cssi/SciSciGPT-SciSciNet huggingface dataset:
Glomerular basement membrane lipidosis in Alagille syndrome

Alagille syndrome is characterized by a paucity of interlobular bile ducts with chronic cholestasis, cardiac, skeletal, and eye abnormalities and is associated predominantly with JAG1 mutations. Various renal abnormalities have been sporadically described. The classic renal histopathology described in Alagille syndrome is mesangiolipidosis, with lipid deposits predominately confined to the mesangium and minimal deposition within the glomerular basement membrane (GBM). We report a 5-year-old girl with Alagille syndrome who presented with persistent subnephrotic proteinuria and renal tubular acidosis. A renal biopsy showed GBM irregularities (mimicking membranous glomerulonephritis), mesangial sclerosis, and focal segmental glomerulosclerosis (FSGS) on light microscopy. Electron microscopy revealed few lipid inclusions within the mesangium but extensive inclusions along the GBM. These findings are mostly consistent with those reported previously in Alagille syndrome. However, the histologic distribution of lipid vacuoles is seemingly reversed in this patient and is uniquely accompanied by FSGS, emphasizing the spectrum of renal histopathology seen in Alagille syndrome. The proteinuria observed in this patient is likely attributed to significant GBM lipid deposition, which over time may contribute to the development of FSGS.
Dynamics of DNA Mismatch Repair Initiation Complex Revealed by Single Molecule Fluorescence

The integrity of the genetic information is dependent on the fidelity of DNA replication and several DNA repair processes. Among these repair systems, DNA mismatch repair (MMR) is responsible for correcting base-base mismatches and small nucleotide insertion/deletion (IDL) mispairs that arise from polymerase misincorporation, elevating fidelity of replication 50-1000 fold. MMR is initiated when MutS binds to mismatched bases on dsDNA. The communication between the mismatch site and a distal strand discrimination signal is required for removing the mismatch from the newly synthesized strand. MutS-MutL-heteroduplex ternary complex is thought to play an key role in the coupling of these two sites on DNA. We used single molecule fluorescence resonance energy transfer (smFRET) to characterize conformational changes in this ternary complex through the process of mismatch recognition, MutS-MutL interaction and large MutS-MutL assembly formation on DNA. We found that the sliding clamp formation of MutS is inhibited by MutL interaction. The initial MutS-MutL complex stays at the mismatch site and recruits more MutS and MutL to form a large protein assembly. The structural information revealed by our single molecule measurements provides constraints for modeling the mechanism of MMR in the initiation stage.
Light Emission from Silicon

The possibility induction of light emission from silicon, an indirect bandgap material in which radiative transitions are unlikely, raises several interesting and technologically important possibilities, especially the fabrication of a truly integrated optoelectronic microchip. In this article, the natural considerations that constrain silicon from emitting light efficiently are examined, as are several engineered solutions to this limitation. These include intrinsic and alloy-induced luminescence; radiatively active impurities; quantum-confined structures, including zone folding and the recent developments in porous silicon; and a hybrid approach, the integration of direct bandgap materials onto silicon.
Cluster Structure and Corralling Effect Driven by Interaction Mismatch in Two Dimensional Mixtures

The formation of clusters with crystal-like order in two dimensions is studied using Monte Carlo simulations. We find that the necessary conditions to induce the formation of clusters of one component is to add a second component that has a larger size and that has a long-range soft repulsive interaction with its own kind but not with the other one. The clusters of the small particles are found to be surrounded by a network of quasi-one-dimensional arrangements of the larger particles. The degree of order of the clusters is found to depend on the concentration of the larger particles. The findings explain recent experimental observations on lipid-poloxamer mixtures and they provide guidelines for how to form ordered clusters of nanoparticles in two dimensions.
Pigs as xenogeneic donors

The success and widespread acceptance of clinical allotransplantation has led to a shortage of cadaveric organs and a resurgence of interest in xenotransplantation. Although swine are generally regarded as the preferred source of xenogeneic organs, the severe immunologic response to swine organs has so far precluded their clinical use. However, the past 10 years have seen many advances in the field, especially the use of genetically modified swine. These include animals transgenic for human complement regulatory proteins, and most recently, animals not expressing the alpha 1,3-galactosyltransferase gene (GalT-KO swine), produced by nuclear transfer. The initial results using GalT-KO swine as donors to nonhuman primates demonstrated survival of a life-supporting renal graft for up to 83 days without rejection when combined with a regimen designed to induce tolerance by vascularized donor thymic grafts. Although the initial results are encouraging, further improvements will be needed to warrant a clinical trial of xenotransplantation. In this review, we discuss immunologic barriers to xenotransplantation and recent attempts to overcome them, strategies to induce tolerance across a xenogenic barrier, and issues that will need to be considered before a clinical trial is attempted.
convergence of difference schemes with high resolution for conservation laws

