cssi/SciSciGPT-SciSciNet huggingface dataset:
Risk Factors and Outcomes Associated With Sepsis After Coronary Artery Bypass and Open Heart Valve Surgeries

Purpose. Sepsis causes significant morbidity and mortality after cardiac surgery and carries a significant burden on health care costs. There is a general association of increased risk of post–card...
Passivity-based Iterative Learning Control Design for Selective Laser Melting

Selective laser melting (SLM) is an additive manufacturing process that creates 3D parts through layer by layer melting and fusion of a metal powder bed. Although a number of finite element models (FEM) have been developed that describe the coupled and complex physics associated with this process, they are typically not suitable for control algorithm design. In this manuscript, a control oriented reduced order model (ROM) to adequately capture these temperature dynamics is proposed and validated against high fidelity FEM simulations. Further, since the laser paths are often repetitive (or consist of repeating sub-trajectories), iterative learning control (ILC) algorithms can be used to obtain suitable laser power profiles to deliver desired temperature field profiles. However, the process is inherently multiple input single output (MISO), therefore, a suitable output is constructed in such a way so as to the make the system passive. A passivity-based ILC law is then designed to drive this synthesized output to a desired profile and a convergence criterion for this law derived. The proposed ILC update law is implemented on both models and the results are compared for a set of candidate laser paths. Finally, the ILC update law is implemented on the high-fidelity FEM to melt a ring geometry to demonstrate the capability of the ILC algorithm to generate optimal laser power profiles for creating complicated geometries on large powder beds.
clustQ: Efficient Protein Decoy Clustering Using Superposition-free Weighted Internal Distance Comparisons

Structure of a protein largely determines its functional properties. Hence, the knowledge of the protein's 3D structure is an important aspect in determining solutions to fundamental biological problems. Structure prediction algorithms generally employ clustering algorithm to select the optimal model for a target from a large number of predicted confirmations (a.k.a. decoy). Despite significant advancement in clustering-based optimal decoy selection methods, these approaches often cannot deliver high performance in terms of the time taken to cluster large number of protein structures owing to the computational cost associated with pairwise structural superpositions. Here, we propose a superposition-free approach to protein decoy clustering, called clustQ, based on weighted internal distance comparisons. Experimental results suggest that the novel weighing scheme is helpful in both reproducing the decoy-native similarity score and estimating pairwise clustering based predicted quality score in a computationally efficient manner. clustQ attains performance comparable to the state-of-the-art multi-model decoy quality estimation methods participating in the latest Critical Assessment of protein Structure Prediction (CASP) experiments irrespective of target difficulty. Moreover, clustQ predicted score offers a unique way to reliably estimate target difficulty without the knowledge of the experimental structure. clustQ is freely available at http://watson.cse.eng.auburn.edu/clustQ/.
Does the “Teer” vocalization deter prospecting female red-winged blackbirds?

A speaker-occupation experiment was conducted to determine whether female red-winged blackbirds (Agelaius phoeniceus) use the aggressive “Teer” vocalization to deter conspecific females that are prospecting for opportunities to settle. In each of 14 trials conducted during the breeding seasons of 1987, 1988, and 1989, tape recordings and a pair of loud speakers were used to “defend” suitable habitat. Observations of female red-winged blackbirds settling on these “speaker territories” and on adjacent control areas showed that speaker territories were settled significantly earlier than silent control territories. Each of the 14 first settlers on speaker territories included at least one speaker location within the bird's display area, and 9 of the 14 included both speaker locations. Additional observations showed that the rate at which prospecting females visited control and speaker territories, and the number of females eventually settling on them, were not significantly different. Finally, females that settled on speaker territories sang Teers at significantly higher rates than those on control territories. These results demonstrate that the Teer alone was not sufficient to deter prospecting female red-winged blackbirds. On the contrary, Teers given in the absence of an actual resident may have attracted settlers. It is suggested that the aggressive Teer vocalization might function to establish dominance relationships among the females sharing a polygynous male's territory.
Sleep Duration and Sleep Quality in Caregivers of Patients With Dementia: A Systematic Review and Meta-analysis

