cssi/SciSciGPT-SciSciNet huggingface dataset:
Terrorism and the Ethics of War: Immunity rights vs. the right of self-defense

If we take rights seriously, how do we resolve the tension between different parts of the right to life? How do we tell which takes precedence in conflict situations? Is it the right of people not to be attacked? Or the right of people to defend themselves when their lives are threatened? A common philosophical method for trying to deal with hard questions like these is to begin with easy cases and see if we can extrapolate from them. Perhaps this familiar strategy can help us to determine whether we should accept absolute noncombatant immunity or recognize exceptions in extreme cases when attacking civilians is the only means of resisting an extraordinary threat. If we decide that defensive rights take precedence, then people who are in dire enough circumstances may have a right to engage in terrorist acts, whether they be bombings of cities by powerful air forces or the use of small bombs in markets and buses. If we decide that immunity rights take precedence, then no matter how dire the circumstances or how severe the threat, no one has a right to protect themselves by killing innocent people. THE SIMPLE MODEL OF JUSTIFIABLE DEFENSE IN ORDINARY LIFE AND IN WAR In standard, uncontroversial cases of justified self-defense, there is no clash between immunity rights and defensive rights. This is what makes these cases uncontroversial. If someone unjustifiably tries to kill you, you have a right to defend yourself from attack and to use lethal force if necessary.
A novel method to recover DD fusion proton CR-39 data corrupted by fast ablator ions at OMEGA and the National Ignition Facility

CR-39 detectors are used routinely in inertial confinement fusion (ICF) experiments as a part of nuclear diagnostics. CR-39 is filtered to stop fast ablator ions which have been accelerated from an ICF implosion due to electric fields caused by laser-plasma interactions. In some experiments, the filtering is insufficient to block these ions and the fusion-product signal tracks are lost in the large background of accelerated ion tracks. A technique for recovering signal in these scenarios has been developed, tested, and implemented successfully. The technique involves removing material from the surface of the CR-39 to a depth beyond the endpoint of the ablator ion tracks. The technique preserves signal magnitude (yield) as well as structure in radiograph images. The technique is effective when signal particle range is at least 10 μm deeper than the necessary bulk material removal.
Optimizing passive quantum clocks

We describe protocols for passive atomic clocks based on quantum interrogation of the atoms. Unlike previous techniques, our protocols are adaptive and take advantage of prior information about the clock's state. To reduce deviations from an ideal clock, each interrogation is optimized by means of a semidefinite program for atomic state preparation and measurement whose objective function depends on the prior information. Our knowledge of the clock's state is maintained according to a Bayesian model that accounts for noise and measurement results. We implement a full simulation of a running clock with power-law noise models and find significant improvements by applying our techniques.
Holograms without Headsets: Projected Augmented Reality with the RoomAlive Toolkit

The RoomAlive Toolkit is an open source SDK that enables developers to create interactive projection mapping applications. The toolkit includes tools to calibrate a network of multiple Kinect sensors and video projectors. It also provides a simple projection mapping sample and Unity3D integration that can be used to develop new immersive augmented reality experiences similar to those of the IllumiRoom [2] and RoomAlive [3] research projects. We demonstrate a RoomAlive installation using three projectors and four cameras.
Network Structure, Strength of Relationships, and Communities’ Success in Project Implementation

Studies of network effectiveness in the collaborative public program setting commonly have found that actors with more organizational partners, more indirect (bridging) ties to other partners, and more cohesive relationships among partners have greater success in implementing projects. This article contributes to this literature by developing and testing hypotheses about how strength of relationships, measured by frequency of contacts, moderates these results. In the context of community water supply projects in Nepal, the article shows that greater frequency of contacts between communities and organizational partners enhances the impact of having more partners and more cohesive relationships among partners but decreases the impact of having more indirect connections. For practitioners and network theorists, these findings highlight the importance of strength of relationships in the link between networks and performance.
Latency, Bandwidth and Power Benefits of the SuperCHIPS Integration Scheme

In this paper, we describe the performance and power benefits of our Fine Pitch integration scheme on a Silicon Interconnect Fabric (Si IF). Here we propose a Simple Universal Parallel intERface (SuperCHIPS) protocol enabled by fine pitch dielet to interconnect fabric assembly. We show the dramatic improvements in bandwidth, latency, and power are achievable through our integration scheme where small dielets (1-25 mm2) are attached to a rigid Silicon Interconnect Fabric (Si-IF) at fine interconnect pitch (2-10 μm) and short inter-die distance (50-500 μm) using solderless metal-to-metal thermal compression bonding (TCB). Our simulations show that links in the Si-IF with short wire-lengths (5-25x improvement in data bandwidth. This can improve system performance (>20x) when compared to PCB-style integration and may even approach single die SoC metrics in some cases. Furthermore our protocol is simple and non-proprietary. We show that this scheme enables heterogeneous system integration using a dielet based assembly method and provides significant reduction in design and validation cost.System-level analysis of heterogeneous integration scheme promises power benefits of more than 15% even for very small systems.
LoopMaker: Automatic Creation of Music Loops from Pre-recorded Music

