cssi/SciSciGPT-SciSciNet huggingface dataset:
By-catch in the Saginaw Bay, Lake Huron commercial trap net fishery

Abstract This study provides species-specific catch and baseline mortality estimates of non-target species (by-catch) for the Saginaw Bay, Lake Huron commercial trap net fishery. By-catch can represent a significant mortality source that is often unknown. By-catch and by-catch mortality rates in the Saginaw Bay commercial trap net fishery, which primarily targets lake whitefish ( Coregonus clupeaformis ), yellow perch ( Perca flavescens ), and channel catfish ( Ictalurus punctatus ), are currently unknown. From May through August 2010, we observed onboard commercial trap net vessels and took species-specific counts of by-catch and estimated initial by-catch mortality (i.e., morbid or floating fish). The high levels of walleye ( Sander vitreus ) catch and mortality observed within inner Saginaw Bay have not been previously documented in the Laurentian Great Lakes. Walleye by-catch averaged 127.3 individuals per trap net lift and 42% of those caught were morbid. The levels of lake trout ( Salvelinus namaycush ) catch observed were within the range observed in previous studies, but mortality (percent) was higher than has been previously observed. Lake trout by-catch averaged 39.4 individuals per lift and 39.2% of those were morbid. Through the use of generalized linear models, this analysis also indicated factors that most influenced catch of non-target species including time of year and soak time (i.e., time interval between trap net lifts). Surface water temperature and trap net depth most influenced mortality. These results may inform fishers and fisheries managers and highlight the need for comprehensive by-catch monitoring throughout the Great Lakes.
Contributions of the different rabbit models to our understanding of rotator cuff pathology

Animal models designed to investigate the biologic aspects of rotator cuff pathology are being used and being developed in the rat, rabbit, dog, and other mammals. The current models have provided valuable information regarding the etiology, pathogenesis, and healing potential of the tendon, as well as effective surgical repair techniques for rotator cuff tears. Rabbit models have primarily been used to describe the muscular changes, rotator cuff enthesis formation, and growth factor expression after rotator cuff injury. This article will serve to review the data obtained from previously described rabbit models and a newly developed rabbit model for studying rotator cuff pathology.
β-Lactoglobulin Gelation and Modification: Effect of Selected Acidulants and Heating Conditions

: The effect of acidulant selection, heating temperature, and heating rate on the properties of low-pH β-lactoglobulin (β-Lg) gels and powders derived from these gels was investigated by rheological and microscopic techniques. As isothermal gelation temperature was increased from 75 to 85 °C, gels made with hydrochloric and lactic acid showed more rapid gel formation and increased stress at gel fracture. Thickening and water-holding properties of powders derived from these gels also increased with temperature. Increases in gel strength and derivatized powder functionality appeared to plateau above 85 °C. Gels and derivatized powders prepared with phosphoric acid exhibited attributes similar to samples prepared with HCl and lactic acid at lower temperatures. The ion-specific ability of phosphate to increase denaturation temperature was responsible for the shift in properties of gels made with phosphoric acid. Microscopy revealed temperature effects on network building block size, but variations in rheological properties could not be linked to changes in gel micrographs. Alteration of heating rates from 2.0 to 0.2 °C/min during gelation affected the observed gelation temperature, but had little effect on final gel mechanical properties. Acid selection and gelation temperature offer alternatives to control β-Lg gel strength and the functional properties of instant thickening protein ingredients.
Depression and pancreatic cancer

Abstract Depression and psychological distress appear to be greater in patients with pancreatic cancer, compared to other equally ill patients with cancer, including those with other abnormal neoplasms. The several hypotheses regarding etiology are unproven, but the possibility of a tumor-related paraneoplastic syndrome which promotes the production of a false neurotransmitter capable of altering mood appears most logical at present. However, patients with pancreatic cancer have tumors with known poor prognosis and they often have pain. Both factors contribute to depression. Management of depression depends upon attention to adequate pain control, use of antidepressants and psychological support. Depression in pancreatic cancer raises challenging questions, both about its cause and treatment. Further research study of its psychological and biological components is important in oncology.
Aerobic glucose disposal in the oyster: An in vivo kinetic analysis

Abstract 1. 1. Aerobic glucose disposal in starved oysters exposed to 1 mM external glucose was 2.29 μg C/g wet wt/min. 2. 2. It was hypothesized that the maximum disposal rate is limited by the maximum rate of transepithelial glucose transport. 3. 3. The major recipients of glucose-carbon were glycogen and amino acids. 4. The rate of glucose-carbon disposal to these two pools was 0.80 and 0.42 μg C/g/min, respectively. 4. 5. The internal energy state determines the pathways of glucose disposal. 5. 6. Disposal of glucose-carbon in “glucose-primed” oysters is primarily into glycogen. 6. 7. In fasted bivalves the disposal is primarily into amino acids and carboxylic acids. 7. 8. The uptake of dissolved glucose has the potential of contributing significantly to growth under conditions where the external glucose concentration is kept artificially high.
Thickness and quality of spin-coated polymer films by two-angle ellipsometry