Importance In the United States, 16 million family caregivers provide long-term care for patients with dementia. Although one’s physical, mental, and cognitive health depends on sleep, many caregivers experience chronic stress, and stress is typically associated with worse sleep quantity and quality. Objective To quantify the extent, nature, and treatability of sleep problems in dementia caregivers. Data Sources PubMed and Scopus databases were systematically searched for articles published through June 2018 using the following keywords:caregiverorspouseorcaretakerANDsleeporcircadianANDdementiaorAlzheimer. Backward citation tracking was performed, and corresponding authors were contacted for additional data to conduct meta-analyses and pooled analyses. Study Selection Two reviewers independently screened 805 studies to identify those that reported sleep duration or sleep quality in caregivers of patients with dementia. Data Extraction and Synthesis Following the PRISMA guidelines, 2 reviewers independently extracted data from all studies and conducted National Heart, Lung, and Blood Institute study quality assessments. Meta-analyses with random-effects models were performed to evaluate sleep duration, sleep quality, and sleep interventions in dementia caregivers. Main Outcomes and Measures Sleep quality and total sleep time were measured by polysomnography, actigraphy, and self-report. Results Thirty-five studies were analyzed with data from 3268 caregivers (pooled mean age [SD of sample means], 63.48 [5.99] years; 76.7% female) were analyzed. Relative to age-matched control noncaregiver adults, caregivers had lower sleep durations akin to losing 2.42 to 3.50 hours each week (Hedgesg = −0.29; 95% CI, −0.48 to −0.09;P = .01). Sleep quality was significantly lower in caregivers (Hedgesg = −0.66; 95% CI, −0.89 to −0.42;P Conclusions and Relevance Sleep debt is known to have cumulative associations with physical, mental, and cognitive health; therefore, poor sleep quality in dementia caregivers should be recognized and addressed. Although the caregiving role is stressful and cognitively demanding by its nature, better sleep quality was observed in caregivers who received low-cost behavioral interventions.
Counting acyclic and strong digraphs by descents

Abstract A descent of a labeled digraph is a directed edge ( s , t ) with s > t . We count strong tournaments, strong digraphs, acyclic digraphs, and forests by descents and edges. To count strong tournaments we use Eulerian generating functions and to count strong and acyclic digraphs we use a new type of generating function that we call a graphic Eulerian generating function.
Groundwater geochemistry and flow in the Spring Mountains, NV: Implications for the Death Valley Regional Flow System

Abstract Groundwater geochemistry and 87Sr/86Sr from spring waters in the Spring Mountains, NV were used to understand how groundwater recharging in the Spring Mountains influences regional groundwater flow in the Death Valley Regional Flow System (DVRFS). Previous researchers hypothesized that groundwater from the Spring Mountains contributes to the DVRFS, an interbasin groundwater flow system (IGF). However, the Spring Mountains are geologically heterogeneous, therefore, a uniform contribution of groundwater flow across the range is unlikely. Here, we use spring water geochemistry, spring water and host rock 87Sr/86Sr, and observations of the surrounding geology to determine what regions of the Spring Mountains are likely to contribute more flow to the DVRFS. Based on geochemical and isotopic evidence, Spring Mountains groundwater can be divided into three flow regions with distinct geochemical signals reflecting silicate or carbonate water-rock interactions and location relative to major thrust faults. The Keystone Thrust flow region (KST) has a 87Sr/86Sr of 0.710–0.711, is recharged by both rain and snow, and weathers both Mesozoic sandstones and Permian and Cambrian carbonate. Central Spring Mountains (CSM) groundwater has a 87Sr/86Sr of ~0.708, is primarily recharged by snow, and weathers Permian and Cambrian limestones and dolostones. The Montgomery Hills (MH) flow region has a 87Sr/86Sr 0.711–0.733, is recharged by both rain and snow, and weathers both Permian and Cambrian carbonates and Precambrian siliciclastics. Groundwater mixing between flow groups occurs along major thrust faults in the study area, as evidenced by 87Sr/86Sr signatures that reflect one flow group and δ18O and δ2H and geochemical signatures that reflect another flow group. The combination of geochemical and isotopic results suggest CSM groundwater is the most likely to reach Death Valley because CSM groundwater composition reflects the geochemical and isotopic signatures of the highly permeable rocks that connect the Spring Mountains to Death Valley. Flow leaving the KST and MH also influences the DVRFS after mixing with CSM groundwater along major thrust faults.
Exploring the use of virtual reality by pre-service elementary teachers for teaching science in the elementary classroom

This research was conducted on two groups of pre-service elementary teachers (PSETs) (N = 38) in a pre/post within-subjects design. Participants were asked to critique, create, and evaluate the use...
Two dimensional models of tumor angiogenesis

Angiogenesis, the formation of new capillaries from pre-existing vessels, is essential for tumor progression. It is critical for the growth of primary cancers. In this thesis, we present a new approach to angiogenesis, based on the theory of reinforced random walks, coupled with a Michaelis-Menten type mechanism. This views the endothelial cell receptors as the catalyst for transforming angiogenic factor into proteolytic enzyme in order to model the first stage. In our model we use a curvature-induced proliferation term for the endothelial cell equation. Our numerical results indicate that the proliferation of endothelial cells is high at the tip. .A,lso, we observe that the tip movement speeds up as it gets close to the tumor. •A. coupled system of ordinary and partial differential equations is derived which, in the pres­ ence of an angiogenic agent, predicts the aggregation of the endothelial cells and the collapse of the vascular lamina, opening a passage into the e.xtracellular matrix (ECM). We have dynam­ ical equations not only in a two-dimensional region,the ECM, but also in a one-dimensional region, the capillary. We also consider the effect of the angiostatin on the endothelial cell proliferation and fibronectin. Our computations are compared with the results of Judah Folkman's classical rabbit eye experiments in which he demonstrated that tumors can produce angiogenic growth factors. Using only classical enzyme kinetics and reinforced random walk cell transport equations, we are able to "predict" how long it should take for a new capillary to grow from the limbus of the rabbit eye to an implanted malignancy. The "predictions" agree very well with the experiments.
Oleanane-type triterpenoid glucuronosides from Glycyrrhiza echinata L. root

