cssi/SciSciGPT-SciSciNet huggingface dataset:
Testing treatment effects in unconfounded studies under model misspecification: Logistic regression, discretization, and their combination

Logistic regression is commonly used to test for treatment effects in observational studies. If the distribution of a continuous covariate differs between treated and control populations, logistic regression yields an invalid hypothesis test even in an uncounfounded study if the link is not logistic. This flaw is not corrected by the commonly used technique of discretizing the covariate into intervals. A valid test can be obtained by discretization followed by regression adjustment within each interval.
A First Principles Examination of Phase Stability in Fcc-Based Ni-V Substitutional Alloys

The phase stability of fcc-based Ni-V substitutional alloys is investigated using linear muffin-tin orbitals total energy (LMTO) calculations. The method of Connolly and Williams (CWM) is used to extract many body interactions from the ground state energies of selected ordered configurations. These interactions are used in conjunction with the cluster variation method (CVM) to calculate the alloy phase diagram. The dependence of the interactions on the choice of configurations used to calculate them is examined.
Affective and Cognitive Effects of Option in an Educational Setting

AbstractOption, found to have enhanced academic performance and attitudes of high school Ss, was reexamined using 811 fifth and sixth graders. Choices of study booklets on a 2-week vocabulary unit resulted in lower learning and retention scores than those obtained in a control where booklets were assigned to students. The affective measures of liking and perceived learning were not significantly affected by option. A model accounting for both positive and negative effects of option is proposed and discussed. Assuming performance is generally a positive linear function of task importance, the model postulates that task-importance under option is a function of the substantialness and expectancy of the option.
A new method for controlling leaching through permeable channels

Abstract In the environment, natural cementation of geological formations occurs constantly over the geological time due to physical, chemical and biological reactions. Although much attention is devoted to these processes, awareness of microbial involvement in mineral consolidation is quite limited. Mineral precipitation is induced as a result of microbial metabolic activities and can persist as a part of the environment. Most deposits are identified as inorganic compounds such as CaC03, phosphorites, or sulfide, with a few organic compounds. These microbiologically induced substances are pollution-free, natural, and ubiquitous in all environments. The process of microbiologically induced mineral precipitation can be employed as a method of selective cementation of highly permeable structures in rock formations to reduce the porosity. The same process can also be used in containing contaminants. This option is studied in this paper. A series of experiments was conducted to investigate the possibility of using microbial plugging of highly permeable channels under various conditions. Results indicate that complete plugging (resulting in nil flow rate) can occur within days of nutrient injection in a sand packed column containing bacteria. The process is highly effective in the presence of fractures which appears to create new nucleation sites for capturing bacteria clusters, leading to improved selective plugging. Finally, a series of batch experiments was conducted to find an optimum pH for bacterial growth as well as mineral precipitation.
Activation of Caspase Pathways during Iron Chelator-mediated Apoptosis

Iron chelators have traditionally been used in the treatment of iron overload. Recently, chelators have also been explored for their ability to limit oxidant damage in cardiovascular, neurologic, and inflammatory disease as well as to serve as anti-cancer agents. To determine the mechanism of cell death induced by iron chelators, we assessed the time course and pathways of caspase activation during apoptosis induced by iron chelators. We report that the chelator tachpyridine sequentially activates caspases 9, 3, and 8. These caspases were also activated by the structurally unrelated chelators dipyridyl and desferrioxamine. The critical role of caspase activation in cell death was supported by microinjection experiments demonstrating that p35, a broad spectrum caspase inhibitor, protected HeLa cells from chelator-induced cell death. Apoptosis mediated by tachpyridine was not prevented by blocking the CD95 death receptor pathway with a Fas-associated death domain protein (FADD) dominant-negative mutant. In contrast, chelator-mediated cell death was blocked in cells microinjected with Bcl-XL and completely inhibited in cells microinjected with a dominant-negative caspase 9 expression vector. Caspase activation was not observed in cells treated with N-methyl tachpyridine, an N-alkylated derivative of tachpyridine which lacks an ability to react with iron. These results suggest that activation of a mitochondrial caspase pathway is an important mechanism by which iron chelators induce cell death.
Continental shelf landscapes of the southeastern United States since the last interglacial

