cssi/SciSciGPT-SciSciNet huggingface dataset:
Angles between infinite dimensional subspaces with applications to the Rayleigh-Ritz and alternating projectors methods ✩

We define angles for infinite dimensional subspaces of Hilbert spaces, inspired by the work of E.J. Hannan, 1961/1962. The angles of Dixmier and Friedrichs, and the gaps are characterized. We establish connections between the angles corresponding to orthogonal complements. The sensitivity of angles with respect to subspaces is estimated. We show that the squared cosines of the angles from one subspace to another can be interpreted as Ritz values in the Rayleigh–Ritz method. The Hausdorff distance between the Ritz values, corresponding to different trial subspaces, is shown to be bounded by a constant times the gap between the subspaces. We prove a similar eigenvalue perturbation bound that involves the gap squared. An ultimate acceleration of the classical alternating projectors method is proposed. Its convergence rate is estimated in terms of the angles. We illustrate the acceleration for a domain decomposition method with a small overlap for the 1D diffusion equation.
Tuning the narrow-band beam position monitor sampling clock to remove the aliasing errors in APS storage ring orbit measurements

The Advanced Photon Source storage ring employs a real-time orbit correction system to reduce orbit motion up to 50 Hz. This system uses up to 142 narrow-band rf beam position monitors (Nbbpms) in a correction algorithm by sampling at a frequency of 1.53 kHz. Several Nbbpms exhibit aliasing errors in orbit measurements, rendering these Nbbpms unusable in real-time orbit feedback. The aliasing errors are caused by beating effects of the internal sampling clocks with various other processing clocks residing within the BPM electronics. A programmable external clock has been employed to move the aliasing errors out of the active frequency band of the real-time feedback system (RTFB) and rms beam motion calculation. This paper discusses the process of tuning and provides test results.
Disinfection of Immature Teeth with a Triple Antibiotic Paste

This study assessed the efficacy of a triple antibiotic paste in the disinfection of immature dog teeth with apical periodontitis. The canals were sampled before (S1) and after (S2) irrigation with 1.25% NaOCL and after dressing with a triple antibiotic paste (S3), consisting of metronidazole, ciprofloxacin, and minocycline. At S1, 100% of the samples cultured positive for bacteria with a mean CFU count of 1.7 10 8 .A t S2, 10% of the samples cultured bacteria-free with a mean CFU count of 1.4 10 4 . At S3, 70% of the samples cultured bacteria-free with a mean CFU count of only 26. Reductions in mean CFU counts between S1 and S2 (p 0.0001) as well as between S2 and S3 (p 0.0001) were statistically significant. These results indicate the effectiveness of a triple antibiotic paste in the disinfection of immature teeth with apical periodontitis.
Theory and practice of simultaneous data reconciliation and gross error detection for chemical processes

Abstract On-line optimization provides a means for maintaining a process near its optimum operating conditions by providing set points to the process’s distributed control system (DCS). To achieve a plant-model matching for optimization, process measurements are necessary. However, a preprocessing of these measurements is required since they usually contain random and—less frequently—gross errors. These errors should be eliminated and the measurements should satisfy process constraints before any evaluation on the process. In this paper, the importance and effectiveness of simultaneous procedures for data reconciliation and gross error detection is established. These procedures depending on the results from robust statistics reduce the effect of the gross errors. They provide comparable results to those from methods such as modified iterative measurement test method (MIMT) without requiring an iterative procedure. In addition to deriving new robust methods, novel gross error detection criteria are described and their performance is tested. The comparative results of the introduced methods are given for five literature and more importantly, two industrial cases. Methods based on the Cauchy distribution and Hampel’s redescending M-estimator give promising results for data reconciliation and gross error detection with less computation.
Stone weathering in a photograph

The appearance of weathering effects on stone is important for creating outdoor scenes in computer graphics. To achieve them, previous research has built upon physical simulation, which, while yielding a degree of realism, is computationally expensive and inapplicable to the situation when the object geometry is unknown. Also, physical simulation requires specific knowledge of the stone properties and environmental processes. In this paper, we present a simple visual simulation pipeline for creating weathering effects on stone within a single image. Two primary effects of stone weathering, i.e., smoothing and roughening, are considered. In addition, erosion on the object silhouette is treated. These challenging effects involve significant geometry changes, which are intractable for previous image-based editing techniques. The effectiveness of our technique is illustrated on a variety of scenes and types of stone. While it can be fully automatic, it also allows easy user interaction.
Immune response of rhesus macaques to recombinant simian immunodeficiency virus gp130 does not protect from challenge infection.