Abstract Phytochemical investigation on Glycyrrhiza echinata L. root resulted in the isolation of five highly polar oleanane glucuronopyranosides [yunganoside G1 (1), yunganoside G2 (2), yunganoside M (3), yunganoside E2 (4), and macedonoside C (5)]. The chemical structures of the isolates were elucidated by NMR and mass spectral data analysis as well as by comparing the relevant data with those of reported in literature. The chemotaxonomic significance of macedonoside C and other saponins in Glycyrrhiza is discussed.
The luxury of doing nothing: inferring luxury from idleness display in travel setting

Extant studies on luxury have focused on exploring motivations and service attributes behind the consumption of luxury travel brands. However, the underlying psychological mechanism of how customer...
Mechanism of negative regulation of NF-κB by N4BP1

Many immune responses depend upon activation of NF-{kappa}B, a key transcription factor in the elicitation of a cytokine response. Here we demonstrate that N4BP1 inhibited TLR-dependent activation of NF-{kappa}B by interacting with the NF-{kappa}B signaling essential modulator (NEMO, also known as I{kappa}B kinase {gamma}) to attenuate NEMO-NEMO dimerization or oligomerization. The UBA-like (ubiquitin associated-like) and CUE-like (ubiquitin conjugation to ER degradation) domains in N4BP1 mediated the interaction with the NEMO COZI domain. Both in vitro and in mice, N4bp1 deficiency specifically enhanced TRIF-independent (TLR2, TLR7, or TLR9-mediated), but not TRIF-dependent (TLR3 or TLR4-mediated), NF-{kappa}B activation leading to increased production of proinflammatory cytokines. In response to TLR4 or TLR3 activation, TRIF caused activation of caspase 8, which cleaved N4BP1 distal to residues D424 and D490 and abolished its inhibitory effect. N4bp1-/- mice also exhibited diminished numbers of T cells in the peripheral blood. Our work identifies N4BP1 as an inhibitory checkpoint protein that must be overcome to activate NF-{kappa}B, and a TRIF-initiated caspase 8-dependent mechanism by which this is accomplished.
Engagement on online social networks during a social crisis: effect of anonymity level

Recent social movements have increasingly used online social networks (OSNs) to spread information and organise activists. Unfortunately, using an OSN during a social crisis also allows for uncertainties and rapid dissemination of misinformation. During the fall of 2015, a student activist group protested and received nationwide attention. At the time, two OSNs were very popular: Twitter, a traditional OSN, and Yik Yak, an anonymous OSN. In this research, we performed a sentiment analysis on datasets from each of these platforms during the social crisis. Our findings suggest that the two platforms are used differently during a social crisis. Posts on traditional OSNs receive more engagement if they have a high total sentiment, but are not overly positive or negative. Anonymous OSN posts see increased engagement with longer messages that are positively or negatively charged. These findings indicate a need for divergent theorising for anonymous OSNs.
COVID-19 cytokine storm: what is in a name?

It is now almost difficult to imagine back to a time before COVID-19 turned the world upside down. The pandemic has taken an enormous toll on patients, families and communities, working fundamental changes into our lives and into our thoughts. The medical community has formed one of many ‘front lines’ in the battle against COVID-19, and our lives and thoughts have been transformed as well. When the COVID-19 story is told, a key subplot will be how physicians and scientists responded to the virus. The report by Caricchio et al 1 in Annals gives us opportunity to consider the medical response to COVID-19, both at a practical level and with respect to the evolving concept of COVID-associated cytokine storm.1 These investigators confronted the pandemic at Temple University, in Philadelphia, one of the early epicentres of COVID-19 in the USA. In a period of 5 weeks beginning in March 2020, the Temple team admitted more than 500 adults with characteristic pulmonary ground-glass opacities, all requiring supplemental oxygen and most positive for SARS-CoV-2 by qPCR. Despite this onslaught, the team still managed to collect and analyse data to ask whether clinical or laboratory parameters accurately predicted the severe inflammatory phenotype referred to here as the ‘COVID-19 cytokine storm’ (COVID-CS). Lacking an accepted gold standard, the investigators employed a consensus of expert rheumatologists and pulmonologists to assign 64 patients (12%) to this category, on the basis of worsening respiratory status and elevation in C reactive protein (CRP), ferritin, D-dimer, lactate dehydrogenase (LDH), and/or troponin. COVID-CS criteria were then tested in a second cohort of 258 Temple patients admitted during a 12-day period later in April. To develop their prediction model, they used univariate logistic regression to identify variables associated with COVID-CS and then principal components analysis to find predictors that clustered together, …
Spatial and temporal dynamics of SAR11 marine bacteria sampled across a nearshore to offshore transect in the tropical Pacific Ocean