Abstract The wide, sediment-starved continental shelf and modern coastal areas of the southeastern United States retain well-preserved but scattered remnants of a submerged paleolandscape. This paper presents a conceptual model of stratigraphic deposition and landscape formation since the last interglacial on the continental shelf of South Carolina, with portions of North Carolina, Georgia, and Florida (USA). Data for this study include multibeam bathymetry surveys, sidescan sonar mosaics, high-resolution subbottom profiles, and ground-truth surveys from − 250 m to the modern tidewater region. Four bathymetric zones are recognized with eleven landforms and landform indicators. The described zones range in depths from the modern shoreline, across the shelf, and over the shelf edge to − 250 m MSL. Relative sea level curves are presented for the area and discussed in conjunction with cultural and climatic events. The potential for preservation of Paleoamerican sites is high at the shelf edge between − 130 m and − 45 m, with Archaic and later occupations likely in depths of less than − 25 m. Prominent vantage points for Paleoamericans (> 11 kya) would have existed at the shelf edge, and tidewater resources would have been available nearby for a period of almost 6 ka. Rapid transgression rates (> 60 km/ka) after the sea level rose over the shelf edge make preservation of tidewater sites less likely on the outer and middle shelf. Searches for the earliest Paleoamericans should focus on promontories at the edge of the shelf and along future discoveries of paleoincisions on the shelf. Mapping and delineating this paleolandscape and associated unconsolidated sedimentary deposits interspersed with rocky plains and ledges will continue to be a priority to marine archeologists, coastal managers, fishery scientists, and marine spatial planners over the next several decades.
Maternal behavior of wild and domestic stocks of Norway rats

The maternal behaviors (nursing, pup-retrieval, and nest-building) of lactating female wild and domestic Norway rats were compared on Days 1, 5, 9, and 13 following parturition. In addition, postpartum aggression was investigated by exposing mothers to strange female intruders on Days 6, 7, and 8. The maternal behaviors of wild and domestic mothers were very similar. However, wild mothers tended to be more efficient in pup-retrieval, whereas domestic females showed shorter latencies for nest construction. Both domestic and field-trapped wild mothers displayed relatively high levels of aggression toward intruders. These results support the hypothesis that domestication has had relatively little impact on maternal behaviors in this species.
On the uniform strong consistency of an estimator of the offspring mean in a branching process with immigration

Abstract For the critical and sub-critical branching process with immigration, the natural estimator of the offspring mean ‘m’ is shown to be strongly consistent uniformly over a whole class of offspring distributions with m ϵ (0, 1] and bounded variance.
Photoinduced addition of nucleophiles to bicyclo[2.2.1]hepta-2,5-diene

Abstract The 1-cyanonaphthalene photosensitized addition of water and methanol to the cation-radical of bicyclo[2.2.1]hepta-2,5-diene is described.
Hole Nucleation and Growth in Free-Standing Polystyrene Ultrathin Films

Nucleation and growth of holes in free-standing ultrathin (<100 nm) polymer films are examinedviaopticalmicroscopyinordertogainabetterunderstandingofthesephenomena.Holenucleation is quantified with a free energy barrier based on a simple capillary model. Additionally, holes are found to grow exponentially in accordance with previous studies in the literature. Ultrathin films of polystyrene (between50and100nm)castviaflowcoatingaresuspendedatoplithographicallypatternedarraysofpillars. The films are then annealed above the glass transition temperature to study the nucleation and growth of holes via optical microscopy. Image analysis is performed tomeasure the density ofnucleated holes as well as hole radius as a function of time. Holes are found to grow exponentially with time in a nonlinear viscoelastic, shearthinningregimeunderhighshearstrain.Theenergybarriermodelisappliedtothenucleationofholesin free-standing thin films and is found to describe the phenomenon well. This analysis of hole nucleation and growth extends the understanding of ongoing research into suspended fiber formation from the melting of free-standing polymer thin films.
Association of Clostridium difficile infection with outcomes of hospitalized solid organ transplant recipients: results from the 2009 Nationwide Inpatient Sample database

Background Diarrhea is a frequent and potentially severe complication in solid organ transplant (SOT) recipients. One of the most common infectious etiologies of diarrhea in these patients is Clostridium difficile. Our objective was to investigate the association of C. difficile infection (CDI) with the outcomes of hospitalized SOT patients. Methods We extracted all adult cases with discharge diagnoses of SOT or CDI from the United States Nationwide Inpatient Sample, Healthcare Cost and Utilization Project, Agency for Healthcare Research and Quality 2009 database. We collected outcome variables (mortality, length of hospital stay [LOS], hospitalization charges, complications of the transplanted organ, and colectomy), demographic information, and comorbidity data for each of the cases. The data were evaluated using univariate and multiple variable regression analyses. Results We identified 49,198 cases with SOT of which 2.7% had CDI. Univariate comparisons of cases with SOT + CDI to those with SOT-only revealed significant differences in the evaluated outcomes including in-hospital mortality (7.4% vs. 2.4%, P < 0.001), LOS (median 9 days vs. 4 days, P < 0.001), charges (median $53,808 vs. $31,488, P < 0.001), organ complications (38.1% vs. 33.9%, P < 0.001), and colectomy (1.1% vs. 0.3%, P < 0.001). Using multiple variable regression analyses, in the SOT cohort (SOT-only and SOT + CDI), CDI was independently associated with greater mortality (adjusted odds ratio [aOR] 2.48, 95% confidence interval [CI] = 2.22, 2.76, P < 0.001), longer LOS (difference 9.6 days, 95% CI = 9.3, 9.9, P < 0.001), higher charges (difference $69,647, 95% CI = $66,190, $73,104, P < 0.001), more complications of the transplanted organ (aOR 1.36, 95% CI = 1.28, 1.44, P < 0.001), and increased need for colectomy (aOR 3.10, 95% CI = 2.35, 4.08, P < 0.001). Conclusions Our results demonstrate that CDI is associated with overall significantly worse outcomes in hospitalized patients with SOT.
Dietary fat and obesity: lack of an important role

