cssi/SciSciGPT-SciSciNet huggingface dataset:
Modeling shear waves through a viscoelastic medium induced by acoustic radiation force

In this study, a finite element model of a tissue-mimicking, viscoelastic phantom with a stiffer cylindrical inclusion subjected to an acoustic radiation force (ARF) is presented, and the resulting shear waves through the heterogeneous media are simulated, analyzed, and compared with experimental data. Six different models for the ARF were considered and compared. Each study used the same finite element model, but applied the following: (1) full radiation push; (2) focal region push; (3) single element focal point source; or (4) various thresholds of the full radiation push. For each case, displacements at discrete locations were determined and compared. The finite element simulation results for the full radiation push matched well with the experimental data with respect to replicating the shear wave speed and attenuation in the peak displacements through the background medium and inclusion, but did not illustrate comparable recovery after the peak displacements. As a result of this study, it has been shown that a focal region or point source push is not adequate to accurately model the effects of the full radiation push, but thresholding the full push can produce comparable results and reduce computation time.
In Vitro Studies of the Prp9·Prp11·Prp21 Complex Indicate a Pathway for U2 Small Nuclear Ribonucleoprotein Activation

Pre-mRNA splicing takes place on a large ribonucleoprotein particle, the spliceosome which contains the five small nuclear ribonucleoproteins (snRNPs), U1, U2, U4, U5, and U6. In Saccharomyces cerevisiae the mRNA splicing factors, Prp9, Prp11, and Prp21, are necessary for addition of the U2 snRNP to the pre-mRNA in an early step of spliceosome assembly. This paper describes a study of interactions between these proteins and their role in spliceosome assembly. The proteins were expressed in Escherichia coli. Prp9 and Prp11 were purified by metal affinity chromatography. Prp21 was purified using a solubilization/renaturation protocol. We have combined these separately purified proteins and present direct evidence of a Prp9zPrp11zPrp21 protein complex that is functional in in vitro splicing assays. Characteristics of this Prp9zPrp11zPrp21 complex were further investigated using proteins synthesized in vitro. In addition, we found that Prp9, Prp11, and Prp21 influence the structure of the U2 snRNP in a manner that alters the accessibility of the branch point pairing region of the U2 snRNA to oligonucleotide- directed RNaseH cleavage. We present a model, based on the data presented here and in the accompanying paper, for a combined role of Prp9, Prp11, Prp21, and Prp5 in activating the U2 snRNP for assembly into the pre-spliceosome.
Disruption of filamentous actin inhibits human macrophage fusion

The foreign body reaction to implanted biomaterials, characterized by the presence of macrophages and foreign body giant cells (FBGC), can result in structural and functional failure of the implant. Recently, we have shown that interleukin-4 and interleukin-13 can independently induce human macrophage fusion to form FBGC via a macrophage mannose receptor (MR) -mediated pathway. The MR is believed to mediate both endocytosis of glycoproteins and phagocytosis of microorganisms, which bear terminal mannose, fucose, N-acetylglucosamine, or glucose residues. Polarization of microfilaments to closely apposed macrophage membranes as observed with fluorescence confocal microscopy led us to ask whether MR-mediated fusion occurred via a filamentous actin-dependent pathway. Cytochalasins B and D and latrunculin-A, agents that disrupt microfilaments, inhibited macrophage fusion in a concentration-dependent manner. The concentrations of cytochalasins D and B that inhibited fusion did not significantly decrease macroph...
Identification of Proteins Whose Synthesis Is Modulated During the Cell Cycle of Saccharomyces cerevisiae

We examined the synthesis and turnover of individual proteins in the Saccharomyces cerevisiae cell cycle. Proteins were pulse-labeled with radioactive isotope (35S or 14C) in cells at discrete cycle stages and then resolved on two-dimensional gels and analyzed by a semiautomatic procedure for quantitating gel electropherogram-autoradiographs. The cells were obtained by one of three methods: (i) isolation of synchronous subpopulations of growing cells by zonal centrifugation.; (ii) fractionation of pulse-labeled steady-state cultures according to cell age; and (iii) synchronization of cells with the mating pheromone, alpha-factor. In confirmation of previous studies, we found that the histones H4, H2A, and H2B were synthesized almost exclusively in the late G1 and early S phases. In addition, we identified eight proteins whose rates of synthesis were modulated in the cell cycle, and nine proteins (of which five, which may well be related, were unstable, with half-lives of 10 to 15 min) that might be regulated in the cell cycle by periodic synthesis, modification, or degradation. Based on the time of maximal labeling in the cell cycle and on experiments with alpha-factor and hydroxyurea, we assigned the cell cycle proteins to two classes: proteins in class I were labeled principally in early G1 phase and at a late stage of the cycle, whereas those in class II were primarily synthesized at times ranging from late G1 to mid S phase. At least one major control point for the cell cycle proteins occurred between "start" and early S phase. A set of stress-responsive proteins was also identified and analyzed. The rates of synthesis of these proteins were affected by certain perturbations that resulted during selection of synchronous cell populations and by heat shock.
Trs20 is required for TRAPP III complex assembly at the PAS and its function in autophagy