Abstract Ellipsometry was used for characterizing the thickness and overall film quality of PMMA films (poly(methyl methacrylate)) spin coated from solutions in chloroform. A new method for solving the equations and a new error minimization algorithm are developed for the determination of the thickness and refractive index of a transparent film from ellipsometry data at two angles of incidence. In the new algorithm, the error in the film parameters is minimized rather than the errors in Δ and Ψ, which is conventionally done. It was found that both the magnitude of the residual and the relative data sensitivity are important when assessing the reliability of the inverted parameters and the quality of a thin film. The substrates were thermally oxidized silicon oxide films on 2 inch silicon wafers, and the oxide thicknesses were about 2500 A. Polymer (PMMA) film thicknesses, ranging from 0.08 to 2 μm, were proportional to c 1.33 ω −0.50 , where c is the initial polymer concentration in solution (1.0–7.5 wt.%) and ω is the spin speed (1000–4000 rev./min) at which the films were coated. The absolute magnitude, rather than the relative magnitude, of the thickness variations influenced the determination of film quality from ellipsometry. Even though the relative film roughnesses were similar, the thinner films were of higher optical quality than the thicker films.
Cervical Carotid Artery Dissection Secondary to Malignant Fibrous Histiocytoma

A rare case of malignant fibrous histiocytoma of the cervical carotid artery is presented. Erosion of the vessel wall by this neoplasm resulted in dissection and pseudoaneurysm formation. The etiology and diagnosis of and the therapeutic alternatives for this unique disorder are discussed briefly.
Initial Therapy for Acquired Immunodeficiency Syndrome-Associated Cryptococcosis With Fluconazole

Background: Published opinion has generally favored amphotericin B over fluconazole as initial therapy for acquired immunodeficiency syndrome—associated cryptococcosis, although data that support this recommendation are limited. Method: Retrospective review of 30 consecutive patients with acquired immunodeficiency syndrome— associated cryptococcosis seen at a single institution over a 1-year period and given fluconazole, 400 mg/d, as initial therapy. Results: No patient died within the first 30 days of therapy, and none of the 14 patients who died within 1 year had clinically detectable infection when last seen or at death. Pretreatment blood cultures were positive in 26 of 27 patients; cerebrospinal fluid cryptococcal antigen titer was greater than 1:1024 in 12 of 23 patients; and five of 30 patients presented with altered mental status. The median CD4 count at diagnosis was 0.042 ×10 9 /L (42/μL). Eight of 25 patients who were followed up for more than 30 days relapsed, as evidenced by a positive culture; all relapses were successfully treated with fluconazole, either by reinstitution of therapy or by increase of dosage. Conclusion: This experience supports the use of fluconazole as initial therapy for acquired immunodeficiency syndrome—associated cryptococcosis. (Arch Intern Med. 1995;155:538-540)
Virus–glycopolymer conjugates by copper(I) catalysis of atom transfer radical polymerization and azide–alkyne cycloaddition

The CuI-catalyzed ATRP and azide–alkyne cycloaddition reactions together provide a versatile method for the synthesis of end-functionalized glycopolymers and their attachment to a suitably modified viral protein scaffold.
Sleep deprivation worsens inflammation and delays recovery in a mouse model of colitis

Background and aim We recently showed that patients with inflammatory bowel disease (IBD) report significantly more sleep disturbances. To determine whether disrupted sleep can affect the severity of inflammation and the course of IBD, we used an animal model of colonic inflammation to determine the effects of acute and chronic intermittent sleep deprivation on the severity of colonic inflammation and tissue damage in colitis and recovery from this damage.
Internal auditing: The emergence of an international profession?

Abstract This study searches for evidence of professionalism in the practice of internal auditing by IIA members in eleven countries: Australia, Canada, France, India, Israel, Italy, Japan, New Zealand, South Africa, the United Kingdom, and the United States. A questionnaire survey investigated (1) the effectiveness of the internal auditor's professional culture to achieve compliance with Internal Auditing Standards; (2) the extent of the internal auditor's independence from management, and (3) the scope of work performed by the internal auditor. The survey reveals wide adherence to the Standards. For most countries, common elements of independence and overall scope of work exist within the boundaries of generally known cultural differences. The findings indicate that evidence of the elements of professionalism is present in the countries surveyed.
NSF-supported undergraduate machine vision research activities

For the past three summers, students at the University of Michigan-Dearborn have been participating in the development and testing of various aspects of machine vision systems with support from the National Science Foundation under the Research Experiences for Undergraduates (REU) program. Much of the work has involved algorithm development since useful work can be performed with a fairly modest programming background. Benchmarking of various algorithms is a related activity that has seen much student participation. To a lesser extent, illumination and optics work has also been performed for the development of experimental setups and actual implementation of vision systems. Over the three-year duration of the program, a total of 34 students participated in these activities. While many of the participants were full-time students at the University of Michigan-Dearborn, others were from engineering colleges over a diverse geographical area. Summaries of a number of the projects is included here. It may be noted that the National Science Foundation has established the REU program to encourage more students to obtain advanced degrees in science and engineering and ultimately to pursue careers in research and development.
MULTI-INSTITUTIONAL VALIDATION STUDY OF NEURAL NETWORKS TO PREDICT DURATION OF STAY AFTER LAPAROSCOPIC RADICAL/SIMPLE OR PARTIAL NEPHRECTOMY

