cssi/SciSciGPT-SciSciNet huggingface dataset:
Communication: A comparison between the solution properties of knotted ring and star polymers.

We computationally investigate the good solvent solution properties of knotted ring and star polymers by combining molecular dynamics (MD) simulation and path-integral calculations. We consider knotted rings having a minimal crossing number mc in the range, 0 ≤ mc ≤ 9, and star polymers having a range of f star arms, 2 ≤ f ≤ 20, attached to a common core monomer particle. After generating configurational ensembles of these polymers by MD, we use the path-integration program ZENO to calculate basic configurational properties, i.e., radius of gyration, hydrodynamic radius, intrinsic viscosity, as well as fluctuations in these properties. Our simulations indicate that the configurational properties of knotted rings and star polymers in solution show a similar decrease with increasing mc and f. Moreover, fluctuations in these properties also decrease with increasing topological complexity. Our findings should be helpful in polymer characterization and more generally for understanding the role of polymer topology in polymer material properties.
AN ECONOMIC ANALYSIS OF THE BULK MILK COLLECTION SYSTEM

Greater investments in farm storage and refrigeration equipment are necessary for farmer participation in a bulk milk procurement program. Economies in operational costs are effected in the collect...
Low-frequency micro-structured mechanical metamaterials

Abstract Mechanical metamaterials with a periodic micro-structure of small length scale ( ≤ 1 cm) and with band gaps at very low frequencies ( ≤ 5 kHz) are designed, fabricated, and experimentally characterized. This is achieved by the addition of a discrete structurally resonant inclusion with a low natural resonance frequency into a hollow cellular structure. The mechanical eigenfrequencies of the cell are calculated based on a finite element simulation of an infinite array with Floquet–Bloch boundary conditions. The unit cell is optimized to demonstrate a measurable low frequency stop band for longitudinal waves. The scattering response for a finitely thick slab of unit cells is estimated using a numerical method. In this method, frequency domain simulations are performed and the scattering matrix is extracted using two velocity measurements within homogeneous external domains on either side of the heterogeneous slab. An example of such micro-structured array was manufactured with 3D printing and its response was measured under water with a solid polymer plate of similar dimensions for comparison. The experimental data is compared with numerical modeling results with particular attention to the effect of macro-scale finite plate resonances as contrasted with micro-structural effects.
Picking Winners in Daily Fantasy Sports Using Integer Programming

We consider the problem of selecting a portfolio of entries of fixed cardinality for contests with top-heavy payoff structures, i.e. most of the winnings go to the top-ranked entries. This framework is general and can be used to model a variety of problems, such as movie studios selecting movies to produce, venture capital firms picking start-up companies to invest in, or individuals selecting lineups for daily fantasy sports contests, which is the example we focus on here. We model the portfolio selection task as a combinatorial optimization problem with a submodular objective function, which is given by the probability of at least one entry winning. We then show that this probability can be approximated using only pairwise marginal probabilities of the entries winning when there is a certain structure on their joint distribution. We consider a model where the entries are jointly Gaussian random variables and present a closed form approximation to the objective function. Building on this, we then consider a scenario where the entries are given by sums of constrained resources and present an integer programming formulation to construct the entries. Our formulation uses principles based on our theoretical analysis to construct entries: we maximize the expected score of an entry subject to a lower bound on its variance and an upper bound on its correlation with previously constructed entries. To demonstrate the effectiveness of our integer programming approach, we apply it to daily fantasy sports contests that have top-heavy payoff structures. We find that our approach performs well in practice. Using our integer programming approach, we are able to rank in the top-ten multiple times in hockey and baseball contests with thousands of competing entries. Our approach can easily be extended to other problems with constrained resources and a top-heavy payoff structure.
The effects of physics-based data augmentation on the generalizability of deep neural networks: Demonstration on nodule false-positive reduction

Purpose An important challenge for deep learning models is generalizing to new datasets that may be acquired with acquisition protocols different from the training set. It is not always feasible to expand training data to the range encountered in clinical practice. We introduce a new technique, physics-based data augmentation (PBDA), that can emulate new computed tomography (CT) data acquisition protocols. We demonstrate two forms of PBDA, emulating increases in slice thickness and reductions of dose, on the specific problem of false-positive reduction in the automatic detection of lung nodules. Methods We worked with CT images from the lung image database consortium (LIDC) collection. We employed a hybrid ensemble convolutional neural network (CNN), which consists of multiple CNN modules (VGG, DenseNet, ResNet), for a classification task of determining whether an image patch was a suspicious nodule or a false positive. To emulate a reduction in tube current, we injected noise by simulating forward projection, noise addition, and backprojection corresponding to 1.5 mAs (a "chest x-ray" dose). To simulate thick slice CT scans from thin slice CT scans, we grouped and averaged spatially contiguous CT within thin slice data. The neural network was trained with 10% of the LIDC dataset that was selected to have either the highest tube current or the thinnest slices. The network was tested on the remaining data. We compared PBDA to a baseline with standard geometric augmentations (such as shifts and rotations) and Gaussian noise addition. Results PBDA improved the performance of the networks when generalizing to the test dataset in a limited number of cases. We found that the best performance was obtained by applying augmentation at very low doses (1.5 mAs), about an order of magnitude less than most screening protocols. In the baseline augmentation, a comparable level of Gaussian noise was injected. For dose reduction PBDA, the average sensitivity of 0.931 for the hybrid ensemble network was not statistically different from the average sensitivity of 0.935 without PBDA. Similarly for slice thickness PBDA, the average sensitivity of 0.900 when augmenting with doubled simulated slice thicknesses was not statistically different from the average sensitivity of 0.895 without PBDA. While there were cases detailed in this paper in which we observed improvements, the overall picture was one that suggests PBDA may not be an effective data enrichment tool. Conclusions PBDA is a newly proposed strategy for mitigating the performance loss of neural networks related to the variation of acquisition protocol between the training dataset and the data that is encountered in deployment or testing. We found that PBDA does not provide robust improvements with the four neural networks (three modules and the ensemble) tested and for the specific task of false-positive reduction in nodule detection.
MKK signaling is required for fibrosarcoma growth and vascularization.