The modular TRAPP complex acts as a guanine-nucleotide exchange factor (GEF) for Ypt/Rab GTPases. Whereas TRAPP I and TRAPP II regulate the exocytic pathway, TRAPP III functions in autophagy. The TRAPP subunit Trs20 is not required for assembly of core TRAPP or its Ypt1 GEF activity. Interestingly, mutations in the human functional ortholog of Trs20, Sedlin, cause spondyloepiphyseal dysplasia tarda (SEDT), a cartilage-specific disorder. We have shown that Trs20 is required for TRAPP II assembly and identified a SEDT-linked mutation, Trs20-D46Y, which causes a defect in this process. Here we show that Trs20 is also required for assembly of TRAPP III at the pre-autophagosomal structure (PAS). First, recombinant Trs85, a TRAPP III-specific subunit, associates with TRAPP only in the presence of Trs20, but not Trs20-D46Y mutant protein. Second, a TRAPP complex with Ypt1 GEF activity co-precipitates with Trs85 from wild type, but not trs20ts mutant, cell lysates. Third, live-cell colocalization analysis indicates that Trs85 recruits core TRAPP to the PAS via the linker protein Trs20. Finally, trs20ts mutant cells are defective in selective and non-selective autophagy. Together, our results show that Trs20 plays a role as an adaptor in the assembly of TRAPP II and TRAPP III complexes, and the SEDT-linked mutation causes a defect in both processes.
Adenotonsillectomy for sleep-disordered breathing in a predominantly obese pediatric population.

Abstract Objectives To determine the efficacy of adenotonsillectomy (T&A) in the treatment of pediatric sleep-disordered breathing, and to determine the natural history in untreated children. Methods The charts of children aged 1–12 who underwent polysomnography (PSG) between 1/2006 and 6/2009 were reviewed to identify children with positive studies. Children not treated by T&A were recruited and matched by age, time since initial PSG, and apnea-hypopnea index (AHI) to children who underwent T&A. All participants were evaluated by a clinical assessment score (CAS-15), follow-up PSG, and the Child Behavior Checklist (CBCL). Results Sixteen matched pairs completed the study. Ten (63%) T&A patients were overweight or obese compared with 14 (88%) untreated patients. There was a greater median improvement in AHI in the surgical group compared to the nonsurgical group (10.3 vs. 6.5, p = 0.044). Although the T&A children were more likely to have a follow-up AHI p p p p p = 0.05) were correlated with change in AHI among T&A subjects. Conclusions T&A was more effective in reducing AHI than no surgery. Median AHI improved in the nonsurgical group, and 4/16 (25%) untreated patients were cured (AHI
Text signals influence team artifacts

This exploratory quasi-experimental investigation describes the influence of text signals on team visual map artifacts. In two course sections, four-member teams were given one of two print-based text passage versions on the course-related topic “Social influence in groups” downloaded from Wikipedia; this text had two paragraphs, each with a prominent heading. Teams in one section (10 teams, 40 participants) were given the version that included the original hyperlinks (HTS) displayed as underlining, while teams in the other section (nine teams, 36 participants) were given an alternate version with the hyperlinks removed but with the same number of important text topics underlined (TTS). Participants worked during class time to create team visual maps of this passage using large sheets of newsprint. Both headings and text topic terms predominated in the TTS team maps, but only hyperlink terms and not headings predominated in the HTS team maps. The team visual map forms, as measured by vector pattern matching and by graph centrality, were also significantly different. Relative to the HTS team maps, on average the TTS team map forms were more complex and more like the expert’s map, while the HTS team map forms were more linear, showing a primacy effect. Further, the HTS team maps were substantially more alike. These results indicate that text signals in these print-based readings strongly influenced team collaboration artifacts.
What Teacher Candidates Learned about Diversity, Social Justice, and Themselves from Service-Learning Experiences.

This article examines how service-learning provides undergraduate teacher candidates opportunities to cultivate deeper understandings of diversity, social justice, and themselves. Participants were from a mid-Atlantic university and a rural southeastern university. Although from different regions, the teacher candidates shared predominantly White, middle-class backgrounds. Three themes framed the discussion—preconceived notions about teaching in diverse settings, how preconceived notions were overcome (or reinforced), and “learning about myself as a teacher.” Findings suggest that service-learning, emphasizing multiculturalism and social justice, has the potential for empowering prospective teachers to confront injustices and to begin deconstructing lifelong attitudes and constructing socially just practices.
Examining the Role of Auditory Sensitivity in the Developmental Weighting Shift

Studies comparing children’s and adults’ labeling of speech stimuli have repeatedly shown that children’s phonological decisions are more strongly related to portions of the signal that involve rapid spectral change (i.e., formant transitions) and less related to other signal components than are adults’ decisions. Such findings have led to a model termed the Developmental Weighting Shift, which suggests that children initially assign particularly strong weight to formant transitions to help delimit individual words in the continuous speech stream but gradually modify these strategies to be more like those of adults as they learn about word-internal structure. The goal of the current study was to test a reasonable alternative: that these apparent age-related differences in perceptual weighting strategies for speech are instead due to age-related differences in auditory sensitivity. To this end, difference limens (DLs) were obtained from children (ages 5 and 7 years) and adults for three types of acoustic p...
Microbiological changes in cottage cheese varieties during storage at +7°C

