen luminance clearly affects the effectiveness of visual masking.White blank screens cause the greatest detriment to scene-recognition performance at all SOAs.Black blank screens cause greater detriment to scene-recognition performance at SOAs<36ms than do gray blank screens set to the mean luminance of the stimuli.Impacts on masking of black and gray blank screens are equivalent after 36ms.
Timing-based detection of packet forwarding in MANETs

In mobile ad hoc networks (MANETs), timing information is easily available due to the use of a shared medium, even when the traffic is encrypted. This paper addresses how such timing information can be used for detecting packet forwarding activities in MANETs.
Obituary: in memoriam, Marcel Rudasingwa (18 June 1955 - 17 November 2014).

Even by the standards of central Africa, Marcel Rudasingwa lived through turbulent times. During the genocide of 1994, when France looked the other way, Belgium withdrew her forces, and Bill Clinton,
Small Molecule Inhibitors of Interaction between ERCC1 and XPA

Accumulation of DNA lesions arising from UV radiation and/or DNA cross-linking agents can cause major disruptions to cell stability. Repair and maintenance of genomic integrity is an important component of cell viability that is in part carried out by heterodimer XPF-ERCC1 in the Nucleotide Excision Repair (NER) pathway. Conversely, the capability to disrupt DNA repair mechanisms may be advantageous in order to overcome resistance of cancer cells to DNA-damaging chemotherapies. Structural studies of the recruitment of XPF-ERCC1 by XPA revealed that a small region of XPA peptide interacts with ERCC1 with submicromolar affinity. This interaction is critical for NER and could potentially be targeted for NER inhibition by small molecules. We have made substantial progress in optimizing small molecules selected from a high-throughput screen for their ability to disrupt ERCC1-XPA binding. Using a combination of structural biology, medicinal chemistry and fluorescence-based binding studies we have improved the binding affinity of the inhibitors by more than an order of magnitude. The ability of these compounds to bind to ERCC1 and displace XPA-peptide with great efficacy may provide a means in sensitizing tumors resistant to certain anti-cancer therapies.
Diversity in receptor-like kinase genes is a major determinant of quantitative resistance to Fusarium oxysporum f.sp. matthioli.

Summary Resistance to wilt fungus Fusarium oxysporum f.sp. matthioli (FOM) is a polygenic trait in Arabidopsis thaliana. RFO3 is one of six quantitative trait loci accounting for the complete resistance of accession Columbia-0 (Col-0) and susceptibility of accession Taynuilt-0 (Ty-0). We find that Col-0 and Ty-0 alleles of RFO3 are representative of two common variants in wild Arabidopsis accessions, that resistance and susceptibility to FOM are ancestral features of the two variants and that resistance from RFO3 is unrivalled by other genes in a genome-wide survey of diversity in accessions. A single receptor-like kinase (RLK) gene in Col-0 is responsible for the resistance of RFO3, although the susceptible Ty-0 allele codes for two RLK homologs. Expression of RFO3 is highest in vascular tissue, which F. oxysporum infects, and root-expressed RFO3 restricts FOM infection of the vascular system. RFO3 confers specific resistance to FOM and provides no resistance to two other crucifer-infecting F. oxysporum pathogens. RFO3's identity, expression and specificity suggest that RFO3 represents diversity in pattern-recognition receptor (PRR) genes. The characteristics of RFO3 and the previously published RFO1 suggest that diversity in RLK PRRs is a major determinant of quantitative resistance in wild plant populations.
A condition based maintenance model for a two-unit series system

This paper discusses a condition based maintenance model with exponential failures and fixed inspection intervals for a two-unit system in series. The condition of each unit, such as vibration or heat, is monitored at equidistant time intervals. The condition indicator variables for each unit are used to decide whether to repair an individual unit or to overhaul the whole system. After a maintenance action is performed the monitored condition indicator variable takes on its initial value. Each unit can fail only once within an inspection interval and when one or both units fail the system fails. The probability of failure is exponential and the failure rate is dependent on the condition. The cost to be minimized is the long-run average cost of maintenance actions and failures. We study the optimal solution to this problem obtained via dynamic programming.
Pseudomonas putida F1 has multiple chemoreceptors with overlapping specificity for organic acids