Time-series surveys of microbial communities coupled with contextual measures of the environment provide a useful approach to dissect the factors determining distributions of microorganisms across ecological niches. Here, monthly time-series samples of surface seawater along a transect spanning the nearshore coastal environment within Kāneʻohe Bay on the island of Oʻahu, Hawaiʻi, and the adjacent offshore environment were collected to investigate the diversity and abundance of SAR11 marine bacteria over a two-year time period. Using 16S ribosomal RNA gene amplicon sequencing, the spatiotemporal distributions of major SAR11 subclades and individual amplicon sequence variants (ASVs) were evaluated. On average, 77% of the SAR11 community was compromised of a small number of ASVs (7 of 106 in total), which were ubiquitously distributed across all samples collected from one or both of the end-member environments sampled in this study (coastal or offshore). SAR11 ASVs were more often restricted spatially to coastal or offshore environments (64 of 106 ASVs) than they were shared among coastal, transition, and offshore environments (39 of 106 ASVs). Overall, offshore SAR11 communities contained a higher diversity of SAR11 ASVs than their nearshore counterparts. This study reveals ecological differentiation of SAR11 marine bacteria across a short physiochemical gradient, further increasing our understanding of how SAR11 genetic diversity partitions into distinct ecological units.
Does the Business Cycle Affect Utilization of Long-Term Care among the Elderly?

Objectives: To estimate the effect of macroeconomic conditions, as measured by unemployment rates, on the probability of receiving long-term care, the amount of care received, and mechanisms that could link care receipt to economic conditions. Methods: The study uses data from the 1998 – 2012 waves of the Health and Retirement Study. Dependent variables are indicators for any use of nursing home care, paid home care and unpaid home care, as well as conditional number of home caregivers and hours. In the regression analysis, effects are estimated using within-state changes in unemployment over time in a state-year fixed effects model. Results: In the full sample, higher unemployment rates are associated with a marginally significant decrease in the probability of being in a nursing home, fewer hours of paid home care and more hours of unpaid home care. The effects appear to be driven by women rather than men and the negative effects of unemployment on utilization of care are larger and more significant among the unmarried. The most likely mechanisms for these effects are significant decreases in both wealth and employment of adult children during recessions. Discussion: Some types of long-term care receipt are sensitive to economic downturns, and this does not appear to be explained by changes in health status or functional limitations over the business cycle. Given that affordability of care is likely to be driving a decrease in care, policy may be required to ensure that the needs of vulnerable elderly are met.
XGBoost Gradient-Boosted Tree Predictions Using Limited Data for Coaxial Rotor Helicopters

The use of finite-state methods is critical to the development of accurate and efficient inflow models used in rotorcraft flight dynamics simulation and control. Recent work in the finite-state fie...
Why Have Divorce Rates Fallen?: The Role of Women’s Age at Marriage

American divorce rates rose from the 1950s to the 1970s peaked around 1980, and have fallen ever since. The mean age at marriage also substantially increased after 1970. I explore the extent to which the rise in age at marriage can explain the decrease in divorce rates for cohorts marrying after 1980 using data from the Survey of Income and Program Participation, 1979 National Longitudinal Survey of Youth, and National Survey of Family Growth. Three different empirical approaches suggest that the increase in women’s age at marriage is the main proximate cause of the fall in divorce rates.
Econometric Methods for Modeling Producer Behavior

Publisher Summary This chapter presents an exposition of econometric methods for modeling producer behavior. The objective of econometric modeling is to determine the nature of substitution among inputs, the character of differences in technology, and the role of economies of scale. The principal contribution of recent advances in methodology has been to exploit the potential of economic theory in achieving this objective. Important innovations in specifying econometric models have arisen from the dual formulation of the theory of production. The chief advantage of this formulation is in generating demands and supplies as the explicit functions of relative prices. By using duality in production theory, these functions can be specified without imposing arbitrary restrictions on the patterns of production. The econometric modeling of producer behavior requires parametric forms for demand and supply functions. The patterns of production can be represented in terms of unknown parameters that specify the responses of demands and supplies to changes in prices, technology, and scale. New measures of substitution, technical change, and economies of scale have provided greater flexibility in the empirical determination of production patterns.
The legal dilemma of partner notification during the HIV epidemic.