Abstract Studies have been made of microbiological changes in cottage cheese varieties during storage at 7°C. Commercially prepared products obtained directly from three manufacturers were at an initial pH in the range 4·6 to 5·1 and differed significantly in their content of sorbic acid/sorbate and of viable lactic streptococci. In many of the varieties that did not contain sorbic acid/sorbate multiplication occurred of Pseudomonas spp., Enterobacteriaceae and yeasts; spoilage occurred in some batches due to formation of a surface film of Pseudomonas fluorescens or of surface colonies of Sporobolomyces roseus and Trichosporon sp. at times equal to, or slightly greater than the recommended storage life. Where high numbers of viable lactic streptococci were present in varieties immediately after manufacture, no marked decrease in pH or increase in titratable acidity was observed during storage at 7°C. In varieties that contained sorbic acid at a concentration higher than approximately 500 mg kg−1 little increase in numbers of bacteria or yeasts was observed during storage at 7°C. Decrease in quality due to separation of whey occurred in some products from each manufacturer, but no clear correlation was observed between separation of whey and pH or the number of lactic streptococci present. Bacteria of public health significance, Escherichia coli type I, Staphylococcus aureus and Vibrio spp. were not detected in these products. Fifty-nine samples produced by six manufacturers, purchased from retail outlets, were examined on the sell-by date; the results confirmed the conclusions drawn from studies during storage.
Turf Wars in Radiology: Introduction

Abstract Turf wars over medical imaging have become ubiquitous. At many centers, radiologists already have lost access to important technologies and their applications. A combination of decreasing revenues in other specialties and a growing attachment to imaging further threatens radiologists' practices in the future. This is the first of an extended series of articles that will address the phenomenon of self-referral—its motivations, extent, and the threats it poses to radiologists. Each article will focus on a specific aspect and provide advice on how radiologists can deal with self-referral in their locales.
A Conceptual Design Methodology for Predicting the Aerodynamics of Upper Surface Blowing on Airfoils and Wings

An aerodynamic analysis methodology for Upper Surface Blowing aerodynamics is presented. This methodology is useful for aerodynamic estimation in the conceptual and preliminary design phases of USB or USB/Distributed Propulsion aircraft concepts. Analytical flow models together with an examination of some two-dimensional experimental data is used to establish the method. The method was then extended to treat fully 3-D wings. Comparisons of the method with experimental data from wind tunnel and flight-testing of USB designs demonstrates its usefulness. Finally, a brief comparison was done with an existing Vortex Lattice Method for USB wings, and the current method demonstrated good agreement.
Probabilistic topological analysis of predictability, sensitivity, and assimilability: Theory and simple illustrative examples

Abstract A probabilistic topological theory is developed to clarify some fundamental aspects of the predictability, sensitivity, and assimilability of initial value problems. In order to measure predictability, sensitivity, and as-similability quantitatively, three indices are introduced. The predictability index is defined in terms of discretized observational error statistics and mapping classifications of the models. Similarly, in addition to the predictability index, the sensitivity and assimilability indices are also defined. The prediction model is simplified to make it easier to handle the nonlinearity of their models. The simplification is a piecewise linear approximation. The nonlinearity condenses into a singularity, fixed point, stationary state, or equilibrium state. The significance and possible advantages of the probabilistic topological analysis are demonstrated by the simple illustrative examples, such as the evolution of globally averaged temperature of a hypothetical planet and homoclini...
Formal and de facto standards and guidelines for personal health records (PHRs)

The objective of this research is to canvas the landscape of existing standards and guidelines relating to electronic personal health records (PHRs). Here, we propose a consensus standard for PHRs consisting of 14 data components, 11 of which should be essential for all PHRs and 3 additional recommended data components, as well as 4 key features. Through a survey of existing commercially PHR vendors, we observe a low level of adoption of existing standards.
The effect of Wolbachia on the lifetime reproductive success of its insect host in the field

Wolbachia is a widespread endosymbiont that induces dramatic manipula- tions of its host's reproduction. Although there has been substantial progress in the developing theory for Wolbachia-host interactions and in measuring the effects of Wolbachia on host fitness in the laboratory, there is a widely recognized need to quantify the effects of Wolbachia on the host fitness in the field. The wasp Anagrus sophiae, an egg parasitoid of planthoppers, carries a Wolbachia strain that induces parthenogenesis, but its effects on the fitness of its Anagrus host are unknown. We developed a method to estimate the realized lifetime reproductive success of female wasps by collecting them soon after they die naturally in the field, counting the number of eggs remaining in their ovaries and quantifying Wolbachia density in their body. We sampled from a highly infected A. sophiae population and found no evidence for Wolbachia virulence and possible evidence for positive effects of Wolbachia on realized reproductive success.
AUTHIGENIC Ti-BEARING CRYSTALS IN A PRECAMBRIAN CLAY FROM BUENOS AIRES PROVINCE, ARGENTINA

