cssi/SciSciGPT-SciSciNet huggingface dataset:
The use of tinted contact lenses in the management of achromatopsia.

Abstract Background Achromatopsia is a congenital, autosomal recessively inherited condition in which cones are either defective or absent. Complete achromatopsia results from having only rods as functioning photoreceptors. Many people with achromatopsia have small amounts of residual cone function that may provide minimal color vision under special circumstances. Clinical findings associated with the condition include reduced visual acuity, nystagmus, a greater than normal incidence of high ametropia, and severe photophobia. The photophobia resulting from achromatopsia can be debilitating even in normal indoor illumination. Tinted contact lenses have been reported to reduce photophobia and improve visual function in these patients. Cases Two cases are reported here. A 32-year-old man presented with reduced and stable visual acuity, complete color blindness, nystagmus, and debilitating photophobia. The second patient was a 23-year-old woman who presented with reduced and stable visual acuity, severely impaired color vision, rotary nystagmus, and significant photophobia. Both of these patients were fit with centrally tinted contact lenses. Although visual acuity did not improve measurably in either patient with tinted compared with clear lenses, both experienced a dramatic reduction in photophobia with the lenses. Conclusion Tinted spectacle or contact lenses may be useful in relieving photophobia associated with a number of cone disorders, including achromatopsia. In addition to decreasing light sensitivity, tinted lenses have been reported to improve visual acuity, decrease the size of central scotomata, enlarge peripheral visual field, and enhance visibility of long wavelength stimuli in bright illumination.
Spherical harmonic-based random fields for aggregates used in concrete

Abstract Two non-Gaussian random field models are developed for characterizing the geometry of star-like inclusions in two-phase or multi-phase materials. For illustration, the models are calibrated to the geometrical features of a population of 128 similar ASTM C57 aggregates used in concrete. The first model is a sum of spherical harmonic functions with random non-Gaussian coefficients. The second model is a nonlinear memoryless mapping of a sum of spherical harmonic functions with Gaussian coefficients. The two random field models are used to develop Monte Carlo algorithms for generating virtual aggregates. By construction, the virtual aggregates capture essential statistics of the target population of aggregates. The performance of the proposed models is assessed by quantitative and qualitative metrics.
Measurement of ventricular function with radionuclide techniques

The noninvasive assessment of resting left ventricular performance has become an integral part of the evaluation of patients with known or suspected cardiac disease, having important diagnostic, therapeutic, and prognostic significance. This article details the wide range of clinical diagnostic possibilities available by dynamic imaging of myocardial function using scintigraphic techniques, including gated planar and tomographic blood pool imaging, first-pass radionuclide angiography, and gated tomographic perfusion imaging. The clinical and technical aspects described should be useful to the cardiologist intent upon supervising the performance of these tests, as well as providing their interpretation.
Comparison of Glycogen and Adenine Nucleotides as Indicators of Metabolic Stress in Mummichogs

Abstract Adenine nucleotide and glycogen concentrations were measured concurrently in white muscle of mummichogs Fundulus heteroclitus after the fish were exposed to stressors that either caused an increase in energy use (metabolic loading) or damaged metabolic function (toxic inhibition). When fish were exposed 4 h to 1% unbleached kraft mill effluent (which causes metabolic loading) in the presence of 6 mg/L dissolved oxygen, glycogen and AMP concentrations significantly (P ≤ 0.05) decreased below control values, whereas ATP, ADP, and total adenylate (TA) concentrations as well as the adenylate energy charge (AEC = [ATP + 1/2ADP]/TA) were unchanged. When dissolved oxygen was below 1 mg/L, the effluent caused significant decreases in glycogen, ATP, and TA, but not in ADP, AMP, or the AEC. The combined effect of effluent and hypoxia caused more significant drops in ATP or TA pool. When fish were exposed to 60 μg/L DDT (a toxic inhibitor) for 4 h, none of the measured energy variables changed even though t...
MALDI AND FAB MASS SPECTROMETRY OF NUCLEOSIDE TRIPHOSPHATES: A COMPARATIVE STUDY

Abstract Comparison of MALDI and FAB mass spectra of dATP, dTTP, dCTP, and dGTP shows that the former technique gives clear molecular ions with minimal fragmentation whereas the latter gives more fragment ions and weaker parent peaks.
Kinetics of nitric oxide formation in premixed laminar flames

The formation of nitric oxide in premixed methane/air in atmospheric-pressure flat flameswas studied at equivalence ratios ranging from 0.89 to 1.15. The peak rates of nitric oxide formation in the flame zone were found to be 1 to 2 orders of magnitude greater than the values in the post-flame zone, and to be consistent with the presence in the flame of oxygen radicals greatly in excess of equilibrium. A fair approximation of the measured rates is provided by the Zeldovich reactions when the free-radical concentrations are derived from the concentration of stable species by use of partial-equilibrium assumptions for the fast-flame reactions. A simplified method of predicting the rates of nitric oxide formation and carbon monoxide burnout in the flame zone provides partial explanation for the results obtained in this study.
In vivo stability of cryoprecipitate fibrinogen.