Previous studies have demonstrated that Pseudomonas putida strains are not only capable of growth on a wide range of organic substrates, but also chemotactic towards many of these compounds. However, in most cases the specific chemoreceptors that are involved have not been identified. The complete genome sequences of P. putida strains F1 and KT2440 revealed that each strain is predicted to encode 27 methyl-accepting chemotaxis proteins (MCPs) or MCP-like proteins, 25 of which are shared by both strains. It was expected that orthologous MCPs in closely related strains of the same species would be functionally equivalent. However, deletion of the gene encoding the P. putida F1 orthologue (locus tag Pput_4520, designated mcfS) of McpS, a known receptor for organic acids in P. putida KT2440, did not result in an obvious chemotaxis phenotype. Therefore, we constructed individual markerless MCP gene deletion mutants in P. putida F1 and screened for defective sensory responses to succinate, malate, fumarate and citrate. This screen resulted in the identification of a receptor, McfQ (locus tag Pput_4894), which responds to citrate and fumarate. An additional receptor, McfR (locus tag Pput_0339), which detects succinate, malate and fumarate, was found by individually expressing each of the 18 genes encoding canonical MCPs from strain F1 in a KT2440 mcpS-deletion mutant. Expression of mcfS in the same mcpS deletion mutant demonstrated that, like McfR, McfS responds to succinate, malate, citrate and fumarate. Therefore, at least three receptors, McfR, McfS, and McfQ, work in concert to detect organic acids in P. putida F1.
Probabilistic Approach to Predicting Fatigue Lives of Corroded 2024-T3

The objective of this work was to develop a probabilistic approach to predict fatigue lives of corroded 2024-T3 aluminum tensile specimens. An experimental program was established to corrode fatigue specimens made of a 2024-T3 sheet separately on the longitudinal-transverse (LT) and longitudinal-short (LS) metallurgical planes in a 3.5% sodium chloride solution for 6 and 8 days. The specimens were fatigue tested to fracture, and the corrosion pits that nucleated fatigue cracks were analyzed with an electron microscope. Corroded material from the fractured specimens was polished on the short-transverse plane and the pits were viewed and photographed under a light microscope. The largest 10% of the collected pits were fit to Gumbel extreme-value distributions. These distributions were used in a Monte Carlo simulation in which 1000 pit areas were selected, modeled as circular surface or corner cracks, and treated as initial flaw sizes. Fatigue life predictions were based on crack propagation life by use of the initial flaw sizes from the Monte Carlo simulation. Predicted cumulative distribution functions of fatigue life were within 22% of the experimental cumulative distribution functions for the LS specimens. The method predicted a reasonable distribution offatigue lives for the 6-day LT specimens but consistently underpredicted the experimental distribution of fatigue lives for the 8-day LT specimens.
Modeling Human Choroidal Melanoma Xenograft Growth in Immunocompromised Rodents to Assess Treatment Efficacy

Purpose. To evaluate potential treatments of primary uveal melanoma in rodent xenograft models, it is necessary to track individual tumor growth during treatment. Previously, high-frequency ultrasound (HF-US) was used to measure tumor volume in nude rats for up to 2 weeks. This study tests the hypothesis that HF-US can be used to repeatedly measure tumor volume for at least a month in both nude rat and severe combined immunodeficiency (SCID) mouse xenograft models of human uveal melanoma, with the goal of modeling tumor growth to evaluate treatment efficacy.
Chiral Amplification with a Stereodynamic Triaryl Probe: Assignment of the Absolute Configuration and Enantiomeric Excess of Amino Alcohols

A stereodynamic, axially chiral triaryl probe is locked into a single conformation upon condensation with two amino alcohol substrates. The well-defined chiral amplification in the diimines formed results in intense Cotton effects at high wavelengths that can be used for in situ CD analysis of the absolute configuration and ee of cyclic and acyclic substrates.
Study of fracture mechanisms of multiphase polymers using the double-notch four-point-bending method

