cssi/SciSciGPT-SciSciNet huggingface dataset:
The Fission Yeast RNA Binding Protein Mmi1 Regulates Meiotic Genes by Controlling Intron Specific Splicing and Polyadenylation Coupled RNA Turnover

The polyA tails of mRNAs are monitored by the exosome as a quality control mechanism. We find that fission yeast, Schizosaccharomyces pombe, adopts this RNA quality control mechanism to regulate a group of 30 or more meiotic genes at the level of both splicing and RNA turnover. In vegetative cells the RNA binding protein Mmi1 binds to the primary transcripts of these genes. We find the novel motif U(U/C/G)AAAC highly over-represented in targets of Mmi1. Mmi1 can specifically regulate the splicing of particular introns in a transcript: it inhibits the splicing of introns that are in the vicinity of putative Mmi1 binding sites, while allowing the splicing of other introns that are far from such sites. In addition, binding of Mmi1, particularly near the 3' end, alters 3' processing to promote extremely long polyA tails of up to a kilobase. The hyperadenylated transcripts are then targeted for degradation by the nuclear exonuclease Rrp6. The nuclear polyA binding protein Pab2 assists this hyperadenylation-mediated RNA decay. Rrp6 also targets other hyperadenylated transcripts, which become hyperadenylated in an unknown, but Mmi1-independent way. Thus, hyperadenylation may be a general signal for RNA degradation. In addition, binding of Mmi1 can affect the efficiency of 3' cleavage. Inactivation of Mmi1 in meiosis allows meiotic expression, through splicing and RNA stabilization, of at least 29 target genes, which are apparently constitutively transcribed.
A New Method to Reduce Cure-Induced Stresses in Thermoset Polymer Composites, Part II: Closed Loop Feedback Control System

A closed loop feedback control system has been developed to obtain cure cycles which reduce the cure-induced stresses in single fiber/matrix model composites. In this feedback system, thermal expansion and stress relaxation are used to counteract the stresses resulting from the chemical shrinkage. The feedback system is applied to two different fibers (carbon and glass) in four different resins [3501-6, 934, and 977-3 epoxies and 5250-4 bismaleimide (BMI)]. The completeness of the cure is verified by comparing glass transition temperature (Tg) for polymers cured using the standard cure cycles (cycles recommended by the prepreg manufactures) and the feedback cure cycles. The durations of the feedback cure cycles are within that of the standard cycles. Test results indicate that feedback cure cycles reduce the curvature of unsymmetrical laminates as a measure of residual stresses.
THERMAL DECAY OF AN INFRARED-LASER-HEATED ARC PLASMA.

A small region of a magnetically confined, fully ionized arc plasma of density 2 \ifmmode\times\else\texttimes\fi{} ${10}^{16}$ ${\mathrm{cm}}^{\ensuremath{-}3}$ and electron temperature of 1.3 to 1.7 eV is heated by 0.7 eV with pulsed C${\mathrm{O}}_{2}$-laser energy. The measured thermal decay is accounted for by classical collisional diffusion along the magnetic field.
Outflow versus Infall in Spiral Galaxies: Metal Absorption in the Halo of NGC 891

United States. National Aeronautics and Space Administration (Hubble Space Telescope Grant)
Clinical implementation of a commercial multileaf collimator: dosimetry, networking, simulation, and quality assurance.

Purpose : Clinical implementation of multileaf collimation (MLC) includes commissioning (including leaf calibration), dosimetric measurements (penumbra, transmission, calculation parameters), shaping methods, networking for file transfer, verification simulation, and development of a quality assurance (QA) program. Differences of MLC and alloy shaping in terms of penumbra and stair-step effects must be analyzed. Methods and Materials : Leaf positions are calibrated to light field. The resultant decrement line, penumbras, leaf transmission data, and isodoses in various planes were measured with film. Penumbra was measured for straight edges and corners, in various media. Ion chambers were used to measure effects of MLC on output, scatter, and depth dose. We maintain midleaf intersection criteria. MLC fields are set 7 mm beyond planning target volumes. After shaping by vendor software or by our three-dimensional planning system, files are transferred to the MLC workstation by means of sharing software, interface cards, and cabling. A MLC emulator was constructed for simulation. Our QA program includes file checks, monthly checks (leaf position accuracy and interlock tests), and annual review. Results : We found the MLC leaf position (light field) corresponds to decrement lines ranging from 50 to 59%. Transmission through MLC (1.5-2.5%) is less than alloy (3.5%). Multileaf penumbra is slightly wider than for alloy. Relative penumbra did not increase in the lung, and composite field dosimetry exhibited negligible differences compared with alloy. Verification simulations provide diagnostic image quality hard copies of the MLC fields. Monitor unit parameters used for alloy held for MLC. Discussion : Clinical implementation for MLC as a block replacement was conducted on a site-by-site basis. Time studies indicate significant (25%) in-room time reductions. Through imaging and dosimetric analysis, the accuracy of field delivery has increased with MLC. The most significant impact of MLC is the ability to increase the number of daily treatment fields, thereby reducing normal tissue dosing, which is vital for dose escalation.
The genetic structure of the incompatibility factors ofSchizophyllum commune: Comparative studies of primary mutations in theB factor