Because of its lower hepatitis risk, cryoprecipitate has been advocated as a substitute for commercial fibrinogen. Previous literature on cryofibrinogen has demonstrated a short blood t t 1/2. rendering it unsuitable for therapeutic/ use. The in vivo clearance of 131I-cryoprecipitate was compared with that of 125I-standard fibrinogen. A small amount of cryoprecipitate was rapidly cleared and apparently was cryofibrinogen. However, the bulk of the cryoprecipitate was cleared with a normal half life, as was cryoprecipitate that was in 10-bag pools. The data indicated cryoprecipitate was an effective in vivo form of fibrinogen and thus the preferred fibrinogen source because of its combining normal t 1/2 with single donor procurement.
Calcium dependence of damage to mouse motor nerve terminals following oxygen/glucose deprivation

Motor nerve terminals are especially sensitive to an ischemia/reperfusion stress. We applied an in vitro model of this stress, oxygen/glucose deprivation (OGD), to mouse neuromuscular preparations to investigate how Ca(2+) contributes to stress-induced motor terminal damage. Measurements using an ionophoretically-injected fluorescent [Ca(2+)] indicator demonstrated an increase in intra-terminal [Ca(2+)] following OGD onset. When OGD was terminated within 20-30min of the increase in resting [Ca(2+)], these changes were sometimes reversible; in other cases [Ca(2+)] remained high and the terminal degenerated. Endplate innervation was assessed morphometrically following 22min OGD and 120min reoxygenation (32.5°C). Stress-induced motor terminal degeneration was Ca(2+)-dependent. Median post-stress endplate occupancy was only 26% when the bath contained the normal 1.8mM Ca(2+), but increased to 81% when Ca(2+) was absent. Removal of Ca(2+) only during OGD was more protective than removal of Ca(2+) only during reoxygenation. Post-stress endplate occupancy was partially preserved by pharmacological inhibition of various routes of Ca(2+) entry into motor terminals, including voltage-dependent Ca(2+) channels (ω-agatoxin-IVA, nimodipine) and the plasma membrane Na(+)/Ca(2+) exchanger (KB-R7943). Inhibition of a Ca(2+)-dependent protease with calpain inhibitor VI was also protective. These results suggest that most of the OGD-induced motor terminal damage is Ca(2+)-dependent, and that inhibition of Ca(2+) entry or Ca(2+)-dependent proteolysis can reduce this damage. There was no significant difference between the response of wild-type and presymptomatic superoxide dismutase 1 G93A mutant terminals to OGD, or in their response to the protective effect of the tested drugs.
Establishing shelters for battered women: Local manifestations of a social movement

This paper analyzes how decentralized social movements manifest themselves on the local level, by studying twenty-five social movement organizations within the battered women's movement. Data consist of in-depth interviews with group members, the study focuses on six issues faced by the groups: how they recognized the need in their communities for alternative services for battered women; how they enlisted community support; how they defined themselves in terms of feminism and the participation of men, how they developed a working relationship with the battered women whom they wanted to help; how they structured their organizations; and how they established goals and strategies. Since the groups were at different stages of development, a dynamic analysis is made of each issue. Groups dealt with the issues on the basis of local resources, values, and other conditions. The movement's structure allowed this independence, which strengthened each group's ability to mobilize resources and accomplish goals. However, it also resulted in local decisions that were often inconsistent with movement goals and weakened the ability of movement leaders to control strategy.
Point defects and diffusion in NiO

Abstract A defect model for NiO is developed and is fit to the electrical-conductivity data [26], the deviation-from-stoichiometry data [7], and the cation-self-diffusion data [14, 17]. This model involves neutral, singly charged, and doubly charged nickel vacancies and charge-compensating electron holes. Both singly and doubly charged cation vacancies are required to explain the data; neutral cation vacancies (if present) are not required by the present data. However, the jump frequencies of the two types of charged cation vacancies are generally not equal; the doubly charged cation vacancy moves with the smaller activation enthalpy. The defect data are quantitatively consistent with the chemical-diffusion data [26] and with a correlation factorƒ v = 0.75.
Optical emissions during plasma assisted chemical vapor deposition of diamond-like carbon films

Abstract The deposition of diamond-like carbon (DLC) films onto silicon wafers and polyethyleneterephthalate (PET) from methanehydrogen gas mixtures by plasma assisted chemical vapor deposition was investigated by optical emission spectroscopy. Film growth rates, crack formation, and average electron energy in the plasma were analyzed for various deposition conditions. The cracks in the DLC films deposited onto PET could be removed by increasing the hydrogen content in the gas mixture. No adjustment of ion energy, substrate temperature control, or addition of inert gas was necessary to avoid crack formation. In the commonly used range of bias voltage above 500 V, the intensity of the Hα line (656.3 nm) correlated well with the film deposition rate. The hydrogen peak intensity can be used for on-line, non-contact, instantaneous monitoring of the deposition rate.
Nutrition in Inflammatory Bowel Disease