Music loops are seamlessly repeatable segments of music that can be used for music composition as well as backing tracks for media such as videos, webpages, and games. They are regularly used by both professional musicians as well as novices with very little experience in audio editing and music composition. The process of creating music loops can be challenging and tedious, particularly for novices. We present LoopMaker, an interactive system that assists users in creating and exploring music loops from pre-recorded music. Our system can be used in a semi-automatic mode in which it refines a user's rough selection of a loop. It can also be used in a fully automatic mode in which it creates a number of loops from a given piece of music and interactively allows the user to explore these loops. Our user study suggests that our system makes the loop creation process significantly faster, easier, and more enjoyable than manual creation for both novices and experts. It also suggests that the quality of these loops are comparable to manually created loops by experts.
Nivolumab use for BRCA gene mutation carriers with recurrent epithelial ovarian cancer: A case series.

Abstract Tumors deficient in DNA mismatch repair are known to display increased susceptibility to immune checkpoint inhibitors due to accumulation of DNA damage and increased neoantigen load. This suggests that deficiency in the BRCA-related DNA repair mechanism may also be a surrogate marker for immunotherapy response. The aim of this study was to examine the efficacy of the immune checkpoint inhibitor, nivolumab, in women with BRCA gene mutations and recurrent mullerian cancer. This retrospective case series followed six BRCA carriers who received nivolumab monotherapy (3.0 mg/kg, intravenous, day 1 and 15, every 4 weeks) as salvage therapy for recurrent epithelial ovarian (n = 5) and fallopian tubal (n = 1) cancers. Toxicity, treatment response, and survival were examined. Median age was 57 (range 51–64). BRCA1 and 2 mutations were equally distributed. All had high-grade serous histology, and all but one had advanced-stage disease at initial diagnosis. The majority had platinum-resistant disease (n = 4). All received salvage therapy prior to nivolumab therapy (median 3 lines), including PARP inhibitors (n = 3). The median number of nivolumab treatment cycles was 9, including 2 women receiving 18 cycles. Three women developed nivolumab-related toxicities, most commonly grade 2 hypothyroidism (n = 2). Median follow-up time was 13.4 months, and there were 3 complete responses, 1 partial response, and 2 patients with progressive disease. Objective response rate was 67% (4 out of 6). In conclusion, our study suggests that nivolumab monotherapy is well-tolerated and may be an effective salvage therapy for BRCA mutation carriers with recurrent epithelial ovarian, fallopian tubal, and primary peritoneal cancers.
A Discrete Search Game

A Hider hides in one of the locations 1,2,…, n. The Seeker searches the locations one after the other with returns allowed. He knows that if he visits location i, he will find the Hider with chance 0 < p i ≤ 1, provided that the Hider is there. The paper provides a method to approximate the value and also characterizes the best among all pure strategies.
Selected Case Studies in the Treatment of the Multiple-Ligament-Injured Knee

This chapter in The Multiple Ligament Injured Knee: A Practical Guide to Management, Second Edition, presents selected cases in treatment of the multiple-ligament-injured knee that are representative of my practice. I have written this chapter in the first person to provide a more personal approach to presenting these topics. These selected cases represent real-life management examples in the treatment of difficult knee ligament instability problems. The format followed will be the same for each case study to provide consistency in the presentation and is outlined as follows: history, physical examination, imaging study findings, surgical timing, graft selection, surgical technique, postoperative rehabilitation program, and results. Details of the surgical technique will not be presented in this chapter since the surgical technique was performed as I have described in the chapters entitled “PCL Based Multiple Ligament Knee Injuries: What I Have Learned,” “Surgical Treatment of Combined PCL ACL Medial and Lateral Side Injuries (Global Laxity): Acute and Chronic,” and “Mechanical Graft Tensioning in Multiple Ligament Knee Surgery” in this textbook. The purpose of this case study chapter is for the reader to gain insight into management and treatment strategy decisions in these complex knee ligament injuries.
At the End of the Peninsula

i Acknowledgments ii Preface iv Introduction 1 Chapter 1: Jower’s 8 Chapter 2: Gas & Coke 23 Chapter 3: The Home Plate 45 Chapter 4: On the Ropes 62 Chapter 5: Wapato 86 Works Consulted 98
Estimating prevalence using composites

We are interested in estimating the fraction of a population that possesses a certain trait, such as the presence of a chemical contaminant in a lake. A composite sample drawn from a population has the trait in question whenever one or more of the individual samples making up the composite has the trait. Let the true fraction of the population that is contaminated be p. Classical estimators of p, such as the MLE and the jackknife, have been shown to be biased. In this study, we introduce a new shrinking estimator which can be used when doing composite sampling. The properties of this estimator are investigated and compared with those of the MLE and the jackknife.
On Constrained Minimum Vertex Covers of Bipartite Graphs: Improved Algorithms