Primary mutations in the three classes of theB factor were detected. The mutations map in the α and β loci of theB factor. The characteristic mating behavior of the mutant strains suggests functional differentiation of the α and β loci. Alternative interpretations are discussed.
Gas-liquid flow patterns in microgravity: Effects of tube diameter, liquid viscosity and surface tension

Abstract Two-phase gas-liquid flow experiments have been developed for use on NASA microgravity aircraft to allow for high speed measurement of void fraction, liquid film thickness and pressure drop as well as high-speed photography of the flow features. Numerous experiments were conducted in order to determine the effect of liquid and gas superficial velocities, tube diameter, liquid viscosity and surface tension on the occurrence of flow patterns in microgravity. The transition from bubble to slug flow was found to be affected by tube diameter for air-water and by changes in liquid viscosity and surface tension. The transition from slug to annular flow was not significantly affected by changes in tube diameter, liquid viscosity or surface tension. Void fraction based transition models were developed to predict microgravity flow patterns. Weber number based transition models were also evaluated
A comparison of three fingerstick, whole blood antibody tests for Helicobacter pylori infection: a United States, multicenter trial

RESULTS: A total of 131 patients participated; 50 (38%) patients had histological evidence of H. pylori infection. Using histology as a gold standard, the sensitivities of FlexPack HP, QuikVue, and Accumeter were 76%, 78%, and 84%, respectively. Specificity was 79% with FlexPack HP and 90% with QuikVue and Accumeter. There were no significant differences in the performance of the three antibody tests though there was a trend toward superior performance for AccuMeter compared to FlexPack HP (p 5 0.019). However, RUT proved superior to FlexPack HP using histology as a gold standard (p 5 0.008). Using either concordant histology and RUT results or a positive histology or RUT to define activeH. pylori infection, there was no statistically significant difference between the antibody tests. CONCLUSIONS: There were no statistically significant differences in the performance of the three antibody tests. These tests proved only marginally sensitive in detecting patients infected with H. pylori. Clinicians should be aware of the limitations of these tests, particularly when using them as a sole means of testing for H. pylori. (Am J Gastroenterol 1999;94:1512‐1516. © 1999 by Am. Coll. of Gastroenterology)
Scaling of spatial correlations in cooperative sequential adsorption with clustering

We examine solvable cooperative sequential adsorption models on a linear lattice where adsorption rates produce strong clustering or island formation. We show that the spatial pair correlations in this regime assume a scaled form for separations comparable to a characteristic length (which diverges in the strong clustering limit). This scaled form is also determined directly from consideration of appropriate solvable continuum grain growth models.
To ITV or Not to ITV: A Comparison of Hybrid and Web-enhanced Approaches to Teaching a Macro-course in Human Behavior in the Social Environment

Hybrid education includes an online component and interaction between students and teacher by televised sound and image. This approach contrasts dramatically with traditional face-to-face teaching and classroom teaching modalities enhanced by Web-based tools. Should educators in “human behavior and the social environment” (HBSE) use hybrid technologies? This study explores the differences and similarities in student satisfaction and learning outcomes between a hybrid and a face-to-face Web-enhanced macro-course in HBSE. Results suggest that hybrid and Web-enhanced course delivery methods do not differently impact student learning. Students did report greater satisfaction with some but not all aspects of the hybrid sections.
A crosstalk aware interconnect with variable cycle transmission

Crosstalk between wires, caused by increased capacitive coupling, is considered one of the major factors that affect the performance of interconnects such as buses. The data-dependent nature of crosstalk-induced delays necessitates bus cycle time to be designed for the worst case crosstalk. However, this pessimism incurs a significant performance penalty. Consequently, we propose a crosstalk aware interconnect that uses a faster clock and dynamically controls the number of cycles required for transmission based on the estimated delay of the data pattern to be transmitted. In order to accomplish this, we designed a crosstalk analyzer circuit that is incorporated into the sender side of the bus and support a variable cycle transmission mechanism. We evaluate the effectiveness of the proposed scheme focusing on the on-chip buses of a microprocessor and by using the SPEC2000 benchmarks. The experimental results show that the proposed approach improves performance by 31.5% as compared to the original pessimistic approach. Furthermore, we employ a coding optimization to enhance the effectiveness of the proposed approach. We also show that the proposed scheme is an area-efficient approach to improving performance as compared to other crosstalk reduction schemes.
Quantification and reduction of bias from sampling larvae to infer population and landscape genetic structure.

A well-designed sampling scheme is critical for obtaining accurate results from population genetic studies. Larval samples contain only the genetic material of successful breeders, often of a single year, and may be biased towards particular families. To quantify the bias of using larval samples to infer population and landscape genetic structure and explore how this bias may be reduced using sibship analysis, we analysed eight microsatellite loci from 484 tissue samples of larvae and adults of Columbia spotted frogs (Rana luteiventris) and long-toed salamanders (Ambystoma macrodactylum) at nine breeding sites in north Idaho. Differences in allele frequencies between adult and larval samples were not detected after full-siblings were removed from the larval data set for Columbia spotted frogs; for long-toed salamanders, these differences remained at two out of four ponds. Data from Columbia spotted frog larvae indicated higher levels of differentiation among populations (median difference in F(ST) = 0.020, P < 0.01), as predicted by population genetic theory, whereas data from larval samples of long-toed salamanders showed some evidence of lower levels of differentiation among populations (median difference in F(ST) = 0.012, P = 0.06). For both species, removing all but one individual from each full-sibling family led to parameter estimates that were closer to those calculated from adult samples for both population and landscape genetic measures. Removal of full-siblings is likely to improve estimates of population genetic parameters; however, knowledge of the species' breeding system is essential for understanding additional sources of bias when inferring population genetic structure from larval samples.
Potential of Müller glia to become neurogenic retinal progenitor cells.