The nutritional impact of inflammatory bowel disease is notable, both in Crohn’s disease and ulcerative colitis. The causes of malnutrition include decreased intake, maldigestion, malabsorption, accelerated nutrient losses, increased requirements, and drug-nutrient interactions. Inflammatory bowel disease causes alterations in body composition and, because of these changes, affects energy expenditure. Various approaches have been most effective in correcting malnutrition, supporting growth, and managing short-bowel syndrome, but the success of primary therapy has been limited.
Cellular, biochemical and functional effects of ozone : new research and perspectives on ozone health effects

Ozone, a toxic component of photochemical oxidant air pollution, has been the focus of considerable research efforts for several decades. In spite of this large body of work, questions remain as to the potential risks to human health represented by chronic low-level exposure to ozone. Newer studies in animals have provided fundamental information on the range of biochemical, functional and morphologic responses to ozone exposure. While the response to ozone exposure is extremely complex, some generalities have emerged which may aid attempts to apply the results of these studies to decisions regarding the protection of human health.
Middlemarch and the problem of other minds heard

(2003). Middlemarch and the problem of other minds heard. Lit: Literature Interpretation Theory: Vol. 14, No. 3, pp. 223-241.
Quantitative Evaluation of Acute Renal Transplant Dysfunction with Low-Dose Three-dimensional MR Renography

Our new quantitative analysis method of MR renography, which includes our multicompartmental tracer kinetic renal model, may help to diagnose noninvasively acute rejection or acute tubular necrosis after kidney transplantation.
Biomarkers of pesticide exposure and diabetes in the 1999-2004 national health and nutrition examination survey.

The associations of 8 pesticides and pesticide metabolites with total diabetes (diagnosed and undiagnosed) and pre-diabetes (glycohemoglobin 5.7–6.4%) were evaluated using the National Health and Nutrition Examination Survey (NHANES), 1999–2004. Six of the pesticides were found to be associated with total diabetes in separate adjusted logistic regressions. These pesticides and pesticide metabolites were beta-hexachlorocyclohexane, p,p′-DDE, p,p′-DDT, oxychlordane, trans-nonachlor, and heptachlor epoxide. When the number of compounds elevated was tested, 4 or more, of the 6, elevated had an odds ratio of 4.99 (95% CI 1.97–12.61) compared to none elevated. When the 6 compounds were tested together in a single combined adjusted logistic regression only oxychlordane, a metabolite of chlordane, and heptachlor epoxide, a metabolite of heptachlor, were significantly associated with total diabetes. In the combined adjusted logistic regression, oxychlordane ≥ 14.5 ng/g lipid adjusted had an odds ratios of 1.90 (95% CI 1.09–3.32) compared to oxychlordane < 14.5 ng/g lipid adjusted, and heptachlor epoxide ≥ 14.6 ng/g lipid adjusted had an odds ratio of 1.70 (95% CI 1.16–2.49) compared to heptachlor epoxide < 14.6 ng/g lipid adjusted. Heptachlor epoxide and p,p′-DDT were significantly associated with pre-diabetes in separate adjusted logistic regressions. When these 2 compounds were tested together only heptachlor epoxide remained significantly associated with pre-diabetes. The evidence supporting the relationship between pesticides and pesticide metabolites, with diabetes, was strongest for heptachlor epoxide and oxychlordane, intermediate for p,p′-DDT, and least for beta-hexachlorocyclohexane, p,p′-DDE, and trans-nonachlor. Mirex and dieldrin were not associated with total diabetes or pre-diabetes.
Ring Resonator Lasers using Passive Waveguides and Integrated Semiconductor Optical Amplifiers

We present a review of our work on ring lasers using passive waveguides and couplers (directional and multimode interference) integrated with semiconductor optical amplifiers (SOAs). Two architectures are given in this paper. The first architecture includes the SOA inside the ring cavity. The second architecture also known as ring resonator coupled laser, consists of passive ring resonators having SOAs in the bus waveguides. The increased photon lifetime in the cavity and the tunability of the ring response can be used to make compact, narrow linewidth, and widely tunable lasers. Four-wave mixing applications are also addressed.
The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like β-grasp domains