The Precambrian Villa Monica Formation clay was analyzed using petrographic and scanning electron microscopy, X-ray diffraction and chemical analysis, with the aim of characterizing the Ti-bearing phases present and determining their possible origin and/or source. Two Ti-bearing minerals were found to be present, rutile and anatase. The crystals are needles between 5 and 15 µm in size, with no evidence of abrasion or corrosion. They are commonly found in association with the (001) faces of illite flakes or in the pores between the flakes. Their disposition is similar in the three quarries studied. No zonation or differential settling due to differences in specific gravity was observed. In addition, chemical analyses indicated a positive correlation between TiO2 and K2O suggesting that both oxides behave similarly after the deposition of the sediment. The TiO2 content in the bulk fraction ranges from 0.8 to 1.98 wt.%, values that are similar to those exhibited in other clay deposits from different ages and geneses. All observations are consistent with an in situ origin of these Ti-bearing phases during post-depositional processes that included recrystallization of existing minerals and crystallization of new phases. The original detrital minerals such as biotite, ilmenite as well as detrital illite, were the primary sources of the TiO2 and of the Fe oxides that coat the clay. Understanding the origin and the reaction mechanisms involved during the post-depositional alteration of the Villa Monica Formation suggests that the Ti-bearing phases in different sediment types were formed by similar mechanisms involving redox processes at low to medium temperatures, even in Precambrian sediments where the presence of rutile could lead to an incorrect assumption of high temperatures involved.
Quark models and polarized electroproduction of the Roper resonance

We calculate the recoil polarization observables for neutral pion electroproduction on the proton. In particular, for theN(938)→N*(1440) transition, we study these observables for several quark models of the resonant amplitudes. We find that the polarization response functions, unlike the unpolarized cross section, have encouragingly large sensitivity to the presence of the Roper. Furthermore, these observables can clearly reveal the presence of a longitudinal coupling.
CITATIONS AND INDIVIDUALS: FIRST AUTHORSHIP ACROSS THE ALPHABET

The presence of a bias in citation counts drawn from sources with first-author citations only are investigated. The study finds systematic bias against authors whose last names begin with letters that occur later in the alphabet, with authors receiving approximately one-half percent less first author citations of the total pieces per letter the later their names are in the alphabet. Given these biases, counts should certainly be used with care. Perhaps there are ways of improving them by either maintaining professionally-based citation counts or by lobbying sources, such as the Social Science Citation Index, to include all authors in their counts.
The clinical continuum of cryopyrinopathies: novel CIAS1 mutations in North American patients and a new cryopyrin model.

Objective The cryopyrinopathies are a group of rare autoinflammatory disorders that are caused by mutations in CIAS1, encoding the cryopyrin protein. However, cryopyrin mutations are found only in 50% of patients with clinically diagnosed cryopyrinopathies. This study was undertaken to investigate the structural effect of disease-causing mutations on cryopyrin, in order to gain better understanding of the impact of disease-associated mutations on protein function. Methods We tested for CIAS1 mutations in 22 patients with neonatal-onset multisystem inflammatory disease/chronic infantile neurologic, cutaneous, articular syndrome, 12 with Muckle-Wells syndrome (MWS), 18 with familial cold-induced autoinflammatory syndrome (FCAS), and 3 probands with MWS/FCAS. In a subset of mutation-negative patients, we screened for mutations in proteins that are either homologous to cryopyrin or involved in the caspase 1/interleukin-1β signaling pathway. CIAS1 and other candidate genes were sequenced, models of cryopyrin domains were constructed using structurally homologous proteins as templates, and disease-causing mutations were mapped. Results Forty patients were mutation positive, and 7 novel mutations, V262A, C259W, L264F, V351L, F443L, F523C, and Y563N, were found in 9 patients. No mutations in any candidate genes were identified. Most mutations mapped to an inner surface of the hexameric ring in the cryopyrin model, consistent with the hypothesis that the mutations disrupt a closed form of cryopyrin, thus potentiating inflammasome assembly. Disease-causing mutations correlated with disease severity only for a subset of known mutations. Conclusion Our modeling provides insight into potential molecular mechanisms by which cryopyrin mutations can inappropriately activate an inflammatory response. A significant number of patients who are clinically diagnosed as having cryopyrinopathies do not have identifiable disease-associated mutations.
Survival following the documentation of platinum and taxane resistance in ovarian cancer: a single institution experience involving multiple phase 2 clinical trials.