The possibility of neural regeneration has gained credence with the identification of neural stem cells seeded within different regions of the adult central nervous system (CNS). Recently, this possibility has received an additional boost from reports that glia, the support cells of the CNS, might provide a source of neural regeneration. We review some of our findings that Muller glia in the chicken retina are a source of proliferating progenitors that can generate neurons. These Muller cells are fully differentiated glial cells that serve functions ascribed to this cell type. In response to damage or exogenous growth factors, Muller glia dedifferentiate, proliferate, express combinations of transcription factors normally expressed by embryonic retinal progenitors, and produce new neurons and glia. In light of these data, the potential of Muller glia as a source of neural regeneration in the retina of nonavian species, namely humans, seems an avenue of investigation that warrants serious consideration.
Lost in the Sauce The Effects of Alcohol on Mind Wandering

Alcohol consumption alters consciousness in ways that make drinking both alluring and hazardous. Recent advances in the study of consciousness using a mind-wandering paradigm permit a rigorous examination of the effects of alcohol on experiential consciousness and metaconsciousness. Fifty-four male social drinkers consumed alcohol (0.82 g/kg) or a placebo beverage and then performed a mind-wandering reading task. This task indexed both self-caught and probe-caught zone-outs to distinguish between mind wandering inside and outside of awareness. Compared with participants who drank the placebo, those who drank alcohol were significantly more likely to report that they were zoning out when probed. After this increase in mind wandering was accounted for, alcohol also lowered the probability of catching oneself zoning out. The results suggest that alcohol increases mind wandering while simultaneously reducing the likelihood of noticing one's mind wandering. Findings are discussed with regard to theories of alcohol and theories of consciousness.
Bayesian Testing and Estimation of Association in a Two-Way Contingency Table

Abstract In a two-way contingency table, one is interested in checking the goodness of fit of simple models such as independence, quasi-independence, symmetry, and constant association, and estimating parameters that describe the association structure of the table. In a large table, one may be interested in detecting a few outlying cells that deviate from the main association pattern in the table. Bayesian tests of these hypotheses are described using a prior defined on the set of interaction terms of the log-linear model. These tests and associated estimation procedures have several advantages over classical fitting/estimation procedures. First, the tests can give measures of evidence in support of simple hypotheses. Second, the Bayes factors can be used to give estimates of association parameters of the table that allow for uncertainty that the hypothesized model is true. These methods are illustrated for a number of tables.
Breastfeeding Supportive Hospital Practices in the US Differ by County Urbanization Level

Background:Breastfeeding rates are lower among infants living in rural areas of the United States, yet there are limited data on whether hospital breastfeeding support differs between rural and urban areas.Objective:This study aimed to describe whether maternity care practices supportive of breastfeeding vary by level of urbanization.Methods:We linked data from the 2007, 2009, and 2011 Maternity Practices in Infant Nutrition and Care (mPINC) surveys with Rural-Urban Continuum Codes to categorize hospital counties as metropolitan urbanized, nonmetropolitan urbanized, less urbanized, and thinly populated.Results:From 2007 to 2011, the average hospital mPINC score, a composite quality score ranging from 0 to 100, increased from 64 to 71 in metropolitan urbanized counties and from 54 to 65 in thinly populated areas. Scores were lowest in thinly populated counties in 2007 and 2009 and in less urbanized counties in 2011. Examination of 2011 mPINC scores by 7 domains of care revealed that hospitals in less urban...
Drosophila and human RecQ5 exist in different isoforms generated by alternative splicing

Members of the RecQ helicase superfamily have been implicated in DNA repair, recombination and replication. Although the genome of the budding yeast Saccharomyces cerevisiae encodes only a single member of this family, there are at least five human RecQ-related genes: RecQL, BLM, WRN, RecQ4 and RecQ5. Mutations in at least three of these are associated with diseases involving a predisposition to malignancies and a cellular phenotype that includes increased chromosome instability. Metazoan RecQ helicases are defined by a core region with characteristic helicase motifs and sequence similarity to Escherichia coli RecQ protein. This core region is typically flanked by extensive, highly charged regions, of largely unknown function. The recently reported human RecQ5, however, has only the core RecQ-homologous region. We describe here the identification of the Drosophila RecQ5 gene. We recovered cDNAs corresponding to three alternative splice forms of the RecQ5 transcript. Two of these generate nearly identical 54 kDa proteins that, like human RecQ5, consist of the helicase core only. The third splice variant encodes a 121 kDa isoform that, like other family members, has a C-terminal extension rich in charged residues. A combination of RACE and cDNA analysis of human RECQ5 demonstrates extensive alternative splicing for this gene also, including some forms lacking helicase motifs and other conserved regions.
Inhibition of the human neutrophil NADPH oxidase by Coxiella burnetii.