Abstract Simian immunodeficiency virus (SIV) infection of rhesus macaques is a model for human immunodeficiency virus (HIV) infection in humans. Inactivated and modified live whole-virus vaccines have provided limited protective immunity against SIV in rhesus macaques. Because of safety concerns in the use of inactivated and live whole-virus vaccines, we evaluated the protective immunity of vaccinia virus recombinants expressing the surface glycoprotein (gp130) of SIVmac and subunit preparations of gp130 expressed in mammalian cells (CHO). Three groups of animals were immunized with recombinant SIV gp130. The first group received SIV gp130 purified from genetically engineered CHO cells (cSIVgp130), the second group was vaccinated with recombinant vaccinia virus expressing SIVmac gp130 (vSIVgp130), and the third group was first primed with vSIVgp130 and then given a booster immunization with cSIVgp130. Although anti-gp130 binding antibodies were elicited in all three groups, neutralizing antibodies were transient or undetectable. None of the immunized animals resisted intravenous challenge with a low dose of cell-free virus. However, the group primed with vSIVgp130 and then boosted with cSIVgp130 had the lowest antigen load (p27) compared with the other groups. The results of these studies suggest that immunization of humans with HIV type 1 surface glycoprotein may not provide protective immunity against virus infection.
Derivation of analytical dyadic Green's function modifications for microstrip attenuation in transmission layered structures

Rigorous derivation of the correction to the dyadic Green's function for a microstrip structure containing complex layered media is carried out for imperfect metallization. A hierarchy of formulas is found consistent with a full-wave electromagnetic code employing zero thickness extent conductors for the guiding structure metal. At the bottom of the hierarchy are formulas which are only dependent on the conductor geometry and material properties. Numerical examples show the sensitivity of the attenuation constant to these formulas.
A spectral method for numerical elastodynamic fracture analysis without spatial replication of the rupture event

Abstract Perrin et al . (1995) and Geubelle and Rice (1995) have introduced a spectral method for numerical solution of two- and three-dimensional elastodynamic fracture problems. The method applies for ruptures confined to a plane separating homogeneous elastic half spaces. In this method, the physical variables, such as the traction components of stress and displacement discontinuity on the rupture plane, are represented as Fourier series in space with time-dependent coefficients. An analytical solution is found for each Fourier mode, in that each Fourier coefficient for stress is expressed by the time convolution of the corresponding coefficient for displacement with a convolution kernel specific to the rupture mode. Once the 2D formulation of the method is known, the method is readily generalizable to 3D problems in that it involves only linear combinations of the convolution kernels found for each rupture mode in 2D. This conceptual simplicity has, however, a major drawback : due to the Fourier series representations of the physical variables, the problem solved is in fact an infinite and periodic replication of rupture events on the fracture plane. So, in order to study the evolution of a single rupture, one has to use a spatial period large enough in order that the waves coming from the replication cracks do not enter the zone of interest during the time duration studied, or provide negligible stress alteration when they do arrive. We show here how to rigorously offset this defect while retaining the modal independence. Once expressed in the spatial domain, the method amounts to truncating in space the space-time convolution kernels, in a manner that provides an exact evaluation for all positions within the rupture domain (where the constitutive law between stress and displacement discontinuity is to be imposed), but not outside. In order for the method to be identical in structure to the method of Perrin et al . (1995) and Geubelle and Rice (1995), the period of the Fourier series is requested to be only twice as large as the rupture domain of interest. The only difference, then, to the original spectral method is that the convolution kernels in the Fourier domain require more elaborate calculations to be established, but this has to be done only once to allow simulations on a given domain.
Fine mapping of QTL for prepulse inhibition in LG/J and SM/J mice using F2 and advanced intercross lines

Prepulse inhibition (PPI) of the startle response is a measure of sensorimotor gating, a process that filters out extraneous sensory, motor and cognitive information. Humans with neurological and psychiatric disorders, including schizophrenia, obsessive-compulsive disorder and Huntington’s disease, exhibit a reduction in PPI. Habituation of the startle response is also disrupted in schizophrenic patients. In order to elucidate the genes involved in sensorimotor gating, we phenotyped 472 mice from an F 2 cross between LG/J × SM/J for PPI and genotyped these mice genome-wide using 162 single nucleotide polymorphism (SNP) markers. We used prepulse intensity levels that were 3, 6 and 12 dB above background (PPI3, PPI6 and PPI12, respectively). We identified a significant quantitative trait locus (QTL) on chromosome 12 for all three prepulse intensities as well as a significant QTL for both PPI6 and PPI12 on chromosome 11. We identified QTLs on chromosomes 7 and 17 for the startle response when sex was included as an interactive covariate and found a QTL for habituation of the startle response on chromosome 4. We also phenotyped 135 mice from an F34 advanced intercross line (AIL) between LG/J × SM/J for PPI and genotyped them at more than 3000 SNP markers. Inclusions of data from the AIL mice reduced the size of several of these QTLs to less than 5 cM. These results will be useful for identifying genes that influence sensorimotor gaiting and show the power of AIL for fine mapping of QTLs.
199: The role of the renin angiotensin system in fetal programming of adult hypertension

three of the populations), are shown in the Table. CONCLUSION: Common genetic variants in circadian clock genes may be associated with maternal glycemia in pregnancy. The different associations in the three populations may result from an interaction with unknown factors which differ between populations. Further studies are needed to examine how genetic and environmental alterations in circadian timing systems may impact maternal-fetal health.
A CLASSIFICATION SCHEME FOR PLANAR 4R, SPHERICAL 4R, AND SPATIAL RCCC LINKAGES TO FACILITATE COMPUTER ANIMATION