Abstract Objectives . There are very limited data in the oncology literature regarding the survival of women with both platinum and taxane-refractory ovarian cancer. Methods . To examine this issue, we retrospectively reviewed the survival of patients treated on one (or more) of four previously reported nonrandomized single-agent phase 2 trials (topotecan, liposomal doxorubicin, gemcitabine, docetaxel), involving women with well-characterized platinum/taxane-resistant ovarian, fallopian tube, and primary peritoneal cancers. Following their most recent treatment with both classes of agents, patients must have either not responded to therapy or experienced a treatment-free interval of Results . The median survival of the 111 patients (median age 61) included in this analysis was 6 months (range 1–37 months). Whereas 36 patients (32%) survived for Conclusion . With currently available antineoplastic drug therapy of platinum/taxane-resistant ovarian cancer, overall survival is relatively short, but a substantial minority of patients can be anticipated to live for periods in excess of 1 year. It remains uncertain whether such unexpectedly prolonged survival results from a biological response to chemotherapy or simply reflects the natural history of disease in a subset of patients with this malignancy.
A Short-Term Double-Blind Trial of Aerosol Triamcinolone Acetonide in Steroid-Dependent Patients with Severe Asthma

Twenty-five steroid-dependent severely asthmatic patients, ranging in age from 20 to 67 years, were hospitalized. Baseline laboratory and pulmonary function testing was followed by reduction of prednisone therapy to 5 mg daily and by entry into a randomized double-blind study of placebo vs active aerosol triamcinolone acetonide (300 µ g four times daily). In this four-week trial, aerosol triamcinolone acetonide further reversed airway obstruction and proved to be an effective substitute for large oral doses of steroids in steroid-dependent patients with severe asthma. No significant improvement occurred in the maximum midexpiratory flow or the maximum velocity of air flow after 50 percent or 75 percent of the vital capacity had been expelled. There was no significant difference in the frequency of untoward effects between the groups taking aerosol triamcinolone acetonide and its vehicle. No patient demonstrated any definite return of adrenal function.
Relation of coronary artery size to one-year clinical events after new device angioplasty of native coronary arteries (a New Approach to Coronary Intervention [NACI] Registry Report).

The influence of vessel size on clinical and angiographic outcomes after new device angioplasty has not been well documented. We reviewed clinical and angiographic outcomes of 2,044 patients undergoing new device angioplasty of native vessels enrolled in the New Approaches to Coronary Interventions (NACI) Registry. Quantitative angiography was performed using standard methods. Patients were divided into 3 groups according to reference vessel diameter (RVD) ( 3.25 mm). Patients with the smallest vessels had a higher incidence of diabetes (26% vs 16%, p 3.25 mm) vessels. Absolute baseline and final minimal lumen diameter (MLD) was also smaller in patients with RVD <2.75 mm despite similar final percent diameter stenosis. Although in-hospital events were similar, patients who underwent interventions in vessels <2.75 mm had an increased incidence of death (p <0.01), surgical revascularization (p <0.05), and target lesion revascularization (TLR) (p <0.01) at 1 year. Multivariate analysis by vessel size showed a stepwise increase in the risk of TLR by 1 year in patients with the smaller RVD (p = 0.0001) and the combined end point of 1 year death/Q wave-myocardial infarction/TLR (p = 0.02). Thus, despite similar early clinical events among patients undergoing new device angioplasty, patients who underwent treatment of smaller vessels had a significantly increased risk of major adverse clinical events and particularly TLR by 1 year after new device angioplasty of native coronary arteries.
Vascular organization of the catfish gill filament.

Light and scanning electron microscopic observations were made on methyl-methacrylate corrosion casts of the blood vessels in the gills of channel catfish (Ictalurus punctatus). The vasculature of the gill filament can be divided into three distinct pathways: 1. the well-known respiratory circulation which includes the afferent filamental artery (AF), afferent lamellar arteriole (AL), lamella (L), efferent lamellar arteriole (EL) and efferent filamental artery (EF), 2. a nutritive pathway from the EF through small nutritive capillaries (NC) and into one of several filamental veins (FV), and 3. an interlamellar circulation in which small prelamellar arterio-venous anastomoses (PAVA) connect the AL into a series of organized vascular spaces (interlamellar vessels, ILV's) that underlie the interlamellar filamental epithelium. Several sinuslike spaces associated with AF, EF and the filamental cartilagenous support were also observed. The physiological significance of these vascular pathways is discussed.
Absolute age of the base of the hominid-bearing beds in Eastern Java

THIS note presents preliminary data on the absolute age of the base of the hominid-bearing beds in Eastern Java. We approached the problem in two steps. First by comparing the stratigraphic sequence of Eastern Java with that of Olduvai Gorge using published data on radiometric dates, magnetic polarity stratigraphy, and the hominid fossil record (Fig. 1). And second, by analysing the planktonic diatom assemblages from the marine intercalations in the lowermost hominid-bearing beds and from the underlying marine sediments from Eastern Java (Fig. 2). The stratigraphy of Olduvai Gorge (Fig. 1) is compiled from various sources1–6. The base of the Gorge is represented by metamorphic rocks6, overlain by ignimbrites whose uppermost part has been K–Ar dated at 2 Myr (refs 5, 6). The sediment sequence from Bed I to the top of the Gorge is represented by volcanogenic, lacustrine and fluvial deposits. The earliest hominid fossils and stone tools occur in the upper part of Bed I, at about 1.8 Myr (refs 1, 4, 5).
Modeling X-ray proximity lithography