Coxiella burnetii is an obligate intracellular Gram-negative pathogen. A notable feature of C. burnetii is its ability to replicate within acidic phagolysosomes; however, the mechanisms utilized in evading host defenses are not well defined. Here, we investigated human neutrophil phagocytosis of C. burnetii (Nine Mile, phase II; NMII) and the effect of phagocytosed organisms on neutrophil reactive oxygen species (ROS) production. We found that opsonization with immune serum substantially enhanced phagocytosis of NMII. Human neutrophils phagocytosing opsonized NMII generated very little ROS compared to cells phagocytosing opsonized Staphylococcus aureus, Escherichia coli, or zymosan. However, phagocytosis of NMII did not affect the subsequent ROS response to a soluble agonist, indicating inhibition was localized to the phagolysosome and was not a global effect. Indeed, analysis of NADPH oxidase assembly in neutrophils after phagocytosis showed that translocation of cytosolic NADPH oxidase proteins, p47phox and p67phox, to the membrane was absent in cells phagocytosing NMII, as compared to cells phagocytosing S. aureus or activated by phorbol myristate acetate. Thus, phagocytosed NMII is able to disrupt assembly of the human neutrophil NADPH oxidase, which represents a novel virulence mechanism for this organism and appears to be a common mechanism of virulence for many intracellular pathogens.
WELT: Using Graphics Generation in Linguistic Fieldwork

We describe the WordsEye Linguistics tool (WELT), a novel tool for the documentation and preservation of endangered languages. WELT is based on WordsEye (Coyne and Sproat, 2001), a text-toscene tool that automatically generates 3D scenes from written input. WELT has two modes of operation. In the first mode, English input automatically generates a picture which can be used to elicit a description in the target language. In the second mode, the linguist formally documents the grammar of an endangered language, thereby creating a system that takes input in the endangered language and generates a picture according to the grammar; the picture can then be used to verify the grammar with native speakers. We will demonstrate WELT’s use on scenarios involving Arrernte and Nahuatl.
Factors Influencing Algal Biomass in Intermittently Connected, Subtropical Coastal Ponds

Microalgae may contribute more to salt marsh productivity than realized, underscoring the importance of understanding algal dynamics in such systems. Benthic and planktonic chlorophyll-a (surrogate for total algal biomass), sediment ash-free dry weight, total suspended solids, salinity, and nutrients were examined in intermittently connected marsh ponds in the subtropical Guadalupe Estuary, Texas, USA to determine the effects of hydrologic connections on algal biomass in this system. From May 2005 to May 2006, several high water events resulting in surface water connections between ponds and nearby tidal creeks occurred, followed by disconnection and, at times, pond desiccation. During periods of disconnection, algal biomass was higher in both the benthos and the water column than during connection events when flushing occurred. Since connection events did not increase NOx, the primary source of dissolved inorganic nitrogen seemed to be nutrient cycling within the ponds. Data at the aggregated level, i.e., chlorophyll-a, indicated this system followed the flood pulse concept. During high water events, algal biomass may be exported to supplement the tidal creek food web (aquatic), whereas during low water events accumulated biomass within the ponds feed the marsh food web (terrestrial), which includes blue crabs (Callinectes sapidus) and the whooping crane (Grus americana).
Trajectory of the main sensory and motor branches of the lumbar plexus outside the psoas muscle related to the lateral retroperitoneal transpsoas approach.

Object. The minimally invasive lateral retroperitoneal transpsoas approach is increasingly used to treat various spinal disorders. Accessing the retroperitoneal space and traversing the abdominal wall poses a risk of injury to the major nervous structures and adds significant morbidity to the procedure. Most of the current literature focuses on the anatomy of the lumbar plexus within the substance of the psoas muscle. However, there is sparse knowledge regarding the trajectory of the lumbar plexus nerves that travel along the retroperitoneum and abdominal wall muscles in relation to the lateral approach to the spine. The objective of this study is to define the anatomical trajectories of the major motor and sensory branches of the lumbar plexus that are located outside the psoas muscle. Methods. Six adult fresh frozen cadaveric specimens were dissected and studied (12 sides). The relationship between the retroperitoneum, abdominal wall muscles, and the lumbar plexus nerves was analyzed in reference to the minimally invasive lateral retroperitoneal approach. Special attention was given to the lumbar plexus nerves that run outside of psoas muscle in the retroperitoneal cavity and within the abdominal muscle wall. Results. The skin and muscles of the abdominal wall and the retroperitoneal cavity were dissected and analyzed with respect to the major motor and sensory branches of the lumbar plexus. The authors identified 4 nerves at risk during the lateral approach to the spine: subcostal, iliohypogastric, ilioinguinal, and lateral femoral cutaneous nerves. The anatomical trajectory of each of these nerves is described starting from the spinal column until their termination or exit from the pelvic cavity. Conclusions. There is risk of direct injury to the main motor/sensory nerves that supply the anterior abdominal muscles during the early stages of the lateral retroperitoneal transpsoas approach while obtaining access to the retroperitoneum. There is also a risk of injury to the ilioinguinal, iliohypogastric, and lateral femoral cutaneous nerves in the retroperitoneal space where they travel obliquely during the blunt retroperitoneal dissection. Moreover, there is a latent possibility of lesioning these nerves with the retractor blades against the anterior iliac crest. (DOI: 10.3171/2010.10.SPINE10395)
Ethanol enhances GABAA receptor function in short sleep and long sleep mouse brain membranes.