The constrained minimum vertex cover problem on bipartite graphs arises from the extensively studied fault coverage problem for reconfigurable arrays. In this paper, we develop a new algorithm for the problem, in which classical results in matching theory and recently developed techniques in parameterized computation are nicely combined and extended. The algorithm is practically efficient with running time bounded by O(1.26k + kn), where k is the size of the constrained minimum vertex cover in the input graph. The algorithm is a significant improvement over the previous algorithms for the problem.
A Two Age Group Population Model

We proceed next to develop a mathematical model for the growth of a population in which newborn animals do not become fertile until a period of time has passed. This situation is rather realistic for many species, including humans. In return for the added realism of the model, certain complications will necessarily arise.
Effects of Stratification: Baroclinic Instability

In Chapters 1 and 2, we have considered the influence of rotation and of shallowness on geophysical flows. The combined effects of the two led to the quasi-geostrophic shallow-water theory of Chapter 3. In this theory, the fluid has constant density and variations of the flow in the vertical are negligibly small. In spite of these idealizations, the theory was able to explain some features of atmospheric and oceanic flows with large horizontal scales, such as planetary waves in the atmosphere and western boundary currents in the ocean.
Global transcriptomic response of Listeria monocytogenes during growth on cantaloupe slices.

Abstract Understanding a pathogen's response to food environments is imperative to develop effective control strategies as well as to elucidate the impact of foods on virulence potential. The purpose of this study was to assess transcriptional response of Listeria monocytogenes after growth in cantaloupe, as well as its impact on survival in synthetic gastric fluid (SGF). The transcriptional profiles of L. monocytogenes grown in cantaloupe or Brain Heart Infusion (BHI) under refrigeration were compared by a custom-designed microarray. A total of 286 and 175 genes were significantly up- and down-regulated, respectively, in L. monocytogenes grown in cantaloupe as compared to BHI (fold change ≥ 2.5 and adj. P
Cyclophilin D, Somehow a Master Regulator of Mitochondrial Function.

Cyclophilin D (CyPD) is an important mitochondrial chaperone protein whose mechanism of action remains a mystery. It is well known for regulating mitochondrial function and coupling of the electron transport chain and ATP synthesis by controlling the mitochondrial permeability transition pore (PTP), but more recent evidence suggests that it may regulate electron transport chain activity. Given its identification as a peptidyl-prolyl, cis-trans isomerase (PPIase), CyPD, is thought to be involved in mitochondrial protein folding, but very few reports demonstrate the presence of this activity. By contrast, CyPD may also perform a scaffolding function, as it binds to a number of important proteins in the mitochondrial matrix and inner mitochondrial membrane. From a clinical perspective, inhibiting CyPD to inhibit PTP opening protects against ischemia–reperfusion injury, making modulation of CyPD activity a potentially important therapeutic goal, but the lack of knowledge about the mechanisms of CyPD’s actions remains problematic for such therapies. Thus, the important yet enigmatic nature of CyPD somehow makes it a master regulator, yet a troublemaker, for mitochondrial function.
Tumor-associated antigens identified early in mouse mammary tumor development can be effective vaccine targets.

Breast cancer vaccines composed of antigens identified by serological analysis of cDNA expression libraries (SEREX) induce antigen specific immune responses in patients but have had disappointing clinical benefits. While many attempts to modify the adjuvants and vaccine method have been tried, one issue not addressed was whether the SEREX tumor-associated antigens identified from late stages of disease were ideal targets. We questioned in the transgenic TgMMTV-neu mouse model whether the antigen repertoire is distinct between early and late stage breast cancer and whether the antigens identified via SEREX from transgenic mice with early or late stage tumors would elicit differential anti-tumor effects to address this question. Three early stage antigens, Pdhx, Stk39, and Otud6B, were identified from a SEREX screen of mice prior to development of palpable lesions. Formulated into a vaccine, each early antigen inhibited tumor growth (p < 0.0001). The antigens identified from mice with late stage tumors (Swap70, Gsn, and Arhgef2) were unable to inhibit tumor growth when used as vaccines (for example Gsn p = 0.26). Each of the three early stage antigens were essential for tumor survival in syngeneic mouse tumor cells and in human breast cancer cell lines across breast cancer subtypes. Silencing protein expression of the early antigens increased apoptosis (p < 0.0001 for all antigens in mouse and p < 0.05 for all antigens in human triple negative breast cancer) and decreased survival (p < 0.0001 for all antigens in mouse and human triple negative and HER2 positive breast cancer). Overexpression of the early stage antigens in women with breast cancer predicted worse prognosis (p = 0.03) while overexpression of late stage antigens did not impact prognosis (p = 0.09). These data suggest that antigens expressed earlier in breast tumor development and functionally relevant to breast tumor growth may be more effective targets for therapeutic breast cancer vaccines than antigens identified in later disease.
“A Song of Ice and Fire”—another verse from the world of ablation