Ubiquitin (Ub)-mediated signaling is one of the hallmarks of all eukaryotes. Prokaryotic homologs of Ub (ThiS and MoaD) and E1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. However, there is no evidence for entire protein modification systems with Ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. Hence, the evolutionary assembly of the eukaryotic Ub-signaling apparatus remains unclear. We systematically analyzed prokaryotic Ub-related β-grasp fold proteins using sensitive sequence profile searches and structural analysis. Consequently, we identified novel Ub-related proteins beyond the characterized ThiS, MoaD, TGS, and YukD domains. To understand their functional associations, we sought and recovered several conserved gene neighborhoods and domain architectures. These included novel associations involving diverse sulfur metabolism proteins, siderophore biosynthesis and the gene encoding the transfer mRNA binding protein SmpB, as well as domain fusions between Ub-like domains and PIN-domain related RNAses. Most strikingly, we found conserved gene neighborhoods in phylogenetically diverse bacteria combining genes for JAB domains (the primary de-ubiquitinating isopeptidases of the proteasomal complex), along with E1-like adenylating enzymes and different Ub-related proteins. Further sequence analysis of other conserved genes in these neighborhoods revealed several Ub-conjugating enzyme/E2-ligase related proteins. Genes for an Ub-like protein and a JAB domain peptidase were also found in the tail assembly gene cluster of certain caudate bacteriophages. These observations imply that members of the Ub family had already formed strong functional associations with E1-like proteins, UBC/E2-related proteins, and JAB peptidases in the bacteria. Several of these Ub-like proteins and the associated protein families are likely to function together in signaling systems just as in eukaryotes.
Rescue of calcineurin Aα(-/-) mice reveals a novel role for the α isoform in the salivary gland.

Calcineurin is an important signal transduction mediator in T cells, neurons, the heart, and kidneys. Recent evidence points to unique actions of the two main isoforms of the catalytic subunit. Although the β isoform is required for T-cell development, α is important in the brain and kidney. In addition, mice lacking α but not β suffer from failure to thrive and early mortality. The purpose of this study was to identify the cause of postnatal death of calcineurin α null (CnAα −/− ) mice and to determine the mechanism of α activity that contributes to the phenotype. CnAα −/− mice and wild-type littermate controls were fed a modified diet and then salivary gland function and histology were examined. In vitro studies were performed to identify the mechanism of α action. Data show that calcineurin is required for normal submandibular gland function and secretion of digestive enzymes. Loss of α does not impair nuclear factor of activated T-cell activity or expression but results in impaired protein trafficking downstream of the inositol trisphosphate receptor. These findings show a novel function of calcineurin in digestion and protein trafficking. Significantly, these data also provide a mechanism to rescue to adulthood a valuable animal model of calcineurin inhibitor-mediated neuronal and renal toxicities.
A Study of the Response of Deep Tropical Clouds to Large-Scale Thermodynamic Forcings. Part II: Sensitivities to Microphysics, Radiation, and Surface Fluxes

Abstract The Goddard Cumulus Ensemble (GCE) model is used to examine the sensitivities of multiday 2D simulations of deep tropical convection to surface fluxes, interactive radiation, and ice microphysical processes. The simulations incorporate large-scale temperature, moisture, and momentum forcings, from the Tropical Ocean Global Atmosphere Coupled Ocean–Atmosphere Response Experiment (TOGA COARE) for the period 19–27 December 1992. This study shows that, when surface fluxes are eliminated, the mean simulated atmosphere is much cooler and drier, convection and CAPE are much weaker, precipitation is less, and low-level to midlevel cloudiness is much greater. Surface fluxes using the TOGA COARE flux algorithm are weaker than with the aerodynamic formulation, but closer to the observed fluxes. In addition, trends similar to those noted above for the case without surface fluxes are produced for the TOGA COARE flux case, albeit to a much lesser extent. The elimination of shortwave and longwave radiation is f...
Inaccurate Doses of Rh Immune Globulin After Rh-Incompatible Fetomaternal Hemorrhage: Survey of Laboratory Practice

Abstract Context.—Rh(D)-negative women with a large fetomaternal hemorrhage (FMH) from an Rh(D)-positive fetus are at risk for anti-D alloimmunization if they do not receive adequate Rh immune globulin (RhIG). Determination of the adequate RhIG dose for these women is a critical laboratory procedure for protecting their future Rh(D)-positive children. Objective.—To determine how often laboratories recommended an inaccurate dose of RhIG for excess FMH. Design.—Nearly 1600 laboratories using the College of American Pathologists' proficiency testing for fetal red blood cell detection were surveyed to determine (1) their calculation method and (2) the number of RhIG doses recommended for a survey specimen, based on their measured percentage of fetal red blood cells. We surveyed nearly 1450 laboratories for their accuracy in determining RhIG dose, using 2 common calculation methods we provided. Results.—The AABB Technical Manual method was used by 67% of responding laboratories. However, 20.7% of laboratories ...
Visual perception and corollary discharge.

Perception depends not only on sensory input but also on the state of the brain receiving that input. A classic example is perception of a stable visual world in spite of the saccadic eye movements that shift the images on the retina. A long-standing hypothesis is that the brain compensates for the disruption of visual input by using advance knowledge of the impending saccade, an internally generated corollary discharge. One possible neuronal mechanism for this compensation has been previously identified in parietal and frontal cortex of monkeys, but the origin of the necessary corollary discharge remained unknown. Here, we consider recent experiments that identified a pathway for a corollary discharge for saccades that extends from the superior colliculus in the midbrain to the frontal eye fields in the cerebral cortex with a relay in the medial dorsal nucleus of the thalamus. We first review the nature of the evidence used to identify a corollary discharge signal in the complexity of the primate brain a...
Fault diagnosis of flash ADC using DNL test