The double-notch four-point-bend technique (DN-4PB) is developed to study the fracture mechanisms of multiphase polymers. This technique is found to be effective for an unambiguous determination of the fracture mechanisms and the sequence of toughening evems of polymer alloys when fracture occurs. The DN-4PB technique is also found to be especially useful for situations where the quantity of the test material is limited and the testing rate is high. The present study demonstrates the usefulness of the DN-4PB technique in a variety of polymeric systems and testing conditions. Requirements for which the DN-4PB technique becomes useful are also addressed.
Treatment of congenital talipes equinovarus (clubfoot)

Abstract Practically all clubfeet can be completely corrected if proper treatment is begun immediately after birth. Good results, without recurrences, are based upon a gradual reduction of the deformity through a systematic series of manipulations and a period of complete or partial immobilization extending approximately to the weight bearing age, eight months. The manipulative attack must be directed against each of the several components of the deformity if the foot is to be restored to normal. Each of these main components, equinus, adduction-abduction and inversion, must be corrected in both the forefoot and the back foot. In equinus the back foot is plantarflexed at the ankle joint and the forefoot is further plantarflexed on the back foot. In adduction-abduction the forefoot is adducted and the calcaneus is abducted. In inversion both the forefoot and the calcaneus are inverted. Weekly manipulations proceed systematically toward a reduction of each of these component distortions and the gain made with each manipulation is maintained by a plaster-of-Paris cast. The manipulative maneuvers are explained in detail. If good dorsiflexion has not been accomplished within five months the closed operation for achillotomy and posterior capsulotomy is indicated so that the infant may enter the weight bearing period with unhampered feet. For the infants in whom the contracture shows a tendency toward recurrence, elastic extension braces are indicated. These are described.
The causation of two scent-marking behaviour patterns in female hamsters (Mesocricetus auratus)

Social, olfactory, and oestrous cycle influences on the frequency of flank-marking and vaginal marking were studied in female hamsters. Vaginal marking was more frequent in the presence of males or their odours than females or their odours. Vaginal marking frequency was greatest the day before oestrus (day 4), intermediate on days 2 and 3, and zero on the oestrous day. The probable sexual advertisement functions of vaginal marking were discussed. In contrast, flank-marking by females was stimulated more by other female odours than by male odours. The frequency of flank-marking was elevated by agonistic encounters and was reduced by sexual encounters. Flank-marking seems to have functions related to functions of aggression among hamsters.
Thailand at the Margins: Internationalization of the State and the Transformation of Labour by Jim Glassman

Despite the 1997 East Asian financial crisis, the 2004 tsunami, and the 2006 military coup that removed Prime Minister Thaksin Shinawatra, Thailand has continued to experience relatively high rates...
Estimators of Generalized Chi-Square Parameters

The maximum likelihood estimators of the parameters of the genalized chi-square distribution are derived and approximated. These estimators are compared with those based on the method of moments.
Cross-Linking of IgE-receptor complexes at the cell surface: Synthesis and characterization of a long bivalent hapten that is capable of triggering mast cells and rat basophilic leukemia cells

Abstract The ability of a series of bivalent haptens to bind and cross-link immunoglobulin E (IgE) in solution and on the surface of cells was examined. Several short ( l -tyrosine (DCT) groups coupled to the α-amino groups of l -cystine was synthesized and characterized. This bivalent hapten [(DCT)2-cystine], binds very tightly to the same monoclonal anti-DNP IgE in solution and cross-links these antibodies to form higher mol. wt aggregates as judged by gel filtration and binding studies. It also stimulates degranulation of both RBL and mast cells sensitized with two different monoclonal anti-DNP IgE antibodies, with the mast cells exhibiting generally greater responsiveness to this ligand. The (DCT)2-cystine bivalent hapten appears to have the structural features necessary for carrying out detailed binding studies with receptor-bound IgE on the cell surface.
Complexity of the EQUATE testing strategy