The debate between the use of radiofrequency (RF) or cryoenergy for ablation near the atrioventricular (AV) conducting system or small coronaries has been fueled by the relative efficacies and risks of the two technologies, particularly in smaller hearts. The manuscript by Schneider et al adds another chapter to that ongoing debate.
Expressing Experience: Language in Ueda Shizuteru’s Philosophy of Zen

As the central figure of the third generation of the Kyoto School of modern Japanese philosophy, UEDA Shizuteru 上田閑照 (b. 1926) has not only followed in the footsteps of his predecessors, NISHIDA Kitarō 西田幾多郎 (1870–1945) and NISHITANI Keiji 西谷啓治 (1900–1990), but has taken several strides forward in their shared pursuit of what can be called a “philosophy of Zen.” The “of” in this phrase should be understood as a “double genitive,” that is, in both its objective and subjective senses. Ueda not only philosophizes about Zen, he also philosophizes from Zen. Like Nishida and Nishitani before him, he has devoted himself to the practice of Zen as well as to the study of Western philosophy. However, what does it mean to speak, much less philosophize, about Zen experience? Ueda has in fact concentrated much of his attention on questions concerning the relation between Zen and philosophy or, more generally, between experience and language. Any development of a “philosophy of Zen,” Ueda recognizes, must begin with the question of what it means to “speak of experience.” What does it mean to express, that is, to speak from and about experience? This question has been at the heart of Ueda’s philosophical path from the beginning. His many works on this topic include a seminal early (1968) essay “Zen and Language,” later re-titled “The Language of Zen” (Ueda 2001: 183–260), articles written in German including “Awakening in Zen Buddhism as a Word-Event” (Ueda 1982a), and a recent article, “Language in a Twofold World,” which Ueda put together to represent his thought in a major anthology of Japanese philosophy (Ueda 2011a). In these and other works, Ueda convincingly demonstrates that the question of the relation between language and experience has always been a pivotal issue for the Zen tradition itself. He also shows how this tradition can help us, in the wake of the “linguistic turn” in philosophy, to return afresh to this fundamental question.
Eustachian tube dysfunction in children with cleft palate: A tympanometric time‐to‐event analysis

OBJECTIVES To characterize the duration of Eustachian tube dysfunction in children with cleft palate compared to those without cleft palate by performing time-to-event analysis on tympanometric data. To determine predictive characteristics of earlier achievement of normal tympanograms in children with cleft palate. METHODS Longitudinal tympanometric data from a minimum of 10 years at a single center were reviewed for children with cleft palate born in the years 2003 through 2007. Children with cleft lip without cleft palate born in the same years were used as a reference group to compare children with similar length of follow-up. The association between time to sustained normal (type A) tympanograms with patient demographics, clinical characteristics, and otologic history was evaluated using time-to-event analysis and compared with log rank tests. Adjusted and unadjusted hazard ratios were estimated using Cox proportional hazard models. RESULTS The median age of achieving a type A tympanogram in children with cleft palate was 9.9 years for one and 12.1 years for both ears, compared to 7.1 and 7.4 years in children with cleft lip only (P < 0.0001). On multivariate analysis, clinical characteristics such as the severity of palatal clefting or the presence of a cleft-associated syndrome/sequence were not predictors of a longer time to a type A tympanogram. CONCLUSION Our results help characterize the observation that there is delayed time to normal Eustachian tube function in children with cleft palate, which is not associated with the degree of palatal clefting. LEVEL OF EVIDENCE 3b Laryngoscope, 130:1044-1050, 2020.
Wafer design valves verification based on ASME B16.34

A flange connection is a very common method of valve attachment to the pipe. The flange is a ring-shaped device designed to be used as an alternative to welding or threading various piping components, including valves. A wafer design is defined as a flangeless design with facing that permits installation between American Society of Mechanical Engineers (ASME) and manufacturer standard (MSS SP) flanges. One advantage of using a wafer design instead of a flanged end design is that smaller face-to-face dimensions save space, and the weight and cost of the valve are lower. This paper compares face-to-face wafer type valves and double flange butterfly valves in class 150 and size ranges between 4″ and 20″ designed according to American Petroleum Institute (API) 609. Using wafer type butterfly valves as per API 609 is very common in the oil and gas industry. However, it is not common to use a wafer type ball valve for saving weight and space. This paper reviews a case study of a wafer ball valve design, including the flange bolt holes inside the body and the closure. The criteria in the ASME B16.34 standard regarding the minimum allowable wall thickness of the valve were used to verify this design. Therefore, this case study can provide a good guideline for verifying the design of wafer type ball valves with the bolt holes inside the body, as per ASME B16.34 criteria.
Pulsed Electrodeposition of Metastable Pd31Bi12 Nanoparticles for Oxygen Reduction Electrocatalysis

Metastable alloys have recently emerged as high-performance catalysts, extending the toolbox of binary alloy materials that can be utilized to mediate electrocatalytic reactions. In particular, nan...
Chapter 10 – ADAPTIVE ANALYSIS