In this paper we develop a complete classification scheme for planar, spherical and spatial four-bar linkages. The goal of this classification is to note all of the subtleties of motion that an arbitrary set of four link lengths can define. A classification should exist only between the mechanisms that exhibit similar ranges of motion at both the input and output. In the planar case, three parameters being identified as either positive, negative, or zero are necessary to completely characterize all possible ranges of motion. In the spherical and spatial cases, four parameters being identified as positive, negative or zero are needed. The result is 27 classifications of planar mechanisms and 81 for spherical and spatial RCCC mechanisms.
Field-Based Simulations of Nanostructured Polyelectrolyte Gels

Nanostructured, responsive hydrogels composed of oppositely charged triblock copolymers with charged end-blocks and neutral, hydrophilic mid-blocks in aqueous solution were recently discovered. Due to electrostatic interactions, the end-blocks microphase separate and form physical cross-links that are bridged by the mid-blocks. Since these hydrogels are hydrophilic and have the ability to respond to a variety of stimuli including temperature and salt concentration, they are promising for a variety of biomedical applications including, but not limited to, drug delivery and tissue scaffolds. For such applications, there is a need to understand how to control the structure of the hydrogel. To this end, we use a new, efficient model along with self-consistent field theory to determine the structure as a function of polymer concentration and end-block fraction. After identifying numerous phases including a sphere phase, a hexagonally packed cylinder phase, a lamellar phase, and regions of phase coexistence, we determine how the polymer functionality can be tuned to manipulate the resulting phase diagram.
The Link Between Inflammatory Disorders and Coronary Heart Disease: a Look at Recent Studies and Novel Drugs in Development

Inflammation is a critical component in the development of coronary heart disease (CHD), specifically in the process of atherogenesis. Human translational and preclinical studies have demonstrated that inflammation contributes to the development, sustainment, and progression of atherosclerosis, and epidemiological studies demonstrate that human diseases associated with increased systemic inflammation increase the risk of CHD-related events. Therefore, over the last decade, multiple clinical studies were designed to target the inflammatory cascade in order to reduce the risk of CHD and to identify which populations may benefit from these preventative treatment strategies. This review briefly summarizes inflammation as a risk factor in atherosclerosis, human disease states associated with accelerated atherosclerosis, and current treatment strategies for CHD targeting the inflammatory cascade.
Manipulation Complexity of Same-System Runoff Elections

Do runoff elections, using the same voting rule as the initial election but just on the winning candidates, increase or decrease the complexity of manipulation? Does allowing revoting in the runoff increase or decrease the complexity relative to just having a runoff without revoting? For both weighted and unweighted voting, we show that even for election systems with simple winner problems the complexity of manipulation, manipulation with runoffs, and manipulation with revoting runoffs are independent. On the other hand, for some important, well-known election systems we determine what holds for each of these cases. For no such systems do we find runoffs lowering complexity, and for some we find that runoffs raise complexity. Ours is the first paper to show that for natural, unweighted election systems, runoffs can increase the manipulation complexity.
Exploring Polypharmacology in Drug Discovery and Repurposing Using the CANDO Platform.

Background Traditional drug discovery approaches focus on a limited set of target molecules for treatment against specific indications/diseases. However, drug absorption, dispersion, metabolism, and excretion (ADME) involve interactions with multiple protein systems. Drugs approved for particular indication(s) may be repurposed as novel therapeutics for others. The severely declining rate of discovery and increasing costs of new drugs illustrate the limitations of the traditional reductionist paradigm in drug discovery. Methods We developed the Computational Analysis of Novel Drug Opportunities (CANDO) platform based on a hypothesis that drugs function by interacting with multiple protein targets to create a molecular interaction signature that can be exploited for therapeutic repurposing and discovery. We compiled a library of compounds that are human ingestible with minimal side effects, followed by an 'all-compounds' vs 'all-proteins' fragment-based multitarget docking with dynamics screen to construct compound-proteome interaction matrices that were then analyzed to determine similarity of drug behavior. The proteomic signature similarity of drugs is then ranked to make putative drug predictions for all indications in a shotgun manner. Results We have previously applied this platform with success in both retrospective benchmarking and prospective validation, and to understand the effect of druggable protein classes on repurposing accuracy. Here we use the CANDO platform to analyze and determine the contribution of multitargeting (polypharmacology) to drug repurposing benchmarking accuracy. Taken together with the previous work, our results indicate that a large number of protein structures with diverse fold space and a specific polypharmacological interactome is necessary for accurate drug predictions using our proteomic and evolutionary drug discovery and repurposing platform. Conclusion These results have implications for future drug development and repurposing in the context of polypharmacology.
Humoral and cellular immune responses to an envelope-associated antigen of herpes simplex virus.