ABSTRACTPurpose: We developed models to predict post-laparoscopic radical or simple nephrectomy (LapNx) and post-laparoscopic partial nephrectomy (LapPNx) hospital duration of stay (DOS).Materials and Methods: We performed a retrospective review (design group) of all 726 patients (July 1997 to April 2004) who underwent LapNx or LapPNx at the Cleveland Clinic Foundation (CCF). Preoperative findings were recorded. Neural network algorithms were designed to predict the DOS before surgery. The models were then tested on a separate 252 patients from 6 different institutions, namely Tulane University Medical School, University of Arkansas for Medical Sciences, Cedars-Sinai Medical Center, University of Iowa, Mayo Clinic at Scottsdale and CCF.Results: In the CCF design groups, the LapNx model accuracy was 73% to 74% and the LapPNx model 73% to 83%. Overall accuracy in the test groups at all 6 institutions was 72% (area under ROC 0.6 to 0.7) for the LapNx model and 52% to 81% (ROC 0.5 to 0.7) for the LapPNx model...
New-onset diabetes after kidney transplant in children

The development of new-onset diabetes after kidney transplantation (NODAT) is associated with reduced graft function, increased cardiovascular morbidity and lower patient survival among adult recipients. In the pediatric population, however, the few studies examining NODAT have yielded inconsistent results. Therefore, the true incidence of NODAT in the pediatric population has been difficult to establish. The identification of children and adolescents at risk for NODAT requires appropriate screening questions and tests pre- and post-kidney transplant. Several risk factors have been implicated in the pathogenesis of NODAT and post-transplant glucose intolerance, including African American race, obesity, family history of diabetes and the type of immunosuppressant regimen. Moreover, uremia per se results in a state of insulin resistance that increases the risk of developing diabetes post-transplant. When an individual becomes glucose intolerant, early lifestyle modification and antihyperglycemic measures with tailoring of the immunosuppressant regimen should be implemented to prevent the development of NODAT. For the child or adolescent with NODAT, antihyperglycemic therapy should be prescribed in order to achieve optimal glycemic control, ultimately reducing complications and improving overall allograft and patient survival. In this article, we review the risk factors, screening methods, diagnosis, management and outcome of children and adolescents with NODAT and post-kidney transplant glucose intolerance.
Elementary network reconstruction: a framework for the analysis of regulatory networks in biological systems.

Abstract Complexity of regulatory networks arises from the high degree of interaction between network components such as DNA, RNA, proteins, and metabolites. We have developed a modeling tool, elementary network reconstruction (ENR), to characterize these networks. ENR is a knowledge-driven, steady state, deterministic, quantitative modeling approach based on linear perturbation theory. In ENR we demonstrate a novel means of expressing control mechanisms by way of dimensionless steady state gains relating input and output variables, which are purely in terms of species abundances (extensive variables). As a result of systematic enumeration of network species in n × n matrix, the two properties of linear perturbation are manifested in graphical representations: transitive property is evident in a special L-shape structure, and additive property is evident in multiple L-shape structures arriving at the same matrix cell. Upon imposing mechanistic (lowest-level) gains, network self-assembly through transitive and additive properties results in elucidation of inherent topology and explicit cataloging of higher level gains, which in turn can be used to predict perturbation results. Application of ENR to the regulatory network behind carbon catabolite repression in Escherichia coli is presented. Through incorporation of known molecular mechanisms governing transient and permanent repressions, the ENR model correctly predicts several key features of this regulatory network, including a 50% downshift in intracellular cAMP level upon exposure to glucose. Since functional genomics studies are mainly concerned with redistribution of species abundances in perturbed systems, ENR could be exploited in the system-level analysis of biological systems.
Therapeutic Failure-Related Hospitalisations in the Frail Elderly

Although therapeutic failure may be a common cause of drug-related morbidity in older adults, few studies have focused on this problem. The study objective was to determine the frequency and types of, and the factors associated with, therapeutic failure leading to hospitalisation in frail, elderly patients, using a new instrument named the Therapeutic Failure Questionnaire (TFQ). The sample included 106 frail, hospitalised elderly patients enrolled in a 1-year-long health service intervention trial at 11 Veterans Affairs Medical Centres. The TFQ was developed by a team of clinicial geriatricians and tested for reliability by two clinical pharmacists and a geriatrician on a sample of 32 patients. To establish validity, a geriatrician retrospectively reviewed the computerised medication records and clinical charts for these patients and applied the TFQ to determine probable therapeutic failures at the time of hospital admission. Inter- and intra-rater reliability for the TFQ were very good = 0.82 for both). Overall, 11% of patients had one or more probable therapeutic failures (TFQ scores between 4 and 7) leading to hospitalisation. Cardiopulmonary disease was a common ‘indicator’ of therapeutic failure and was often the result of non-adherence. The only factor associated with therapeutic failure occurrence was severe chronic kidney disease (crude odds ratio 5.87; 95% CI 1.20, 28.69; p = 0.01). The TFQ was able to identify several cases of probable therapeutic failure leading to hospitalisation in frail, elderly patients. Non-adherence to effective therapies for chronic serious cardiopulmonary disease was a common cause of therapeutic failure and represents a target for interventions to reduce hospitalisation. Further research on the occurrence, risk factors for and types of therapeutic failure is needed in a larger cohort of older non-veterans.
A New Eddy-Covariance Method Using Empirical Mode Decomposition