Publisher Summary The use of uniform mesh refinement has proven not to be cost effective. It appears that there will be significant future improvements and efficiencies based on the use of adaptive finite element methods for analysis and design. One price that will be paid for these new approaches is a more heavy reliance on mathematics, such as functional analysis, norms, and interpolation theory. That is because of all adaptive methods are built on some concepts for estimating and automatically reducing the error in a solution. Another price is an increase in the complexity of the computational methods and the supporting data base. This chapter outlines some of their basic theoretical and computational aspects that are needed for two- and three-dimensional analysis and design tools. The adaptive methods fall into the categories of the h-method, p-method, r-method, and hp-method. The r-method is not a commonly used method while the h-method is probably the most widely used adaptive method. The hp-method is the least commonly used method.
Reliability-Aware Energy-Efficient Scheduling for (m, k)-Constrained Real-Time Systems Through Shared Time Slots

Abstract While energy consumption is the primary concern for the design of real-time systems, reliability and Quality of Service (QoS) are becoming increasingly important in the development of today’s pervasive computing systems. In this paper, we present a reliability-aware energy management (RAEM) scheme for minimizing the energy consumption for (m, k)-constrained real-time systems, which requires that at least m out of any k consecutive jobs of a real-time task meet their deadlines. In order to meet the (m, k)-constraints while preserving the system reliability, we propose to reserve shared recovery space for real-time tasks based on window-constraints that could be transferred to the corresponding (m, k)-constraints. Moreover, we propose efficient online scheduling techniques to boost the energy saving through shared slack reclamation. Through extensive simulations, our experimental results demonstrate that the proposed techniques significantly outperformed the previous research in reducing energy consumption for real-time systems while satisfying the (m, k)-constraints under the reliability requirement.
Variable inbreeding depression may explain associations between the mating system and herbicide resistance

Abstract Inbreeding depression is a central parameter underlying mating system variation in nature and one that can be altered by environmental stress. Although a variety of systems show that inbreeding depression tends to increase under stressful conditions, we have very little understanding across most organisms how the level of inbreeding depression may change as a result of adaptation to stressors. In this work we examined the potential that inbreeding depression varied among lineages of Ipomoea purpurea artificially evolved to exhibit divergent levels of herbicide resistance. We examined inbreeding depression in a variety of fitness-related traits in both the growth chamber and in the field. We paired our examination of inbreeding depression in fitness-related traits with an examination of gene expression changes associated with the level of herbicide resistance, breeding history (inbred or outcrossed), and the interaction of the breeding system and the level of herbicide resistance. We found that, while inbreeding depression was present across many of the traits, lineages artificially selected for increased herbicide resistance often showed no evidence of inbreeding depression in the presence of herbicide, and in fact, showed evidence of outbreeding depression in some traits compared to non-selected control lines and lineages selected for increased herbicide susceptibility. Further, at the transcriptome level, the resistant selection lines had differing patterns of gene expression according to breeding type (inbred vs outcrossed) compared to the control and susceptible selection lines. Our data together indicate that inbreeding depression may be lessened in populations that are adapting to regimes of strong selection.
Exploring the Efficiency of Self-Organizing Software Teams with Game Theory

Over the last two decades, software development has moved away from centralized, plan-based management toward agile methodologies such as Scrum. Agile methodologies are founded on a shared set of core principles, including self-organizing software development teams. Such teams are promoted as a way to increase both developer productivity and team morale, which is echoed by academic research. However, recent works on agile neglect to consider strategic behavior among developers, particularly during task assignment–one of the primary functions of a self-organizing team. This paper argues that self-organizing software teams could be readily modeled using game theory, providing insight into how agile developers may act when behaving strategically. We support our argument by presenting a general model for self-assignment of development tasks based on and extending concepts drawn from established game theory research. We further introduce the software engineering community to two metrics drawn from game theory—the price-of-stability and price-of-anarchy—which can be used to gauge the efficiencies of self-organizing teams compared to centralized management. We demonstrate how these metrics can be used in a case study evaluating the hypothesis that smaller teams self-organize more efficiently than larger teams, with conditional support for that hypothesis. Our game-theoretic framework provides new perspective for the software engineering community, opening many avenues for future research.
Institutional Foundations of the American Revolution: Legislative Politics in Colonial North America

Institutional Foundations of the American Revolution: Legislative Politics in Colonial North America
The Renin-Angiotensin-Aldosterone System and Sodium Appetite in Rats

Richter (1) was the first to show that bilateral adrenalectomy induced a specific appetite for sodium chloride (NaCl) solutions in rats. This appetite was normalized by adrenal cortical transplants, implicating an hormonal factor which we now recognize as aldosterone. Accordingly, administration of graded doses of aldosterone or of desoxycorticosterone acetate (DOCA) to adrenalectomized rats produced a graded reduction in salt appetite (Figure 1, top panel). However, doses of DOCA in excess of about 1 mg/kg/day increased NaCl intake, resulting in a U-shaped dose-response relationship. In these experiments 0.15 M NaCl solution was given in simultaneous choice with distilled water, the intake of which was the mirror image of the NaCl curve (Figure 1, lower panel). High doses of aldosterone or DOCA also induce sodium appetite in intact rats (2,3).
Modernizing the c++ interface to MPI