On a specific level this article addresses the issue of whether states should mandate HIV testing and notification of prospective or current marital partners, or non-marital partners with whom the testing-positive person is involved in a sexual relationship. But on a broader level, this article advocates governments taking a reasonable and deliberate approach to public health pandemics and that all government action be coordinated at the local level, accompanied by education of the population. This article also speaks to what is called the “HIV exception,” which characterizes the more restrained approach taken by public health officials when compared to other public health pandemics in the past, measles, polio, and tuberculosis being examples. Overall, the government demonstrated restraint when employing the segregations of infected portions of the population and acting upon suspicions of infection to stigmatize persons and communities. Statistics reveal that initially, HIV was confined to the gay male population and then spread. Perhaps if those affected had been different, there would have been more hysteria and greater punitive government reaction. The article concludes with a recommendation for community involvement, education, and reasonableness in the response to public health emergencies, particularly in regards to whether there should be mandatory partner notification.
Signal transduction in the interferon system.

Abstract Interferons (IFNs) comprise a family of secreted proteins that function as important biologic response modifiers in vertebrates. Interferons are produced in response to viral and other microbial infections, they bind to specific receptors on the surface of target cells, and they induce rapid activation of gene transcription. Interferon-stimulated genes modulate many biologic effects of IFNs. Characterization of the molecular mechanisms of IFN-induced gene activation led to the discovery of two distinct families of proteins, known as the Janus family kinases (Jaks) and the signal transducers and activators of transcription (Stats). These signaling proteins transduce intracellular signals from IFN receptors to the nucleus and activate transcription of IFN-stimulated genes. Subsequent studies have shown that many cytokines, hormones, and growth factors signal their target cells through the Jak-Stat signal transduction pathway. Significant molecular cross-talk between Jaks and Stats recruited to IFN receptors in response to IFN-alpha stimulation and other signaling pathways may be involved in the etiology of some of the side effects associated with IFN-alpha therapy.
Mapping Educational Standards to the Big6

Information literacy is arguably the essential 21st century skill set for all students, and as such, it is important that students have a solid grounding in information problem-solving, the application of information literacy skills. A wide variety of authorities have called for these skills to be incorporated into educational standards both in the United States and in Europe. This paper compares the American Association of School Librarians (AASL) information literacy standards to the Big6 model of information problem-solving to determine the extent that these standards engage with all aspects of the information problem-solving process—especially the stage of Evaluation. Findings indicate that Evaluation and Task Definition seem to be under-emphasized in the AASL standards and missing entirely from the CCSS and should be addressed in research, policy, and practice.
Treatment of Bipolar Disorder During Pregnancy

The treatment of bipolar disorder during pregnancy or in those women who wish to conceive poses a unique set of dilemmas with which clinicians should be familiar. Given the teratogenicity of some psychotropic medications used to treat bipolar disorder and incomplete reproductive safety data for agents frequently employed to manage the illness, patients and clinicians should collaborate as they weigh options regarding appropriate pharmacologic therapy during pregnancy. Ultimately, risk-benefit decisions are made that must factor in the risk of relapse of psychiatric illness during pregnancy and its attendant morbidity versus the risk of fetal exposure to these agents. No clinical decision is risk-free, and patients with comparable information about risks and benefits of treatment options may make different decisions. However, awareness of the latest reproductive safety data across the family of compounds used to treat bipolar disorder, including antipsychotics, antidepressants, mood stabilizers, and anticonvulsants, allows for the most informed decisions. This article (1) describes the treatment dilemmas faced by bipolar women who are either pregnant or who wish to conceive, (2) reviews the teratogenic risks associated with commonly used psychotropic medications used to treat the illness, and (3) provides some clinical guidelines for treating this population during pregnancy.
A case-based framework for workflow model management

Case-oriented workflow modeling provides flexibility in specifying and executing workflows because it is possible to consider unique, organization-specific business process conditions and thereby minimize exceptions. However, it is a laborious task for a workflow designer to derive a case-oriented workflow model from a business specification, resulting in high modeling overhead. Recent commercial systems are providing generic templates of common business processes which may be adapted to an organizations requirements. These templates, called cases, can be modified individually or multiple cases may be composed into a more complex workflow and then the assembled workflow may be modified as needed to meet the business specification. In this paper, we propose a novel framework for case-oriented retrieval, instantiation and reuse of workflow models utilizing Case-Based Reasoning (CBR) techniques. We describe key modules of a prototypical implementation to facilitate model management activities such as model retrieval, reuse and composition of component case models from a workflow repository.
Theories of budgetary tradeoffs