The percentage of dietary energy from fat has been suggested to be an important determinant of body fat, and this presumed effect has been used to promote low-fat diets. In short-term randomized trials, a small reduction in body weight is typically seen in individuals randomized to diets with a lower percentage of calories from fat. However, in trials lasting for 1 year or longer, fat consumption within the range of 18-40% of energy had consistently had little if any effect on body fatness. The weighted mean difference was -0.25 kg overall and +1.8 kg for trials with a control group that received a comparable intensity intervention (i.e. less weight loss on the low-fat diets). Moreover, in the USA and other affluent countries, a substantial decline in the percentage of energy from fat during the past two decades has corresponded with a massive increase in obesity. Diets high in fat do not account for the high prevalence of excess body fat in Western countries; red uctions in the percentage of energy from fat will have no important benefits and could further exacerbate this problem. Keywords: adiposity; diet; fat; obesity; overweight
Massively parallel high-energy time-dependent wave-packet calculations

The exact solution of the time-dependent Schrodinger equation is obtained using a parallel implementation of the standard grid techniques. Most of the operations involved in this calculation may be executed concurrently for each of the grid points. For the few operations which may not be executed concurrently, we have implemented parallel algorithms. In our two-dimensional implementation on the Connection Machine, we have obtained optimal speed-up — that is, by usingN processors we achieve a speed-up which is proportional toN. In addition to the discussion of our 2-dimensional implementation, we shall discuss our proposed 3-dimensional implementation of these grid techniques.
Parallel discrete event simulation of Transaction Level Models

Describing Multi-Processor Systems-on-Chip (MPSoC) at the abstract Electronic System Level (ESL) is one task, validating them efficiently is another. Here, fast and accurate system-level simulation is critical. Recently, Parallel Discrete Event Simulation (PDES) has gained significant attraction again as it promises to utilize the existing parallelism in today's multicore CPU hosts. This paper discusses the parallel simulation of Transaction-Level Models (TLMs) described in System-Level Description Languages (SLDLs), such as SystemC and SpecC.We review how PDES exploits the explicit parallelism in the ESL design models and uses the parallel processing units available on multicore host PCs to significantly reduce the simulation time. We show experimental results for two highly parallel benchmarks as well as for two actual embedded applications.
Complete high temperature expansions for one-loop finite temperature effects

We develop exact, simple closed form expressions for partition functions associated with relativistic bosons and fermions in odd spatial dimensions. These expressions, valid at high temperature, include the effects of a nontrivial Polyakov loop and generalize well-known high temperature expansions. The key technical point is the proof of a set of Bessel function identities which resum low temperature expansions into high temperature expansions. The complete expressions for these partition functions can be used to obtain one-loop finite temperature contributions to effective potentials, and thus free energies and pressures.
Effect of hydrogen peroxide administration on life span, superoxide dismutase, catalase, and glutathione in the adult housefly, Musca domestica

The general objective of this study was to further elucidate the relationship between oxidative stress and the aging process. H2O2 is known to be a progenator of reactive oxygen species, such as hydroxyl free radical, by various mechanisms involving, among others, a superoxide anion radical-driven Fenton cycle, or splitting of the 0−0 bond by hemoproteins. Effects of H2O2 administration on life span, activities of superoxide dismutase, catalase, concentrations of endogenous H2O2, and glutathione in the housefly are described. Adult male flies were given various concentrations of H2O2, ranging from 0 to 100 mM H2O2, in their drinking water. Life span was shortened by H2O2 intake except in 10 mM H2O2 administrated flies, which exhibited the longest life span. Flies administered mM H2O2 also contained the highest concentration of reduced glutathione (GSH). Superoxide dismutase and catalase activities were not affected by H2O2 intake. Compensatory elevation in GSH may be responsible for the increase in life span observed in 10 mM H2O2 administered flies.
Identification of spherical virus particles in digitized images of entire electron micrographs.