Advanced semiconductor circuits, such as DRAMs, are based on very complex fabrication processes. Because of the cost and complexity involved, it is rapidly becoming impossible to adopt a "trial-and-error" approach in the development stage of a new process. Fortunately, the advances in computer power spurred by the new semiconductor devices have made it possible to compute the response of complex systems in a reasonable time on workstations. Thus, the study of a virtual representation of the process (that is, a model) can represent a solution to the high cost of process development--of course, after verification of the model accuracy through controlled experiments. A correct physical interpretation of the process under study is necessary in order to implement a model that is both accurate and extendible. This is particularly true for new approaches, such as those involved in X-ray lithography. We have studied the process of image formation in X-ray lithography and have implemented several models to predict the intensity distribution at the wafer plane. The models can be applied to the definition of an optimal exposure system that will provide the maximum exposure latitude, and to the study of new types of X-ray masks.
The use of progenitor cell/biodegradable MMP2–PLGA polymer constructs to enhance cellular integration and retinal repopulation

The inability of the adult mammalian retina to regenerate can be partly attributed to the expression of injury-induced inhibitory extracellular matrix (ECM) and cell adhesion molecules. In particular, photoreceptor degeneration stimulates deposition of the inhibitory ECM proteins neurocan and CD44 at the outer limits of the dystrophic retina, where they act as a barrier against cellular migration and axonal extension. We have previously shown that degradation of these molecules, via induction of MMP2, promotes host-donor integration and retinal repopulation following transplantation. Here we present a biodegradable/biocompatible polymer scaffold that has the ability to deliver MMP2, in conjunction with retinal progenitor cells, directly to the site of retinal injury in an attempt to enhance cellular integration and promote retinal repopulation. Pre-activated MMP2, loaded into a PLGA polymer, maintained its activity throughout polymer fabrication and hydrolysis. Following delivery, significant degradation of CD44 and neurocan from the outer limits of the dystrophic retina, without further disruption of retinal architecture, was observed. As a result, the number of retinal progenitor cells that migrated beyond the glial barrier into the degenerating host increased significantly. These cells took up residence in the retinal outer nuclear layer, adopted appropriate photoreceptor morphology and expressed the mature photoreceptor markers recoverin and rhodopsin. Thus, we have created a cell delivery platform that upon transplantation provides controlled release of active-MMP2 directly to the site of retinal injury, stimulating inhibitory ECM barrier removal and enhancement of stem cell integration and retinal repopulation.
What can DNA tell us about biological invasions

It is often hoped that population genetics can answer questions about the demographic and geographic dynamics of recent biological invasions. Conversely, invasions with well-known histories are sometimes billed as opportunities to test methods of population genetic inference. In both cases, underappreciated limitations constrain the usefulness of genetic methods. The most significant is that human-caused invasions have occurred on historical timescales that are orders of magnitude smaller than the timescales of mutation and genetic drift for most multicellular organisms. Analyses based on the neutral theory of molecular evolution cannot resolve such rapid dynamics. Invasion histories cannot be reconstructed in the same way as biogeographic changes occurring over millenia. Analyses assuming equilibrium between mutation, drift, gene flow, and selection will rarely be applicable, and even methods designed for explicitly non-equilibrium questions often require longer timescales than the few generations of most invasions of current concern. We identified only a few population genetic questions that are tractable over such short timescales. These include comparison of alternative hypotheses for the geographic origin of an invasion, testing for bottlenecks, and hybridization between native and invasive species. When proposing population genetic analysis of a biological invasion, we recommend that biologists ask (i) whether the questions to be addressed will materially affect management practice or policy, and (ii) whether the proposed analyses can really be expected to address important population genetic questions. Despite our own enthusiasm for population genetic research, we conclude that genetic analysis of biological invasions is justified only under exceptional circumstances.
Identification and characterization of the murine ortholog (brms1) of breast-cancer metastasis suppressor 1 (BRMS1).

We have cloned a novel metastasis-suppressor gene (BRMS1) by differential display, comparing metastatic human breast carcinoma cell line MDA-MB-435 to its metastasis-suppressed human chromosome 11 microcell hybrid. Screening of a murine cDNA library led to the identification of a 1.4 kb cDNA with a sequence revealing 85% homology to human BRMS1 within the open reading frame. The predicted protein sequence for the murine ortholog is 95% identical, suggesting that it is strongly conserved across these 2 species. The cloned cDNA was used to screen a murine strain SV129 BAC library to obtain brms1 genomic DNA. Three BAC clones [226(I4), 226(H4) and 239(N7)] were confirmed to encode the entire brms1 gene. Detailed analysis of BAC clone 226(I4) shows that the gene spans 8.5 kb and, like the human gene, is organized into 10 exons and 9 introns. While the exons share a high degree of homology, there are greater differences when comparing intron structures between the human and murine genes. The 5′ upstream region shares about 64% homology with its human counterpart, retaining several of the many putative regulatory elements. Like the human genomic BRMS1, the murine ortholog of the iGnT gene is found upstream of brms1 and the murine ortholog of the RIN1 gene is found downstream of brms1.brms1 was then tested for suppression of metastasis of mouse mammary carcinoma cell line 66cl4 in syngeneic BALB/c mice. Transfection with brms1 did not inhibit 66cl4 primary tumor formation but significantly suppressed its metastatic capability. This suggests that the murine ortholog functions similarly to BRMS1. © 2002 Wiley-Liss, Inc.
Gas-phase 13C chemical shifts in the zero-pressure limit: refinements to the absolute shielding scale for 13C