We are concerned with the convergence of Lax-Wendroff type schemes with high resolution to the entropy solutions for conservation laws. These schemes include the original Lax-Wendroff scheme proposed by Lax and Wendroff in 1960 and its two step versions-the Richtmyer scheme and the MacCormack scheme. For the convex scalar conservation laws with algebraic growth flux functions, we prove the convergence of these schemes to the weak solutions satisfying appropriate entropy inequalities. The proof is based on detailed L P estimates of the approximate solutions, H -1 compactness estimates of the corresponding entropy dissipation measures, and some compensated compactness frameworks. Then these techniques are generalized to study the convergence problem for the nonconvex scalar case and the hyperbolic systems of conservation laws.
Dissolution Rates of Amorphous Al- and Fe-Phosphates and their Relevance to Phosphate Mobility on Mars

Phosphate is an essential nutrient for life on Earth, and therefore if life exists or ever existed on Mars it may have required phosphate. Amorphous Al- and Fe-phosphates rapidly precipitate from acidic solutions and amorphous Al-phosphates likely control phosphate concentrations in some natural waters on Earth. The amorphous fraction of martian soils has also been shown to be enriched in P, and amorphous phosphates are therefore also likely important in the phosphate cycle on Mars. Despite this importance, however, few dissolution rates exist for amorphous Al- and Fe-phosphates. In this study, dissolution rates of amorphous Al- and Fe-phosphates were measured in flow-through reactors from steady state concentrations of Al, Fe, and P. A pH-dependent rate law, log R = log k – n pH was determined from the dissolution rates, where R is the dissolution rate, k is the intrinsic rate constant, and n is the reaction order with respect to H+. For amorphous Al-phosphate, log k = −6.539 ± 1.529 and n = 2.391 ± 0.493. For amorphous Fe-phosphate, log k = −13.031 ± 0.558 and n = 1.376 ± 0.221. The amorphous Al-phosphate dissolves stoichiometrically under all experimental conditions measured, and the amorphous Fe-phosphate dissolves non-stoichiometrically, approaching stoichiometric dissolution as pH decreases, due potentially to Fe oxyhydroxides precipitating and armoring grain surfaces. Perhaps due to these effects, amorphous Al-phosphate dissolution rates are approximately three orders of magnitude faster than the amorphous Fe-phosphate dissolution rates measured under these experimental conditions. Amorphous Al-phosphate dissolution rates measured in this study are also faster than published dissolution rates for the crystalline Al-phosphate variscite. The rapid dissolution rates measured in this study therefore suggest that, if these phases are present on Mars, phosphate would be rapidly released into acidic environments.
Chronic granulomatous disease: a review of the infectious and inflammatory complications

Chronic Granulomatous Disease is the most commonly encountered immunodeficiency involving the phagocyte, and is characterized by repeated infections with bacterial and fungal pathogens, as well as the formation of granulomas in tissue. The disease is the result of a disorder of the NADPH oxidase system, culminating in an inability of the phagocyte to generate superoxide, leading to the defective killing of pathogenic organisms. This can lead to infections with Staphylococcus aureus, Psedomonas species, Nocardia species, and fungi (such as Aspergillus species and Candida albicans). Involvement of vital or large organs can contribute to morbidity and/or mortality in the affected patients. Major advances have occurred in the diagnosis and treatment of this disease, with the potential for gene therapy or stem cell transplantation looming on the horizon.
Replication-Independent Long-Distance Trafficking by Viral RNAs in Nicotiana benthamiana

Viruses with separately encapsidated genomes could have their genomes introduced into different leaves of a plant, thus necessitating long-distance trafficking of the viral RNAs for successful infection. To examine this possibility, individual or combinations of genome segments from the tripartite Brome mosaic virus (BMV) were transiently expressed in leaves of Nicotiana benthamiana plants using engineered Agrobacterium tumefaciens. BMV RNA3 was found to traffic from the initial site of expression to other leaves of the plant, as detected by RNA gel blot analyses and also by the expression of an endoplasmic reticulum-targeted green fluorescent protein. When RNA3 trafficked into leaves containing the BMV replication enzymes, RNA replication, transcription, and virion production were observed. RNA3 trafficking occurred even when it did not encode the movement or capsid proteins. However, coexpression of the movement protein increased the trafficking of BMV RNAs. BMV RNA1 and RNA2 could also traffic throughout the plant, but less efficiently than RNA3. All three BMV RNAs trafficked bidirectionally to sink leaves near the apical meristem as well as to the source leaves at the bottom of the stem, suggesting that trafficking used the phloem. These results demonstrate that BMV RNAs can use a replication-independent mechanism to traffic in N. benthamiana.
Learning semantic definitions of online information sources