Abstract New methods are described that should facilitate high-resolution (5–10 A) image reconstructions from low-dose, low-contrast electron micrographs of frozen-hydrated specimens and processing of large, digital images produced by new imaging devices and modern electron microscopes. Existing techniques for automatic selection of images of individual biological macromolecules from electron micrographs are inefficient or unreliable. We describe the Crosspoint method (CP), which produces good quality solutions with relatively small miss rates and few false hits, and an extension of this method along with a procedure for refining its solution. Two algorithms for processing large images, one based on image subsampling, the other on image decomposition, are described. A large image is first compressed (e.g., by subsampling) and the CP method is applied to the compressed image to produce an initial solution. The information gathered at this stage is used to cut the original image into subimages and then to refine the particle coordinates in each subimage. An interactive environment for experimenting with particle identification methods is described.
A macroscopic derivation of Onsager's relations

Abstract It was proposed by Tribus in 1961 that the familiar coupling of diffusive flows might be a direct result of certain thermostatic analogs. It is shown herein that the Tribus proposal leads to a macroscopic theorem for non-oscillatory processes. The Onsager relations for such processes in isotropic media result as a corollary.
Thermogenic and hemodynamic effects of ingesting a pre-workout supplement with and without synephrine

Background A number of nutritional strategies have been developed to optimize nutrient delivery prior to exercise. As a result, a number of pre-workout supplements have been developed to increase energy availability, promote vasodilation, and/ or positively affect exercise capacity. The purpose of this study was to examine the acute effects of ingesting a preworkout dietary supplement with and without synephrine on energy metabolism and cardiovascular hemodynamics. Methods
Mass spectral analysis and fragment ion structure of fusarochromanone.

Fusarochromanone is a mycotoxin produced by Fusarium equiseti that is implicated in the poultry disease tibial dyschrondroplasia. Electron impact ionization tandem mass spectrometry was used to elucidate probable structures of fragment ions found at m/z 274, 275, 261, 233, 218 and 191 and for devising an analytical rationale for the metabolites of the parent compound. In addition, a sensitive, qualitative liquid chromatographic technique using direct injection continuous-flow fast atom bombardment for the detection of fusarochromanone in corn was devised. Analysis was carried out on a hybrid tandem instrument (VG-7070EQ) using open tubular columns (75 microns i.d.) with direct-flow open-loop injection. The limit of detection of the pure compound was 500 pg in the selected ion monitoring mode. A 50 p.p.b. (500 pg injected) of the pure compound added to ground corn samples was the lowest detectable amount in a biological matrix.
Community partnered projects: a case study of a collaborative effort to improve sanitation in a marginalized community in northwest Mexico

There is a growing recognition in developing countries that community participation in water and sanitation projects is a necessary strategy in sustainable development. The main advantage of following such an approach is that, if participation can encourage a sense of ownership of the projects, the benefits of the project are more likely to extend over the long term. The case study at hand focuses on the challenges faced in implementing a wastewater treatment system to solve an environmental and public health problem in a rural community, Rosario de Tesopaco, in northwest Mexico. Until recently, the community has been unable to implement an effective plan to treat the wastewater generated in the community. The problems faced by the community can be attributed to the political arrangement of water and sanitation decentralization in Mexico that occurred in the mid 1980’s, whereby communities were required to meet wastewater treatment standards, but were not given the technical and political guidance needed to achieve this goal. However, in this instance, cooperation between the authorities in Rosario de Tesopaco, the federal agency for social development, and an academic institution has led to the successful design and approval of a wastewater treatment project. This achievement can be attributed to the use of an effective collaborative strategy, tailoring the project to the needs and capacity of the local community, positioning the community as the leaders and owners of the project. A model for following this strategy for developing rural sanitation projects in Mexico is proposed.
Smart and designer structural material systems

An efficient civil infrastructure system is essential to every country's productivity, security, and quality of life. Basic research and development in smart structures and designer materials have shown great potential for enhancing the functionality, serviceability, and increased lifespan of civil infrastructure systems. New construction and the intelligent renewal of ageing and deteriorating civil infrastructure systems include efficient and innovative use of high-performance designer materials, sensors, actuators, and mechanical and structural systems. High-performance designer materials, in particular, require new methods of computational materials science, some of which are described herein. In this paper, some examples of National Science Foundation (NSF) funded awards, some examples of National Institute of Standards and Technology (NIST) ‘designer material’ projects, and future research needs, as well as new research initiatives on nanotechnology, are presented.
PERSONAL NOSTALGIA, WORLD VIEW, MEMORY, AND EMOTIONALITY

Batcho's 1995 Nostalgia Inventory was completed by 210 respondents, 88 males and 122 females, ranging in age from 5 to 79 years old. Subjects scoring high on the Nostalgia Inventory rated the past more favorably than did subjects scoring low on the inventory but did not differ in ratings of the present or future. High-scoring individuals rated themselves more emotional, with stronger memories, need for achievement, and preference for activities with other people, but not as less happy, risk or thrill seeking, religious, logical, easily bored, or expecting to succeed. In a second study, 113 undergraduates, 32 men and 81 women, completed measures of nostalgia, memory, and personality. High-scoring subjects showed no advantage in free recall over low-scoring subjects but recalled more people-oriented autobiographical memories. Individuals scoring high on nostalgia were no more optimistic, pessimistic, or negatively emotional but scored higher on a measure of emotional intensity. Personal nostalgia was distinguished from social-historical nostalgia and world view. Results were discussed with respect to major theoretical approaches.
N-(4-hydroxyphenyl)retinamide: a synthetic analog of vitamin A that is a potent inhibitor of prostaglandin biosynthesis