The Message Passing Interface (MPI) is the de facto standard for writing message passing applications. Much of MPI's power stems from its ability to provide a high-performance, consistent interface across C, Fortran, and C++. Unfortunately, with cross-language consistency at the forefront, MPI tends to support only the lowest common denominator of the three languages, providing a level of abstraction far lower than typical C++ libraries. For instance, MPI does not inherently support standard C++ constructs such as containers and iterators, nor does it provide seamless support for user-defined classes. To map these common C++ constructs into MPI, programmers must often write non-trivial boiler-plate code and weaken the type-safety guarantees provided by C++. This paper describes several ideas for modernizing the C++ interface to MPI, providing a more natural syntax along with seamless support for user-defined types and C++ Standard Library constructs. We also sketch the C++ techniques required to implement this interface and provide a preliminary performance evaluation illustrating that our modern interface does not imply unnecessary overhead.
Role of Pipecolic Acid in the Biosynthesis of Lysine in Rhodotorula glutinis

The role of pipecolic acid in the biosynthesis of lysine was investigated in Rhodotorula glutinis, an aerobic red yeast. Supplementation of pipecolic acid in the minimal medium supported the growth of mutants lys2, lys3, and lys5; α-aminoadipic acid supported the growth of lys5; but neither α-aminoadipic acid nor pipecolic acid supported the growth of mutants MNNG42 and MNNG37. During the growth of the appropriate mutants, pipecolic acid was removed from the growth medium and the intracellular pool. In tracer experiments, radioactivity from [14C]pipecolic acid was selectively incorporated into the cellular lysine of lys5 and the wild-type strain. l-Pipecolic acid-dependent enzyme activity did not require any cofactor and was inhibited by mercuric chloride and potassium cyanide. This activity was present in the wild-type strain and all of the mutants tested and was repressed in mutant lys5 when grown in the presence of higher concentration of lysine. The reaction product of pipecolic acid was converted to saccharopine by lys5 enzyme in the presence of glutamate and reduced nicotin-amide adenine dinucleotide phosphate. Mutant MNNG37 lacked the saccharopine dehydrogenase activity, indicating that this step is involved in the conversion of α-aminoadipic acid and pipecolic acid to lysine. Mutants MNNG37 and MNNG42 accumulated a p-dimethylaminobenzaldehyde-reacting product in the culture supernatant and in the intracellular pool. Chromatographic properties of the p-dimethylaminobenzaldehyde adduct and that of the pipecolic acid-dependent reaction product were similar. The reaction product and the accumulation product were characterized on the basis of mass and absorption spectra as α-aminoadipic-semialdehyde, which in solution remains in equilibrium with Δ1-piperideine-6-carboxylic acid. Since α-aminoadipic-semialdehyde is a known intermediate of the α-aminoadipic acid pathway for the biosynthesis of lysine, it is concluded that pipecolic acid is converted to lysine in R. glutinis via α-aminoadipic-semialdehyde and saccharopine.
Toward Better Drugs for Less

The Truth About the Drug Companies How They Deceive Us and What To Do About It . by Marcia Angell . Random House, New York, 2004. 325 pp. $24.95, C$34.95. ISBN 0-375-50846-5. Powerful Medicines The Benefits, Risks, and Costs of Prescription Drugs. By Jerry Avorn . Knopf, New York, 2004. 457 pp. $27.50, C$39.95. ISBN 0-375-41483-5. Angell offers an expose of the pharmaceutical industry, which she describes as "primarily a marketing machine to sell drugs of dubious benefit." Avorn discusses how prescription drugs are approved, promoted, and used. To contain costs, he argues for an agenda of comparative studies that would inform physicians, patients, and those who pay the bills.
Robust control design with real parameter uncertainty using absolute stability

The purpose of this thesis is to investigate an extension of mu theory for robust control design by considering systems with linear and nonlinear real parameter uncertainties. In the process, explicit connections are made between mixed mu and absolute stability theory. In particular, it is shown that the upper bounds for mixed mu are a generalization of results from absolute stability theory. Both state space and frequency domain criteria are developed for several nonlinearities and stability multipliers using the wealth of literature on absolute stability theory and the concepts of supply rates and storage functions. The state space conditions are expressed in terms of Riccati equations and parameter-dependent Lyapunov functions. For controller synthesis, these stability conditions are used to form an overbound of the H2 performance objective. A geometric interpretation of the equivalent frequency domain criteria in terms of off-axis circles clarifies the important role of the multiplier and shows that both the magnitude and phase of the uncertainty are considered. A numerical algorithm is developed to design robust controllers that minimize the bound on an H2 cost functional and satisfy an analysis test based on the Popov stability multiplier. The controller and multiplier coefficients are optimized simultaneously, which avoids the iteration and curve-fitting procedures required by the D-K procedure of mu synthesis. Several benchmark problems and experiments on the Middeck Active Control Experiment at M.I.T. demonstrate that these controllers achieve good robust performance and guaranteed stability bounds.
Disaster Resilience of Critical Water Infrastructure Systems