The Internet contains a very large number of information sources providing many types of data from weather forecasts to travel deals and financial information. These sources can be accessed via Web-forms, Web Services, RSS feeds and so on. In order to make automated use of these sources, we need to model them semantically, but writing semantic descriptions for Web Services is both tedious and error prone. In this paper we investigate the problem of automatically generating such models. We introduce a framework for learning Datalog definitions of Web sources. In order to learn these definitions, our system actively invokes the sources and compares the data they produce with that of known sources of information. It then performs an inductive logic search through the space of plausible source definitions in order to learn the best possible semantic model for each new source. In this paper we perform an empirical evaluation of the system using real-world Web sources. The evaluation demonstrates the effectiveness of the approach, showing that we can automatically learn complex models for real sources in reasonable time. We also compare our system with a complex schema matching system, showing that our approach can handle the kinds of problems tackled by the latter.
Generating Queries with Cardinality Constraints for DBMS Testing

Good testing coverage of novel database techniques, such as multidimensional histograms or changes in the execution engine, is a complex problem. In this work, we argue that this task requires generating query instances, not randomly, but based on a given set of constraints. Specifically, obtaining query instances that satisfy cardinality constraints on their subexpressions is an important challenge. We show that this problem is inherently hard, and develop heuristics that effectively find approximate solutions
Twelve tips for getting started using mixed methods in medical education research.

Background: Mixed methods research, which is gaining popularity in medical education, provides a new and comprehensive approach for addressing teaching, learning, and evaluation issues in the field. Aim: The aim of this article is to provide medical education researchers with 12 tips, based on consideration of current literature in the health professions and in educational research, for conducting and disseminating mixed methods research. Conclusion: Engaging in mixed methods research requires consideration of several major components: the mixed methods paradigm, types of problems, mixed method designs, collaboration, and developing or extending theory. Mixed methods is an ideal tool for addressing a full range of problems in medical education to include development of theory and improving practice.
To unify structured and unstructured P2P systems

Most of current peer-to-peer designs build their own system overlays independent of the physical one. Nodes within unstructured systems form a random overlay, on the contrary, structured designs normally organize peers into an elegant identifier ring. However, all of those overlays are far from the physical one. Noticed that the system overlay is crucial for building a distributed system, this paper proposes to build system overlays based on the physical overlay. By making full use of physical network characteristics and taking advantages of both structured and unstructured protocols, a network-based peer-to-peer system is built in this paper. Not only the system is highly efficient (the stretch is equal to one), but also it can adapt extremely system churning. The most important is that the maintenance overhead is very low, even under highly dynamic environment.
Computational analysis of the interfacial bonding between feed-powder particles and the substrate in the cold-gas dynamic-spray process

The cold-gas dynamic-spray process is analyzed by numerical modeling of the impact between a single spherical feed-powder particle and a semi-infinite substrate. The numerical modeling approach is applied to the copper‐aluminum system to help explain experimentally observed higher deposition efficiencies of the copper deposition on aluminum than the ones associated with the aluminum deposition on copper. To properly account for the high strain, high strain-rate deformation behavior of the two materials, the appropriate linear-elastic rate-dependent, temperature-dependent, strain-hardening materials constitutive models are used. The results obtained indicate that the two main factors contributing to the observed higher deposition efficiency in the case of copper deposition on aluminum are larger particle/substrate interfacial area and higher contact pressures. Both of these are the result of a larger kinetic energy associated with a heavier copper feed-powder particle. The character of the dominant particle/substrate bonding mechanism is also discussed in the present paper. It is argued that an interfacial instability which can lead to the formation of interfacial roll-ups and vortices can play a significant role in attaining the high strength of interfacial bonding. # 2003 Elsevier Science B.V. All rights reserved.
Lifelong voluntary exercise in the mouse prevents age-related alterations in gene expression in the heart

We present the first quantitative gene expression analysis of cardiac aging under conditions of sedentary and active lifestyles using high-density oligonucleotide arrays representing 11,904 cDNAs a...
Interactions Between Vasoconstrictors and Vasodilators in Regulating Hemodynamics of Distinct Vascular Beds

We examined whether interactions between angiotensin II (Ang II), endothelin (ET), nitric oxide (NO), and prostaglandins (PGs) differentially regulate perfusion to distinct vascular beds. For this, we blocked either angiotensin AT1 or ET receptors or both and then sequentially inhibited NO and PG synthesis in anesthetized dogs. Blocking Ang II or ET had similar effects on systemic hemodynamics: Mean arterial pressure fell slightly without altering cardiac output. Blocking both caused a synergistic fall in mean arterial pressure and increased cardiac output. Pulmonary vascular resistance was not altered by blocking Ang II, ET, or both but progressively increased during NO and PG blockade in group 2 (which had unblocked ET receptors), suggesting that endogenous ET exerts pulmonary vasoconstriction that is tempered by NO and PGs. In the kidney, blocking Ang II increased regional blood flow (RBF), glomerular filtration rate (GFR), and fractional excretion of sodium (FENa). In contrast, blocking ET did not alter RBF, and it decreased GFR and FENa. Combined Ang II and ET blockade markedly increased RBF without altering GFR, and FENa was maintained at the levels as when only ET was blocked. Sequentially inhibiting NO and PGs decreased RBF when Ang II or ET were blocked but had little effect when both were blocked. Finally, Ang II or ET blockade did not alter iliac blood flow. Inhibiting NO and PGs decreased iliac blood flow when Ang II or ET but not both were blocked. These results suggest that regional differences in the interactions between endogenous Ang II, ET, NO, and PGs are important determinants in systemic, pulmonary, and regional hemodynamics.
New imaging modalities for laser-based systems