Abstract In Madin-Darby canine kidney (MDCK) cells, 4-hydroxyphenyl retinamide, at levels ranging from 0.025 to 3.1 μM, inhibited serum- and TPA-stimulated biosynthesis of prostaglandin F 2α , prostaglandin I 2 (measured as 6-keto-prostaglandin Fl.) and prostaglandin E2 but did not inhibit serum- or TPA-stimulated deacylation of cellular phospholipids. 4-Hydroxyphenyl retinamide was also a potent inhibitor of prostaglandin E 2 and prostaglandin F 2α production by serum-stimulated methylcholanthrene-transformed mouse fibroblasts (MC5-5), normal human fibroblasts (D-550), “spindle-shaped” smooth muscle cells present in the intima layer of rabbit aorta (R-1), and thromboxane production by melittin-stimulated mouse lymphoma cells (WEHI-5). In the presence of 10% fetal bovine serum, 4-hydroxyphenyl retinamide inhibited prostaglandin production by MDCK cells 4 times less effectively than indomethacin and about 50 times more effectively than aspirin; while in the absence of serum, the inhibiting effectiveness of 4-hydroxyphenyl retinamide was equal to that of indomethacin.
Performance evaluation of hybrid spread spectrum based wireless smart meter sensor network with multi-user detection techniques

Smart grid is the process of revitalizing the 20th century aging power grid by leveraging the communication, networking and information technological advancements of the 21st century. In the communication and networking industry, the buzz word “smart grid” initiated a discussion on the selection of the appropriate communication and networking technologies for different smart grid applications. In a recent study, a trustworthy source compared different technologies like GPRS, RF mesh, PLC and 3G cellular technologies and concluded that the 3G cellular technologies meet the requirements of distribution side smart grid applications [1]. Even though 3G cellular technologies meet the requirements of smart grid applications, based on the data size specifications of smart grid applications given in [2], an analysis on the use of the current state of the art 3G cellular technologies for smart grid applications gives an indication that their usage results in high data overhead, high latency and high power consumption (during power outage) for data transfer [3]. Therefore, in our prior work we have proposed a Hybrid Spread Spectrum (HSS) based smart meter network design that can reduce the overhead, latency and power consumption in data transfer when compared to the 3G cellular technologies [3].
A Triad Interaction in the Fingers Subdomain of DNA Polymerase Beta Controls Polymerase Activity

DNA polymerase beta (pol beta) is the main polymerase involved in the base excision repair pathway responsible for repairing damaged bases in the DNA. Previous studies on the H285D mutant of pol beta suggested that the C-terminal region of the polymerase is important for polymerase function. In this study, the C-terminal region of pol beta was mutated to assess its role in polymerization. Kinetic experiments showed that the C-terminal region is required for wild-type polymerase activity. Additionally, an interaction between the fingers and palm subdomain revealed itself to be required for polymerase activity. The E316R mutant of pol beta was shown to have a 29 000-fold reduction in polymerization rate with no reduction in nucleotide binding, suggesting that there exists a noncovalent mechanistic step between nucleotide binding and nucleophilic attack of the primer 3′-hydroxyl group on the α-PO4 of the nucleotide. Molecular modeling studies of the E316R mutant demonstrate that disrupting the interaction be...
Lys583 in the Third Extracellular Loop of the Lutropin/Choriogonadotropin Receptor Is Critical for Signaling

The lutropin/choriogonadotropin receptor (LH/CG-R) contains a relatively large extracellular domain, in addition to the seven transmembrane helices (TMH), three extracellular loops (ECL), and three intracellular loops typical of G protein-coupled receptors. While high affinity ligand binding has been attributed to the N-terminal extracellular domain, there is evidence that portions of the three ECLs may function in ligand binding and transmembrane signaling. We have investigated the role of several ionizable amino acid residues of rat LH/CG-R in human choriogonadotropin (hCG) binding and hCG-mediated cAMP production. COS-7 cells were transfected with the pSVL expression vector containing cDNAs of either wild-type or mutant rat LH/CG-R. Several point mutants of Lys583, located at the interface of ECL III and TMH VII, bound hCG like wild-type receptor but exhibited greatly diminished ligand-mediated signaling. Neither the point mutant, Lys401-->Asp (ECL I), nor the double mutant, Asp397-->Lys/Lys583-->Asp (ECLs I and III, respectively, showed significant hCG binding to intact cells; in detergent-solubilized cells, only the double mutant bound hCG. The mutants Arg341-->Glu (interface of the extracellular domain and TMH I) and Lys488-->Glu (ECL II) proved to be similar to wild-type receptor in binding and signaling. Our results establish that Lys583 is important in signaling but not ligand binding. Its location on the opposite side of the membrane from GS precludes a direct interaction, thus emphasizing the importance of a conformational change in the receptor and suggesting that ligand binding to receptor and ligand-mediated receptor activation are dissociable phenomena.
What a Tangled Web We Weave: Emerging Resistance Mechanisms to Inhibition of the Phosphoinositide 3-Kinase Pathway