Abstract Most testing methods do not fare well with software whose modules contain data and operations at widely varying levels of abstraction. With the evolution of new design techniques and new languages that encourage the use of more abstract data types, it is becoming increasingly important that testing methods begin to deal with abstraction in a reasonable and consistent manner. The EQUATE testing strategy offers strong support for data and functional abstraction. EQUATE selects a number of test locations throughout the program and chooses a set of expressions derived from the abstract syntax tree of the module being tested. Test data is required that distinguishes these expressions from one another at every test location. The time complexity of EQUATE is at worst O(Lp2) and the space complexity O(Lp3) where Lp is the length of the program under test.
ReMail: a reinvented email prototype

The Collaborative User Experience Research group has been investigating how people use email and how we might design and build a better email system. In this demonstration, we will show a prototype email client developed as part of a larger project on "reinventing email." Among other new capabilities, this integrated prototype incorporates 1) novel visualizations of the documents within mail databases to aid understanding and navigation, 2) advanced text analysis of the content of email messages, and 3) several unique features for helping users manage their attention.
Adaptive Robust Precision Motion Control of a Piezoelectric Positioning Stage

Positioning stages using piezoelectric stack actuators (PEA) have very high theoretical bandwidth and resolution. However, it is difficult to achieve precise dynamic motion tracking using traditional linear controllers such as PID due to the inherent hysteresis nonlinearity of piezoelectric materials and the phase lag associated with such controllers. In this paper, it is demonstrated that, in the frequency range for which only the piezoelectric dynamics dominates, high tracking accuracy is possible through an intelligent integration of advanced adaptive robust control strategy with a control-oriented modeling of nonlinear piezoelectric effects. Specifically, the fast and slow dynamics of the total stage displacement due to various piezoelectric effects including the rate-dependent hysteresis nonlinearity, the drifting, and the broad spectrum of domain switching time constants are first identified. With a control oriented modeling in mind, a simple first-order nonlinear model with unknown parameters and bounded disturbances is used to capture the essence of those fast and slow dynamics. An adaptive robust controller (ARC) is subsequently designed to compensate for the effect of unknown model parameters and bounded disturbances effectively, which provides an online adaptation-based dynamic model compensation that minimizes tracking errors. Experimental results from tracking control of sinusoidal trajectories up to 100 Hz and point-to-point trajectories show that tracking accuracy down to the same magnitude of sensor noise is achieved, demonstrating the effectiveness of the approach.
Efficient mode selection for block-based motion compensated video coding

A method for efficiently selecting the operating modes within a block-based multi-mode video compression system is described. For a given image region, the optimum combination of modes is selected so as to minimize the overall distortion for a given bit-rate budget. Necessary conditions for optimizing the encoder operation are derived within a rate-constrained product code framework. When rate and distortion dependencies exist between adjacent blocks, the ensuing encoder complexity is surmounted using a dynamic programming strategy based on the Viterbi algorithm so as to achieve the optimum selection of macroblock modes. Results are provided for the emerging H.263 video coding standard.
A regression model for time series of counts

SUMMARY This paper discusses a model for regression analysis with a time series of counts. Correlation is assumed to arise from an unobservable process added to the linear predictor in a log linear model. An estimating equation approach used for parameter estimation leads to an iterative weighted and filtered least-squares algorithm. Asymptotic properties for the regression coefficients are presented. We illustrate the technique with an analysis of trends in U.S. polio incidence since 1970.
Approximate Calibration-Free Trajectory Reconstruction in a Wireless Network

The problem of location tracking of a mobile station in a wireless network has received considerable attention in recent literature. In many installations, a mobile station transmits a radio frequency signal which is received at a number of base stations, from which location estimation follows. Such an application requires some form of signal-distance calibration, either an empirical signal map, or a model-based method which relies on functional relationships between signal and distance derivable from physical principles. In this paper, we propose an alternative approach in which a time series of received signal strength (RSS) measurements is mapped onto a plane in a manner which preserves the general topological and directional properties of any trajectory of a mobile station. This is accomplished without requiring a signal-distance calibration, or even exact knowledge of the base station locations. A detailed proof of the stability properties of the mapping is given. An implementation protocol is developed, and illustrated with numerical examples.
The Lesser-Known Protostome Taxa: An Introduction and a Tribute to Robert P. Higgins