We introduce a new eddy-covariance method that uses a spectral decomposition algorithm called empirical mode decomposition. The technique is able to calculate contribu- tions to near-surface fluxes from different periodic components. Unlike traditional Fourier methods, this method allows for non-orthogonal contributions to the total flux, which are shown to be errors due to the undersampling of low-frequency processes. Inspection of the non-orthogonal terms with relation to sampling duration and periodicity reveals that a mea- sured periodic process requires approximately six cycles in order to be sufficiently sampled. This determines the maximum eddy size sufficiently measured given a particular sampling duration.
Reduction in growth of hybrid poplar following field exposure to low levels of O3 and (or) SO2

A field fumigation system was modified from one described elsewhere, and used to expose unenclosed hybrid poplar plants (Populus deltoides × trichocarpa) to low levels of O3 and (or) SO2. A 3 × 3 factorial design was employed, allowing for analysis of individual effects and potential interactions between the two pollutants. Two experiments were conducted during the summer of 1980. During the experiments, levels of ambient SO2 and O3 were near zero (<0.01 ppm) and low (mean, 0.04 ppm), respectively. Pollutant treatments included exposure to ambient air or to ambient air plus additional O3 and SO2 for 5–6 h/day. Fumigations with O3 and SO2 were made on 17 of 27 (first experiment) and 13 of 20 (second experiment) days, respectively. Exposure to two greater than ambient levels of O3 (mean concentrations, 0.06 or 0.08 ppm) and (or) SO2 (mean concentrations, 0.06 or 0.11 ppm) resulted in reductions in growth, dry matter accumulation, and leaf longevity. No significant interactions between the pollutants were ob...
Commercialization of oil-seed biotechnology economic implications for secondary agricultural areas

Progress in commercialization of biotechnology in production of oil palm, rapeseed, and soybeans has been remarkable, and the supply of vegetable oils is likely to increase. Some of the new cultivars of the oilbearing crops offer an opportunity to expand agricultural production in marginal agricultural areas, but many will cause land diversion to other purposes. The long-term changes in the location of production will depend on the biological nature of the crop (annual vs perennial) and the future changes in demand. Aging populations in developed countries will pay more attention to nutritional qualities of vegetable oils. An increase industrial use of vegetable oil may require breeding for oil characteristics that are useful to industry.
Sharding social networks

Online social networking platforms regularly support hundreds of millions of users, who in aggregate generate substantially more data than can be stored on any single physical server. As such, user data are distributed, or sharded, across many machines. A key requirement in this setting is rapid retrieval not only of a given user's information, but also of all data associated with his or her social contacts, suggesting that one should consider the topology of the social network in selecting a sharding policy. In this paper we formalize the problem of efficiently sharding large social network databases, and evaluate several sharding strategies, both analytically and empirically. We find that random sharding---the de facto standard---results in provably poor performance even when frequently accessed nodes are replicated to many shards. By contrast, we demonstrate that one can substantially reduce querying costs by identifying and assigning tightly knit communities to shards. In particular, our theoretical analysis motivates a novel, scalable sharding algorithm that outperforms both random and location-based sharding schemes.
Indigenous Land Use in the Ecuadorian Amazon: A Cross-cultural and Multilevel Analysis

Among the remaining tropical forests of lowland Latin America, many are inhabited by indigenous peoples, and the sustainability of their land uses is a point of heated debate in the conservation community. Numerous small-scale studies have documented changes in indigenous land use in individual communities in the context of expanding frontier settlements and markets, but few studies have included larger populations or multiple ethnic groups. In this paper we use data from a regional-scale survey of five indigenous populations in the Northern Ecuadorian Amazon to describe their agricultural land use practices and investigate the factors that affect those practices. We find the areas cultivated by indigenous households to be small compared to those of nearby mestizo colonists, but a large proportion of indigenous cultivated area is in commercial land uses. We also construct multilevel statistical models to investigate the household and community-level factors that affect indigenous land use. The results reveal significant influences on cultivated area from contextual factors such as access to markets, oil company activities, and the land tenure regime, as well as from household characteristics such as demographic composition, participation in alternative livelihood activities, and human, social and physical capitals. Overall the results are most consistent with market integration as an underlying driver of land use change in indigenous territories of the study area.
Quantitation of rheumatoid factor by laser nephelometry.