Background: SS and LS mice have been used to explore the genetic and neurochemical bases for differences in sensitivity to ethanol. The present study investigated the effects of ethanol on GABAA receptor function in microsacs from these genotypes. The purpose was to test a key element of the hypothesis that differences between these lines in sensitivity to ethanol-induced enhancement of GABAA receptor function underlie their selected differences in sensitivity to ethanol-induced loss of righting reflex (LORR). Methods: The effects of ethanol on GABA-activated 36Cl− uptake in brain membranes (microsacs) isolated from male SS and LS mice were tested using a chloride flux filtration assay. Results: Ethanol significantly enhanced GABA-activated 36Cl− uptake in SS microsacs at concentrations of 100–300 mM. Ethanol did not significantly affect GABA-activated chloride uptake in this preparation at concentrations of 25 and 50 mM. Ethanol significantly enhanced GABA-activated 36Cl− uptake in LS microsacs at concentrations of 25–100 mM, but not at 200 mM. Conclusion: The present studies are the first to show a statistically significant effect of ethanol on GABA-activated chloride uptake in both SS and LS mice with a clear difference between the genotypes in threshold. The relative threshold differences between SS and LS microsacs in sensitivity to ethanol indicate that selection for resistance to ethanol-induced LORR in SS mice has shifted the ethanol-GABAA receptor concentration-response curve to the right. The findings add key evidence that supports a cause-effect relationship between sensitivity to ethanol-induced potentiation of GABAA receptor function and genetically determined sensitivity to ethanol's behavioral effects.
Sulfur Dioxide Treatment Alters Wine Microbial Diversity and Fermentation Progression in a Dose-Dependent Fashion

The use of sulfur dioxide (SO2) as an antimicrobial in winemaking is a well-established, common practice. Although much is known about the antimicrobial effects of SO2 at single concentrations, little is known about its effects on microbial growth dynamics across a range of concentrations or when used in conjunction with yeast inoculation. Using high-throughput marker-gene sequencing, we investigated the cumulative impacts of yeast inoculation and SO2 treatments across a broad concentration range (0 to 150 mg/L SO2) on the bacterial and fungal communities in wine fermentations. Our results indicated a dose-dependent effect of SO2, with lactic acid bacteria and Gluconobacter proliferating in fermentations with
Maximizing efficiency of solar-powered systems by load matching

Solar power is an important source of renewable energy for many low-power systems. Matching the power consumption level with the supply level can make a great difference in the efficiency of power utilization. This paper proposes a source-tracking power management strategy that maximizes the panel's total energy output under a given solar profile by load matching. The power efficiency was validated by extensive measurement. Compared to a conventional solar powered system, our load matching strategy improves the power utilization by 132% for a portable system performing image processing and wireless communication tasks.
Late 20th Century benthic foraminiferal distribution in Central San Francisco Bay, California: Influence of the Trochammina hadai invasion

The distribution of foraminifera in most of San Francisco Bay is well documented, but this is not the case for the subembayment known as Central Bay. To resolve this, 55 grab samples obtained in 1998 were analyzed to characterize the foraminiferal fauna in the surface sediments of the area. Thirty-five species were identified, including the invasive Japanese species Trochammina hadai that was introduced into the bay in the early 1980s. A cluster analysis of the samples from Central Bay produced three groups (biofacies) and one outlier. The Shallow Subtidal Biofacies is characterized by a marsh to shallow-subtidal agglutinated fauna, domi- nated by T. hadai but also including T. inflata, T. macrescens, Haplophragmoides subinvolutum, and Miliammina fusca. The Intermedi- ate Subtidal Biofacies, the Intermediate Subtidal Outlier, and the Deep Subtidal Biofacies are dominated by calcareous taxa, most notably Ammonia tepida, Elphidium excavatum, and Elphidiella hannai. Ammonia tepida is most abundant in the warmer, intermediate depths of eastern Central Bay, abundances of E. excavatum peak in the cooler estuarine water near Alcatraz Island, and E. hannai thrives in the cold water west of Angel Island in a transitional setting between the deep subtidal estuarine and the nearshore marine envi- ronments. The recovery of oceanic species as far east as Angel Island indicate that western Central Bay is the most marine-influenced region of San Francisco Bay. Samples collected from 1965 onward were also compared with those from 1998 to investigate how the distribution of benthic foraminifera in Central Bay has changed over the latter half of the 20th Century, particularly in response to the invasion by Trochammina hadai. In 1998, T. hadai was recovered at 46 of 55 sites in Central Bay, comprising from 0.3 to 97% (mean = 23%) of the foraminiferal fauna. With the species' affiliation for shallow environments, it is not unexpected that it dominated the fauna of the Shal- low Subtidal Biofacies (68-97%, mean = 77%) and was also a significant component of the Intermediate Subtidal Biofacies (7-51%, av- eraging 28%). In the deeper waters west of Alcatraz Island, the abundance of T. hadai was significantly less (mean = 8%), most likely reflecting allochthonous specimens that were the result of post-mortem transport. A cluster analysis clearly distinguishes pre- and post-invasion biofacies, illustrating how dominant T. hadai has become in Central Bay.
Consumer Demand for Food and Food Safety: Models and Applications