SYNOPSIS. Most biologists are familiar only with a few of the approximately 40 extant animal phyla. The purpose of this symposium was to renew interest in the lesser-known invertebrate taxa, encourage their use in research and teaching and to promote the relevance of high-level systematic studies. This paper reviews the two major views of metazoan evolutionary relationships with particular attention to the lesser-known taxa and to some of the new and/or conflicting terminology used in current animal phylogenetic study. The current use of lesser-known taxa in research is briefly described, and the discussion that followed the symposium is summarized. The paper concludes with a brief history of the symposium and a tribute to Robert P. Higgins, who organized three ‘‘Symposia on the Lesser-Known Invertebrates’’ over the past 25 yr.
Extraction of Hand Gestures with Adaptive Skin Color Models and Its Applications to Meeting Analysis

We present an adaptive skin color model for hand gesture tracking which is applied to cross-modal analysis of planning meetings. We build a skin color model with the Gaussian distribution and a skin color filter for each participant in meetings. By combining with the Vector Coherence Mapping (VCM) algorithm, we track hand motion and obtain 3D trajectories. The hand gesture stream is extracted from hand motion trajectories. Different skin color models are created for different people to handle the differences of skin color. We update each model dynamically to adapt changes of environments. A parallel system has been implemented to track and extract hand motion trajectories. Examples of hand motion gesture tracking in meeting environments are provided. The applications of the adaptive skin color model can increase the speed of hand tracking.
Trace-driven co-simulation of high-performance computing systems using OMNeT++

In the context of developing next-generation high-performance computing systems, there is often a need for an "end-to-end" simulation tool that can simulate the behaviour of a full application on a reasonably faithful model of the actual system. Considering the ever-increasing levels of parallelism, we take a communication-centric view of the system based on collecting application traces at the message-passing interface level. We present an integrated toolchain that enables the evaluation of the impact of all interconnection network aspects on the performance of parallel applications. The network simulator, based on OMNeT++, provides a socket-based co-simulation interface to the MPI task simulator, which replays traces obtained using an instrumentation package. Both simulators generate output that can be evaluated with a visualization tool. A set of additional tools is provided to translate generic topology files to OMNeT's ned format, import route files at run time, perform routing optimizations, and generate particular topologies. We also present several examples of results obtained that provide insights that would not have been possible without this integrated environment.
Activities of the Porphyromonas gingivalis PrtP proteinase determined by construction of prtP-deficient mutants and expression of the gene in Bacteroides species.

PrtP is a major cysteine proteinase of Porphyromonas gingivalis. The gene encoding this proteinase, prtP, was cloned into the Escherichia coli-Bacteroides shuttle vectors pFD288 and pFD340 and was expressed in Bacteroides cells, apparently under the control of its own promoter, when in pFD288, or a Bacteroides promoter present on pFD340. Proteolytically active PrtP was detected by fibrinogen zymography in cells or spent growth medium of several Bacteroides species harboring the recombinant plasmids. The proteinase was recovered from Bacteroides fragilis ATCC 25285(pFD340-prtP) cells by 3-[(3-cholamidopropyl)-dimethyl-ammonio]-1-propanesulfonate (CHAPS) extraction and characterized with regard to exopeptidase specificity and sensitivity to proteinase inhibitors. Lys-amidolytic activity, but not Arg-amidolytic activity, was detected. PrtP was activated by cysteine and, to a lesser extent, dithiothreitol, and it was stimulated by glycine-containing compounds. It also was inhibited by Nα-p-tosyl-l-lysine chloromethyl ketone (TLCK) and, to a lesser extent, H-d-Tyr-l-Pro-l-arginyl chloromethyl ketone (YPRCK) and was relatively insensitive to EDTA and leupeptin. Neither B. fragilis ATCC 25285(pFD340-prtP) cells nor the CHAPS extract effected hemagglutination of sheep red blood cells or collagen cleavage, but the cells did cleave gelatin. Furthermore, P. gingivalis W12, ATCC 33277, KDP110, and HG66 with knockout mutations in prtP were constructed by allelic replacement. Unlike the parent strains, the mutant strains produced beige colonies on plates containing sheep blood. These strains also were affected in their ability to effect hemagglutination, cleave collagen, and cleave a Lys-specific peptide substrate. This report presents the results of the first characterization of the PrtP proteinase clearly in the absence of any influence by other P. gingivalis proteins and describes the properties of P. gingivalis cells defective in the production of PrtP.
Timing of Adjuvant Surgical Oophorectomy in the Menstrual Cycle and Disease-Free and Overall Survival in Premenopausal Women With Operable Breast Cancer