The literature on defense-welfare tradeoffs has not been characterized by an emphasis on theory development. Indeed, most work has concentrated on using increasingly sophisticated statistical techniques to isolate empirical relationships in spending data on various countries. Unfortunately, however, this empirical enterprise has proven inconclusive, with some studies finding trade-offs and others not. In this paper, we suggest that a greater focus on theory development may help to resolve some of the empirical conflicts in this literature. In particular, we argue that there are at least two substantial bodies of theoretical work available that, while relevant to guns-butter questions, have remained to a large extent unexploited. One conclusion that we draw from this exercise is that the discussion of tradeoffs should probably move away form its current focus on primarily direct exchanges between spending on guns and butter, and instead begin to explore more indirect links which are acting through the economy.
The rediscovery of time

Publisher Summary This chapter discusses the role of probability and irreversibility in the conception of the universe. Different approaches to this question are well exemplified by the three excerpts from Einstein (1916), Kuznetzov (1987), Lucretius (∼ −60 BC). The analogy between Einstein and Lucretius is that the precise time of elementary processes is determined by chance. The basic problem is the conflictual situation between the static description proposed by classical physics, based on deterministic and time-reversible laws, and the world as it is known now, which includes probability and irreversibility as basic elements. According to the standard model, the entropy of the universe would remain constant, while its temperature decreases with the adiabatic expansion of the universe. the classical view expresses a dualistic structure: the phenomenological level corresponds indeed to irreversible and stochastic laws, while at the fundamental level, classical or quantum, there are time-reversible, deterministic laws.
Biology and Violence: From Birth to Adulthood

Foreword Marvin E. Wolfgang Preface Introduction 1. Biological and environmental influences on crime 2. Violent criminals as children and as adults 3. Intelligence and crime 4. Biological and environmental predictors of crime 5. Case studies of violent and career criminals 6. Biology and responsibility Appendix: selection and distribution of Biosocial Project variables References Author index Subject index.
Finding Data in DNA: Computer Forensic Investigations of Living Organisms

Recent advances in genetic engineering have allowed the insertion of artificial DNA strands into the living cells of organisms. Several methods have been developed to insert information into a DNA sequence for the purpose of data storage, watermarking, or communication of secret messages. The ability to detect, extract, and decode messages from DNA is important for forensic data collection and for data security. We have developed a software toolkit that detects the presence of a hidden message within a DNA sequence, and deciphers that message. In order to decode a message we are modifying several existing cryptanalysis tools that have been developed for solving simple substitution ciphers and compare their performance.
Achieving dependable systems by synergistic development of architectures and assurance cases

Assurance Based Development (ABD) is an approach to the construction of critical computing systems in which the system and an argument that it meets its assurance goals are developed simultaneously. ABD touches all aspects of the system lifecycle, but in this paper we focus on how the evolving assurance argument can guide architectural choices to increase system dependability. The goals with this approach to architectural choice are twofold. The first is to develop the architecture so that it provides the required evidence. The second is to refine the assurance case as architectural choices are made so that the evidence that will be provided supports the assurance claims. Combining development and assurance in this way facilitates detection--and thereby avoidance--of potential assurance difficulties as they arise, rather than after development is complete.
Computational quality of service for scientific components.

Scientific computing on massively parallel computers presents unique challenges to component-based software engineering (CBSE). While CBSE is at least as enabling for scientific computing as it is for other arenas, the requirements are different. We briefly discuss how these requirements shape the Common Component Architecture, and we describe some recent research on quality-of-service issues to address the computational performance and accuracy of scientific simulations.
Inductors with high L and Q: polymeric magnetics

The demonstration of organic magnetic materials has offered the challenge of finding polymer (organic) materials in which there is sufficient electronic exchange as well as stability in both thermally and chemically. This paper gives an overview of the synthesis of promising new complex polymer building blocks that have allowed the fabrication of high Q and L inductors. New materials from the saccharide, epoxy, and other polymers materials are also explained. Some devices made from these materials are discussed.
Normal Forms and Lie Groupoid Theory

In these lectures I discuss the Linearization Theorem for Lie groupoids, and its relation to the various classical linearization theorems for submersions, foliations and group actions. In particular, I explain in some detail the recent metric approach to this problem proposed in [6].
The Impact of Structural Reforms on Poverty : A Simple Methodology with Extensions

Structural reforms are often designed to change the prices of key goods and services. Since the overall intention of such reforms is the reduction of poverty, it is important to understand how the resulting price changes affect the poor. However, organizations seeking to provide timely advice to policymakers in developing countries often do not have the data and resources needed to undertake the most sophisticated approaches to such analysis. McCulloch outlines a simple methodology based on the analysis of household survey data to estimate the first-order impact of a variety of structural reforms. He also elaborates on the ways in which this methodology may be extended in a flexible way to account for particular features of a country in question. Finally, he outlines the direction of some extensions on the approach to tackle dynamics, risk, and qualitative poverty analysis.
Automating the layout of reconfigurable subsystems via template reduction