Invisible hazards and imperfect knowledge and information about foodborne risks make food safety an explosive issue that can disrupt markets and cause substantial economic losses for everyone from farm input suppliers to consumers. The Alar scare in red apples is one recent example. But the range of commodities under scrutiny by consumers includes almost all commodities: fish (federal inspection), poultry (salmonella), fresh eggs (salmonella), red meat (subtherapeutic feeding of antibiotics), pesticide residues (fresh fruits and vegetables and animal feed), and bio-engineered growth promotants (BST in milk). One can also include more general diet and health concerns under the guise of food safety, such as cholesterol, fat, sugar, alcohol, and cigarette smoking.
Mitochondrial Reactive Oxygen Species Mediate Cardiac Structural, Functional, and Mitochondrial Consequences of Diet-Induced Metabolic Heart Disease.

Background Mitochondrial reactive oxygen species (ROS) are associated with metabolic heart disease (MHD). However, the mechanism by which ROS cause MHD is unknown. We tested the hypothesis that mitochondrial ROS are a key mediator of MHD. Methods and Results Mice fed a high‐fat high‐sucrose (HFHS) diet develop MHD with cardiac diastolic and mitochondrial dysfunction that is associated with oxidative posttranslational modifications of cardiac mitochondrial proteins. Transgenic mice that express catalase in mitochondria and wild‐type mice were fed an HFHS or control diet for 4 months. Cardiac mitochondria from HFHS‐fed wild‐type mice had a 3‐fold greater rate of H 2 O 2 production ( P =0.001 versus control diet fed), a 30% decrease in complex II substrate–driven oxygen consumption ( P =0.006), 21% to 23% decreases in complex I and II substrate–driven ATP synthesis ( P =0.01), and a 62% decrease in complex II activity ( P =0.002). In transgenic mice that express catalase in mitochondria, all HFHS diet–induced mitochondrial abnormalities were ameliorated, as were left ventricular hypertrophy and diastolic dysfunction. In HFHS‐fed wild‐type mice complex II substrate–driven ATP synthesis and activity were restored ex vivo by dithiothreitol (5 mmol/L), suggesting a role for reversible cysteine oxidative posttranslational modifications. In vitro site‐directed mutation of complex II subunit B Cys100 or Cys103 to redox‐insensitive serines prevented complex II dysfunction induced by ROS or high glucose/high palmitate in the medium. Conclusion Mitochondrial ROS are pathogenic in MHD and contribute to mitochondrial dysfunction, at least in part, by causing oxidative posttranslational modifications of complex I and II proteins including reversible oxidative posttranslational modifications of complex II subunit B Cys100 and Cys103.
Structural Insight into Substrate Selectivity of Erwinia chrysanthemi l-Asparaginase

l-Asparaginases of bacterial origin are a mainstay of acute lymphoblastic leukemia treatment. The mechanism of action of these enzyme drugs is associated with their capacity to deplete the amino acid l-asparagine from the blood. However, clinical use of bacterial l-asparaginases is complicated by their dual l-asparaginase and l-glutaminase activities. The latter, even though representing only ∼10% of the overall activity, is partially responsible for the observed toxic side effects. Hence, l-asparaginases devoid of l-glutaminase activity hold potential as safer drugs. Understanding the key determinants of l-asparaginase substrate specificity is a prerequisite step toward the development of enzyme variants with reduced toxicity. Here we present crystal structures of the Erwinia chrysanthemi l-asparaginase in complex with l-aspartic acid and with l-glutamic acid. These structures reveal two enzyme conformations—open and closed—corresponding to the inactive and active states, respectively. The binding of lig...
Men's attitudes towards contraception in sub-Saharan Africa : original research

This paper examines male attitudes towards family planning in Sub-Saharan Africa. Studying attitudes is ideal as they can be calculated for all men, at any point in their lives, regardless of marital status, sexual activity, or fertility desires. We find that positive attitudes towards family planning have increased across Sub-Saharan Africa in the last two decades. We analyze both the association of positive attitudes with a variety of demographic characteristics (age, marital status, education, and religion) and the relationships with multiple forms of discussion about family planning (radio, television, friends, and partners). We find higher approval at older ages and higher levels of education, and lower levels of approval among Muslims compared to Christians. Interactions between characteristics and discussion of family planning demonstrate that hearing or talking about contraception has different associations for different groups. This paper offers a new way to explore fertility and reproductive health in Sub-Saharan Africa. Cet article examine les attitudes des hommes envers la planification familiale en Afrique subsaharienne. etudier les attitudes est ideal, car elles peuvent etre calculees pour tous les hommes, a tout moment de leur vie, independamment de l'etat civil, l'activite sexuelle, ou les desirs de fecondite. Nous constatons que des attitudes positives envers la planification familiale ont augmente dans toute l'Afrique sub-saharienne au cours des deux dernieres decennies. Nous analysons a la fois l'association des attitudes positives et une variete de caracteristiques demographiques (âge, 'etat civil, education et religion) et les relations avec les multiples formes de discussion sur la planification familiale (radio, television, amis et partenaires). Nous constatons qu'il y a beaucoup plus d'approbation a un âge avance et a des niveaux plus eleves de l'education, et qu'il y a des niveaux bas d'approbation parmi les musulmans par rapport aux chretiens. Les interactions entre les caracteristiques et la discussion de la planification familiale demontrent qu'entendre parler ou de parler de la contraception a de differentes associations pour les differents groupes. Cet article propose une nouvelle facon d'explorer la fecondite et la sante de la reproduction en Afrique sub-saharienne.
Discrete Pathophysiology is Uncommon in Patients with Nonspecific Arm Pain