The phosphoinositide 3-kinase (PI3K) pathway is one of the most frequently mutated pathways in cancer, and is actively being pursued as a therapeutic target. Despite the importance of the PI3K pathway in cancer, durable responses to PI3K pathway-targeted therapies are uncommon with monotherapy. Several in vitro and xenograft models have elucidated compensatory signaling and genomic changes which may limit the therapeutic effectiveness of PI3K inhibitors in the clinic. Future clinical trials with prospective evaluation of tumor signaling and genomic changes are likely to identify novel resistance mechanisms as well as subsets of patients who may derive maximal benefit from PI3K pathway inhibitors. Significance: There are multiple ongoing clinical trials targeting the PI3K pathway members in several malignancies. This review summarizes the known mechanisms of resistance to targeting the PI3K pathway. Understanding of resistance mechanisms will help to inform more rational clinical trial design to optimize the clinical impact of targeting the PI3K pathway in cancer. Cancer Discov; 3(12); 1345–54. ©2013 AACR .
Prosodic effects on word reduction.

It is widely known that English-speaking children reduce words by omitting syllables in certain predictable patterns (e.g., banana --> nana). One way to better understand the nature of phonological reductions in children is to examine adults' word reduction behavior. This study explored whether adults produce predictable output patterns when reducing words. Undergraduate participants heard a list of polysyllabic words varying systematically across syllable number and primary stress location and were asked to generate a "reduced" form, similar to common English reductions (e.g., rhinoceros --> rhino). Regardless of stress and syllable number, participants reduced the stimulus words significantly more often to left-headed disyllabic or monosyllabic feet, retaining stressed syllables and omitting unstressed syllables. The general bias found was similar to that which children exhibit in natural speech, namely, to maintain well-formed prosodic patterns and preserve salient syllables. On the other hand, a tendency to preserve word-initial instead of word-final syllables was also found, suggesting subtle differences in language processing between children and adults. The current study contributes to the psycholinguistic literature on adults' syllable omissions in abbreviations and fast-speech registers by examining the processing strategies that adults may use when reducing words.
An interlaboratory comparison of 16S rRNA gene‐based terminal restriction fragment length polymorphism and sequencing methods for assessing microbial diversity of seafloor basalts

We present an interlaboratory comparison between full-length 16S rRNA gene sequence analysis and terminal restriction fragment length polymorphism (TRFLP) for microbial communities hosted on seafloor basaltic lavas, with the goal of evaluating how similarly these two different DNA-based methods used in two independent labs would estimate the microbial diversity of the same basalt samples. Two samples were selected for these analyses based on differences detected in the overall levels of microbial diversity between them. Richness estimators indicate that TRFLP analysis significantly underestimates the richness of the relatively high-diversity seafloor basalt microbial community: at least 50% of species from the high-diversity site are missed by TRFLP. However, both methods reveal similar dominant species from the samples, and they predict similar levels of relative diversity between the two samples. Importantly, these results suggest that DNA-extraction or PCR-related bias between the two laboratories is minimal. We conclude that TRFLP may be useful for relative comparisons of diversity between basalt samples, for identifying dominant species, and for estimating the richness and evenness of low-diversity, skewed populations of seafloor basalt microbial communities, but that TRFLP may miss a majority of species in relatively highly diverse samples.
Broadband circular polarizers using plasmonic metasurfaces

In nature, circular polarization detection is unique to bio-systems, since human eyes cannot detect polarization information. Various animal species successfully use it for defense, signaling and orientation. It may be of great interest to reproduce these functionalities in artificial photonic devices, being able to distinguish different handedness of circular polarization, and to possibly integrate this operation with other photonic systems. However, currently available artificial circular polarizers are inherently narrow bandwidth, bulky and with poor efficiency. Here, we put forward some exciting ideas to employ individual and stacked plasmonic metasurfaces to generate or to filter circular polarizations. We model a single ultrathin metasurface as a shunt circuit element in terms of its admittance tensor and show that under certain conditions one can exploit the exotic features of plasmonic materials to realize ultrathin circular polarization filters with broad bandwidth of operation.
Interacting effects of soil fertility and atmospheric CO2 on leaf area growth and carbon gain physiology in Populus × euramericana (Dode) Guinier