AbstractCritical water infrastructure systems (e.g., drinking water treatment, transmission, and distribution; and wastewater and stormwater collection and treatment) are critical functions of a healthy society. Disaster resilience of these infrastructure systems during and after hazards is vital for the response and recovery to the event. Critical aspects of resiliency such as planning for hazardous conditions and taking into account interdependences with the electrical infrastructure must be understood so that water infrastructure system managers can improve system resiliency. These aspects are not always initially clear until the system is exposed to a hazard, which is why we can learn so much from recent disasters. This paper outlines and quantifies the key aspects of water infrastructure system resiliency (e.g., water system redundancy, wastewater system storage, etc.) to allow for comparison. An analysis of these parameters using historical hazardous events (i.e., hurricanes Katrina and Rita) is pre...
Immunological Response of the Rabbit to Vi Antigen

Vi antibody response of rabbits varied depending on whether Vi antigen was administered in particulate or soluble state. Vi antigen in particulate form induced hemagglutinins, bacterial agglutinins, and passive cutaneous anaphylaxis (PCA) antibodies, whereas soluble Vi antigen induced only hemagglutinins. Guinea pigs passively sensitized with antisera against particulate Vi antigen gave PCA reactions when challenged with either soluble or cellular Vi antigen; antisera against soluble Vi antigen were negative for PCA. The specificity of PCA was demonstrated by its dependence on the Vi concentration and by absorption of PCA activity from antisera with V-form cells of Salmonella typhosa.
Very Large Scale Visualization Methods for Astrophysical Data

We address the problem of interacting with scenes that contain a very large range of scales. Computer graphics environments normally deal with only a limited range of orders of magnitude before numerical error and other anomalies begin to be apparent, and the effects vary widely from environment to environment. Applications such as astrophysics, where a single scene could in principle contain visible objects from the subatomic scale to the intergalactic scale, provide a good proving ground for the multiple scale problem. In this context, we examine methods for interacting continuously with simultaneously active astronomical data sets ranging over 40 or more orders of magnitude. Our approach relies on utilizing a single scale of order 1.0 for the definition of all data sets. Where a single object, like a planet or a galaxy, may require moving in neighborhoods of vastly different scales, we employ multiple scale representations for the single object; normally, these are sparse in all but a few neighborhoods. By keying the changes of scale to the pixel size, we can restrict all data set scaling to roughly four orders of magnitude. Navigation problems are solved by designing constraint spaces that adjust properly to the large scale changes, keeping navigation sensitivity at a relatively constant speed in the user’s screen space.
Automated trust negotiation

Distributed software subjects face the problem of determining one another's trustworthiness. The problem considered is managing the exchange of credentials between strangers for the purpose of property-based authentication and authorization when credentials are sensitive. An architecture for trust negotiation between client and server is presented. The notion of a trust negotiation strategy is introduced and examined with respect to an abstract model of trust negotiation. Two strategies with very different properties are defined and analyzed. A language of credential expressions is presented, with two example negotiations illustrating the two negotiation strategies. Ongoing work on policies governing credential disclosure and trust negotiation is summarized.
Influence of alkyl chain length compatibility on microemulsion structure and solubilization

The solubilization capacity of water/oil microemulsions formed with fatty acid soaps and alcohols was studied as a function of alkyl chain length of oil (C8 to C16), soap (C14 and C18), and alcohol (C4 to C7). For n-butanol with both soaps, the maximum amount of water solubilized in the microemulsion continuously decreased with increasing oil chain length whereas for n-heptanol the solubilization capacity continuously increased. For pentanol with both soaps and for hexanol with sodium stearate, the solubilization reached a maximum when the oil chain length, lo, plus that of the alcohol, la, was equal to that of the surfactant, ls, (i.e., la + lo = ls). When excess water was added to these systems, a birefringent aqueous phase in equilibrium with an isotropic upper phase formed if la + lo < ls whereas a different phase behavior, namely, the formation of two isotropic phases, was observed if la + lo ⩾ ls. Both of these observations indicate a chain length compatibility effect similar to that observed in monolayers, foams, emulsions, and lubricants. The solubilization behavior is interpreted in terms of partitioning of alcohol among oil, water, and the interface depending upon the chain length of oil and alcohol, as well as in terms of molecular packing at the interface in relation to the disorder produced by the chain length compatibility effect. It was concluded from the oil-alcohol titration study that the molar ratio of alcohol to soap at the interface increases with oil chain length. We propose that the increase in the alcohol/soap molar ratio leads to increased spacing between carboxyl groups resulting in a greater degree of ionization. Electrical resistance and dielectric constant measurements yielded results consistent with this interpretation. At a given water/oil ratio, the electrical resistance of microemulsions decreases, the dielectric constant increases, and the thickness of ionic atmosphere within the water droplets increases as the oil chain length is increased. These phenomena are consistent with the concept that microemulsions form, and vary their structure, under the influence of surfactant and alcohol partitioning between aqueous and oleic phases and the consequent interfacial activity of both species. Here, the partitioning of alcohol and soap is subtly varied by changing the oil chain length.
Dendritic cell vaccination induces cross-reactive cytotoxic T lymphocytes specific for wild-type and natural variant human immunodeficiency virus type 1 epitopes in HLA-A*0201/Kb transgenic mice.