323 Fibrosarcoma is a malignant tumor derived from fibrous connective tissue and characterized by immature proliferating fibroblasts or undifferentiated anaplastic spindle cells. We have hypothesized that signaling through multiple MKK pathways is essential for growth and vascularization of fibrosarcomas. We tested this using anthrax lethal toxin (LeTx), a protease that cleaves and inactivates MKKs. Western blots confirmed that the phosphorylation levels of ERK, JNK and p38 MAPK in fibrosarcoma cell lines in vitro were reduced after 72 hours LeTx treatment. Concomitant with inhibition of MKK signaling, LeTx also blocked soft agar colony formation and proliferation but appeared to be neither cytotoxic nor cytostatic, causing only a minor G1 phase block and lengthened cell cycle progression. Because growth proliferation can be affected by autocrine growth factors we examined the effects of LeTx upon cytokine release from these cells. We observed that LeTx could decrease the release of many pro-angiogenic factors, notably VEGF. The effects of LeTx on fibrosarcoma growth and vascularization were also evaluated in vivo using a xenograft model. Both tumor volume and mean vascular density were significantly decreased by LeTx treatment. These changes correlated with altered in vivo cytokine expression. In conclusion, our results are consistent with the hypothesis that MKK signaling is required for the growth and vascularizaion of fibrosarcomas both in vitro and invivo.
Prospective evaluation of drug-drug interactions in ambulatory cancer patients initiated on prophylactic anticoagulation.

IntroductionDrug options for VTE prophylaxis are increasing for ambulatory cancer patients and data regarding anticoagulant-drug interactions and their relationship to VTE and bleeding are needed t...
Do nothing but observe microprolactinomas: when and how to replace sex hormones?

Hyperprolactinemia is associated with suppression of the hypothalamic- pituitary–gonadal axis and consequent hypogonadism, manifesting loss of libido, infertility and osteoporosis long-term in both male and female patients, with associated menstrual irregularities, amenorrhea and galactorrhea in women and erectile dysfunction in men. The primary goals of therapy in patients harboring prolactinoma are control of tumor size and normalization of serum PRL, with restoration of gonadal and sexual function and fertility. Clinical manifestations of hypogonadism have variable consequences depending on the age and sex of the patient and desire for fertility. Careful consideration of clinical consequences of hyperprolactinemia in relation to age and sex should help guide therapeutic decision making. Another important consideration in attaining our treatment goals in patients harboring microprolactinomas, is the observation that greater than 90% of microprolactinomas do not enlarge, when followed for 10 years. Treatment options for the management of microprolactinomas include observation alone, with monitoring of serum prolactin levels every 6–12 months, vs initiation of dopamine agonist therapy vs gonadal steroid hormone replacement (using the oral contraceptive or other combination estrogen and progesterone replacement regimens in females or testosterone replacement therapy in males). In the present review, current data related to clinical consequences of microprolactinomas and treatment outcomes at different stages in the lifespan are reviewed, with a suggested algorithm as to whether to treat or not, and an appropriate therapeutic regimen to institute.
Pharmacokinetics of a weekly transdermal delivery system of tenofovir alafenamide in hairless rats

Tenofovir alafenamide (TAF) is a potent prodrug of tenofovir (TFV) for HIV prophylaxis, and HIV and HBV treatment. Compared to oral daily doses, transdermal administration of TAF may be more advantageous for long-term adherence by offering sustained drug delivery and reduced dosing frequency. Here, we described the plasma pharmacokinetics (PK) of an optimized once-weekly suspension transdermal delivery system (TDS) for TAF (96 mg/25 cm2 of TDS) in female hairless rats. Over the study period, the TAF TDS delivered an overall low level of TAF (median: 1.43 [0.02-3.28] ng/mL) and a sustained level of the stable metabolite and parent drug, TFV. Relative to the projected exposure corresponding to six-day oral daily doses, a comparable TAF exposure but a substantially lower TFV exposure was resulted from the TAF TDS, suggesting a lower risk of TFV-associated adverse effects. TAF, TFV, and phosphorylated TFVs (TFV-monophosphate and diphosphate) were found distributed in vaginal tissue, the portal of entry for HIV during male-to-female sexual transmission. Skin adhesion and tolerance were acceptable given the animal model used. PK evaluation of the TAF TDS in hairless rats demonstrates the proof of concept that transdermal delivery can be an alternative route for a sustained, once-weekly systemic delivery of TAF.
"Us vs. Them" Pair Housing: Effects on Body Weight, Open Field Behavior, and Gut Microbiota in Rats Selectively Bred on a Taste Phenotype