were detected in both guinea pigs and rabbits after immunization with the antigen. In a standard assay of cellular immunity to herpes simplex virus, the antigen stimulated blast transformation of herpes simplex virus-reactive splenic lymphocytes in vitro. Furthermore, immunization of rabbits with the envelope-associated antigen protected the animals from a lethal dose of live herpes simplex virus. Thus an antigen of herpes simplex virus can be prepared which contains neither infectious nor noninfectious viral particles and which stimulates immunity to the virus in laboratory animals. Previous investigations in our laboratory have shown that an envelope-associated antigen can be obtained from partially purified preparations of herpes simplex virus (HSV) after treatment with diethyl ether and alkaline buffer. This antigen has been shown to be noninfectious, to contain neither enveloped virus nor nucleocapsids, and to be nonreactive in CF tests with antisera to partially purified capsids [1]. We have also shown that the antigen is a useful CF reagent for detection of recent HSV infection [2] and for detection of type-specific antibody in sera from immunized animals and from humans previously infected with HSV [3]. In the present study, we have evaluated the humoral and cellular immune responses of animals immunized with envelope-associated antigen and have tested the protective effect of such immunization against an otherwise lethal challenge with HSV.
Remembering for empire: The war with Tripoli and the battle of Derna in US memory

In 2004, the Smithsonian debuted “The Price of Freedom: Americans at War,” a permanent exhibition at the National Museum of American History in Washington DC. The exhibit occasioned strong criticism for its privatization of public memory and glorification of militarism. What has gone unexamined, however, is the curious absence of the 1801–1805 War with Tripoli from the exhibit. This war has long been invoked as an important lesson in US exceptionalism. The assault and short occupation of the coastal town of Derna by US-led forces in 1805 holds particular significance and commemorations of the battle during the twentieth century were important in the formation of attitudes that informed US approaches to empire before, during, and after the Cold War.
Binding of factor VIIa to tissue factor permits rapid antithrombin III/heparin inhibition of factor VIIa

Because free factor VIIa is inactivated only very slowly by a plasma concentration of antithrombin III (AT III) even in the presence of heparin, it has been assumed that AT III plays no significant role in regulating the initiation of tissue factor-dependent blood coagulation. However, in the present study, we present evidence that factor VIIa bound to tissue factor, unlike free factor VIIa, is readily inactivated by AT III in the presence of heparin. In a reaction mixture containing calcium ions and approximately equimolar concentrations of relipidated tissue factor (8.9 nmol/L) and factor VIIa (10 nmol/L), AT III (100 micrograms/mL) plus heparin (1 U/mL) inhibited 50% of the factor VIIa coagulant activity of the reaction mixture within 5 minutes. AT III/heparin was also shown to inhibit the catalytic activity towards factor X of factor VIIa/tissue factor complexes formed on monolayers of an ovarian carcinoma cell line (OC-2008) that constitutively expresses surface membrane tissue factor. AT III, even in the absence of exogenously added heparin, substantially inhibited the functional activity of factor VIIa/cell surface tissue factor complexes on intact monolayers. AT III alone and AT III/heparin, to a greater extent, also inhibited factor VIIa on “nonfunctional” factor VIIa/tissue factor complexes on intact monolayers, with resultant inhibition of their expression of factor VIIa/tissue factor catalytic activity toward factor X after cell lysis. The potential physiologic significance of these findings is discussed.
Iterative Temporal Planning in Uncertain Environments With Partial Satisfaction Guarantees

This paper introduces a motion-planning framework for a hybrid system with general continuous dynamics to satisfy a temporal logic specification consisting of cosafety and safety components in a partially unknown environment. The framework employs a multilayered synergistic planner to generate trajectories that satisfy the specification and adopt an iterative replanning strategy to deal with unknown obstacles. When the discovery of an obstacle renders the specification unsatisfiable, a division between the constraints in the specification is considered. The cosafety component of the specification is treated as a soft constraint, whose partial satisfaction is allowed, while the safety component is viewed as a hard constraint, whose violation is forbidden. To partially satisfy the cosafety component, inspirations are taken from indoor-robotic scenarios, and three types of (unexpressed) restrictions on the ordering of subtasks in the specification are considered. For each type, a partial satisfaction method is introduced, which guarantees the generation of trajectories that do not violate the safety constraints while attending to partially satisfying the cosafety requirements with respect to the chosen restriction type. The efficacy of the framework is illustrated through case studies on a hybrid car-like robot in an office environment.
In Vivo Models of Ovarian Toxicity