Laser nephelometry is a sensitive technique for measuring the degree of light scatter caused by the interaction of rheumatoid factors with heat aggregated human IgG. In measuring the rheumatoid factor (RF) level in rheumatoid serum and synovial fluid, it was found that nephelometry measured the combined amounts of IgM-RF and IgG-RF. However, on an equivalent weight basis, IgM-RF produced at least 17 times more scatter than IgG-RF. Low molecular weight IgM-RF had minimal light scattering activity in this assay. The total serum RF level, measured by nephelometry and expressed in terms of μg/ml of IgM-RF equivalents, correlated strongly with IgM-RF measured by solid phase radioimmunoassay (r=0.97, n=30, P<0.001) and an equation was derived to equate the two variables. It is concluded that the nephelometric RF test is a simple and rapid method to measure the total polyclonal RF level in various biological fluids, although monoclonal or an occasional polyclonal preparation of rheumatoid factor may give atypical results.
Economists and the Media

When my colleagues at The New York Times use the word "academic," they intend no compliment; they mean irrelevant. And when my former colleagues in the academy describe someone's work as "journalistic," they invariably mean shallow. One way to frame discussion for this symposium is to ask how well economists who deal with the media bridge the gap between thoughtful irrelevance and engrossing superficiality. From my vantage point, the answer is remarkably well. . . . As a journalist, I could stop here, having rendered a clear editorial opinion, . . . . but academics, even retired ones, yearn to criticize. So here goes.
Stress Management Interventions for HIV+ Adults: A Meta-Analysis of Randomized Controlled Trials, 1989 to 2006

Objective: Numerous studies document that stress accelerates disease processes in a variety of diseases including HIV. As a result, investigators have developed and evaluated interventions to reduce stress as a means to improve health among persons living with HIV. Therefore, the current meta-analysis examines the impact of stress-management interventions at improving psychological, immunological, hormonal, and other behavioral health outcomes among HIV+ adults.
Conjugate heat transfer from a translating drop in an electric field at low Peclet number

Abstract The conjugate heat exchange with transient interfacial temperature between a translating liquid drop and its host fluid in a uniform electric field is considered. Singular perturbation is developed to obtain the temperature within the domain of the continuous phase whereas regular perturbation is used to obtain the solution inside the drop with the help of the method of weighted residuals. This method proves to be powerful for the solution of problems with time-dependent non-homogeneities arising within the governing equation and/or the boundary conditions. The temperature is computed up to and including the first order in the Peclet number; however, higher order is also performed for the host phase in order to examine the influence of an external field upon the total transport rates. In the first order solution, the effects of an electric field were to alter the temperature inside and outside the droplet as well as the heat flux, but the net heat transfer rate, which is totally controlled by conduction and convection, remains unchanged. Beyond the first order approximation, the contribution to the net heat transfer due to the electric field becomes assessable.
Molecular Orbital Functional Groups. 3. Subspectrality in the Eigenvalues of Linear Polyene Molecules and Related Aspects

Embedding and McClelland right-hand mirror-plane fragments are MO functional groups. Molecular graphs having common embedding and right-hand mirror-plane fragments are subspectral in those eigenvalues and have a greater degree of similarity. Collections of subspectral structures are tabulated.
Quantitative classification as a tool to show change in an urbanizing watershed

Quantitative classification of Landsat Thematic Mapper (TM and ETM+) imagery can provide a very useful medium for showing urban change at a watershed scale. It shows both the nature and the degree of urbanization with a resolution equivalent to that of the original TM image. Estimates of urbanization-related factors such as surface imperviousness and canopy cover can be coupled to illustrate the process of urban growth in the watershed using change vector analysis. When used together and combined with standard GIS data sets such as digital line graphs and digital elevation models, quantitative classification can provide the parameters needed to run standard hydrological models that can be used to describe or to forecast the effects of urbanization on area streams. Watersheds provide a meaningful scale for the analysis of the connections between urbanization and the environmental changes it brings. The study area for this paper is the Tinker's Creek watershed in northeast Ohio, USA. Tinker's Creek is one o...
Directed migration of positively selected thymocytes visualized in real time.

Development of many vertebrate tissues involves long-range cell migrations. In most cases, these migrations have been inferred from analysis of single time points and the migration process has not been directly observed and quantitated in real time. In the mammalian adult thymus, immature CD4+CD8+ double-positive (DP) thymocytes are found in the outer cortex, whereas after T cell antigen receptor (TCR) repertoire selection, CD4+CD8– and CD4–CD8+ single-positive (SP) thymocytes are found in the central medulla. Here we have used two-photon laser-scanning microscopy and quantitative analysis of four-dimensional cell migration data to investigate the movement of thymocytes through the cortex in real time within intact thymic lobes. We show that prior to positive selection, cortical thymocytes exhibit random walk migration. In contrast, positive selection is correlated with the appearance of a thymocyte population displaying rapid, directed migration toward the medulla. These studies provide our first glimpse into the dynamics of developmentally programmed, long-range cell migration in the mammalian thymus.
Time-Resolved Three-Dimensional Molecular Tracking in Live Cells

We report a method for tracking individual quantum dot (QD) labeled proteins inside of live cells that uses four overlapping confocal volume elements and active feedback once every 5 ms to follow three-dimensional molecular motion. This method has substantial advantages over three-dimensional molecular tracking methods based upon charge-coupled device cameras, including increased Z-tracking range (10 μm demonstrated here), substantially lower excitation powers (15 μW used here), and the ability to perform time-resolved spectroscopy (such as fluorescence lifetime measurements or fluorescence correlation spectroscopy) on the molecules being tracked. In particular, we show for the first time fluorescence photon antibunching of individual QD labeled proteins in live cells and demonstrate the ability to track individual dye-labeled nucleotides (Cy5-dUTP) at biologically relevant transport rates. To demonstrate the power of these methods for exploring the spatiotemporal dynamics of live cells, we follow individ...
Hierarchical models for mapping Ohio lung cancer rates