Taste is increasingly recognized as being related to reward, risk, and social processes beyond the ingestive domain. Occidental High (HiS) and Low (LoS) Saccharin Consuming rats have been selectively bred for more than 25 years to study those relationships. The present study examined LoS and HiS rats' sensitivity to a social partner's lineage. The role of gut microbiome transfer between lines was also explored as a possible mediating mechanism. Rats were pair-housed with a rat from either their own line (same-line condition) or the other line (other-line condition); weight gain, saccharin intake, acoustic startle, and open field behavior were measured. Results show for the first time that the lines express different behavioral strategies in a novel open field. In addition, weight gain and open field measures indicate that other-line housing was stressful. Saccharin intake, however, was unaffected by housing condition. A previous finding that the lines possess different gut microbiota was replicated. Although microbial transfer occurred between social partners, no clear evidence was obtained that housing-condition effects on weight gain or behavior were mediated by microbial transfer. Overall, these findings add to the characterization of non-gustatory correlates of a taste phenotype and suggest that rats differing strikingly on the taste phenotype and/or its correlates may be socially incompatible.
Paying attention to climate change: Positive images of climate change solutions capture attention

Abstract The impact of anthropogenic climate change is an ever-pressing challenge facing the global community. Making changes to minimize the negative effects of climate change is critical. Visual images of climate change are emotionally salient and have been found to capture attention. However, the degree to which emotional valence (i.e., positive or negative) and aspect of climate change (i.e., potential cause, effect, or solution) influence attentional capture by climate change relevant images is unknown. Across three experiments, we addressed this knowledge gap by measuring attention to these types of images with a dot-probe task. We found a consistent capture of attention by emotionally positive images of climate change solutions (e.g., windmills and solar panels), but not emotionally negative images of causes (e.g., industrial pollution) and effects (e.g., natural disasters and melting polar ice caps) of climate change. Negative images of climate change were found to produce a general slowing of reaction time, which may reflect a “freezing” response. Individual differences in attentional capture by climate change images were related to environmental disposition. Our results suggest that positive images of climate change solutions are attention grabbing and in turn may be the most suitable images to motivate environmentally friendly action or behavior.
Attitudes toward COVID-19 illness and COVID-19 vaccination among pregnant women: a cross-sectional multicenter study during August-December 2020

ObjectiveEvaluate pregnant womens attitudes toward COVID-19 illness and vaccination and identify factors associated with vaccine acceptability. Study DesignCross-sectional survey among pregnant women enrolled in a prospective COVID-19 cohort study in Salt Lake City, UT, Birmingham, AL, and New York, NY, August 9- December 10, 2020. Women were eligible if they were 18-50 years old and <28 weeks of gestation. Upon enrollment, women completed surveys regarding concerns about COVID-19 illness and likelihood of getting COVID-19 vaccine if one were available during pregnancy. Vaccine acceptability was defined as a response of "very likely" or "somewhat likely" on a 4-point Likert scale. Factors associated with vaccine acceptability were assessed with multivariable logistic regression. ResultsOf 939 pregnant women eligible for the main cohort study, 915 (97%) consented to participate. Among these 915 women, 39% self-identified as White, 23% Black, 33% Hispanic, and 4% Other. Sixty-two percent received an influenza vaccine last season. Seventy-two percent worried about getting sick with COVID-19. If they were to get sick, 92% worried about harm to their pregnancy and 80% about harm to themselves. Only 41% reported they would get a vaccine. Of women who were unlikely to get vaccinated, the most frequently cited concern was vaccine safety for their pregnancy (82%). Non-Hispanic Black and Hispanic women had lower odds of accepting a vaccine compared with non-Hispanic White women (adjusted odds ratios (aOR) 0.4, 95%CI 0.2-0.6 for both). Receipt of influenza vaccine during the previous season was associated with higher odds of vaccine acceptability (aOR 2.1, 95%CI 1.5-3.0). ConclusionAlthough most pregnant women worried about COVID-19 illness, <50% were willing to get vaccinated during pregnancy. Racial and ethnic disparities in plans to accept COVID-19 vaccine highlight the need to prioritize strategies to address perceived barriers among groups at high risk for COVID-19.
Disordered Regions in Crystalline Silicon at High Temperatures

If we start with a perfect crystal at 0 K and raise its temperature to some finite temperature T, the crystalline order will be disrupted by the thermal creation of defects.
Changing Our Economic Outlook