This paper describes a technique which uses the differential non linearity (DNL) test data for fault location and identification of the analog components of a flash ADC. In a flash ADC, a fault in the analog subcircuit is uniquely reflected in the transfer function and therefore also in DNL data. This property is exploited to locate a fault and to identify the error value in analog components of the flash ADC. The technique proposed here relies only on DNL test data. Thus the diagnosis can be carried out using at-operating-speed test data. The paper presents relationship between each fault case and its respective DNL pattern. Fault simulation results of a small flash ADC are presented. >
Mixing and Phasing of Roles Among Volunteers, Staff, and Participants in Faith-Based Programs:

In this grounded theory research project, face-to-face interviews were conducted with program participants, board members, administrators, coordinators, and collaborators in 15 faith-based programs. Findings concerning the roles played by participants, volunteers, and paid staff reveal the wearing of multiple hats, facilitated by a tendency toward cross-training, role diffusion, and doing what is needed. Boundaries created by roles appear to be less important than pragmatically responding to meet human needs. The moral imperative or faith-based nature of the work appears to be a recruiting tool for both paid staff and volunteers, as well as an expressed personal benefit for both. Challenges include turnover among paid staff and volunteers, heavy reliance on volunteers, and low pay. Psychological contracting with a faith-based community may be related to the ability to cope with fluid role expectations and associated ambiguities.
Inferred Eastern Extent, Overthrust Belt, Central Utah: ABSTRACT

Structural and stratigraphic relations in the Wasatch Plateau, the Gunnison Plateau, and the northwestern Cedar Hills suggest a new interpretation of the easternmost limit of thrusting during Late Cretaceous foreland deformation in central Utah. Steep to overturned dips in the Upper Cretaceous Indianola Group within this region are interpreted to reflect involvement of foreland basin clastics in thrust-related structures that deformed the flank of the foreland basin. A subhorizontal overlap assemblage of inferred Paleocene age indicates that the post-thrust erosion surface sloped gently eastward into the foreland basin. Northeast-striking, southeast-facing homoclines of Indianola Group strata rest disconformably on Jurassic beds. However, favorable horizons within the Arapien Shale of the Jurassic sequence served as a zone of regional decollement, along which younger formations were detached and transported eastward with respect to underlying autochthonous units. The decollement zone was deformed internally by multiple thrusts and by east-vergent isoclinal folds subsequently complicated by local diapiric modifications. Most exposures of the Indianola Group are thus wholly or partly allochthonous. Folds involving Indianola strata apparently include: (1) fully detached ramp anticlines associated with subsurface thrust faults that underlie the southern Wasatch Mountains, Gunnison Plateau, and Sanpete Va ley; and (2) partly detached frontal anticlines associated with blind thrusts that approach the surface beneath the Sanpete Valley and the western margin of the Wasatch Plateau. Structures inferred locally are consistent with documented patterns of deformation involving foreland clastics elsewhere in the overthrust belt and should influence exploration strategy in central Utah. End_of_Article - Last_Page 592------------
Analysis of tabular methods for modular reduction

Alternate table lookup schemes for the operation z mod p are presented and compared. The cases of a single table and two tables, including some new schemes, are analyzed completely and closed-form solutions for optimal designs are derived. Extension of the analysis and design techniques to more elaborate decomposition schemes are also discussed briefly. A novel multi-operand modular addition scheme is presented that can be used in implementing some multi-table schemes. >
The evolution of tamoxifen therapy in breast cancer: selective oestrogen-receptor modulators and downregulators

Tamoxifen is the most widely used hormonal treatment for all stages of breast cancer and has been approved for the prevention of breast cancer in high-risk women. The observation that tamoxifen acts as an antioestrogen on the breast but has paradoxical oestrogenic effects on bones and lipids heralded the development of the selective oestrogen-receptor modulators (SERM). Raloxifene, another of these drugs, is being used to prevent osteoporosis in postmenopausal women, but it seems, like tamoxifen, to prevent breast cancer. The molecular basis for these target-site-specific actions remains unclear but may involve the relative expressions of coregulatory proteins in target tissues. Several new SERM agents are in clinical development in an attempt to decrease the unwanted effects. Furthermore, two different classes of hormonal agents, the aromatase inhibitors and oestrogen-receptor downregulators, which have no oestrogen-like properties at any site, are promising new treatments for breast cancer.
Trawl fisheries, catch shares and the protection of benthic marine ecosystems: Has ownership generated incentives for seafloor stewardship?