Laser-based electro-optical sensors can gather spatial information (imagery) as well as a variety of other types of information. These include motion detection (including vibration), color sensing, and sensing of the effects of the illuminated object on the polarization of the incident illumination. Such systems can have several advantages over sensors that rely on reflected or emitted light. Laser-based systems can gather a full 3D image of an object on a single pulse. The sensors can gather this information in a covert manner because of the high directionality of the laser illumination. Also, a laser-based sensor can gather information with high resolution. In addition, the ability to control the illumination source, the receiver, and the optical aperture can lead to new sensing modalities. We describe various spatial and non-spatial sensing concepts and discuss hardware implementations. In particular we highlight the ability of laser-based systems to produce imagery at very low light levels. The utility of low light level imagery in 2D is discussed and the potential benefits of 3D low light level imagery is assessed. The effect of intervening obscurants on low light level systems are considered. Characteristics of systems that can implement such concepts are also described.
Severe Lead Poisoning in Pregnancy

Background.— Lead freely crosses the placenta. Consequently, gestational lead poisoning is not only harmful to the woman but also to the developing fetus, invariably producing congenital lead poisoning. The scope and consequences of severe lead poisoning in pregnancy (blood lead level ≥45 μg/dL) have not been well characterized. Methods.— We reviewed our experience in the management of women with severe gestational lead poisoning. Additionally, we reviewed the literature on this disorder in an effort to identify patterns in etiology and outcome. Results.— Over a 3-year period treatment was provided to 7 severely lead-poisoned women. A 25-year review of the medical literature identified an additional 8 cases. Among these 15 women, 70% were Hispanic, all of whom developed lead poisoning from the ingestion of soil, clay, or pottery ( "tierra" ). Other sources of lead poisoning were paint chip ingestion (n = 2), household renovation, and use of a complementary-alternative medication (bone meal). Lead poisoning was discovered in the third trimester in 12 (86%) subjects after the women presented with subtle but characteristic findings of severe lead poisoning, including malaise, anemia, or basophilic stippling on blood smear; one woman was identified when she presented after a generalized seizure, having a blood lead level of 104 μg/dL. Five women received chelation therapy during pregnancy with CaNa 2 EDTA, dimercaprol, or succimer. At delivery mean maternal blood lead level was 55 μg/dL, whereas mean neonatal lead level was 74 μg/dL ( P = .009). Thirteen neonates underwent chelation, all within the first 28 days of life. No infant in the current series had an identifiable birth defect. Conclusions.— On the basis of this experience we conclude that severe lead poisoning in pregnant women has the following characteristics: 1) it most often occurs because of intentional pica, 2) its presenting features are subtle, often consisting only of malaise and anemia, and 3) blood lead levels in the neonate are higher than simultaneous maternal lead levels.
Electronic Structure of (n,0) Zigzag Carbon Nanotubes: Cluster and Crystal Approach

We study the electronic structure of (n,0) zigzag carbon nanotubes by means of two complementary numerical methods. Using the semiempirical PM3 method, we carry out quantum-chemical calculations for tube fragments of different symmetry and size, which represent these tubes. Using the tight-binding method, we proceed in parallel to determine the band structure of these tubes. The effect of cluster size on the structure of frontier orbitals and on the cluster stability is investigated for the (6,0) tube. We show that the highest occupied molecular orbitals (HOMOs) and the lowest unoccupied molecular orbitals (LUMOs) of the (n,0) tube fragments are localized on the edge atoms. The comparison between the band structure of the (6,0) tube and the molecular orbitals of the (6,0) tube fragment with 13 carbon hexagons along the tube axis indicates that the spatial
Sexual dimorphism in the tooth-crown diameters of the deciduous teeth.