The success of cancer treatment results in female survivors who wrestle with long-term reproductive side effects of chemotherapy. An ideal ovoprotective drug would be mechanism-based, requiring increased knowledge of the action of chemotherapy drugs on the ovary. The strengths and weaknesses of relevant animal models in researching the mechanism of chemotherapy ovarian toxicity and developing ovoprotective therapies are discussed. Emerging in vivo rodent studies reveal that chemotherapeutic agents target multiple ovarian cell types. Most in vivo data assess either acute or long-term ovoprotection from a single chemotherapeutic agent, but direct cross-study efficacy comparisons are difficult due to disparate animal ages and endpoints. Nonetheless, in vivo proof-of-concept studies of some promising ovoprotectants in mice have led to normal offspring. Non-human primate models are necessary to evaluate chemotherapy-induced ovarian toxicity in vivo if the development of ovoprotective agents is to become a clinical reality. Future research on ovarian chemoprotection and design of novel chemotherapeutic agents that are not ovotoxic will transform clinical oncofertility practices for female cancer patients.
A History and Objectives of Primatology

This chapter reviews the history and objectives of primatology. The science of primatology is concerned with the study of those mammals that are most closely related to human beings. The closest mammal relatives constitute the order Primates, which includes four main living groups: prosimians, monkeys of the old and new worlds, greater and lesser apes, and humans. Primatology as a distinctive field within biology did not exist until the second half of the 1950s but today primatology has blossomed into an important subdiscipline of biology and has developed different focal points, such as the study of primate morphology, history, and function as well as primate social behavior and molecular primatology. The thought processes leading to the development of primatology took root when Darwin's theory of evolution by natural selection was first applied to interpret the comparative biology of humans and apes. Many of the topics have been discussed that remained important in primatology up to the present day.
Endothelial Cell-Specific Deletion of P2Y2 Receptor Promotes Plaque Stability in Atherosclerosis-Susceptible ApoE-Null Mice

Objective— Nucleotide P2Y2 receptor (P2Y2R) contributes to vascular inflammation by increasing vascular cell adhesion molecule-1 expression in endothelial cells (EC), and global P2Y2R deficiency prevents fatty streak formation in apolipoprotein E null (ApoE−/−) mice. Because P2Y2R is ubiquitously expressed in vascular cells, we investigated the contribution of endothelial P2Y2R in the pathogenesis of atherosclerosis. Approach and Results— EC-specific P2Y2R-deficient mice were generated by breeding VEcadherin5-Cre mice with the P2Y2R floxed mice. Endothelial P2Y2R deficiency reduced endothelial nitric oxide synthase activity and significantly altered ATP- and UTP-induced vasorelaxation without affecting vasodilatory responses to acetylcholine. Telemetric blood pressure and echocardiography measurements indicated that EC-specific P2Y2R-deficient mice did not develop hypertension. We investigated the role of endothelial P2Y2R in the development of atherosclerotic lesions by crossing the EC-specific P2Y2R knockout mice onto an ApoE−/− background and evaluated lesion development after feeding a standard chow diet for 25 weeks. Histopathologic examination demonstrated reduced atherosclerotic lesions in the aortic sinus and entire aorta, decreased macrophage infiltration, and increased smooth muscle cell and collagen content, leading to the formation of a subendothelial fibrous cap in EC-specific P2Y2R-deficient ApoE−/− mice. Expression and proteolytic activity of matrix metalloproteinase-2 was significantly reduced in atherosclerotic lesions from EC-specific P2Y2R-deficient ApoE−/− mice. Furthermore, EC-specific P2Y2R deficiency inhibited nitric oxide production, leading to significant increase in smooth muscle cell migration out of aortic explants. Conclusions— EC-specific P2Y2R deficiency reduces atherosclerotic burden and promotes plaque stability in ApoE−/− mice through impaired macrophage infiltration acting together with reduced matrix metalloproteinase-2 activity and increased smooth muscle cell migration.
Sickle Cell Vaso-Occlusion Is Triggered by E-Selectin Ligand Signaling and Propagated by the Leukocyte Integrin Mac-1.

Abstract Vasoocclusion (VOC) is the leading cause of morbidity and mortality in patients with sickle cell disease (SCD). Intravital microscopy studies in a murine model of SCD have revealed that capture of sickle red blood cells (RBC) by intravascular adherent leukocytes (WBC) plays an important role in VOC, and that deficiency in both P-and E-selectins protect from VOC. Here, we have investigated the cellular and molecular mechanisms leading to sickle RBCs interactions with adherent WBCs. Intravital microscopy analyses of the individual role of P- or E-selectin revealed, unexpectedly, a profound reduction in RBC-WBC interactions in Berkeley sickle mice lacking E-selectin (Sele−/−; >97% reduction), whereas the protection was only partial in the absence of endothelial P-selectin. Since E-selectin is expressed exclusively on the endothelium, and its deficiency does not alter WBC recruitment, we hypothesized that E-selectin might provide activation signals to neutrophils that allow them to capture RBCs. During our studies, we observed that RBC-WBC interactions are not exclusive of sickle animals but are also present in wild-type B6 mice treated with TNF-α, suggesting that this phenomenon accompanies a physiological inflammatory response. We found that RBC-WBC interactions in B6 mice occur at a lower frequency than in sickle mice and that these interactions are also reduced in Sele−/− mice (60% reduction; p
INJURY AND REPAIR OF SEVERAL SALMONELLA SEROTYPES AFTER FREEZING AND THAWING IN MILK SOLIDS