The mapping of geographical variation in disease occurrence plays an important role in assessing environmental justice (i.e. the equitable sharing of adverse effects of pollution across socio-demographic subpopulations). Bayes and empirical Bayes methods can be used to obtain stable small-area estimates while retaining geographic and demographic resolution. In this study, we focus on modelling spatial patterns of disease rates, incorporating demographic variables of interest such as gender and race. We employ a Bayesian hierarchical modelling approach, which uses a Markov chain Monte Carlo computational method to obtain the joint posterior distribution of the model parameters. We use this approach to construct smoothed maps of lung cancer mortality in Ohio counties in 1988. Our approach also facilitates a cross-validatory comparison between the normal and Poisson likelihoods often fit uncritically to data of this type. Finally, we uncover evidence of changing spatial structure in the rates over the 21-year period 1968-1988, suggesting a spatio-temporal hierarchical model as a new possibility.
'Before I didn't understand anything about white people, but now, I speak English': Negotiating globally mediated discourses of race, language, and nation

This article explores the ways in which Mexican transmigrants in the USA discursively construct national identities in relation to the mediated message of a television advertisement for an English-language self-study program marketed to Spanish speakers, called Ingles Sin Barreras. Using narrative analysis of the advertisement and critical discourse analysis of a focus group, the author considers the ways in which identities and ideologies of language and language learning come to be intertwined and circulate across national boundaries.
Abstract IA3-3: Genetic testing for breast and ovarian cancer: From risk assessment to therapeutic targeting

Germline genetic variation can be used in a number of ways to improve the care of patients. First, such information can be used to predict the development of disease. Knowledge of risk can lead to targeted preventative strategies. Finally, understanding the genetic etiology for the development of an individual9s cancer has the potential to lead to targeted drug development. Inherited BRCA1 and BRCA2 mutations are a model for this paradigm. Since these genes were identified in 1994 and 1995, much work has been done to establish mutation-associated cancer risks and potential management strategies. Deleterious mutations in both genes are associated with a high risk of breast and ovarian cancer, as well as lower risks of other tumor types. Risk-reducing salpingo-oophorectomy significantly reduces the risk of breast and ovarian cancer in mutation carriers and work is ongoing to establish the optimal timing of this procedure as well as the potential for hormone replacement therapy. Women with BRCA1 or BRCA2 mutations require increased breast screening with the addition of breast MRI at the minimum. Prophylactic mastectomy is a valid option. More recently attention has turned to the impact of the biological basis of disease in BRCA1/2 mutation carriers with breast and ovarian cancer on decisions regarding systemic therapy. Due to the role of BRCA1 and BRCA2 proteins in cellular functions such as homologous DNA repair, an enhanced sensitivity to platinum agents and reduced sensitivity to spindle poisons has been postulated and supported by in vitro studies and early clinical data. An additional pathway to target that has been recently identified is poly(ADP-ribose) polymerase (PARP). PARP is a key enzyme in the base-excision repair pathway. In vitro, PARP inhibitors given to BRCA1 or BRCA2 deficient cell lines have led to cell death through synthetic lethality. Early clinical trials have demonstrated efficacy for PARP inhibitors in BRCA1 and BRCA2 mutation carriers with advanced breast and ovarian cancer, with objective response rates in heavily pretreated patients of greater than 40%. Genetic testing for BRCA1 and BRCA2 mutations can be seen as a model for translating the biology of a disease into risk assessment, prevention and treatment, thus demonstrating the potential for inherited genetics to directly impact the care of patients. Citation Information: Clin Cancer Res 2010;16(14 Suppl):IA3-3.
The effect of thiols on the dehalogenation of 5-iodo and 5-bromouracil.

Abstract The 5-iodo- and 5-bromo- analogs of uracil are dehalogenated in the presence of both cysteine and 2-mercaptoethanol to yield uracil. Presumably, the reaction involves the initial addition of the thiol group across the 5,6 double bond of the halopyrimidine to yield the corresponding 5-halo, 5,6-dihydrouracil-6-thioether which then dehalogenates to yield uracil. Under comparable conditions, cysteine causes more rapid dehalogenation of both halouracils than does 2-mercaptoethanol. Thiol containing compounds catalyze hydrogen-deuterium exchange at carbon five of uracil (1–3) and have been implicated as having a catalytic effect in the deamination of cytosine (4,5). Presumably, these reactions involve the reversible nucleophilic addition of the thiol group across the 5,6 double bond of the pyrimidine to yield the corresponding 5,6 dihydropyrimidine with a substituted thioether group on carbon six. This pathway is supported by comparable reactions involving the addition of bisulfite to the pyrimidine ring system (6–10). Different from the bisulfite addition compounds, the thioether containing dihydropyrimidine adducts have not been isolated and characterized; however, 5′-deoxy-5′,6-epithio-5,6-dihydro-2′,3′-0-isopropylideneuridine resulting from the intramolecular attack of the 5′ thiol group on carbon six of the uracil ring system of 5′-deoxy-5′-thio-2′,3′-0-isopropylideneuridine has been isolated and characterized (11). In a recent communication, we reported that bisulfite buffer systems catalyze the dehalogenation of 5-iodo-, 5-bromo-, and 5-chlorouracil (12). The object of this work is to demonstrate that cysteine and 2-mercaptoethanol, sulfur nucleophiles with more physiological importance than bisulfite, also cause halopyrimidine dehalogenation under nearly physiological conditions of temperature and pH.
Genetic and Epigenetic Fine-Mapping of Causal Autoimmune Disease Variants