Background: Nonspecific symptoms are common in all areas of medicine. Patients and caregivers can be frustrated when an illness cannot be reduced to a discrete pathophysiological process that corresponds with the symptoms. We therefore asked the following questions: 1) Which demographic factors and psychological comorbidities are associated with change from an initial diagnosis of nonspecific arm pain to eventual identification of discrete pathophysiology that corresponds with symptoms? 2) What is the percentage of patients eventually diagnosed with discrete pathophysiology, what are those pathologies, and do they account for the symptoms? Methods: We evaluated 634 patients with an isolated diagnosis of nonspecific upper extremity pain to see if discrete pathophysiology was diagnosed on subsequent visits to the same hand surgeon, a different hand surgeon, or any physician within our health system for the same pain. Results: There were too few patients with discrete pathophysiology at follow-up to address the primary study question. Definite discrete pathophysiology that corresponded with the symptoms was identified in subsequent evaluations by the index surgeon in one patient (0.16% of all patients) and cured with surgery (nodular fasciitis). Subsequent doctors identified possible discrete pathophysiology in one patient and speculative pathophysiology in four patients and the index surgeon identified possible discrete pathophysiology in four patients, but the five discrete diagnoses accounted for only a fraction of the symptoms. Conclusion: Nonspecific diagnoses are not harmful. Prospective randomized research is merited to determine if nonspecific, descriptive diagnoses are better for patients than specific diagnoses that imply pathophysiology in the absence of discrete verifiable pathophysiology.
Nonsterol Isoprenoids Activate Human Constitutive Androstane Receptor in an Isoform-Selective Manner in Primary Cultured Mouse Hepatocytes

Our laboratory previously reported that accumulation of nonsterol isoprenoids following treatment with the squalene synthase inhibitor, squalestatin 1 (SQ1) markedly induced cytochrome P450 (CYP)2B1 mRNA and reporter activity in primary cultured rat hepatocytes, which was dependent on activation of the constitutive androstane receptor (CAR). The objective of the current study was to evaluate whether isoprenoids likewise activate murine CAR (mCAR) or one or more isoforms of human CAR (hCAR) produced by alternative splicing (SPTV, hCAR2; APYLT, hCAR3). We found that SQ1 significantly induced Cyp2b10 mRNA (∼3.5-fold) in primary hepatocytes isolated from both CAR-wild-type and humanized CAR transgenic mice, whereas the 3-hydroxy-3-methylglutaryl-CoA reductase inhibitor pravastatin had no effect. In the absence of CAR, basal Cyp2b10 mRNA levels were reduced by 28-fold and the effect of SQ1 on Cyp2b10 induction was attenuated. Cotransfection with an expression plasmid for hCAR1, but not hCAR2 or hCAR3, mediated SQ1-induced CYP2B1 and CYP2B6 reporter activation in hepatocytes isolated from CAR-knockout mice. This effect was also observed following treatment with the isoprenoid trans,trans-farnesol. The direct agonist CITCO increased interaction of hCAR1, hCAR2, and hCAR3 with steroid receptor coactivator-1. However, no significant effect on coactivator recruitment was observed with SQ1, suggesting an indirect activation mechanism. Further results from an in vitro ligand binding assay demonstrated that neither farnesol nor other isoprenoids are direct ligands for hCAR1. Collectively, our findings demonstrate that SQ1 activates CYP2B transcriptional responses through farnesol metabolism in an hCAR1-dependent manner. Further, this effect probably occurs through an indirect mechanism.
Ultrasound to video registration using a bi-plane transrectal probe with photoacoustic markers

Modern surgical scenarios typically provide surgeons with additional information through fusion of video and other imaging modalities. To provide this information, the tools and devices used in surgery must be registered together with interventional guidance equipment and surgical navigation systems. In this work, we focus explicitly on registering ultrasound with a stereo camera system using photoacoustic markers. Previous work has shown that photoacoustic markers can be used in this registration task to achieve target registration errors lower than the current available systems. Photoacoustic markers are defined as a set of non-collinear laser spots projected onto some surface. They can be simultaneously visualized by a stereo camera system and an ultrasound transducer because of the photoacoustic effect. In more recent work, the three-dimensional ultrasound volume was replaced by images from a single ultrasound image pose from a convex array transducer. The feasibility of this approach was demonstrated, but the accuracy was lacking due to the physical limitations of the convex array transducer. In this work, we propose the use of a bi-plane transrectal ultrasound transducer. The main advantage of using this type of transducer is that the ultrasound elements are no longer restricted to a single plane. While this development would be limited to prostate applications, liver and kidney applications are also feasible if a suitable transducer is built. This work is demonstrated in two experiments, one without photoacoustic sources and one with. The resulting target registration error for these experiments were 1.07mm±0.35mm and 1.27mm±0.47mm respectively, both of which are better than current available navigation systems.
Comparison of Tensile Testing Flow Stress to Orthogonal Plate Machining Flow Stress in FCC, BCC, and HCP Materials at Various Levels of Hardness Using a Videographic Quick Stop Device