Background For women with hormone receptor-positive, operable breast cancer, surgical oophorectomy plus tamoxifen is an effective adjuvant therapy. We conducted a phase III randomized clinical trial to test the hypothesis that oophorectomy surgery performed during the luteal phase of the menstrual cycle was associated with better outcomes. Methods Seven hundred forty premenopausal women entered a clinical trial in which those women estimated not to be in the luteal phase of their menstrual cycle for the next one to six days (n = 509) were randomly assigned to receive treatment with surgical oophorectomy either delayed to be during a five-day window in the history-estimated midluteal phase of the menstrual cycles, or in the next one to six days. Women who were estimated to be in the luteal phase of the menstrual cycle for the next one to six days (n = 231) were excluded from random assignment and received immediate surgical treatments. All patients began tamoxifen within 6 days of surgery and continued this for 5 years. Kaplan-Meier methods, the log-rank test, and multivariable Cox regression models were used to assess differences in five-year disease-free survival (DFS) between the groups. All statistical tests were two-sided. Results The randomized midluteal phase surgery group had a five-year DFS of 64%, compared with 71% for the immediate surgery random assignment group (hazard ratio [HR] = 1.24, 95% confidence interval [CI] = 0.91 to 1.68, P = .18). Multivariable Cox regression models, which included important prognostic variables, gave similar results (aHR = 1.28, 95% CI = 0.94 to 1.76, P = .12). For overall survival, the univariate hazard ratio was 1.33 (95% CI = 0.94 to 1.89, P = .11) and the multivariable aHR was 1.43 (95% CI = 1.00 to 2.06, P = .05). Better DFS for follicular phase surgery, which was unanticipated, proved consistent across multiple exploratory analyses. Conclusions The hypothesized benefit of adjuvant luteal phase oophorectomy was not shown in this large trial.
The Importance of Prolonged Binding to Antigen-Presenting Cells for T Cell Fate Decisions

How critical is it for T cells to stably arrest on antigen-presenting cells? In this issue of Immunity, Scholer et al. (2008) demonstrate profound effector and memory defects for CD8(+) T cells encountering "nonsticky" antigen-presenting cells lacking intercellular adhesion molecule-1.
Exploiting parallel microprocessor microarchitectures with a compiler code generator

With advances in VLSI technology, microprocessor designers can provide more microarchitectural parallelism to increase performance. We have identified four major forms of such parallelism: multiple microoperations issued per cycle, multiple result distribution buses, multiple execution units, and pipelined execution units. The experiments reported in this paper address two important issues: The effects of these forms and the appropriate balance among them. A central microarchitecture is identified as the comparison basis. We separately vary each form of the microarchitectural parallelism in the central to measure their individual effects on performance. In addition, we vary two forms of the microarchitectural parallelism in the central to derive an appropriate balance between them. To make fair comparisons, our compiler generates different code sequences optimized for different microarchitectural configurations. For each given set of technology constraints, these experiments can be used to derive a cost-effective microarchitecture to execute each given set of workload programs at high speed.
Cloning and expression of the Listeria monocytogenes scott A ptsH and ptsI genes, coding for HPr and enzyme I, respectively, of the phosphotransferase system.