Mesiodistal and buccolingual crown dimensions of the right de- ciduous teeth of 133 white children were analyzed for information on sexual di- morphism and sex discrimination using discriminant analysis. Even though con- sistent differences were found for only 15 out of 20 paired measurements, five of them significant at p = 0.05 or better, discriminant analysis showed the possi- bility of correctly sexing up to 75% of the juvenile sample, using a maximum of seven deciduous teeth. Discriminant functions have become a wide- ly used method for the sexual diagnosis of human skeletal remains (Pons, '55; Thieme and Schull, '57; Giles, '64, '66, '70; Giles and Elliot, '63; Van Vark, '70; Ditch and Rose, '72; Van Gerven, '72; Garn et al., '77). Recently, several investigators have had success with discriminant functions based on the tooth- crown diameters of the permanent teeth alone (Ditch and Rose, '72; Garn et al., '77). Al- though these investigators did not discuss the obvious implications of their results for the sexual diagnosis of the remains of children, it is apparent that discriminant functions of the human dentition may provide reliable non- radiographic means for sexing immature skeletons. The sexual identification of immature re- mains has been an important problem in phy- sical anthropology for many years. Various workers have attempted to use size dimorph- ism in the dentition as an aid to sexing the remains of children. Bailit and Hunt ('64) achieved 58% accuracy by comparing the de- velopmental ages of the individual dentitions with published male and female standards of tooth formation from radiographs. These au- thors assigned to the individual the sex of the standard which caused the least variation among teeth. The discriminant functions em- ployed by Ditch and Rose ('72) and Garn et al. ('77) improved the accuracy of sexing of older children to 85% or better. However, their dis- AM. J. PHYS. ANTHROP. (1978) 48: 77-82. criminant functions were based on the perma- nent teeth and would sex few children less than 12 years of age. If sexual dimorphism in tooth-crown size is as pronounced in the de- ciduous dentition as it is in the permanent dentition, then it may be possible to correctly assess the sex of children as young as two years. Percent sexual dimorphism between the male and female means for the dental mea- surements is presented together with tests for the significance of the differences of the means. Five sets of discriminant functions are calculated to determine the most reliable com- bination of measurements for sexing the de- ciduous dentition. One set of discriminant functions is based on the 20 dental measure- ments used in this paper, the other four sets of functions include only ten measurements each; these four sets are the maxillary teeth, the mandibular teeth, all mesiodistal mea- surements, and all buccolingual measure- ments.
Real Time Metagenomics

Summary: Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex). Here we present a novel approach to annotate metagenomes using unique k-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that k-mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy. A last-common ancestor approach was also developed to describe the members of the community. Availability and implementation: This open-source application was implemented in Perl and can be accessed via a user-friendly website at http://edwards.sdsu.edu/rtmg. In addition, code to access the annotation servers is available for download from http://www.theseed.org/. FIGfams and k-mers are available for download from ftp://ftp.theseed.org/FIGfams/. Contact: redwards@mail.sdsu.edu Supplementary information:Supplementary data are available at Bioinformatics online.
HISTORY, POLITICS, AND CLAIMS OF MAN-MADE GLOBAL WARMING

Claims that a man-made global warming catastrophe is imminent have two major aspects: the scientific support offered for the claims, and the political proposals brought forth in response to the claims. The central questions are whether non-scientists should accept the claims themselves as true, and whether they should support the political proposals attached to them. Predictions of a coming disaster are shown to be a-historical in both the long term and the short term, to involve shifting predictions that are contrary to evidence, and to be opposed by many scientists. The political proposals to alleviate this alleged problem—especially plans by the U.S. Environmental Protection Agency—are shown to offer no alternative to fossil fuels, and to portend a major economic decline and permanent losses of liberty. The anthropogenic global warming claims are largely motivated not by science, but by a desire for socialist intervention on a national and a global scale. Neither the claims to an impending climate catastrophe nor the political proposals attached to those claims should be accepted.
Coupling of angiotensin II AT1 receptors to neuronal NHE activity and carrier-mediated norepinephrine release in myocardial ischemia

In ischemia, cardiac sympathetic nerve endings (cSNE) release excessive amounts of norepinephrine (NE) via the nonexocytotic Na+-dependent NE transporter (NET). NET, normally responsible for NE reu...
The Slingerland Tests Reliability and Validity

This study analyzed the reliability and validity of two widely–used screening tests for academic readiness and for specific language disability: the Pre–Reading Screening Procedures and the Slingerland Screening Tests for Identifying Children with Specific Language Disability. These tests were administered to 1021 heterogeneous students in grades one through six. Student background data, handwriting samples, and Comprehensive Tests of Basic Skills scores were also collected and analyzed. The study's design allowed researchers to develop estimates of reliability (alpha, test–retest, and inter–rater) and validity, including factor analysis. The results indicate that reliability and validity coefficients are well within acceptable limits for the purposes of the tests, and that educational programming decisions can confidently be based on the test results.
The Political Scientist as a Blogger

In November 2007, I helped found a blog, The Monkey Cage, with two of my colleagues, David Park and Lee Sigelman. This site joined a nascent political science blogosphere that is now composed of at least 80 blogs (Farrell and Sides 2010). The goals of The Monkey Cage are to publicize political science research and use this research to comment on current events. Although blogging is a promising way for scholars to promote their work to a larger audience, political scientists have been slow to take up this medium. To be sure, blogging is not without its challenges, particularly in terms of the time and energy needed to maintain a site. But blogging can also have its benefits by not only helping political science reach a broader audience, but also aiding individual scholars' research, teaching, and service goals.
An Efficient Exhaustive Anytime Sampling Algorithm for Influence Diagrams