Abstract Dendritic cells (DC) are highly efficient at inducing primary T cell responses. Consequently, DC are being investigated for their potential to prevent and/or treat human immunodeficiency virus type 1 (HIV-1) infection. In the current study, we examined the capacity of DC to elicit CD8+ cytotoxic T lymphocyte (CTL) reactivity against an HLA-A*0201-restricted HIV-1 reverse transcriptase (pol) epitope (residues 476–484) and two naturally occurring variants. Previous work demonstrated that the wild-type pol epitope is recognized by CTLs from HIV-1-infected individuals, whereas the variant pol epitopes are not, despite binding to HLA-A*0201. In agreement with these observations, parenteral administration of wild-type pol peptide induced HLA-A*0201-restricted CTL activity in A2Kb transgenic mice. In contrast, similar treatment with the two variant pol peptides failed to stimulate CTL reactivity, and this lack of immunogenicity correlated with reduced peptide:HLA-A*0201 complex stability. However, CTL responses were induced in A2Kb transgenic mice upon adoptive transfer of syngeneic bone marrow DC pulsed with the variant pol peptides. Furthermore, DC pulsed with the wild-type pol peptide elicited CTLs that cross-reacted with the variant pol epitopes. These results demonstrate that DC effectively expand the T cell repertoire of a given epitope to include cross-reactive T cell clonotypes. Accordingly, DC vaccination may aid in immune recognition of HIV-1 escape variants by broadening the T cell response.
A computer-based system for collection and analysis of circadian rest-activity data.

A computer-based system for collection and analysis of circadian rest-activity data was developed. The system has the advantage of a minimal amount of interface hardware and uses standard laboratory computer equipment permitting easy collection and automatic visualization and analysis of the data. The flexibility of the programs allows manipulation of the presentation format as needed and further refinements of the data analyses are possible.
Clinical Aspects of Cholecystokinin Release and Gallbladder Contraction

The development of sensitive and specific radioimmunoassays for cholecystokinin (CCK) and reliable techniques to quantitate gallbladder emptying has enabled studies to elucidate the physiology and pathophysiology of CCK secretion and gallbladder contraction. Both CCK and the cholinergic system are involved in the regulation of postprandial gallbladder emptying. CCK is the major factor responsible for gallbladder contraction during the intestinal phase of digestion The cholinergic system regulates gallbladder contraction during the cephalic and possibly also the gastric phase of digestion and modulates the gallbladder responsiveness to CCK during the intestinal phase. In recent years, research has focused on various pathophysiological conditions suspected to be accompanied by alterations in gallbladder motility and CCK secretion. Abnormalities of CCK secretion or gallbladder sensitivity to CCK have been described in coeliac disease, gallstone disease, pancreatic insufficiency, postgastrectomy, postvagotomy...
On the timing and place of action during embryogenesis of the female-sterile mutants fused and rudimentary Drosophila melanogaster☆☆☆

The genes fused and rudimentary were studied using gynandromorphs. Aged homozygous (experimentals) and heterozygous (controls) fu59 (from two different fu59 stocks) and r9 females were mated to Xc2cv v f males, and their daughters were examined for mosaic spots resulting from the elimination of the Xc2 chromosome. It was established that this elimination probably occurred at the second cleavage division. If the genes fu59 or r9 act before blastula formation there should be no difference in the types of gynanders recovered in experimental and control crosses, since the wild-type gene product would be distributed randomly among the cells of the blastoderm, regardless of the location of mutant nuclei. Since no gynanders with large mosaic spots were obtained from the experimental crosses, it was concluded that both fused and rudimentary do not act or the gene product is not released from the nucleus until after blastula formation. In addition, only gynanders with mosaic spots located on their abdomens were obtained from the experimental crosses, while all types of gynanders were found in the controls. It was concluded that either the genes fused and rudimentary are activated only in head and thorax tissue, or normal embryogenesis in the abdominal region of the zygote is not critical for the survival of the embryo. The gynandromorphs also provide data indicating that the reduction of ocellar size and bristle number, and of scutellar bristle number in fused as well as the formation of fused wings are autonomous; the data confirmed previous reports of autonomy of rudimentary wings.
Metastasis to a brooke heostomy—An unusual cause of stomal dysfunction

Malignant obstruction of a Brooke ileostomy is a very uncommon occurrence. This situation was encountered in a patient with chronic ulcerative colitis who had undergone a proctocolectomy for carcinoma of the rectum. Such an occurrence has not been described before in the English medical literature