SUMMARY Two important processes which may limit productivity gains in forest ecosystems with rising atmospheric CO2are reduction in photosynthetic capacity following prolonged exposure to high CO2 and diminution of positive growth responses when soil nutrients, particularly N, are limiting. To examine the interacting effects of soil fertility and CO2 enrichment on photosynthesis and growth in trees we grew hybrid poplar (Populus × euramericana) for 158 d in the field at ambient and twice ambient CO2 and in soil with low or high N availability. We measured the timing and rate of canopy development, the seasonal dynamics of leaf level photosynthetic capacity, respiration, and N and carbohydrate concentration, and final above- and belowground dry weight. Single leaf net CO2 assimilation (A) increased at elevated CO2 over the majority of the growing season in both fertility treatments. At high fertility, the maximum size of individual leaves, total leaf number, and seasonal leaf area duration (LAD) also increased at elevated CO2, leading to a 49% increase in total dry weight. In contrast, at low fertility leaf area growth was unaffected by CO2 treatment. Total dry weight nonetheless increased 25% due to CO2 effects on A. Photosynthetic capacity (A at constant internal p(CO2), ((C1)) was reduced in high CO2 plants after 100 d growth at low fertility and 135 d growth at high fertility. Analysis of A responses to changing C1 indicated that this negative adjustment of photosynthesis was due to a reduction in the maximum rate of CO2 fixation by Rubisco. Maximum rate of electron transport and phosphate regeneration capacity were either unaffected or declined at elevated CO2. Carbon dioxide effects on leaf respiration were most pronounced at high fertility, with increased respiration mid-season and no change (area basis) or reduced (mass basis) respiration late-season in elevated compared to ambient CO2 plants. This temporal variation correlated with changes in leaf N concentration and leaf mass per area. Our results demonstrate the importance of considering both structural and physiological pathways of net C gain in predicting tree responses to rising CO2 under conditions of suboptimal soil fertility.
Saliva Collection and Quantification from Adult Butterflies (Lepidoptera)

The coilable proboscis is possessed by over 99% of lepidopteran species and is a key innovation contributing to the success of Lepidoptera as the second larg est insect order (Krenn, 2010; Kristensen, 1984; Pogue, 2009). Study of the struc ture and function of the proboscis is applicable to lepidopteran systematics, natural history (Krenn, 2010), and to the design of microfluidic devices (Tsai et al., 2011; Monaenkova, 2012). Saliva plays an important role in proboscis function (Krenn, 2010). Saliva is exuded from the food canal of the proboscis through the tip and through slits between the plate-like dorsal legulae and hook-like ventral legulae. The cuticular surface of the proboscis varies along its length, and has microchannels and grooves which could direct saliva between dorsal and ventral sides (Lehnert et al., 2013). Saliva appears as droplets on the surface of the proboscis during as sem bly (Krenn, 1997), repair (Lehnert et al., 2014), and feeding (Lehnert et al., 2014). Methods used for collection of butterfly saliva have included rinsing the proboscis with water or buffer (Eberhard et al., 2007), or prompting saliva deposition onto glass (Tokarev et al., 2013). In this paper I describe a new procedure for collecting the saliva of adult butterflies directly from the proboscis into capil lary tubes, and I report the volumes of saliva collected from different species. I also report the appearance of a yellow liquid exuded from the proboscis by some lepidopteran adults.
Selective overexpression of inflammatory molecules in hearts from brain-dead rats.

Abstract Background: Inflammatory processes that occur before, during, and after surgery may contribute to damage of transplanted hearts and their ability to withstand acute and chronic rejection. Methods: We determined the expression of mRNA for 10 inflammatory indicator molecules in hearts from brain-dead animals in which stable circulation was maintained. To produce brain death in male rats ( n = 11), we inflated an intracranial balloon with saline (245 μl ± 27 μl) to produce apnea and areflexia. Mean arterial pressure was maintained at 80 ± 2 mm Hg for 6 hours. Controls ( n = 11) received a burr hole but no balloon (mean arterial pressure, 94 ± 1 mm Hg). We measured expression of each indicator molecule mRNA relative to expression of glyceraldehyde-3-phosphate dehydrogenase mRNA using reverse-transcriptase polymerase chain reaction. Results: Relative expression of intercellular adhesion molecule-1, vascular adhesion molecule-1, interleukin-1β, and interleukin-6 mRNAs differed significantly (2.4 –4.6 times higher) between brain-dead and control hearts ( p t -test). Conclusion: Increases in the inflammatory cytokine, interleukin-1β, whose mRNA also increased, may mediate the overexpression of the adhesion molecule and interleukin-6 mRNAs. The data suggest that endothelial cells become inflamed during brain death, even when the circulation is stable, which may lead to leukocyte–endothelial interactions during brain death or after graft transplantation.
Reduction of Soybean Yield Components by Megacopta cribraria (Hemiptera: Plataspidae)

ABSTRACT Since its discovery in the United States, the invasive plataspid Megacopta cribraria (F.) (Hemiptera: Plataspidae) has infested soybean [Glycine max (L.) Merrill] fields in often alarming numbers in parts of the southeastern United States. Although a known feeder on soybean, reports of its pest status in its native Asian range are conflicting, and little information exists documenting its impact on soybean yields. Our objective was to examine the relationship between M. cribraria density and soybean yield loss. M. cribraria adults and nymphs were confined to small soybean plots by using walk-in field cages from late vegetative stage to harvest in 2011 and 2012. Adults (0, 5, or 25 per plant) were added at late vegetative stages, and their progeny were allowed to complete a full generation within the caged plots. Densities reached as high as 182.5 +/- 23.1 (SEM) nymphs and adults per plant, and soybean yield was reduced by as much as 59.6% at the highest density treatment. The yield components seeds per pod and individual seed weight were reduced as M. cribraria densities increased, but pods per plant and protein and oil content were not affected. Preliminary economic injury level curves for a range of grain prices and management costs were calculated based on 2012 yield loss data combined with population monitoring. M. cribraria is capable of causing severe reductions in soybean yields at densities that are relevant within its invasive U.S. range.
Myosin light chain kinase functions downstream of Ras/ERK to promote migration of urokinase-type plasminogen activator-stimulated cells in an integrin-selective manner.