This discussion begins by examining the broad macro influences in the social character of the country, linking demographic and economic changes to the current and future uses of historic properties. Regional strengths and weaknesses due to population shifts provide an explanation of the status of many areas, once agricultural or industrial, but now dependent on the service sector. Preservation economics closely examines the idea of why an “obsolete” property is often endangered. In truth, these sites can be more accurately described as suffering from inattention, physical deterioration, functional inadequacy, or social and aesthetic unacceptability, all of which can be addressed and remedied. The economic arguments for continued use of properties are also linked to job creation, and savings in energy, time, transportation costs, and materials.
Decisions Detained: The Courts’ Embrace of Complexity in Guantánamo-Related Litigation

This Article explores the judicial embrace of complexity in the context of Guantanamo-related litigation. First, the Article sets out a conception of war as defined by the three limiting factors of time, space, and means and the conceptual challenge to each that a war against terrorism has posed. Second, the Article examines a number of key judicial decisions implicating post-9/11 detention at Guantanamo to reveal how courts have shied away from delving too deeply into the first two factors while concentrating on the third. Next, the Article suggests institutional reasons for that emphasis: in particular, the avoidance of issues potentially considered political questions, and the evasion of clear and potentially unwinnable conflict with other branches. Fourth, the Article explores the benefits of that choice to a handful of detainees by demonstrating how the choice has allowed the courts to intervene in case-specific ways and, in so doing, to secure the release of a few detainees. Finally, the Article reveals the costs of that choice by showing how uncertainty has repeatedly traveled up and down the judicial hierarchy, delaying resolution of central issues that, indeed, remain unsettled today, all the while potentially endangering the judiciary’s institutional standing in war-time. Throughout, the Article argues that courts have refused to define time or space as limiting factors in the war against terrorism, instead focusing on the means employed. Emphasizing that distinctly difficult defining factor has made the courts’ task easier, enabling them to issue narrow rulings through reinterpretable opinions. Institutional reasons explain this judicial approach: in particular, the courts have sought to avoid clear intrusion into the sphere of political questions as well as to evade clear and potentially unenforceable conflict with the political branches. While the benefits of this approach have included particularized judicial intervention, the costs have loomed far larger, including persistent uncertainty and potential institutional diminution for the judiciary.
Inheritance as an Incremental Modification Mechanism or What Like Is and Isn't Like

Incremental modification is a fundamental mechanism not only in software systems, but also in physical and mathematical systems. Inheritance owes its importance in large measure to its flexibility as a discrete incremental modification mechanism. Four increasingly permissive properties of incremental modification realizable by inheritance are examined: behavior compatibility, signature compatibility, name compatibility, and cancellation. Inheritance for entities with finite sets of attributes is defined and characterized as incremental modification with deferred binding of self-reference. Types denned as predicates for type checking are contrasted with classes defined as templates for object generation. Mathematical, operational, and conceptual models of inheritance are then examined in detail, leading to a discussion of algebraic models of behavioral compatibility, horizontal and vertical signature modification, algorithmically defined name modification, additive and subtractive exceptions, abstract inheritance networks, and parametric polymorphism. Liketypes are defined as a symmetrical general form of incremental modification that provide a framework for modeling similarity. The combination of safe behaviorally compatible changes and less safe radical incremental changes in a single programming language is considered.
Fuel cell commercialization: hydrogen infrastructure economic and technical barriers

Fuel cells have the potential to provide a significant shift in global politics as the United States shift to a hydrogen-fueled economy and alter its dependency on foreign petroleum. Fuel cells, however, despite their potential to provide US energy security and providing a key technology against global warming, must overcome several economic and technical barriers, one of which is the development of a hydrogen fuel infrastructure. This paper provides a basic overview of these barriers and summarizes the necessary challenges.
Stereotactic body radiotherapy for prostate cancer: current results of a phase II trial

The hypofractionation of stereotactic body radiotherapy (SBRT) for prostate cancer has become a broad topic, and there are many aspects to consider before accepting this treatment into our clinics. Among the considerations are the data from the Stanford phase II trial, a seminal investigation into this area, which will be presented and reviewed here. A single-arm, prospective phase II trial was initiated at Stanford in December of 2003. This trial uses SBRT as monotherapy for 'low-risk' prostate cancer patients, and 69 patients have been entered to date. We have analyzed the patient data for the first 5 years of this study. For study entry, patients were required to have clinical stage T1c or T2a disease, prostate-specific antigen (PSA) ≤ 10 and a Gleason score of 3 + 3 (or 3 + 4 if the higher grade portion was of small volume, usually <25% of the cores involved). No prior treatment was permitted, including the use of transurethral resections or androgen deprivation therapies. A low urinary IPSS score of < 20 was required for study entry as well. The prescription dose was 7.25 Gy for 5 fractions for a total dose of 36.25 Gy. This was normalized to cover ≥ 95% of the planning target volume with 100% of the prescription dose. Patients were treated using CyberKnife technology. To date, excellent PSA responses have been observed in patients with lower-risk disease selected for treatment and receiving 36.25 Gy in 5 fractions. To date, sexual quality of life outcomes have also been approximately comparable to other radiotherapy approaches. Rates of late GI and GU toxicity have been relatively low and generally comparable to dose-escalated approaches using conventional fractionation.
Modern‐age buildup of CO2 and its effects on seawater acidity and salinity

