cssi/SciSciGPT-SciSciNet huggingface dataset:
LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo.

Long terminal repeat retrotransposons are the most abundant transposons in plants. They play important roles in alternative splicing, recombination, gene regulation, and defense mechanisms. Large-scale sequencing projects for plant genomes are currently underway. Software tools are important for annotating long terminal repeat retrotransposons in these newly available genomes. However, the available tools are not very sensitive to known elements and perform inconsistently on different genomes. Some are hard to install or obsolete. They may struggle to process large plant genomes. None can be executed in parallel out of the box and very few have features to support visual review of new elements. To overcome these limitations, we developed LtrDetector, which uses techniques inspired by signal-processing. We compared LtrDetector to LTR_Finder and LTRharvest, the two most successful predecessor tools, on six plant genomes. For each organism, we constructed a ground truth data set based on queries from a consensus sequence database. According to this evaluation, LtrDetector was the most sensitive tool, achieving 16–23% improvement in sensitivity over LTRharvest and 21% improvement over LTR_Finder. All three tools had low false positive rates, with LtrDetector achieving 98.2% precision, in between its two competitors. Overall, LtrDetector provides the best compromise between high sensitivity and low false positive rate while requiring moderate time and utilizing memory available on personal computers. LtrDetector uses a novel methodology revolving around k-mer distributions, which allows it to produce high-quality results using relatively lightweight procedures. It is easy to install and use. It is not species specific, performing well using its default parameters on genomes of varying size and repeat content. It is automatically configured for parallel execution and runs efficiently on an ordinary personal computer. It includes a k-mer scores visualization tool to facilitate manual review of the identified elements. These features make LtrDetector an attractive tool for future annotation projects involving long terminal repeat retrotransposons.
Spiritual Care in the Perinatal Period

In perinatal palliative care, the loss of a baby is a deeply profound experience that calls upon our sense of meaning through religious and spiritual means. Clinicians need to recognize this anguish as spiritual distress in order to help alleviate it as much as possible. Although having a professional clinically trained chaplain (a spiritual specialist) is ideal for a palliative care team, practitioners of perinatal palliative care must be comfortable dealing with spiritual and religious issues as they arise in their everyday work. Clinicians must feel comfortable as a spiritual generalist for when, or if, they do not have access to a spiritual specialist.
Abstract IA14: Molecular programs defining tumor-specific T-cell dysfunction and reprogrammability

Tumor-specific T cells in solid tumors are dysfunctional, allowing tumors to progress. The epigenetic regulation determining T-cell dysfunction and therapeutic reprogrammability is not well understood. We recently found that T-cell dysfunction is a dynamic antigen-driven differentiation program initiated early during tumorigenesis: initially, T cells enter a plastic dysfunctional state from which they can be functionally rescued, but with time and continued tumor antigen encounter, they ultimately enter a fixed dysfunctional state that is resistant to reprogramming. We found that plasticity and imprinting of dysfunction is determined by epigenetic programs, and we identified surface markers associated with plastic and fixed chromatin states that demarcated reprogrammable from non-reprogrammable PD1hi dysfunctional T cells within heterogeneous T-cell populations. Moreover, we recently identified the nuclear factor Tox as a critical regulator of tumor-specific T-cell differentiation. New insights into the epigenetic and molecular programs underlying tumor-specific T-cell differentiation and dysfunction will be discussed. Citation Format: Andrea Schietinger. Molecular programs defining tumor-specific T-cell dysfunction and reprogrammability [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr IA14.
KEOPS complex expression in the frontal cortex in major depression and schizophrenia.

Objectives Recently, the presence of a complete five subunit Kinase, Endopeptidase and Other Proteins of small Size (KEOPS) complex was confirmed in humans. The highly conserved KEOPS protein complex has established roles in tRNA modification, protein translation and telomere homeostasis in yeast, but little is known about KEOPS mRNA expression and function in human brain and disease. Here, we characterise KEOPS expression in post-mortem tissue from subjects diagnosed with major depression (MDD) and schizophrenia and assess whether KEOPS is associated with telomere length dysregulation in neuropsychiatric disorders. Methods We assessed mRNA expression of KEOPS complex subunits TP53RK, TPRKB, GON7, LAGE3, OSGEP, and OSGEP mitochondrial ortholog OSGEPL1 in the dorsolateral prefrontal cortex (DLPFC) of subjects with MDD, schizophrenia and matched non-psychiatrically ill controls (n = 20 per group) using qPCR. We conducted bioinformatic analysis using Kaleidoscope, data mining post-mortem transcriptomic datasets to characterise KEOPS expression in human brain. Finally, we assayed relative telomere length in the DLPFC using a qPCR-based assay and carried out correlation analysis with KEOPS subunit mRNA expression to determine if the KEOPS complex is associated with telomere length dysregulation in neuropsychiatric disorders. Results There were no significant changes in KEOPS mRNA expression in the DLPFC in MDD or schizophrenia compared to non-psychiatrically ill controls. Relative telomere length was not significantly altered in MDD or schizophrenia, nor was there an association between relative telomere length and KEOPS subunit gene expression in these subjects. Conclusions This study is the first to describe KEOPS complex expression in post-mortem brain and neuropsychiatric disorders. KEOPS subunit mRNA expression is not significantly altered in the DLPFC in MDD or schizophrenia. Unlike in yeast, the KEOPS complex does not appear to play a role in telomere length regulation in humans or in neuropsychiatric disorders.
Can the Trade-off Theory Explain Debt Structure?