The phosphoenolpyruvate (PEP)-dependent phosphotransferase system (PTS) utilizes high-energy phosphate present in PEP to drive the uptake of several different carbohydrates in bacteria. In order to examine the role of the PTS in the physiology of Listeria monocytogenes , we identified the ptsH and ptsI genes encoding the HPr and enzyme I proteins, respectively, of the PTS. Nucleotide sequence analysis indicated that the predicted proteins are nearly 70% similar to HPr and enzyme I proteins from other organisms. Purified L. monocytogenes HPr overexpressed in Escherichia coli was also capable of complementing an HPr defect in heterologous extracts of Staphylococcus aureus ptsH mutants. Additional studies of the transcriptional organization and control indicated that the ptsH and ptsI genes are organized into a transcription unit that is under the control of a consensus-like promoter and that expression of these genes is mediated by glucose availability and pH or by by-products of glucose metabolism.
The Overrated adversary: Rhodes and Ottoman naval power

This essay examines the relative power of the Rhodian and Ottoman fleets in the first decades of the sixteenth century, taking as its context the commercial and diplomatic relations of the eastern Levantine states. After the Aegean wars of 1499–1503 Rhodes failed to mobilize a Christian alliance against the Ottomans. Nor did the rise of Ismail Safavi in Iran provide the hoped for relief from Ottoman expansion. While the Ottoman state was preoccupied with the succession struggle for Bayezid's throne and with plans to extend its hegemony to the Indian Ocean, Rhodes was fighting for survival. Although the development of the Ottoman fleet provoked great fear in Rhodes, Venice and the Mamluk kingdom, Ottoman naval power until the conquest of Cairo in 151J was directed primarily to defensive and transport activities. Further the Ottoman fleet provided security against corsairs for merchant shipping. By supporting the corsair activities of Order members, Rhodes alienated the Mamluk state, Venice and France (allpotential allies in an anti-Ottoman coalition) but refrained from directly challenging the Ottoman navy. Naval engagements during this period cannot be understood without taking into consideration the prolonged conditions of grain shortage in the Aegean and eastern Mediterranean. Both aggressive and defensive measures taken by the Ottoman, Venetian and Rhodian fleets Were ordinarily related to the competition for foodstuffs during this period rather than the conquest of territory or the establishment of commercial dominance (as in the Indian Ocean).
On material velocities and non-locality in the thermo-mechanics of continua

Abstract Following is a discussion of several issues surrounding the continuum modeling of discrete particulate systems, particularly the uncertainty in the definition of continuum-level material particles and velocities. The work is motivated in part by various proposals for the introduction of supplemental velocity fields into the thermo-mechanics of single-component fluids. A review and modification are given of the relevant continuum field equations, based on the Eulerian rather than the conventional Lagrangian description, and a connection is made to the well-known statistical mechanics of Kirkwood and coworkers for point-particles. The Noetherian technique of Green and Naghdi is employed to derive the momentum balance directly from the particle-level energy balance, and it is shown that non-barycentric effects in particle motion engender stress asymmetry. It is conjectured that this and related effects are generally bound up with higher-gradient effects and the breakdown of the simple-material model for continuum thermo-mechanics. To illustrate this, a theory of non-local linear viscoelasticity is presented and compared with Brenner’s “bi-velocity hydrodynamics” and Muller’s “extended thermodynamics” for heat flux and stress. These models are shown to represent expansions in spatial wave vector, representing a Knudsen number, and temporal frequency, representing a Deborah number. Suggestions are made for further work to explore the associated effects of couple-stress and the consequences of departures of entropy flux from heat flux.
Insulin-Like Growth Factor 1 Mediates Negative Feedback to Somatotroph GH Expression via POU1F1/CREB Binding Protein Interactions

Circulating insulin-like growth factor 1 (IGF-1) has been shown to act as a negative feedback regulator of growth hormone (GH) gene expression; however, the mechanism of this negative feedback is poorly understood. Activation and regulation of GH gene expression require the binding of the transcription factor POU1F1 to the GH promoter along with cyclic AMP (cAMP) response element binding protein (CREB) binding protein (CBP). We investigate the role of CBP as a target of IGF-1 somatotroph regulation using the MtT/S somatotroph cell line. IGF-1 significantly inhibits basal GH mRNA levels but not POU1F1 levels. Chromatin immunoprecipitation assays demonstrate inhibition of CBP binding to the GH promoter after IGF-1 treatment. We hypothesized that IGF-1 receptor (IGF-1R) signaling disrupts the POU1F1/CBP complex to inhibit gene expression. In support, the use of a mutant CBP (S436A) construct, which lacks a critical phosphorylation site, leads to the loss of IGF-1 inhibition. The studies of CBP (S436A) knock-in mice show elevated serum GH levels, a greater response to GH releasing hormone (GHRH) stimulation along with lower weight gain, and decreased body fat. Our data confirm the inhibitory effects of IGF-1 on GH expression at the level of the promoter and provide evidence of CBP's role as a target of IGF-1R signaling.
Size reduction of a microstrip antenna using a corrugated surface