[1] The impacts of increases in atmospheric CO2 since the midst of the 18th century on average seawater salinity and acidity are evaluated. Assuming that the rise in the planetary mean surface temperature continues unabated, and that it eventually causes the melting of terrestrial ice and permanent snow, it is calculated that the average seawater salinity would be lowered not more than 0.61‰ from its current 35‰. It is also calculated –using an equilibrium model of aqueous carbonate species in seawater open to the atmosphere- that the increase in atmospheric CO2 from 280 ppmv (representative of 18th-century conditions) to 380 ppmv (representative of current conditions) raises the average seawater acidity approximately 0.09 pH units across the range of seawater temperature considered (0 to 30°C). A doubling of CO2 from 380 ppmv to 760 ppmv (the 2 × CO2 scenario) increases the seawater acidity approximately 0.19 pH units across the same range of seawater temperature. In the latter case, the predicted increase in acidity results in a pH within the water-quality limits for seawater of 6.5 and 8.5 and a change in pH less than 0.20 pH units. This paper's results concerning average seawater salinity and acidity show that, on a global scale and over the time scales considered (hundreds of years), there would not be accentuated changes in either seawater salinity or acidity from the observed or hypothesized rises in atmospheric CO2 concentrations.
Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes

Due to the high cost and low reproducibility of many microarray experiments, it is not surprising to find a limited number of patient samples in each study, and very few common identified marker genes among different studies involving patients with the same disease. Therefore, it is of great interest and challenge to merge data sets from multiple studies to increase the sample size, which may in turn increase the power of statistical inferences. In this study, we combined two lung cancer studies using micorarray GeneChip®, employed two gene shaving methods and a two-step survival test to identify genes with expression patterns that can distinguish diseased from normal samples, and to indicate patient survival, respectively. In addition to common data transformation and normalization procedures, we applied a distribution transformation method to integrate the two data sets. Gene shaving (GS) methods based on Random Forests (RF) and Fisher's Linear Discrimination (FLD) were then applied separately to the joint data set for cancer gene selection. The two methods discovered 13 and 10 marker genes (5 in common), respectively, with expression patterns differentiating diseased from normal samples. Among these marker genes, 8 and 7 were found to be cancer-related in other published reports. Furthermore, based on these marker genes, the classifiers we built from one data set predicted the other data set with more than 98% accuracy. Using the univariate Cox proportional hazard regression model, the expression patterns of 36 genes were found to be significantly correlated with patient survival (p < 0.05). Twenty-six of these 36 genes were reported as survival-related genes from the literature, including 7 known tumor-suppressor genes and 9 oncogenes. Additional principal component regression analysis further reduced the gene list from 36 to 16. This study provided a valuable method of integrating microarray data sets with different origins, and new methods of selecting a minimum number of marker genes to aid in cancer diagnosis. After careful data integration, the classification method developed from one data set can be applied to the other with high prediction accuracy.
Graetz–Brinkman problem in laminar core-annular flow of two immiscible liquids

Abstract Thermally-developing flow with the inclusion of the viscous dissipation is known as the Graetz–Brinkman problem. Here, the problem of thermally-developing, hydrodynamically-developed laminar core-annular flow in a circular duct with a prescribed inlet temperature distribution and viscous dissipation is considered. Both fluids are assumed to be Newtonian, and the effects of interfacial waves, flow eccentricity, and axial heat conduction are neglected. An external convection boundary condition is considered, which recovers the constant wall temperature boundary condition as the Biot number approaches infinity. The problem is solved using a combined analytical and numerical solution, with a general inlet temperature distribution expanded by the method of quasi-orthogonal functions. Results are presented for the case of an oil-water flow, with oil occupying the core region of the flow. The effects of the different boundary conditions and the inlet temperature distribution of the fluid are discussed and compared to the well-known results for the single-fluid Graetz–Brinkman problem.
Joint spacing as a method of locating faults

Contour maps showing areas of equal joint spacing in outcrop can provide important evidence for locating faults at the surface in areas of extensive alluvial and vegetative cover. The technique has been applied to an area of detailed joint mapping in the Allegheny Plateau of south-central New York and contiguous northern Pennsylvania. Contour maps of joint spacing indicate that the spacing between joints, within a joint set, increases as some faults or fault zones are approached. The maximum spacing of joints is adjacent to faults. A contour map of the northwest-striking joints appears to identify and delineate thrust faults (that is, east-striking faults), whereas a contour map of the northeast-striking joints seems to show tear faults (that is, north-striking faults). Although not all known faults are indicated by this technique, several mapped faults as well as several suspected faults are apparent on the contour maps.
Viscous forces on acoustically levitated gas bubbles

Abstract When a gas bubble is subjected to an oscillating acoustic field in a gravitational environment, it seeks a location where time-averaged net force vanishes (‘acoustic levitation’). At this location, the bubble undergoes periodic, coupled volumetric pulsation and translational motion. In this study, we extend the existing inviscid theory of acoustic levitation to include viscous drag forces arising from translational motion. Equilibrium locations are computed and compared with predictions from inviscid theory. It is found that the effects are quite small, producing negligible effect on the levitation position.
Sequence and expression of NUC1, the gene encoding the mitochondrial nuclease in Saccharomyces cerevisiae.