Genome-wide association studies have identified loci underlying human diseases, but the causal nucleotide changes and mechanisms remain largely unknown. Here we developed a fine-mapping algorithm to identify candidate causal variants for 21 autoimmune diseases from genotyping data. We integrated these predictions with transcription and cis-regulatory element annotations, derived by mapping RNA and chromatin in primary immune cells, including resting and stimulated CD4(+) T-cell subsets, regulatory T cells, CD8(+) T cells, B cells, and monocytes. We find that ∼90% of causal variants are non-coding, with ∼60% mapping to immune-cell enhancers, many of which gain histone acetylation and transcribe enhancer-associated RNA upon immune stimulation. Causal variants tend to occur near binding sites for master regulators of immune differentiation and stimulus-dependent gene activation, but only 10-20% directly alter recognizable transcription factor binding motifs. Rather, most non-coding risk variants, including those that alter gene expression, affect non-canonical sequence determinants not well-explained by current gene regulatory models.
Computational investigation of adsorption of molecular hydrogen on lithium-doped corannulene.

Density functional theory and classical molecular dynamics simulations are used to investigate the prospect of lithium-doped corannulene as adsorbent material for H2 gas. Potential energy surface scans at the level of B3LYP/6-311G(d,p) show an enhanced interaction of molecular hydrogen with lithium-atom-doped corannulene complexes with respect to that found in undoped corannulene. MP2(FC)/6-31G(d,p) optimizations of 4H2−(Li2−C20H10) yield H2 binding energies of −1.48 kcal/mol for the H2−Li interaction and −0.92 kcal/mol for the H2−C interaction, whereas values of −0.94 and −0.83 kcal/mol were reported (J. Phys. Chem. B 2006, 110, 7688−7694) for physisorption of H2 on the concave and the convex side of corannulene using MP2(full)/6-31G(d), respectively. Classical molecular dynamics simulations predict hydrogen uptakes in Li-doped corannulene assemblies that are significantly enhanced with respect to that found in undoped molecules, and the hydrogen uptake ability is dependent on the concentration of lithiu...
Banking Reforms for the 21st Century: A Perfectly Stable Banking System Based on Financial Innovations

Although bank loans themselves are somewhat illiquid because of private information, most of their cashflows are not. Recent financial innovations allow commercial loans to be liquefied via credit derivatives and actual and synthetic securitizations. The loan originating bank holds the remaining illiquid equity tranche containing the concentrated credit risk, private information rent and the ‘excess spread’ that incentivize the bank to continue to monitor and service the loans. Empirically, we find that the average size of the equity tranche is about 3% for the representative commercial loan portfolios in our sample. The liquefaction of bank loans makes possible a banking system that restricts the guaranteed accounts to be backed by 100% reserves and the non-guaranteed deposits to be backed by liquid securitized loan tranches, while retaining the deposit-lending synergy. Such a system is perfectly safe without deposit insurance and it renders banks bankruptcy-remote without sacrificing a bank's traditional role as a financial intermediary.
Likewise, as Technical Experts, But Not (At All) by Way of Culture (2012-2013).

For more information on this video, see Gabrielle Gopinath's "Skin Deep: Surfacing with Leigh-Ann Pahapill," included in this edition of Contemporaneity.
Reinnervation of denervated iris by transplanted sympathetic ganglia: Effect of neuronal age

Abstract Neuronal outgrowth in vivo is aggressive postnatally, but is diminished with increasing age. This may be attributable to intrinsic features of the neuron or its interaction with other components of the developing organism. The purpose of this study was to determine if there is an age-dependent reduction in the intrinsic ability of sympathetic neurons to initiate fiber outgrowth. Superior cervical ganglia from donor rats aged 3–4, 11–12, 27–28 and 45–46 days were removed and transplanted to the anterior chamber of the sympathectomized eye of host rats 85–89 days of age. Ganglia with host irides were removed at 3, 6 and 10 days post-transplant and whole mounts were analysed using catecholamine histofluorescence for maximum sympathetic fiber density, length and initial rate of outgrowth. Fluorescent fibers were present in host irides of donors of all ages and at all post-transplant times. However, maximum fiber density was less for the 3–4 day-old donor ganglia (e.g. 43–71% of 11–46-day-old donor ganglia at 600 μm, 10 days post-transplant). Maximum fiber length was also less in the youngest group (e.g. 35–49% of 11–46-day-old donor ganglia, 10 days post-transplant). Further, the initial rate of outgrowth was decreased for the 3–4-day-old donor ganglia (128±46 μm/day for the 3–4-day-old ganglia vs 253±48 μm/day for the 11–12-day-old ganglia, 307±35 μm/day for the 27–28-day-old ganglia and 260±22 μm/day for the 45–46-day-old ganglia). We conclude that the capacity for neuronal outgrowth is limited in the early postnatal period, but rapidly attains the mature level by the second postnatal week. Therefore, diminished outgrowth in mature rats does not appear to be due to a decrease in the intrinsic ability of sympathetic nerves to initiate fiber outgrowth, but is attributable to other factors.
Exact soliton solutions for a class of coupled field equations