Abstract 13 C chemical shifts have been measured relative to 13 CO in the zero-pressure limit for over twenty molecules for which theoretical calculations of 13 C nuclear shielding have recently been reported. Rovibrational averaging effects on the spin-rotation constant in 13 C 16 O have been used to find σ e ( 13 C in 13 C 16 O) = 3.0 ± 1.2 ppm and σ 0 ( 13 C in 13 C 16 O) = 1.0 ± 1.2 ppm. With the latter, the σ 0 values for the 13 C nuclei in this work have been determined absolutely and compared with calculated values. Agreement is generally good in most cases except where low-lying n → π ★ transitions contribute significantly to the paramagnetic shielding.
Daily scrums in a distributed environment

Agile product teams tend to be collocated in an effort to facilitate communication and collaboration between members, but today, remote workforces are a reality. Agilists that are looking to use Scrum typically find advice that is relevant to collocated teams, but don't find much that deals with issues of remote teams. As we move more and more toward distributed teams we need to identify best practices for working with remote (perhaps culturally different) teammates. We need to look at our methods and the possibility of modifying our practices to better fit with multiple time zones, cultural differences and tools that need to go beyond "stories on the wall".
A New Subgenus and Species of Murine Opossum (Genus Marmosa) from Peru

A new subgenus of Marmosa and its type species are described from Peru. Morphological characters separating the new subgenus from currently recognized subgenera of murine opossums are presented. Characters separating the new species from other species of Marmosa found to be sympatric with it are also discussed.
Interactive conversion of sequential to multitasking FORTRAN

Fully automated compilation of sequential Fortran to efficient multitasking code is impractical; tools need to be developed to aid users in interactively converting sequential to multitasking Fortran. This paper reports on experience using an interactive Parallelizing Assistant Tool (PAT) to convert sequential Fortran applications (ranging from short benchmarks to large application programs) to Cray microtasking Fortran, and discusses the advantages and limitations of interactive parallelization. We also introduce a taxonomy of task parallelization.
Centaurin-like protein Cnt5 contributes to arsenic and cadmium resistance in fission yeast.

Arsenic (As) and cadmium (Cd) are two of the most hazardous substances in the environment and have been implicated in a number of human diseases including cancer. Their mechanisms of toxicity and subsequent carcinogenesis are not understood. To identify the genes involved in As/Cd detoxification, we screened a random insertional mutagenesis library of Schizosaccharomyces pombe for mutants that are hypersensitive to As/Cd. Mutations were mapped to spc1 + ( sty1 +) and SPBC17G9.08c . Spc1 is a stress-activated protein kinase orthologous to human p38. A fragment of SPBC17G9.08c was previously identified as csx2 , a high-copy suppressor of cut6 that encodes an acetyl-CoA carboxylase involved in fatty acid biosynthesis. SPBC17G9.08c is a member of the centaurin ADP ribosylation factor GTPase activating protein family found in a variety of fungi, plants and metazoans, but not in Saccharomyces cerevisiae . Cnt5, so named because its closest human homolog is centaurin β-5, binds to phosphatidic acid and phosphatidyl serine in vitro . Microscopic localization of Cnt5-GFP indicates significant redistribution of Cnt5 from the cytoplasm to the cell membranes in response to As stress. These data suggest a model in which Cnt5 contributes to As/Cd resistance by maintaining membrane integrity or by modulating membrane trafficking.
Transactional Memory: The Hardware-Software Interface

As multicore chips become ubiquitous, the need to provide architectural support for practical parallel programming is reaching critical. Conventional lock-based concurrency control techniques are difficult to use, requiring the programmer to navigate through the minefield of coarse-versus fine-grained locks, deadlock, livelock, lock convoying, and priority inversion. This explicit management of concurrency is beyond the reach of the average programmer, threatening to waste the additional parallelism available with multicore architectures. This comprehensive architecture supports nested transactions, transactional handlers, and two-phase commit. The result is a seamless integration of transactional memory with modern programming languages and runtime environments
A New Model for Predicting Solubilities and Enthalpies of Solution for a Given Solute in a Series of Solvents

The unified solvation model Δχ = PS‘ + EA*EB + CA*CB + W, used to predict solvent dependence of dissolved solutes, is extended to enthalpies of solution and solubilities, by predicting the energetic component for forming a cavity in the solvent. The energy to create the cavity is given without adding a new solvent parameter using the term, QS‘2, where the S‘2 values are the square of the previously reported USM solvent polarity parameters, S‘. Q is the solute-dependent cavity formation term. The resultant unified solvation cavity model (USCM) is applied successfully to 350 enthalpies and free energies (solubilities) of solution in effect unifying the separate areas of solvation polarity probes and regular solution theory. The resulting empirical parameters for all 35 solutes studied are consistent with the intuitive concepts that cavity formation, QS‘2, and separation of solid or liquid solute molecules upon dissolution, W, are endothermic processes, while nonspecific solvation of the solute, PS‘, is exot...
1183 MICROBIOLOGIC AND CLINICAL CHARACTERIZATION OF COAGULASE-NBGATIVE STAPHYLOCOCCI FROM CEREBROSPINAL FLUID SHUNTS