The focus of this work is the automatic generation of mask layouts, which is performed by the VLSI layouts, which is performed by the VLSI generator. This paper also presents method of automating the layout process, the template reduction method. The goal of the template reduction is not only the removal of unneeded routing resource, but also the removal of unneeded functional units. Benchmarking results show that template reduction method is able to reduce the number of functional units by an average of 45% and the routing resources by an average of 75%. It is found that the template reduction method produces circuits that are on average 53.4% smaller and 13.9% faster than the unreduced template.
Integrating Commodity and Conservation Programs: Design Options and Outcomes

Can a single program support farm income and encourage producers to adopt environmentally sound farming practices? While simple in concept, attempting to roll the farm income support features of existing commodity programs and conservation payments into a single program raises questions. Exactly how would farm commodity and conservation payments be combined? What difference would it make for environmental gain and farm income support? This report approaches the questions in two ways. First, spending patterns in existing commodity and conservation programs are analyzed to determine the extent to which producers who are currently receiving commodity payments also receive conservation payments. Then, a number of hypothetical program scenarios are devised and analyzed to estimate how emphasis on current income support recipients would differ from a combined program that focuses on achieving cost-effective environmental gain. The results show that policymakers face significant tradeoffs between environmental (conservation) objectives and farm income support objectives in designing a program that provides both income support and environmental gain.
Industry trade-balance and domestic merger policy: some empirical evidence from the U.S

Die ‚anti-trust’-Literatur bezogen auf eine offene Volkswirtschaft sagt wenig dazu aus, welche Rolle die Leistungsbilanz fur die Fusionspolitik eines Landes spielt. In diesem Papier wird anhand von Paneldaten, in denen die Berichte der Fusionskontrolle in unterschiedlichen Industrien der U.S.A. uber einen Zeitraum von 1997-2001 zusammengestellt sind, empirisch getestet, welchen Effekt die Leistungsbilanzen - nach Industriezweigen unterteilt - auf das Niveau der ‚antitrust’- Kontrolle haben. Die Ergebnisse der Tests deuten an, dass mit groserem Leistungsbilanzgewicht auch eine strengere ‚anti-trust’-Kontrolle einhergeht. Folglich ist eine ‚strategische’ Fusionspolitik der U.S.A. nicht zu erkennen. Stattdessen scheint die US-amerikanische Fusionspolitik stark vom Verbrauchernutzen geleitet zu sein, trotz der Verheisung internationaler Wettbewerbsvorteile.
Rater Bias Models

Raters' response tendencies, standards, or expectations can result in the tendency to consistently overestimate or underestimate the behavior of targets. Such rater biases can influence the outcomes of behavioral genetic studies. Quantitative genetic models allow researchers to determine the significance of rater biases and estimate genetic and environmental influences on behaviors controlling for bias. Keywords: twin studies; shared environmental variance; nonshared environmental variance
ANOMALOUSLY WEAK DYNAMICAL FRICTION IN HALOS

A bar rotating in a pressure-supported halo generally loses angular momentum and slows down due to dynamical friction. Valenzuela & Klypin report a counter-example of a bar that rotates in a dense halo with little friction for several Gyr, and argue that their result invalidates the claim by Debattista & Sellwood that fast bars in real galaxies require a low halo density. We show that it is possible for friction to cease for a while should the pattern speed of the bar fluctuate upward. The reduced friction is due to an anomalous gradient in the phase-space density of particles at the principal resonance created by the earlier evolution. The result obtained by Valenzuela & Klypin is probably an artifact of their adaptive mesh refinement method, but anyway could not persist in a real galaxy. The conclusion by Debattista & Sellwood still stands.
Integral representations of functions and Addison-type series for mathematical constants

Abstract We generalize techniques of Addison to a vastly larger context. We obtain integral representations in terms of the first periodic Bernoulli polynomial for a number of important special functions including the Lerch zeta-, polylogarithm, Dirichlet L - and Clausen functions. These results then enable a variety of Addison-type series representations of functions. Moreover, we obtain integral representations and Addison-type series for a variety of mathematical constants.
Friction Between Polymer Brushes

A type of static friction between two polymer brush coated surfaces, resulting from fluctuations from mean field theory is found, but with creep-like motion for forces below the force of static friction, which is much more rapid than the usual creep between solid surfaces in contact.
CRASHWORTHINESS ANALYSIS OF FIELD INVESTIGATION OF BUSINESS AIRCRAFT ACCIDENTS