Summary. We describe an efficient sampling algorithm for solving influence diagrams that achieves its efficiency by testing candidate decision strategies against the same set of samples and, effectively, reusing samples for each of the strategies. We show how by following this procedure we not only save a significant amount of computation but also produce better quality anytime behavior. Our algorithm is exhaustive in the sense of computing the expected utility of each of the possible decision strategies.
The subsea-bed option

Among the alternatives to mined geologic disposal listed in Chapter 3, the most attractive is burial of HLW under the floor of the deep ocean. The immediately obvious merit of this suggestion is removal of the waste far from any inhabited area; one immediately obvious disadvantage is the need for complex political negotiations to legitimize such use of international waters. Despite this potential difficulty, subsea-bed disposal is appealing enough to have been the subject of serious study in several nations for more than a decade; in the United States it is widely regarded as a possible substitute for additional repositories on land a few decades hence. In this chapter we return to the subsea-bed option for a closer look.
Processing gradable adjectives in context: A Visual World study

Both relative adjectives (RAs) like big and absolute adjectives (AAs) like empty are sensitive to the context: in the former case, the context determines how much size is required to count as big; in the latter, the context determines how much deviation from total emptiness is allowed to count as empty. Whereas it is generally agreed that the role of context with RAs is to fix the value of a threshold variable, the status of absolute adjective thresholds, and therefore the role of context in their interpretation, remains an object of debate. Some researchers have argued that all gradable adjectives have context-sensitive threshold variables that are assigned values by the same mechanisms ( Lassiter & Goodman 2013 ). Others have claimed that AAs have fixed, endpoint-oriented meanings and that sensitivity to context arises from pragmatic reasoning about imprecision ( Kennedy 2007 ; Syrett, Kennedy & Lidz 2009 ; van Rooij 2011 ; Burnett 2014 ; Qing & Franke 2014 ). In an eye-tracking Visual World experiment, we investigate RAs and AAs used as restrictive modifiers. We find that target identification is significantly faster for both types of adjectives when the visual context supports a restrictive interpretation of the predicate, although this effect is considerably delayed in the case of AAs. We conclude that for RAs, the target facilitation effect is driven by the lexical semantics of the predicate itself. However, it is argued that the extra processing cost observed with AAs results from pragmatic reasoning about imprecision.
Solanaceae — a model for linking genomics with biodiversity: Conference Reviews

Recent progress in understanding the phylogeny of the economically important plant family Solanaceae makes this an ideal time to develop models for linking the new data on plant genomics with the huge diversity of naturally occurring species in the family. Phylogenetics provides the framework with which to investigate these linkages but, critically, good species-level descriptive resources for the Solanaceae community are currently missing. Phylogeny in the family as a whole is briefly reviewed, and the new NSF Planetary Biodiversity Inventories project ‘PBI: Solanum—a worldwide treatment’ is described. The aims of this project are to provide species-level information across the global scope of the genus Solanum and to make this available over the Internet. The project is in its infancy, but will make available nomenclatural information, descriptions, keys and illustrative material for all of the approximately 1500 species of Solanum. With this project, the opportunity of linking valid, up-to-date taxonomic information about wild species of Solanum with the genomic information being generated about the economically important species of the genus (potato, tomato and eggplant) can be realized. The phylogenetic framework in which the PBI project is set is also of enormous potential benefit to other workers on Solanum. The community of biologists working with Solanaceae has a unique opportunity to effectively link genomics and taxonomy for better understanding of this important family, taking plant biology to a new level for the next century. Copyright © 2004 John Wiley & Sons, Ltd.
Sexual selection on skeletal shape in Carnivora

Lifetime reproductive success of males is often dependent upon the ability to physically compete for mates. However, species variation in social structure leads to differences in the relative importance of intraspecific aggression. Here, we present a large comparative dataset on sexual dimorphism in skeletal shape in Carnivora to test the hypotheses that carnivorans exhibit sexual dimorphism in skeletal anatomy that is reflective of greater specialization for physical aggression in males relative to females and that this dimorphism is associated with the intensity of sexual selection. We tested these hypotheses using a set of functional indices predicted to improve aggressive performance. Our results indicate that skeletal shape dimorphism is widespread within our sample. Functional traits thought to enhance aggressive performance are more pronounced in males. Phylogenetic model selection suggests that the evolution of this dimorphism is driven by sexual selection, with the best-fitting model indicating greater dimorphism in polygynous versus nonpolygynous species. Skeletal shape dimorphism is correlated with body size dimorphism, a common indicator of the intensity of male-male competition, but not with mean body size. These results represent the first evidence of sexual dimorphism in the primary locomotor system of a large sample of mammals.
Single-pixel hyperspectral imaging for real-time cancer detection: detecting damage in ex vivo porcine tissue samples