Abstract Proponents of catch share-based fisheries have claimed ecological stewardship can result from the assignment of individual catch quotas. This claim is examined by analyzing the distribution of benthic habitat protection measures adopted by quota-owning industry sectors within the exclusive economic zones (EEZs) of the U.S. (Alaska), New Zealand, and high seas seamounts within the Southern Indian Ocean Deepsea Fishers Association (SIODFA) competence area. Results suggest the protection of both benthic ecosystems and essential fish habitat (EFH) are marginal at best when quota owners have primacy in determining the boundaries of bottom trawl closures. The majority of the areas in these three regions that are closed to trawling are too deep to fish, may not contain vulnerable marine ecosystems, and do not have high abundances of commercially important species. “Freezing the footprint” of bottom trawling is not the best method for benthic habitat protection in areas where the fishing industry is actively fishing vulnerable habitats. Analytical methods should be applied to help determine boundaries of future bottom trawl closures rather than allowing the fishing industry to place benthic protection areas (BPAs) in areas where they are not interested in fishing.
Information measures of Dirichlet distribution with applications

We explore properties of information measures of the Dirichlet family and related distributions. Representations of the information measures of the Dirichlet family in terms of the information measures of the gamma family reflect the characterization of Dirichlet distribution in terms of the ratios of independent gamma distributions to their sum. We present measures of information provided by a multinomial vector about the multinomial parameters under the Dirichlet prior and measures of information loss due to aggregation of Dirichlet components and the multinomial categories. New information characterizations of the bivariate Dirichlet distribution in terms of survival and hazard gradient constraints are given. The information analysis of contingency tables is briefly described. An example illustrates applications of Dirichlet prior for inferences about information measures of contingency tables and Kendall's tau for ordinal data. Results that compare solicitation of the mean and mode vectors for the Dirichlet model are given and are illustrated through an example from a study of business executives' environmental uncertainty in the aftermath of 9/11 terrorist attacks. The probability integral transformation is proposed for facilitating implementation of the maximum entropy Dirichlet process prior procedure for inference about the fit of continuous distributions to the data. Copyright © 2011 John Wiley & Sons, Ltd.
eSNaPD: A Versatile, Web-Based Bioinformatics Platform for Surveying and Mining Natural Product Biosynthetic Diversity from Metagenomes

Summary Environmental Surveyor of Natural Product Diversity (eSNaPD) is a web-based bioinformatics and data aggregation platform that aids in the discovery of gene clusters encoding both novel natural products and new congeners of medicinally relevant natural products using (meta)genomic sequence data. Using PCR-generated sequence tags, the eSNaPD data-analysis pipeline profiles biosynthetic diversity hidden within (meta)genomes by comparing sequence tags to a reference data set of characterized gene clusters. Sample mapping, molecule discovery, library mapping, and new clade visualization modules facilitate the interrogation of large (meta)genomic sequence data sets for diverse downstream analyses, including, but not limited to, the identification of environments rich in untapped biosynthetic diversity, targeted molecule discovery efforts, and chemical ecology studies. eSNaPD is designed to generate a global atlas of biosynthetic diversity that can facilitate a systematic, sequence-based interrogation of nature's biosynthetic potential.
Cutis marmorata telangiectatica congenita: a prospective study of 27 cases and review of the literature with proposal of diagnostic criteria

Summary Background. Cutis marmorata telangiectatica congenita (CMTC) is a congenital vascular anomaly of unknown aetiology. About 300 cases have been reported in the literature. The rate of associated anomalies varies between 20% and 70%. Methods. We report a series of 27 children with CMTC, 18 of whom were followedup prospectively for a median of 22 months (range 2 months–5.3 years). Results. Both genders were equally affected (13 male ⁄ 14 female). The legs were involved in 20 cases (74%), the arms in 10 (37%), the face in 4 (15%) and the trunk in 18 (67%). There were 20 (74%) patients who presented with involvement of both trunk and limbs, a further 20 patients had lesions affecting the limb on only one side of the body, and 7 children (26%) had bilateral lesions; 1 child had generalized CMTC lesions. The involved areas covered a mean of 18% of body surface area (range 3–90). Associated anomalies were found in 15 patients (56%), with some exhibiting more than one. There was body asymmetry (hypertropy or hypotrophy of the affected limb) in nine patients (33%), seven patients had a variety of other malformations (congenital glaucoma, syndactyly, lipoma, macrocephaly, renal hypoplasia, Kartagener’s syndrome), and other vascular lesions were present in four patients (15%). There was no correlation between the extent of skin lesions and likelihood of associated anomalies. On follow-up, fading of skin lesions was noted in 67% of our patients. Conclusion. Body asymmetry is the most common anomaly associated with CMTC; other associations might be pure chance. In order to separate CMTC from other vas
Effect of solid flow above a subducting slab on water distribution and melting at convergent plate boundaries

[1] Hydrous fluids derived by dehydration of the downgoing slab at convergent plate boundaries are thought to provoke wet melting in the wedge above the downgoing plate. We have investigated the distribution of hydrous fluid and subsequent melt in the wedge using two-dimensional models that include solid mantle flow and associated temperature distributions along with buoyant fluid migration and melting. Solid mantle flow deflects hydrous fluid from their buoyant vertical migration through the wedge. Melting therefore does not occur directly above the region where hydrous fluids are released from the slab. A melting front develops where hydrous fluids first encounter mantle material hot enough to melt. Wet melting is influenced by solid flow through the advection of fertile mantle material into the wet melting region and the removal of depleted material. The region of maximum melting occurs where the maximum flux of water from slab mineral dehydration reaches the wet melting region. The extent of melting (F) and melt production rates increase with increasing convergence rate and grain size due to increased temperatures along the melting front and to increased fractions of water reaching the melting front, respectively. The position of isotherms above the wet solidus varies with increasing slab dip and thereby also influences F and melt production rates. Applying the understanding of wet melting from this study to geochemical studies of the Aleutians may help elucidate the processes influencing fluid migration and melt production in that region. Estimates of the timescale of fluid migration, seismic velocity variation, and attenuation are also investigated.
A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing

SUMMARY: Currently available bisulfite sequencing tools frequently suffer from low mapping rates and low methylation calls, especially for data generated from the Illumina sequencer, NextSeq. Here we introduce a sequential trimming-and-retrieving alignment approach for investigating DNA methylation patterns, which significantly improves the number of mapped reads and covered CpG sites. The method is implemented in an automated analysis toolkit for processing bisulfite sequencing reads. Availability: http://mysbfiles.stonybrook.edu/~xuefenwang/software.html https://github.com/xfwang/BStools CONTACT: xuefeng.wang@stonybrook.edu SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.
HIV Increases HCV Replication in a TGF-β1–Dependent Manner

Background & Aims: Human immunodeficiency virus (HIV) coinfection increases hepatitis C virus (HCV)-related progression of hepatic fibrosis, increases HCV persistence, and decreases response rates to interferon-based anti-HCV therapy. It has remained unclear how HIV, a nonhepatotropic virus, accelerates the progression of liver disease by HCV. Methods: We explored the possibility that circulating HIV and/or its proteins contribute to the pathogenesis of HCV through engagement of extracellular coreceptors on hepatocytes. Results: In this study, we found that inactivated HIV or gp120 increases HCV replication and enhances HCV-regulated transforming growth factor (TGF)-β1 expression in both a replicon and an infectious model of HCV. This proviral effect of HIV and gp120 on HCV replication is neutralized by antibodies to CCR5 or CXCR4. However, HIV and gp120 did not alter type I interferon-mediated signaling in these HCV models, indicating that HIV regulates HCV replication through an alternative mechanism. Interestingly, we found that human TGF-β1 also enhanced HCV replication. The effect of HIV on HCV replication was blocked by a neutralizing antibody to TGF-β1, indicating that its effects on HCV replication are TGF-β1 dependent. Conclusions: These results suggest a novel mechanism by which HIV not only enhances HCV replication but also contributes to progression of hepatic fibrosis.
Variability in ammonium nitrate formation and nitric acid depletion with altitude and location over California

[1] Spatial variations in the partitioning of nitrate between gas phase nitric acid (HNO3) and particulate ammonium nitrate were observed using airborne measurements of trace gas mixing ratios, particle size distributions, and particle composition. During the Intercontinental Transport and Chemical Transformation experiment in April and May 2002 the NOAA WP-3 aircraft flew up to 8 km altitude on 11 research flights from Monterey, California. The formation of semivolatile aerosols was studied by examining the enhancement of fine-particulate ammonium nitrate and depletion of gas-phase HNO3 over the San Joaquin Valley, Los Angeles Basin, and Mojave Desert. Gas-phase particle precursors, HNO3 and ammonia (NH3), were converted to particulate ammonium nitrate at higher altitudes within the boundary layer. These particle layers were a consequence of lower ambient temperatures that caused a reduction of the dissociation constant for ammonium nitrate aerosol so that gas phase HNO3 was depleted and particle mass was formed. The resulting vertical gradients in particulate matter and HNO3 were observed in well-mixed boundary layers where other directly emitted trace gases (CO) and secondary pollutants (O3) exhibited no vertical gradients. Hence the equilibrium between the gas and particle phases occurred faster than boundary layer mixing times and chemical rather than meteorological effects were responsible for the layers of enhanced particulate matter aloft. Coincident HNO3 depletion and ammonium nitrate formation was also observed downwind from regions characterized by large agricultural NH3 emissions in the Los Angeles Basin and San Joaquin Valley.
A project component in a web engineering course

Web applications are an extremely important and ubiquitous part of today's world. Students must not only know how to develop them from a technical perspective, but in doing so need to understand how to follow the proper principles of software engineering — delivering the project on time, on budget, and in a high quality manner. At the Department of Software Engineering at the Rochester Institute of Technology, we offer a Web Engineering course which not only introduces students to a variety of web technologies, but more importantly it shows them how to use them in a collaborative environment while properly utilizing web engineering methodologies. The course includes a significant project component requiring students to use a variety of contemporary technologies and resources to create a robust web application. The main premise of the project is for each group to create a web portal using both custom-built and already existing components. The project takes place over the entire 15 week course term, includes multiple releases, and has students work in teams of 4–5. This innovative project component has received significant praise from both students and faculty members while fulfilling an emerging area of our curriculum. Students enjoy the real-world nature of the project and the ability to work with contemporary technologies in a format which closely mimics what they will see in industry. This paper outlines the educational objectives, project details, some sample project results of our class offering, as well as student feedback about the project. The goal of this work is to share the project, its importance, and lessons learned for use at other institutions with similar educational goals.
Choosing Customized Marketing Offers to Attract a Desirable Mix of Customers