Abstract The DNA sequence and studies on the expression of the NUC1 gene from Saccharomyces cerevisiae are presented. The NUC1 locus is located in the distal portion of the left arm of Chromosome X and encodes the major nuclease found in mitochondria. The inferred amino acid sequence of NUC1 predicts that the nuclease is basic, rich in prolines, of average hydrophobicity, and has a molecular weight for the primary translation product of 37,209 daltons. NUC1 is very poorly expressed, consistent with the codon usage bias determined from the DNA sequence and our previous determination of the number of enzyme molecules per cell. Mapping of the 5' terminus of the NUC1 mRNA reveals that the mRNA has a long 400 base untranslated leader in which are found three open reading frames, each initiated by an AUG. The possibility that these upstream open reading frames contribute to the poor expression of the NUC1 gene is discussed.
The cone threshold: Spatial interactions of rod and cone adapting signals

Steady small blue adapting fields that stimulated only rods produced large threshold elevations for a superimposed tiny red flash that stimulated cones. The threshold elevation differed considerably between observers, confirming the results of Buck (Topical Meeting on Recent Advances in Vision, abstract in Technical Digest, 1980; Invest. Ophthal, visual Sci., Suppl. 20, 207, 1981). A red annulus that stimulated cones reduced slightly the threshold elevation produced by the small rod adapting field. Similarly, when the cone threshold was elevated by a small red field that stimulated only cones, a blue annulus that stimulated rods slightly reduced the threshold of the red cone test flash. These effects, although weak, demonstrate lateral sensitizing interactions between a cone center field and rod annulus, and vice versa, when the cone threshold is assessed with a tiny red flash.
Interferon-induced indoleamine 2,3-dioxygenase activity inhibits Chlamydia psittaci replication in human macrophages.

ABSTRACT Interferon-γ (IFN-γ) previously has been shown to inhibit the replication of Chlamydia psittaci in epithelial cells by inducing indoleamine 2,3-dioxygenase, the enzyme that decyclizes tryptophan to N-formylkynurenine. The role of indoleamine 2,3-dioxygenase in IFN-mediated inhibition of C. psittaci in human macrophages has now been examined. Peripheral blood monocytes from normal donors were isolated and cultivated 10–14 days to allow differentiation to macrophages. Cells were then treated with either IFN-γ or IFN-β for 48 h before infection with sufficient C. psittaci to infect approximately 30% of the cells. Infected cells were incubated 24 h, at which time coverslips were fixed, stained with Giemsa, and examined for development of C. psittaci inclusions by light microscopy. Complete inhibition of inclusion development was observed with IFN-γ. In the absence of lipopolysaccharide, inhibition of C. psittaci by IFN-γ was variable; however, in the presence of lipopolysaccharide, IFN-γ also complet...
The separation of ionic forms of phosphatidylserine by column chromatography

Abstract Two ionic forms of brain phosphatidylserine have been separated by column chromatography on silicic acid. The free acid form of this phosphatide is readily eluted with chloroform-methanol 4:1 whereas the sodium salt form required a more polar solvent for elution. The two forms of phosphatidylserine were identified by chemical, spectral, and chromatographic analyses.
Maternal urinary tract infections and selected cardiovascular malformations.

BACKGROUND: In a population-based case-control study, we investigated the association between congenital cardiovascular malformations (CVMs) and maternal urinary tract infections (UTIs). METHODS: Within the National Birth Defects Prevention Study, 3,690 women who had singleton livebirths with nonsyndromic CVMs, and 4,760 women who had infants without birth defects were identified. Affected infants had: conotruncal, septal, anomalous pulmonary venous return, atrioventricular septal defects, or left- or right-sided obstructive heart defects. Mothers had a UTI if they reported having at least one infection during the first trimester. Adjusted ORs and 95% CIs were computed to determine the association between CVMs and UTIs. Stratified analyses were conducted to investigate if sulfonamide use and/or fever modified the effect between CVMs and UTIs. RESULTS: Women who had offspring with either left ventricular outflow tract obstructive defects or atrioventricular septal defects were more likely than controls to report a UTI. These associations remained among women who did not have fever or used sulfonamides. Maternal use of sulfonamides during the UTI did not appear to modify the relationship between CVM subtypes and maternal UTIs. CONCLUSIONS: In the National Birth Defects Prevention Study there was little evidence to support an association between CVMs and UTIs during the first trimester of pregnancy. Associations between left ventricular outflow tract obstructive defects and maternal UTI as well as between atrioventricular septal defects and maternal UTI were found. Our findings, while not conclusive, suggest that the possible association between maternal UTI and CVMs should be investigated further. Birth Defects Research (Part A), 2008. © 2008 Wiley-Liss, Inc.
SPATIAL AND TEMPORAL VARIATION IN CALCIUM AND ALUMINUM IN NORTHERN HARDWOOD FOREST FLOORS