We are developing a single-pixel hyperspectral imaging system based on compressive sensing that acquires spatial and spectral information simultaneously. Our spectral imaging system uses autofluorescencent emission from collagen (400 nm) and NAD(P)H (475 nm), as well as, differences in the optical reflectance spectra as diagnostics for differentiating between healthy and diseased tissue. In this study, we demonstrate the ability of our imaging system to discriminate between healthy and damaged porcine epidermal tissue. Healthy porcine epidermal tissue samples (n=11) were imaged ex vivo using our hyperspectral system. The amount of NAD(P)H emission and the reflectance properties were approximately constant across the surface of healthy tissue samples. The tissue samples were then thermally damaged using an 1850 nm thulium fiber laser and re-imaged after laser irradiation. The damaged regions were clearly visible in the hyperspectral images as the thermal damage altered the fluorescent emission of NAD(P)H and changed the scattering properties of the tissue. The extent of the damaged regions was determined based on the hyperspectral images and these estimates were compared to damage extents measured in white light images acquired with a traditional camera. The extent of damage determined via hyperspectral imaging was in good agreement with estimates based on white light imaging indicating that our system is capable of differentiating between healthy and damaged tissue. Possible applications of our single pixel hyperspectral imaging system range from real-time determination of tumor margins during surgery to the use of this technique in the pathology lab to aid with cancer diagnosis and staging.
Plaque morphology predictors of side branch occlusion after provisional stenting in coronary bifurcation lesion: Results of optical coherence tomography bifurcation study (ORBID)

Objectives The aim of this study was to identify the predictors of side branch (SB) ostial stenosis developed after provisional stenting of the main vessel (MV) using optical coherence tomography (OCT). Background Provisional stenting remains the main approach to treatment of bifurcation lesions; however, it may result in the narrowing of SB ostium. There is little information about underlying plaque morphology of the MV lesion and its potential impact on the SB after provisional stenting. Methods Patients with stable coronary disease with angiographic MV lesion not involving SB were included in a prospective single center study. The primary outcome was significant SB ostium stenosis (SBOS), defined as residual stenosis of >50% after MV stenting. Results Thirty bifurcation lesions in 30 patients were analyzed in the study. Poststenting significant SBOS was observed in 30% of patients. The MV lesions with SBOS > 50% were characterized by a higher prevalence of lipid rich plaques (100 vs. 64%, p = 0.040) and spotty calcifications (60 vs. 0%, p = 0.005). Maximal lipid arcs were greater (257° vs. 132°, p = 0.001) and lipid volume index was higher (1380 vs. 574, p = 0.012) in the SBOS >50% group. Multivariate logistic regression analysis identified maximal lipid arc (odds ratio (OR): 1.014, p = 0.038) and the presence of lipid plaque contralateral to SB ostium (OR: 8.14, p = 0.046) before stenting as independent predictors of significant SBOS after PCI. Conclusions High lipid content of the MV lesion and a contralateral location of lipid in the bifurcation area may contribute to SBOS after provisional stenting. © 2016 Wiley Periodicals, Inc.
Congenital pseudarthrosis of the Tibia

Congenital pseudarthrosis of the tibia is characterized by anterolateral deformity of the tibia and shortening of the limb. Its etiology remains unclear. Although several classification systems have been proposed, none provides specific guidelines for management. Treatment remains challenging. The goal is to obtain and maintain union while minimizing deformity. The basic biologic considerations with surgical intervention include resection of the pseudarthrosis and bridging of the defect with stable fixation. Intramedullary stabilization, free vascularized fibula, and Ilizarov external fixation are among the most frequently used methods of treatment. In addition, bone morphogenetic protein recently has shown promise. Nevertheless, despite improvements in healing rates with congenital pseudarthrosis of the tibia, the potential for amputation in failed cases persists.
Competition between sp3-C-N vs sp3-C-F reductive elimination from PdIV complexes

This communication describes the design of a model system that allows direct investigation of competing sp3-C–N and sp3-C–F bond-forming reductive elimination from a PdIV fluoro sulfonamide complex. The reductive elimination selectivity varies dramatically as a function of reaction additives. A mechanism is proposed that provides a rationale for these effects.
Obtaining Longitudinal Built Environment Data Retrospectively across 25 years in Four US Cities.