During the period 1964-1977 some 7,351 aircraft engaged in business flying, and 883 in corporate/executive operations, were involved in accidents reported by the NTSB. These accidents were reviewed utilizing the University of Michigan Computerized Accident Files to provide an overall view of the incidence and nature of business/executive aircraft accidents relative to occupant crash injuries. In addition more detailed case studies of selected accidents investigated are provided to illustrate specific types of crashworthiness, occupant protection, or post-crash emergency egress findings applicable to business/executive operations. Emergency egress problems involving smoke and fire are discussed. Data from 1975-1977 indicate that the chances of being fatally injured in an accident is significantly greater than receiving serious injury, suggesting a lack of crashworthy performance which may be predicted to improve as more accidents occur in which crew shoulder harnesses are installed and worn.
On the nature of progress

We identify a simple relationship that unifies seemingly unrelated progress conditions ranging from the deadlock-free and starvation-free properties common to lock-based systems, to non-blocking conditions such as obstruction-freedom, lock-freedom, and wait-freedom. Properties can be classified along two dimensions based on the demands they make on the operating system scheduler. A gap in the classification reveals a new non-blocking progress condition, weaker than obstruction-freedom, which we call clash-freedom. The classification provides an intuitively-appealing explanation why programmers continue to devise data structures that mix both blocking and non-blocking progress conditions. It also explains why the wait-free property is a natural basis for the consensus hierarchy: a theory of shared-memory computation requires an independent progress condition, not one that makes demands of the operating system scheduler.
When is a Trigonometric Polynomial Not a Trigonometric Polynomial

As an application of Bezout's theorem from algebraic geometry, we show that the standard notion of a trigonometric polynomial does not agree with a more naive, but reasonable notion of trigonometri...
Thermodynamics of Mechanosensitivity

Publisher Summary This chapter describes the phenomenon of mechanosensitivity in terms of basic membrane forces: (1) membrane tension, (2) line tension, and (2) membrane torque. Their geometrical counterparts are in‐plane area, length of the border between the channel and lipid and the channel shape. A separate position is occupied by the length of the channel. The hydrophobic mismatch between channel and lipid bilayer generates a force normal to the bilayer that pulls the parts of the channel into membrane or pushes them out. The resulting effect was parameterized by the line tension representing the energy of mismatch. This approach provides a simple and efficient method of analysis of mechanosensitive (MS) channels—for example the gating process of MS channels changes with bilayer thickness and stiffness. The effects were mediated through the line tension and this parameter was found using existing experimental data.
Biology at Berkeley

This paper is concerned with the reorganization of biology at Berkeley, begun in the late 1970s and early 1980s, and now well along. Key to the initiation of change was the appointment of a Chancellor and Vice-chancellor who were committed to the changes, and the enlistment of outstanding biologists already at Berkeley to design the reform and carry it through. The paper raises the following questions: what led to the momentous changes in this leading research university; what actually happened as a result of the reform; what the key forces were that made the reform possible; and what, if anything, are the implications of the reform for other universities in the United States and in other countries.
Capital Flows: Issues and Policies

This paper presents an analytical overview of recent contributions to the literature on the policy implications of capital flows in emerging and developing countries, focusing specifically on capital inflows as well as on the links between inflows and subsequent capital-flow reversals. The objective is to clarify the policy challenges that such inflows pose and to evaluate the policy alternatives available to the recipient countries to cope with those challenges. A large menu of possible policy responses to large capital inflows is considered, and experience with the use of such policies is reviewed. A policy “decision tree”—i.e., an algorithm for determining how to deploy policies in response to an exogenous inflow episode—is developed, and strategies to achieve resilience to both inflows and outflows in a world where exogenous events may frequently drive capital flows in both directions are discussed.
Vapor‐phase transport in the near‐drift environment at Yucca Mountain

[1] A key issue regarding the performance of the potential high-level radioactive waste repository at Yucca Mountain, Nevada, is the likelihood of precipitation percolating a vertical distance of ∼300 m through fractured unsaturated rock into drifts containing waste packages. Water enhances waste package corrosion and is required for transport of released radionuclides. To evaluate the propensity for seepage into tunnels at Yucca Mountain, a 5-m-diameter, 2.7-km-long tunnel, commonly referred to as the Cross Drift (CD), was excavated in 1998, branching off from the main Exploratory Studies Facility tunnel. Sections of this tunnel have been isolated from ventilation for extended periods over the last 4 years. We present continuous measurements of relative humidity and temperature and periodic observations of liquid water in the CD over two periods. During this observation duration the terminal section of the drift was partitioned into four sections by bulkheads, and ventilation to these sections was minimized to a few days. We compare these observations to results from analytical and numerical models to investigate processes associated with the movement of water vapor between the tunnel bore and the surrounding fractured rock formation. Observations from this effort indicate that fractures can be primary paths for unsaturated zone vapor flow in the immediate vicinity of emplacement drifts. Observations, measurements, and analysis indicate the need for a model that includes fracture-dominated vapor transport as a significant contributor to total water flow into the drifts.