Acid rain results in losses of exchangeable base cations from soils, but the mechanism of base cation displacement from the forest floor is not clear, and has been hypothesized to involve mobilization of aluminum from the mineral soil. We attempted to test the hypothesis that losses of calcium from the forest floor were balanced by increases in Al in NewHampshire northern hardwoods. We measured exchangeable (six stands) and acid extractable (13 stands) Ca and Al in horizons of the forest floor over an interval of 15 years. Our sampling scheme was quite intensive, involving 50 or 60 blocks per stand, composited in groups of 10 for chemical analysis. Even at this level of effort, few stands exhibited changes large enough to be significant. Because of high spatial variability, differences would have had to be greater than about 50% to be statistically detectable. Differences in Ca and Al concentrations between Oi, Oe, Oa, and A horizons, however, were readily detected. Acid-extractable Al increased with depth, while Ca concentrations decreased; Ca-to-Al ratios decreased from 8.3 (charge basis) in the Oi to 0.2 in the A horizon. Therefore, a small change in sampling depth, or the inclusion of more or less A horizon material in the forest floor, could cause large differences in measured Ca and Al concentrations. To detect small changes in exchangeable cations over time would require sampling very intensively with careful control for comparability of horizons.
CO2 Lasers and Temperature Changes of Titanium Implants

Lasers may be useful in uncovering submerged implants or in removing contaminants from “ailing” implants. The purposes of this study were to record temperature changes at the bone-titanium implant interface when using a CO2 laser to: 1) uncover the implant at second stage surgery; and 2) “decontaminate” exposed implant threads. Scanning electron microscopy (SEM) was used to characterize surface changes of lased implants, both uncontaminated or contaminated with blood or saliva. In part one, 28 titanium implants, measuring 3.75 mm by 7 to 20 mm, were placed into room temperature, fresh, resected pig mandibles and covered with a flap of gingiva. The overlying tissue was removed with a CO2 laser at different power levels. Bone-implant interface temperatures were measured with a thermocouple near the top of the implant, and 5 to 7 mm apical to the osseous crest. The effects of implant size, power level, tissue thickness, and operation time were evaluated. In part two, 5 mm by 4 mm bony dehiscences were create...
Diarrhetic Shellfish Poisoning, Washington, USA, 2011

Diarrhetic shellfish poisoning is a gastrointestinal illness caused by consumption of bivalves contaminated with dinophysistoxins. We report an illness cluster in the United States in which toxins were confirmed in shellfish from a commercial harvest area, leading to product recall. Ongoing surveillance is needed to prevent similar illness outbreaks.
Desipramine desensitizes β-adrenergic signal transduction in salivary glands: differential regulation with age

We previously reported that the tricyclic antidepressant, desipramine desensitizes beta-adrenergic signal transduction in parotid and submandibular salivary glands. To determine the consequences of repeated desipramine administration on beta-adrenergic signal transduction in salivary glands from aged rats and whether the recovery after drug withdrawal is impaired, we assessed the effects of 28-day desipramine administration and the reversibility of this treatment following a 15-day washout period on beta-adrenoceptors and adenylyl cyclase activity in parotid and submandibular glands from F-344 rats of 6, 12 and 24 months of age. beta-Adrenoceptors were also assessed in the cerebral cortex. Desipramine administration down-regulated receptor number and attenuated isoproterenol-stimulated adenylyl cyclase activity in all three ages of rats. However, the reduction in isoproterenol-stimulated adenylyl cyclase activity was greater than the loss of receptor number. Desipramine administration attenuated the efficacy of NaF-stimulated activity with no change in forskolin-stimulated adenylyl cyclase activity. These data suggest that in addition to desensitizing beta-adrenergic-mediated signal transduction, desipramine impaired G-protein-mediated adenylyl cyclase stimulation. The recovery from desipramine desensitization was age dependent. beta-Adrenoceptor density recovered more slowly in the cerebral cortex and the submandibular gland in 24-month-old rats than in 6-month-old rats. In contrast, in 12-month-old rats, there was a receptor up-regulation and adenylyl cyclase supersensitivity. These data indicate that the capacity for receptor modulation is age dependent and suggest that desipramine treatment may down-regulate stimulatory G protein.
STAT3-mediated transcription of Bcl-2, Mcl-1 and c-IAP2 prevents apoptosis in polyamine-depleted cells