Background: Neighborhood transportation infrastructure and public recreational facilities are theorized to improve the activity, weight, and cardiometabolic profiles of individuals living in close proximity to these resources. However, owing to data limitations, there has not been adequate study of the influence of timing and placement of new infrastructure on health over time. Methods: This protocol details methods of the Four Cities Study to perform retrospective field audits in order to capitalize on existing longitudinal health data from the Coronary Artery Risk Development in Young Adults (CARDIA) Study. We developed and verified measures of recreation facilities (trails, parks) and transportation infrastructure (bus, light rail, bicycle parking, bicycle paths) in Birmingham, AL, Chicago, IL, Minneapolis, MN, and Oakland, CA. We identify introductions, renovations, and closures between 1985-2010 to develop measures of facility and infrastructure change. Ultimately, these data were linked to CARDIA sites’ respondents’ geographic locations over the 25-year study period to examine associations with health behaviors and outcomes. Results: Data available for retrospective audits was inconsistent by city, primarily due to record-keeping differences. We found large increases in bicycle infrastructure, with the exception of Birmingham, AL. Excluding the addition of a new rail line in Minneapolis, MN, few changes occurred in bus service, rail, and parks. Conclusion: Our method represents innovation toward the collection of retrospective neighborhood data for use in longitudinal analyses. The data produced give insight into the way neighborhood infrastructure has changed over time and the potential relationship between these changes and health behaviors.
Abstract A22: Functional long noncoding RNAs in castration-resistant prostate cancer

Prostate cancer progression from an androgen-dependent state to an androgen-independent phase, which is also referred to castration-resistant prostate cancer (CRPC), not only results in cancer refractory to androgen deprivation therapy but also marks lethal prognosis. Androgen receptor (AR) plays central roles in both normal prostate development and prostate cancer progression. Aberrant androgen/AR signaling activity is often associated with the development of CRPC, such as increased synthesis of steroid hormone, increased expression of AR, emergence of specific AR variants etc. However, deeper understanding of detailed mechanism of CRPC development is still necessary in order to discover novel effective drug targets for the treatment of CRPC. Recent studies suggest that long non-coding RNA (lncRNA) can be extensively functional rather than just transcriptional noise and lncRNAs are also widely involved in the pathogenesis of different types of cancers including prostate cancer. To further investigate the potential role of lncRNAs during prostate cancer progression, we profiled lncRNA transcriptome using RNA-seq in prostate cancer cells in the presence or absence of androgen treatment. In combination with AR cistrome data, we identified a set of lncRNAs that are directly regulated by androgen/AR signaling. A specific lncRNA was identified as androgen/AR repressed target gene in androgen-dependent cells while showing significant higher expression in androgen-independent cells that mimics CRPC state. Interestingly, knockdown of this lncRNA specifically attenuates the growth of androgen-independent cells while has little effect on androgen-dependent cells. To understand the detailed mechanism, we identified the downstream target genes using RNA-seq upon silencing this lncRNA in either androgen-dependent or -independent cells. Moreover, this lncRNA is located in a region that is frequently amplified in CRPC and highly expressed in a subset of CRPC patients. We suggest that this lncRNA, along with other androgen/AR targets, may play a role during the development of CRPC and could serve as a potential drug target for the treatment of CRPC. Note: This abstract was not presented at the conference. Citation Format: Teng Fei, Yiwen Chen, Xiaole Shirley Liu, Myles Brown. Functional long noncoding RNAs in castration-resistant prostate cancer. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A22.
Neurophysiologic monitoring of patients with head injuries.

Despite new technologic developments designed to analyze the brain’s electrical activity, monitoring the electroencephalogram or evoked potentials has not yet provided important information with regard to acute management of patients with head injury. Measurement of cerebral blood flow as well as jugular oxygen saturation is of more practical importance. Particularly when monitored continuously, these measures can provide useful information about the use of hyperventilation and control of elevated systemic arterial pressure.
Voice, Perceived Fairness, Agency Trust, and Acceptance of Management Decisions Among Minnesota Anglers

ABSTRACTAlthough researchers agree that public participation in natural resource decision making is critical to institutional acceptance by stakeholders and the general public, the processes to gain public perceptions of fairness, agency trust, and acceptance of management decisions are not clear. Using results from a mail survey of Minnesota resident anglers, we used structural equation modeling to examine how instrumental versus symbolic motives related to anglers’ perceptions of agency fairness, trustworthiness, and ultimately acceptance of fisheries management decisions. We applied laboratory research on relationships among procedural fairness, trust, and management acceptance, and then tested models incorporating anglers’ perceptions of voice for anglers and nonanglers in management decisions. Results suggested that trust fully mediated the relationship between procedural fairness and management acceptance. Angler perceptions of angler and nonangler voice both related to views of procedural fairness,...
Tomography: the Cormack algorithm revisited

Summary form only given. The Cormack algorithm for doing tomography is easily extended from parallel geometry to fan geometry. After a Fourier transform of the data (in rotation angle space) one is required to solve a truncated system before back Fourier transforming to object space. This is carried out by doing a Galerkin discretization and converting the system to a system of matrix equations, which are solved by singular value decomposition (SVD). All of the SVD work on all N+1 kernels, can be done once and stored. Some reconstructions derived from very noisy data have been obtained. >