Abstract Exact soliton solutions are provided for a class of nonlinear coupled field equations arising in the study of organic conductors, quantum fields and plasma systems.
Stress Tolerance of Misfolded Carboxypeptidase Y Requires Maintenance of Protein Trafficking and Degradative Pathways

The accumulation of aberrantly folded proteins can lead to cell dysfunction and death. Currently, the mechanisms of toxicity and cellular defenses against their effects remain incompletely understood. In the endoplasmic reticulum (ER), stress caused by misfolded proteins activates the unfolded protein response (UPR). The UPR is an ER-to-nucleus signal transduction pathway that regulates a wide variety of target genes to maintain cellular homeostasis. We studied the effects of ER stress in budding yeast through expression of the well-characterized misfolded protein, CPY*. By challenging cells within their physiological limits to resist stress, we show that the UPR is required to maintain essential functions including protein translocation, glycosylation, degradation, and transport. Under stress, the ER-associated degradation (ERAD) pathway for misfolded proteins is saturable. To maintain homeostasis, an "overflow" pathway dependent on the UPR transports excess substrate to the vacuole for turnover. The importance of this pathway was revealed through mutant strains compromised in the vesicular trafficking of excess CPY*. Expression of CPY* at levels tolerated by wild-type cells was toxic to these strains despite retaining the ability to activate the UPR.
The Influences of the Relationship between Primary and Secondary Process Content on Aesthetic Success in Novels

Previous studies have indicated that primary and secondary process content, two processes theorized to play an important role in the creation of an artistic work and of which some residue is though...
The distribution of colloidal and particulate bioactive metals in Narragansett Bay, RI

Abstract The bioactive metals Fe, Mn, Cu, Zn and Ni in Narragansett Bay, RI, were partitioned into soluble, colloidal and particulate size fractions using a combination of conventional and cross-flow filtrations. Particulate samples (0.2–8.0 μm; >8 μm) were chemically fractionated into acetic-acid reactive and non-reactive metals. Conventional “dissolved” samples ( Mn>Zn>Cu>Ni with concentrations in the 0.2–0.8 μm fraction being generally higher than in the >8.0 μm fraction. The acid leachable fraction of the particulate phase increased from ∼32%–80% in the order Fe 8.0 μm) being generally less labile than small particulates (0.2–8.0 μm). The colloidal phase represented an average 4%–96% of the “dissolved” metals, ranging in importance from Fe (96%)>Cu (44%)>Ni (25%)>Zn (7%)>Mn (4%). Although generally small, the colloidal fraction of Zn and Mn was highest in a region of the bay where biomass typically is high. Changes in soluble and colloidal fractions along a transect through the bay indicate that a significant proportion of Fe, Cu and Ni were transferred from “dissolved” to particulate size fractions via colloid aggregation. Predicting colloidal metal concentrations from measurements of particulate mass ( C p ) and literature values of colloid metal partition coefficients ( K c ) underestimated the measured concentrations by 5–50×. Acetic acid leachable metal concentrations in the small particle (0.2–8 μm) phase correlated well with metal concentrations in the larger (8 kDa–0.2 μm) colloid fraction ( r =0.91–0.99). In contrast, metals in the smaller colloid fraction (1–8 kDa) were for the most part independent of any measured parameters. Metals were not distributed equally between colloidal size classes; colloidal Zn was associated with larger colloids (>90%), Fe and Ni were associated primarily with larger colloids (∼70–85%) but also with the smaller colloid fraction, while ≳70% of colloidal Cu was associated with smaller colloids. The non-uniform distribution of metals within colloidal size classes indicates that metal:colloid associations are regulated by specific interactions. These findings suggest that it is inappropriate to employ single, non-specific sorbing metal tracers (e.g. Th) to delimit the pathways and kinetics of bioactive metal interactions with marine colloids.
The glycosyl-phosphatidylinositol anchor of membrane proteins.

Description des groupements fonctionnels glycosyl-phosphatidylinositol se liant aux extremites C terminales des proteines procaryotiques ou eucaryotiques. Identification des proteines modifiees. Analyse de leur structure chimique. Developpement de methodes permettant leur determination et leur identification. Etude de la synthese des groupements se greffant aux proteines (phenomene posttraductionnel, precurseur, interaction mecanisme…), de leur degradation (activite enzymatique impliquee) et de leur fonction (phylogenese, proprietes physiques, interaction et activation cellulaire, regulation hormonale)