Freezing and thawing of Salmonella anatum cells induced increased sensitivity to selective agents in the plating medium. Selective plating media containing the bile salt sodium desoxycholate were most inhibitory. Injury was demonstrated in 11 Salmonella serotypes. The percent injury ranged from 20% (Salmonella heidelberg) to about 60% (Salmonella pullorum, Salmonella anatum, Salmonella infantis, and Salmonella cubana). The percent death ranged from 10% (Salmonella meleagridis and Salmonella infantis) to 27% (Salmonella pullorum and Salmonella oranienburg). The data indicated that 2,4-dinitrophenol prevented repair of injury in all serotypes that exhibited at least 25% injury. This suggested the importance of energy synthesis in the repair process.
Java thread and process performance for parallel machine learning on multicore HPC clusters

The growing use of Big Data frameworks on large machines highlights the importance of performance issues and the value of High Performance Computing (HPC) technology. This paper looks carefully at three major frameworks Spark, Flink and Message Passing Interface (MPI) both in scaling across nodes and internally over the many cores inside modern nodes. We focus on the special challenges of the Java Virtual Machine (JVM) using an Intel Haswell HPC cluster with 24 cores per node. Two parallel machine learning algorithms, K-Means clustering and Multidimensional Scaling (MDS) are used in our performance studies. We identify three major issues — thread models, affinity patterns, and communication mechanisms — as factors affecting performance by large factors and show how to optimize them so that Java can match the performance of traditional HPC languages like C. Further we suggest approaches that preserve the user interface and elegant dataflow approach of Flink and Spark but modify the runtime so that these Big Data frameworks can achieve excellent performance and realize the goals of HPC-Big Data convergence.
Situational Context for Ranking in Personal Search

Modern search engines leverage a variety of sources, beyond the conventional query-document content similarity, to improve their ranking performance. Among them, query context has attracted attention in prior work. Previously, query context was mainly modeled by user search history, either long-term or short-term, to help the ranking of future queries. In this paper, we focus on situational context, i.e., the contextual features of the current search request that are independent from both query content and user history. As an example, situational context can depend on search request time and location. We propose two context-aware ranking models based on neural networks. The first model learns a low-dimensional deep representation from the combination of contextual features. The second model extends the first one by leveraging binarized contextual features in addition to the high-level abstractions learned using a deep network. The existing context-aware ranking models are mainly based on search history, especially click data that can be gathered from the search engine logs. Although context-aware models have been widely explored in web search, their influence on search scenarios where click data is highly sparse is relatively unstudied. The focus of this paper, personal search (e.g., email search or on-device search), is one of such scenarios. We evaluate our models using the click data collected from one of the world's largest personal search engines. The experiments demonstrate that the proposed models significantly outperform the baselines which do not take context into account. These results indicate the importance of situational context for personal search, and open up a venue for further exploration of situational context in other search scenarios.
Developing a de-centralized cycle-free nash bargaining arterial traffic signal controller

This paper presents a novel de-centralized cycle-free traffic signal controller that adapts to changes in traffic demand. Traffic signal timing optimization is achieved using a Nash Bargaining game-theoretic framework, where each phase is modeled as a player in a game in which the players cooperate to reach a mutual agreement. The Nash bargaining solution is applied to obtain the optimal control strategy, considering a flexible phasing sequence and free cycle length. The system is implemented and evaluated in the INTEGRATION microscopic traffic assignment and simulation software. The proposed control approach is compared to the operation of an optimum fixed-time coordinated plan, a centralized adaptive phase split controller, a decentralized phase split and cycle length controller, and a fully coordinated adaptive phase split, cycle length, and offset optimization controller to evaluate the performance of the proposed decentralized controller. The simulation results were tested on an arterial network located in the heart of downtown Blacksburg, Virginia, USA. The simulation results show significant reductions in the average travel time ranging from 7% to 21%, a reduction in the total delay ranging from 36% to 67%, and a reduction in the emission levels ranging from 6% to 13%. Analysis of variance, Tukey, and pairwise comparison tests were conducted, to examine the statistically significant difference of the proposed controller. The results demonstrate that the proposed decentralized controller produces major improvements over other state-of-the-art centralized and de-centralized control approaches.
Momentum exchange theory of photon diffraction