1183 MICROBIOLOGIC AND CLINICAL CHARACTERIZATION OF COAGULASE-NBGATIVE STAPHYLOCOCCI FROM CEREBROSPINAL FLUID SHUNTS
An optimization neural network for smartphone data protection

Since the launch of iPhones in 2007, smartphones become very popular these days. Because of their small sizes and high mobility, smartphones are easily lost or stolen. When people lost their smartphones, they are worried the private data stored in the phones may be revealed to strangers. This research proposes a novel approach for mobile data protection. Mobile usage data is first collected and usage patterns are then discovered and saved. An optimization Hopfield neural network is proposed to match the usage data with the stored usage patterns. When an unusual usage pattern such as an unlawful user trying to access the mobile data is detected, the device will automatically lock itself down until a further action is taken. Experimental results show this method is effective and convenient for mobile data protection.
Electronic Kapitza conductance at a diamond-Pb interface.

In recent experiments it was found that the Kapitza conductance between diamond and Pb at room temperature is as much as 100 times larger than predicted by the acoustic mismatch model. Because the diamond and Pb are in intimate contact, the phonon modes near the interface are joint vibrational modes, extending a phonon mean free path on each side of the interface. Since the phonon mean-free path at room temperature is of the order of 4000 \AA{} in diamond but only of the order of 10 \AA{} in Pb, the energy of a joint mode resides primarily in the diamond. Consequently, the thermal population of a joint mode is determined by the temperature of the diamond. It is shown here that the direct energy transfer between metallic electrons at the Pb temperature and joint vibrational modes at the diamond temperature explains the observed heat conduction across the interface.
An art gallery theorem for line segments in the plane

Abstract Given a set L of n non-intersecting line segments in the plane, we show that it is possible to choose a set S of at most ⌞n/2⌟ segments such that for each segment l of L there exists a point pl on one of the segments in S which sees every point of l. That is, for any point p on segment l the segment p l p does not intersect the interior of any line segment other than those containing p and pl. This bound is also shown to be tight. Thus, by imagining that each segment of S contains an edge guard, we conclude that ⌞n/2⌟ edge guards are sometimes necessary and always sufficient to guard any set of n segments in the plane.
Targeting Astrocytomas and Invading Immune Cells with Cannabinoids: A Promising Therapeutic Avenue

The last quarter century has borne witness to great advances in both the detection and treatment of numerous cancers. Even so, malignancies of the central nervous system, especially high-grade astrocytomas, continue to thwart our best efforts toward effective chemotherapeutic strategies. With prognosis remaining bleak, the time for serious consideration of alternative therapies has arrived. Various preparations of the marijuana plant, Cannabis sativa, and related synthetic and endogenous compounds, may constitute just such an alternative. Cannabinoids, although much maligned historically for their psychotropic effects and clear abuse potential, have long been used medicinally and are now staging an impressive comeback, as recent studies have begun to explore their powerful anti-tumoral properties. In this study, we review in vitro and in vivo evidence supporting the use of cannabinoids for treatment of brain tumors. We further propose the continued intense investigation of cannabinoid efficacies as novel anti-cancer agents, especially in models recapitulating such properties within the unique environment of the brain.
GLOBAL OPTIMUM PROTEIN THREADING WITH GAPPED ALIGNMENT AND EMPIRICAL PAIR SCORE FUNCTIONS

We describe a branch-and-bound search algorithm for finding the exact global optimum gapped sequence-structure alignment ("threading") between a protein sequence and a protein core or structural model, using an arbitrary amino acid pair score function (e.g. contact potentials, knowledge-based potentials, potentials of mean force, etc.). The search method imposes minimal conditions on how structural environments are defined or the form of the score function, and allows arbitrary sequence-specific functions for scoring loops and active site residues. Consequently the search method can be used with many different score functions and threading methodologies; this paper illustrates five from the literature. On a desktop workstation running LISP, we have found the global optimum protein sequence-structure alignment in NP-hard search spaces as large as 9.6 x 10(31), at rates ranging as high as 6.8 x 10(28) equivalent threadings per second (most of which are pruned before they ever are examined explicitly). Continuing the procedure past the global optimum enumerates successive candidate threadings in monotonically increasing score order. We give efficient algorithms for search space size, uniform random sampling, segment placement probabilities, mean, standard deviation and partition function. The method should prove useful for structure prediction, as well as for critical evaluation of new pair score functions.
Who’s in control? Teachers from five countries share perspectives on power dynamics in the learning environment:

This article explores perspectives and strands of thought among teachers from five countries about power dynamics in learning environments, perspectives on power of dominant cultures and impacts of...