Since the 1970s, there has been a significant interest in microstrip antennas because they exhibit many desirable characteristics such as low-profile, low weight, conformability and ease of fabrication. Such characteristics are attractive for many applications especially those which have weight and space limitations. For such applications, reducing the size of the antenna element is the primary concern. Many methods have been used to miniaturize microstrip antennas such as material loading, the use of slots to increase the current path length [1] and even the use of shorting pins [2]. In this paper, the use of a corrugated surface for miniaturizing a microstrip antenna is presented and discussed. In addition, its implementation using standard printed circuit board (PCB) fabrication techniques is presented.
Continuous- and semicontinuous-flow blood centrifugation systems: therapeutic applications, with plasma-, platelet, lympha-, and eosinapheresis.

Blood centrifugation, with a continuous-flow or semicontinuous-flow system, was used in the treatment of 17 patients with various hematologic disorders. Total plasma exchange (TPE) controlled symptoms of hyperviscosity and arrested bleeding in three patients. In two patients, TPE made it possible to perform urgent surgical procedures. It was a very valuable adjuvant in the treatment of the one patient with a Factor VIII inhibitor. Eosinapheresis was not of significant value in the therapy of syndromes associated with eosinophilia. Lymphapheresis significantly reduced peripheral lymphocytosis, aiding in the chemotherapeutic control of chronic lymphosarcoma cell leukemia in one patient. It was of questionable value in the maintenance therapy of two patients with Sezary syndrome. Plateletapheresis significantly reduced peripheral platelet count in thrombocytosis, making it possible to minimize the chemotherapeutic dose and permitting urgent surgical procedures in two patients.
Inactivation of β-lactamases from Enterobacter cloacae by monophosphams

Amongst the monocyclic beta-lactam antibiotics, selected monophosphams were potent mechanism-based inactivators of the P99 and E2 cephalosporinases of Enterobacter cloacae. Inhibition of these enzymes was time-dependent with second order rate constants for inactivation of 100,000 to 20,000,000 l/mol/min. After incubation for 24 h at least 99% of the enzymatic activity was inhibited when enzyme was exposed to a ten-fold excess of inactivator. Amongst the monophosphams three classes of inhibitors were seen: irreversible inactivators as described above, transient inactivators and competitive (inhibitory) substrates.
Deep Convection in the Labrador Sea as Observed by Lagrangian Floats

Abstract During the winters of 1997 and 1998, a total of 24 Lagrangian floats were deployed in the Labrador Sea. These floats were designed to match the buoyancy and compressibility of seawater. They measured temperature and three-dimensional position (pressure for vertical position and RAFOS acoustic tracking for latitude and longitude) as they followed water motions three-dimensionally. This data provides direct observation of mixed layer depth and excellent estimates of vertical velocity. Floats were repeatedly carried across the convecting layer by vertical velocities averaging several centimeters per second with vertical excursions of up to one kilometer. In the horizontal, several scales of eddy motion were resolved, as was a possible float predilection toward remaining in water preconditioned for convection. Heat flux estimates from this data reveal entrainment and surface heat fluxes similar in magnitude. The mixed layer acts as a vertical conveyor belt of temperature, transporting heat from depth...
Age-associated cardiovascular changes are the substrate for poor prognosis with myocardial infarction.

Advanced age is a powerful independent predictor of short-term mortality and morbidity in post-infarct patients [(1–3)][1]. Randomized studies, including thousands of patients, indicate 10-fold increases in death, clinical heart failure (HF), and cardiogenic shock as age increases from 85