Momentum exchange theory (MET) provides an alternative picture for optical diffraction based on a distribution of photon paths through momentum transfer probabilities determined at the scattering aperture. This is contrasted with classical optical wave theory that uses the Huygens–Fresnel principle and sums the phased contributions of wavelets at the point of detection. Single-slit, multiple-slit (Talbot effect), and straight-edge diffraction provide significant clues to the geometric parameters controlling momentum transfer probabilities and the relation to Fresnel zone numbers. Momentum transfer is primarily dependent on preferred momentum states at the aperture and the specific location and distance for momentum exchange. Diffraction by an opaque disc provides insight to negative (attractive) dispersions. MET should simplify the analysis of a broadened set of aperture configurations and experimental conditions.
Have we done our last amniocentesis? Updates on cell-free DNA for Down syndrome screening

Prenatal aneuploidy screening changed significantly in 2012 when cell-free fetal deoxyribonucleic acid (DNA) was introduced as a noninvasive prenatal test. A noninvasive prenatal test detects cell free fragments of fetal DNA from the placenta circulating in maternal blood that coexist with cell-free DNA (cfDNA) of maternal origin. Using next-generation sequencing, the noninvasive prenatal test compares maternal and fetal cfDNA ratios for chromosomes of interest (i.e., 21, 18, 13, X, and Y) to assess chromosomal aneuploidy. Compared to traditional screening using ultrasound and serum markers, the noninvasive prenatal test has superior test characteristics, including a higher detection rate and positive predictive value, and a lower false-positive rate. The noninvasive prenatal test is already used for primary screening in high-risk women and is rapidly expanding to all women. Given its increasing use, understanding the noninvasive prenatal test's limitations is critical. Discordant results (i.e. noninvasive prenatal test is positive for aneuploidy with a normal fetal karyotype) can occur because of biological processes such as aneuploidy confined to the placenta, a vanished twin, maternal aneuploidy or maternal cancer. Use of the noninvasive prenatal test for screening beyond the most common aneuploidies is not recommended. The noninvasive prenatal test is a major advance in prenatal aneuploidy screening but it is not diagnostic and does not replace invasive testing (i.e. chorionic villous sampling or amniocentesis) for confirmation of fetal chromosomal disorders.
Properties of the ambient noise field recorded at the 150 m isobath during the 2016–2017 Canadian Basin Acoustic Propagation Experiment

The Applied Research Laboratories at the University of Texas at Austin (ARL:UT) deployed two passive acoustic recording systems along the 150 m isobath of the Chukchi Shelf during the 2016–2017 Canadian Basin Acoustic Propagation Experiment (CANAPE). The first system was a single-hydrophone recorder located on the seafloor, while the Persistent Acoustic Observation System (PECOS) contained a horizontal line array of hydrophones along the seabed and a vertical line array spanning a portion of the water column. The systems were deployed and recovered during open-water conditions, but remained in place during the ice-formation, ice-covered, and ice-melt time periods. This talk presents initial findings of the statistical ambient noise levels during the year-long experiment, presents beam-noise levels recorded by PECOS, and qualitatively discusses the natural, biologic, and anthropogenic sounds present in the acoustic recordings. [Work sponsored by ONR.]
Safety of Dynamic Magnetic Resonance Imaging of the Cervical Spine in Children Performed without Neurosurgical Supervision.

Objective The need for neurosurgical supervision as well as the general safety and utility of dynamic magnetic resonance imaging (MRI) of the cervical spine in children remains controversial. We present the largest descriptive cohort study of cervical flexion-extension MRI scans in pediatric patients to help elucidate the safety and utility of this technique. Methods We retrospectively reviewed all cervical spine MRI scans performed at Lucile Packard Children's Hospital at Stanford from 2009 to 2015. We identified 66 dynamic cervical MRI scans performed in 45 children and 2 young adults for further study. Results General anesthesia was used in 43 scans. The neuroradiology team performed all scans with no direct supervision by the neurosurgery team. There were no adverse events. Dynamic MRI detected significant instability that was not clearly seen on dynamic radiographs (5 patients) and cord compression not seen on static MRI (9 patients). One patient with asymptomatic instability found on flexion-extension radiographs had no cord compression with movement on MRI and was managed conservatively. Two neonates with significant congenital malformations of the cervical spine were cleared for operative positioning for cardiac procedures based on flexion-extension MRI. Conclusions Dynamic MRI is a safe tool for evaluating the cervical spine and cervicomedullary junction in various pediatric populations and can be performed safely without direct neurosurgical supervision. We describe for the first time the use of flexion-extension MRI to clear neonates with severe congenital cervical spine abnormalities for complex operative positioning and further care in the intensive care unit.
Pass GO and collect $610: modified Monopoly for teaching inequality