Urokinase-type plasminogen activator (uPA) activates the mitogen activated protein (MAP) kinases, extracellular signal-regulated kinase (ERK) 1 and 2, in diverse cell types. In this study, we demonstrate that uPA stimulates migration of MCF-7 breast cancer cells, HT 1080 fibrosarcoma cells, and uPAR-overexpressing MCF-7 cells by a mechanism that depends on uPA receptor (uPAR)-ligation and ERK activation. Ras and MAP kinase kinase (MEK) were necessary and sufficient for uPA-induced ERK activation and stimulation of cellular migration, as demonstrated in experiments with dominant-negative and constitutively active mutants of these signaling proteins. Myosin light chain kinase (MLCK) was also required for uPA-stimulated cellular migration, as determined in experiments with three separate MLCK inhibitors. When MCF-7 cells were treated with uPA, MLCK was phosphorylated by a MEK-dependent pathway and apparently activated, since serine-phosphorylation of myosin II regulatory light chain (RLC) was also increased. Despite the transient nature of ERK phosphorylation, MLCK remained phosphorylated for at least 6 h. The uPA-induced increase in MCF-7 cell migration was observed selectively on vitronectin-coated surfaces and was mediated by a β1-integrin (probably αVβ1) and αVβ5. When MCF-7 cells were transfected to express αVβ3 and treated with uPA, ERK was still phosphorylated; however, the cells did not demonstrate increased migration. Neutralizing the function of αVβ3, with blocking antibody, restored the ability of uPA to promote cellular migration. Thus, we have demonstrated that uPA promotes cellular migration, in an integrin-selective manner, by initiating a uPAR-dependent signaling cascade in which Ras, MEK, ERK, and MLCK serve as essential downstream effectors.
Sharing Stories of the 9/11 Experience: An Exploratory Study of the Tribute Walking Tour Program

The objective of this study is to explore the perceived benefits of sharing one's personal story of trauma and loss with a public audience. A group of 103 volunteer docents who were directly affected by the September 11 terrorist attacks were surveyed about their experiences conducting walking tours around the World Trade Center site. Analysis of quantitative and qualitative data revealed four primary benefits of the program: ability to interact with visitors, ability to educate, ability to make sense of events, and ability to find something positive in the experience. Results are discussed in terms of healing and meaning reconstruction.
Scattering suppression and wideband tunability of a flexible mantle cloak for finite-length conducting rods

A simple, thin, flexible mantle cloak for conducting rods based on scattering cancellation is analyzed, designed and experimentally realized. We show strong scattering suppression at all angles of incidence, for both far-field plane-wave and near-field Gaussian excitations. The required effective shunt surface impedance is realized by a subwavelength patch array, targeting the suppression of the dominant omnidirectional scattering contribution of a conductive rod. Full-wave simulations predict a total radar cross-section reduction better than 14 dB in the lossless case and nearly 8 dB when considering a lossy substrate in the cover. Measurements of the realized cloak are consistent and validate these numerical predictions. The proposed geometry is also shown to be an ideal platform for monolithic integration of varactor diodes, allowing real-time tuning of the effective surface capacitance of the cloak. We show with numerical simulations the possibility of tunable scattering suppression over 1 GHz of bandwidth by seamlessly integrating varactor diodes in our mantle cloak design.
A learning based algorithm for automatic extraction of the cortical sulci

This paper presents a learning based method for automatic extraction of the major cortical sulci from MRI volumes or extracted surfaces. Instead of using a few pre-defined rules such as the mean curvature properties, to detect the major sulci, the algorithm learns a discriminative model by selecting and combining features from a large pool of candidates. We used the Probabilistic Boosting Tree algorithm [16] to learn the model, which implicitly discovers and combines rules based on manually annotated sulci traced by neuroanatomists. The algorithm almost has no parameters to tune and is fast because of the adoption of integral volume and 3D Haar filters. For a given approximately registered MRI volume, the algorithm computes the probability of how likely it is that each voxel lies on a major sulcus curve. Dynamic programming is then applied to extract the curve based on the probability map and a shape prior. Because the algorithm can be applied to MRI volumes directly, there is no need to perform preprocessing such as tissue segmentation or mapping to a canonical space. The learning aspect makes the approach flexible and it also works on extracted cortical surfaces.