Basic and advanced metal cutting research has been an ongoing effort since Cocquilhat’s early work directed towards measuring the work required to remove a given volume of material when drilling in the year 1851. Over the 150+ years since his experiments, one of the persistent issues in metal cutting has been how best to determine the flow stress in a metal undergoing cutting. In all the many models proposed since then, the flow stress of metal flowing in front of a cutting tool has not proven to be the same as the flow stress of metal undergoing a tensile pull. This paper examines the flow stress phenomenon using an improved Videographic Quick Stop equipment at Auburn University.The orthogonal machining plates and tensile specimens were all cut from the same stock. Tensile testing of the stock was performed immediately prior to the machining of the plates in a standard MTS load frame to allow actual metal cutting experiments to be performed and compared to actual load frame data from the same stock.Machining was conducted in a specially modified Cincinnati Horizontal Milling machine using an improved Videographic Quick Stop Device (VQSD) to capture the geometry of the cutting formation simultaneously with the forces in the X, Y and Z-axes using a standard Kistler force plate dynamometer. Utilizing the VQSD greatly increases the number of replicates available for statistical analysis by the metal cutting researcher. This allows for comprehensive multivariate analysis of the data with high confidence (> 95%) in the meaning of the results obtained, along with for powerful regression.The results of the data collection and statistical analysis are then used to populate the various historical models predicting the flow stress in metal cutting. The results indicate that one model is superior to all the other models in predicting the flow stress as predicted by the accompanying tensile test data. Further improvements in this model may lead to instantaneous tensile strength measurement when metal cutting with the need for load frames. This in turn would allow optimization of cutting conditions to match material conditions, resulting in a better product and longer-lived tools.Copyright © 2015 by ASME
TV'S Clean Little War

(1991). TV'S Clean Little War. Bulletin of the Atomic Scientists: Vol. 47, No. 4, pp. 16-19.
Effects of Piston Uplift, Piston Friction, and Machine Deflection in Reduced Triaxial Extension Testing

A series of Reduced Triaxial Extension (RTE) tests were conducted on dummy (brass) and null (water) samples to determine the effects of (corrections required for) piston uplift, piston friction and system compliance associated with RTE tests. During the consolidation stage of RTE tests, the sample may be consolidated in isotropic or anisotropic stress conditions. During the shearing stage of an RTE test, the sample is unloaded in the axial direction by decreasing the deviator stress while the radial stress remains constant. Ten (10) tests were conducted on a brass “dummy” sample. The device was assembled in the same manner as for tests conducted on soil samples. The tests simulated the backpressure saturation and consolidation stages of testing. For various effective stresses (cell pressure and backpressure combinations) the load associated with piston uplift and piston friction was measured. Correlations were developed for piston uplift and piston friction. Eleven (11) tests were on “dummy” ice samples The samples, used as place holders, were set-up in the same manner as for tests conducted on soil samples then allowed to melt before shearing. For various effective stresses the load associated with machine deflection was measured. The contribution of the membrane elongation and filter paper were determined.
Focal Epidemic of Sarcoptid (Acarina: Sarcoptidae) Mite Infestation in an Insular Population of White-Footed Mice

The abrupt and focal emergence of an infestation of sarcoptid mites was documented during long-term studies of populations of the white-footed mouse, Peromyscus leucopus (Rafinesque), on Nantucket Island, MA. From 1985 to 1996, > 1,000 trap nights were recorded each year in 2 permanently situated sampling grids that were sampled monthly from April through November. In April 1995, prominent excrescences were first noted on the pinnae of mice trapped solely from 1 of the 2 sites. Histopathology of the lesions suggested infestation with Notoedres spp. Of 140 unique captures of mice during 1995-1997, 77% were infested as determined by the presence or absence of macroscopic ear lesions. Both sexes were likely to be infested, but juvenile mice were twice as likely to be noninfested. No lesions were noted in 103 mice concurrently sampled from a grid situated 15 km away, nor in mice from other sites in coastal New England. The origin of this epidemic remains obscure. This unusual infestation exemplifies the emergence of zoonotic infections, but at the level of an enzootic cycle.
A User-centered Design for the Addition of Interactive Masking Capability within an existing Web GIS

This article presents a case study of how a user-centered design (UCD) approach was utilized during the addition of interactive masking capability to an existing web-based geographic information system (Web GIS). By analyzing and discussing specific aspects of the user-developer dialog within the context of a Web GIS software development life cycle, this article presents a case study for similar systems. The results of the UCD methodology is a discussion that presents a shift from an initial design to a new design that, based on user feedback, furthers the utility and usability of interactive masking within the Web GIS.