Modified versions of the board game Monopoly have been used to teach inequality. This paper reviews modifications suggested in the pedagogical literature and then reports survey-based results on whether playing a modified version of the game affected students' objective perceptions or subjective attitudes towards inequality. Our survey results suggest that, compared to a group of students who received only a traditional lecture on inequality statistics, students who played the modified Monopoly game saw larger improvements in their objective perceptions of the actual extent of income and wealth inequality and, also, bigger changes in their subjective attitudes about the importance of inheritance, luck, and hard work to real-world success. Yet, attitudes were not dramatically affected by playing the game and misperceptions about basic inequality statistics remained, so higher impact approaches to teaching inequality are still needed.
From Deficit Thinking to Counter Storying: A Narrative Inquiry of Nontraditional Student Experience within Undergraduate Engineering Education

This paper reports on narrative inquiry research conducted with nontraditional undergraduates as they pursued a common goal of becoming engineers. Participants were enrolled in a two-year engineering transfer program offered in the evenings, via synchronous broadcast distance instruction, by a public, land-grant university situated in the western United States. The purpose of the research was to understand the experiences of nontraditional students during the two-year program, which they accessed at regional campuses within or near their local communities, and later as they transitioned to the four-year university campus located in another city away from these communities. In this paper, personal, social, and institutional tensions, arising from instances of deficit thinking and emerging from within the participants’ lived and told stories, are identified and examined. Despite deep, personal reactions to the bias they experienced, participants overcame perceptions of personal deficiency to pursue and achieve their goal of becoming engineers. Participant counter stories further revealed ways in which their unique life experiences alternately served to enhance and deepen their engineering education.
Can Bacteria Evolve Anticancer Phenotypes

Can bacteria evolve anticancer phenotypes when growing together with cancer cells? Three hypotheses have been developed to address this question. First, based on an analogy of bacterial biofilm development from planktonic cells to carcinogenesis from metastatic cells, there seems to be an evolutionary relationship between bacteria and cancer. Such an analogy in lifestyle suggests that bacteria and cancer may compete with each other while encountering nutrient needs or anti-­proliferation drug treatment. These thoughts lead to the second hypothesis that bacteria can form biofilms on cancer cells under treatment of DNA replication inhibitory anticancer drugs, thereby impairing metastasis. Under such treatment, bacteria may be able to adhere to and invade into cancer cells—thus resulting in advantageous bacterial phenotypes—so that bacteria survive the drug attack. This hypothesis proposes that bacteria, growing with cancer cells and replication inhibition drugs, undergo the SOS response through which the evolution of the anticancer phenotypes is facilitated.
Noise Sensitivity Evaluation of Autoregressive Features Extracted from Structure Vibration

In the past few decades many types of structural damage indices based on structural health monitoring signals have been proposed, requiring performance evaluation and comparison studies on these indices in a quantitative manner. One tool to help accomplish this objective is analytical sensitivity analysis, which has been successfully used to evaluate the influences of system operational parameters on observable characteristics in many fields of study. In this chapter, the sensitivity expressions of two damage features, namely the Mahalanobis distance of autoregressive coefficients and Cosh distance of autoregressive spectra, will be derived with respect to the measurement noise level. The effectiveness of the proposed methods is illustrated in a numerical case study on a 10 DOF system, where their results are compared with those from direct simulation and theoretical calculation.
Recovery of Function, Neural Basis of

The study of recovery of function is important to help ameliorate the effects of brain damage. This article examines the factors that can influence and promote recovery of function by classifying explanations of recovery of function according to the mechanisms of vicariation, diaschesis, reorganization, and substitution. These theories are not mutually exclusive, sometimes sharing common mechanisms. Finally, the study of recovery of function also yields a basic understanding of normal brain organization and localization.
Improved Arrangement and Capacity for Medication Transactions: A Pilot Study to Determine the Impact of New Technology on Medication Storage and Accessibility.

Purpose: A new-generation automated dispensing cabinet (ADC) deployment is described. Methods: A single-center retrospective-prospective pilot product performance study was conducted, and prospecti...
Consensus of Nonidentical Euler–Lagrange Systems Under Switching Directed Graphs

This paper studies the consensus problem of nonidentical Euler–Lagrange systems with parametric uncertainties, under switching directed graphs. We present an adaptive distributed control algorithm that solves this problem in the leaderless scenario, under weak assumptions on the switching interconnection between agents. It is shown that the proposed consensus protocol achieves consensus without using neighbor's velocity information and accounts for the discontinuity of the input torque that results from the switching interaction between agents. Simulation results are given to illustrate the effectiveness of the proposed control schemes.
Salvage prostate brachytherapy after definitive external radiation: tried and now tested.

Definitive external beam radiation therapy (EBRT) has long been one of the standard treatment modalities for prostate cancer. However, 15–75% of patients will experience a disease recurrence depending on such factors as the risk group, use and length of androgen deprivation therapy (ADT) and radiation dose (1). Approximately 25% of patients with biochemical recurrence will have local clinical disease progression within 5 years (2).