This paper studies the marketing problem of a firm trying to obtain an attractive mix of customers by making customized offers. The firm values the average features of the acquired set of customers, makes decisions with uncertainty about whether and which customers will accept offers, is risk averse, and faces a resource constraint. These features do not allow the application of standard procedures, so we develop methods tailored to the stochastic nature of the problem in order to be computationally feasible. These methods include calculating probabilistic guarantees for the approximate utility function and bounds on the optimal value. Our approach overcomes both the Optimizer's Curse and the computational difficulty of enumeration techniques for this problem. We apply the approach to an MBA admission process and implement adjusted scholarship decisions. We demonstrate the methodology can generate statistically significant improvements over current management decisions. By comparing our solution to what management would do on its own, we provide insight into the nature of mistakes management made in this complex decision environment. We believe that the methodology proposed here, i.e., the model, the probabilistic guarantees, and the computational approach, will prove to be valuable in a variety of different applications.
Digital-Friendly but Learning-Focused: Action and Readings for Excellent Teaching

SUBJECT AREA: classroom teaching. Being digital (or at least heading there) is perhaps the most interesting forward-looking issue in the development of excellent teachers today. Society is awash in progressively higher tides of new information technology. For teachers, this creates a race to adapt, cheered by students who value flexibility and novelty, and by corporate partners who want their new recruits trained in the latest and greatest. However fleet of foot the instructor might be, the workout required to keep up with the pack is nontrivial. There is always new software or systems lying around the bend. The price tag for it all requires smelling salts for Deans. And though the invention and experimentation brings tangible rewards to the teaching enterprise, it also carries unintended adverse side effects. The finish line to this race keeps moving outward. And besides, as Gertrude Stein might have asked, is there a there there? I think the answer is "yes" though its shape is not obvious today. And getting there successfully depends crucially on the distinction between wisdom, knowledge, and information. This note offers some suggestions to guide the journey. Past columns by Robert Bruner may be found by search at the SSRN website at: http://papers.ssrn.com/sol3/search.taf or by going to his Author Page at SSRN at: http://papers.ssrn.com/sol3/cf_dev/AbsByAuth.cfm?per_id=66030
Orientation to Education as a Factor in the School Maladjustment of Lower-Class Children

E| VEN taking an extremely crude index of school achievement, that of grade placement, for every age level the average grade of middle-class urban children is higher than that of lower-class children. (See Tables 1, 2, and 3.) These differences can be observed at 7 and 8 years of age as well as at 17. Apparently whatever produces the difference starts operating to differentiate lower-class from middle-class children from the early grades. Another way of looking at class selectivity of the educational process is to observe the proportion of lower-class boys in high school a generation ago (Tables 4 and 5) or in college today.' Why are middle-class children more successful in their studies? Why do lower-class children drop out at younger ages and complete fewer grades? One hypothesis is that school teachers are middleclass in their values, if not in their origins, and penalize those students who do not exhibit the middle-class traits of cleanliness, punctuality, and neatness or who do exhibit the lower-class traits of uninhibited sexualtty and aggression.2 Some social scientists believe that lower-class children, even though they may have the intellectual potentialities for high levels of academic achievement, lose interest in school or never become interested because they resent the personal rejection of their teachers. Such rejection is, they say, motivated by the teachers' mistaken notion that lower-class children are deliberately defying them. Davis and Havighurst show that children are the prisoners of their experience and that lower-class children behave the way they do, not because of any initial desire to defy school authorities, but rather because of their lower-class childhood training.' According to this hypothesis, teacher rejection makes the lower-class boy resentful and rebellious. His attitude is, "If you don't like me, I won't cooperate." Unfortunately for him, however, school achievement is related to later occupational advancement. Failure to cooperate with the teacher cuts off the lower-class boy from a business or professional career. Professor August Hollingshead describes what happens to lower-class boys from a small town in Illinois who withdraw from school to escape the psychic punishment meted out by the teachers and upper-class children.
Release and Recovery of Phosphorus-32 Tagged Jack Pine Budworm Larvae in the Field (Lepidoptera: Tortricidae)

Late-stage larvae of the genus Choristoneura drop readily from their host trees when disturbed. This phenomenon has been discussed for the spruce budworm by Craighead (1924), Wellington and Henson (1947), and Morris and Mott (1963). Some larvae are able to return to the tree crowns, but many are lost to predators or are unable to reestablish on suitable host plants. Larvae of the jack pine budworm, C. pinus pinus Freeman, exhibit similar behavior (Jennings 1971). If a large proportion of the larvae can be stimulated to drop from the host trees, and if few are able to return, the dropping behavior may be used advantageously to reduce populations. This note reports information on return of larvae from the ground to overstory jack pines.