Activation of STAT3 (signal transducer and activator of transcription 3) plays a crucial role in cell survival and proliferation. The aim of the present study was to clarify the role of STAT3 signalling in the protection of polyamine-depleted intestinal epithelial cells against TNF-α (tumour necrosis factor-α)-induced apoptosis. Polyamine depletion by DFMO (α-difluoromethylornithine) caused phosphorylation of STAT3 at Tyr-705 and Ser-727. Phospho-Tyr-705 STAT3 was immunolocalized at the cell periphery and nucleus, whereas phospho-Ser-727 STAT3 was predominantly detected in the nucleus of polyamine-depleted cells. Sustained phosphorylation of STAT3 at tyrosine residues was observed in polyamine-depleted cells after exposure to TNF-α. Inhibition of STAT3 activation by AG490 or cell-membrane-permeant inhibitory peptide (PpYLKTK; where pY represents phospho-Tyr) increased the sensitivity of polyamine-depleted cells to apoptosis. Expression of DN-STAT3 (dominant negative-STAT3) completely eliminated the protective effect of DFMO against TNF-α-induced apoptosis. Polyamine depletion increased mRNA and protein levels for Bcl-2, Mcl-1 (myeloid cell leukaemia-1) and c-IAP2 (inhibitor of apoptosis protein-2). Significantly higher levels of Bcl-2 and c-IAP2 proteins were observed in polyamine-depleted cells before and after 9 h of TNF-α treatment. Inhibition of STAT3 by AG490 and DN-STAT3 decreased Bcl-2 promoter activity. DN-STAT3 decreased mRNA and protein levels for Bcl-2, Mcl-1 and c-IAP2 in polyamine-depleted cells. siRNA (small interfering RNA)-mediated inhibition of Bcl-2, Mcl-1 and c-IAP2 protein levels increased TNF-α-induced apoptosis. DN-STAT3 induced the activation of caspase-3 and PARP [poly(ADP-ribose) polymerase] cleavage in polyamine-depleted cells. These results suggest that activation of STAT3 in response to polyamine depletion increases the transcription and subsequent expression of anti-apoptotic Bcl-2 and IAP family proteins and thereby promotes survival of cells against TNF-α-induced apoptosis.
Object Motion: A World View

Moving objects are detected by virtue of their shifting image on the retina. But to know how objects are moving in the world, we must take into account the rotation of our eyes, as well as the rotation of our head. A recent paper describes neurons that carry out this computation.
Does reverse growth dominance develop in old plantations of Eucalyptus saligna

Abstract Patterns of stand growth and dominance among individual trees change through stand development. We tested a prediction that large, old plantations of Eucalyptus saligna (Sm.) in Hawaii and Brazil would show a pattern of “reverse” growth dominance, with the largest trees contributing more to stand biomass than to current stand increment. This pattern might develop if the largest trees accounted for a large portion of the total resource use of the stand, but were less efficient at utilizing resources to produce stemwood. The 70-year-old plantation in Hawaii had a stem mass of 610 Mg/ha, compared with 325 Mg/ha in the 66-year-old Brazil plantation. Cumulative frequency plots for both sites showed that dominant trees comprised a very large proportion of total stand mass; the largest 20% of the trees accounted for 50% and 30% of the total stand mass in Hawaii and Brazil, respectively. Contrary to expectations, the largest trees continued to produce a disproportionately large amount of total stand growth, with the largest 20% of trees accounting for 60% (Hawaii) and 40% (Brazil) of stand growth. The frequency distributions resulted in positive growth dominance coefficients (similar to Gini coefficients) of 0.14 for Hawaii and 0.09 for Brazil, rather than negative values that would indicate that reverse growth dominance. The failure of these monoculture Eucalyptus stands to develop reverse growth dominance contrasts starkly with a variety of studies with pine species, which tend to show neutral-to-reverse growth dominance. Indeed, continued dominance of large trees suggests the trees might respond well to silvicultural treatments such as thinning or fertilization. Future work that contrasts patterns of growth dominance among species will be important as a foundation for developing generalizations about trends in growth dominance with stand development.
Digital calibration system enabling real-time on-orbit beamforming

Real-time On-orbit digital beamforming, combined with lightweight, large aperture reflectors, enable SweepSAR architectures, which promise significant increases in instrument capability for solid earth and biomass remote sensing. These new instrument concepts require new methods for calibrating the multiple channels, which are combined on-board, in real-time. The benefit of this effort is that it enables a new class of lightweight radar architecture, Digital Beamforming with SweepSAR, providing significantly larger swath coverage than conventional SAR architectures for reduced mass and cost.
A multi-scale accuracy assessment of the MODIS irrigated agriculture data-set (MIrAD) for the state of Nebraska, USA

Accurate and timely information about the geographic distribution of irrigated cropland is important for a range of applications including crop assessments, water resources management, drought monitoring, and environmental modeling. In the United States, a consistent, seamless irrigated agricultural lands map was not available until the development of the 250-m moderate resolution imaging spectroradiometer (MODIS) irrigated agriculture data-set (MIrAD), which was developed from time-series MODIS normalized difference vegetation index, county-level crop area statistics, and land use/land cover (LULC) data using an automated county-level classification approach. This study performed a detailed multi-scale assessment of the MIrAD over the state of Nebraska, which is extensively irrigated, to determine the thematic accuracy of classified irrigation patterns at various spatial scales (i.e., landscape, field, and subfield) and over various crop types. The MIrAD was found to map comparable irrigated cropland pat...