We examine the optimal mixture and priority structure of bank and market debt using a tradeoff model where banks have the unique ability to renegotiate outside formal bankruptcy. Flexible bank debt offers a superior tradeoff between tax shields and bankruptcy costs. Ease of renegotiation limits bank debt capacity, however. Optimal debt structure hinges upon which party has bargaining power in private workouts. Weak firms have high bank debt capacity and utilize bank debt exclusively. Strong firms lever up to their (lower) bank debt capacity, augment with market debt, and place the bank senior. Therefore, the tradeoff theory offers an explanation for: (i) why young/small firms use bank debt exclusively; (ii) why large/mature firms employ mixed debt financing; and (iii) why bank debt is senior. The tradeoff theory also generates predictions consistent with international evidence. In countries where the bankruptcy regime entails soft (tough) enforcement of contractual priority, bank debt capacity is low (high), implying greater (less) reliance on market debt.
Social Engineering: The Looming Threat

Social Engineering can be performed using many different vectors. A range of people are subject to one of these attacks. Cyber attacks are normally seen as highly technological attacks carried out by someone with a great knowledge of computer systems. These attacks can be as simple as going through the garbage for information or looking over someone’s shoulder and reading the content on their monitor. Social Engineering attacks are an attack that is going to become a greater threat and require more attention with the increased use of IoT devices used for communication. These attacks tend to follow an attack framework to accomplish a goal involving destruction, unauthorized access or to obtain monetary value. The prevention of these attacks starts with the human hence the use of the word social. Mitigation relies on educating the persons the attack will be intended for as well as being able to identify the specific attack and acting accordingly. This paper will focus on the explanation and implementation of the Social Engineering Attack Framework as well as the mitigations to the different types of attacks.
A Fundamental Flaw with UNCITRAL's Approach to Cross-Border Secured Transactions: The Failure to Address Creditor Due Diligence Issues

The development of Article 9 of the Uniform Commercial Code in the 195'0s addressed the problems faced by commercial businesses and lawyers in dealing with the differing laws of 50 states. The UCC solved a massive transaction cost problem by unifying 50 laws into one uniform code. Seeking to emulate the success of Article 9, various international organizations have attempted to develop a harmonized or more uniform approach to international secured transactions. One such organization is the United Nations Commission on International Trade Law ("UNCITRAL"). UNCITRAL has developed a Legislative Guide on Secured Transactions (the "Legislative Guide"). The goal of the Legislative Guide is to reduce the transaction costs of cross-border lending, and thereby increase such lending. The proponents of international efforts such as the Legislative Guide find encouragement in America's adoption of the Uniform Commercial Code, and view their efforts as the initial steps to accomplishing the global equivalent of a uniform code. The thesis of this paper, however, is that efforts such as the Legislative Guide lack a crucial feature of the Uniform Commercial Code. This paper contends that the success of Article 9 of the Uniform Commercial Code is the result, in large part, of its role in guiding the due diligence efforts of lenders in determining whether to make a loan or not. In effect, Article 9 says to lenders: If you conduct due diligence, as guided by Article 9, you will have assurance that you have a valid security interest with the priority you seek. The Legislative Guide does little to address due diligence issues. For this reason, it cannot have the force and vitality of Article 9, and cannot achieve what Article 9 has achieved. This paper further questions whether the Legislative Guide is necessary at all, because the international capital markets have devised powerful means to enable banks to engage in cross-border secured lending without the need for such empty efforts as the Legislative Guide.
Numerical simulations show potential for strong nonisothermal effects during fluid leakage from a geologic disposal reservoir for CO2

Leakage of CO 2 from a primary disposal reservoir is presumed to occur along a fault or fracture zone, which has been modeled as a slab of porous and permeable material embedded in wall rocks of negligibly small permeability. Numerical simulations presented here include multiphase flow, boiling of liquid CO 2 , transitions between supercritical and subcritical conditions, phase partitioning between CO 2 and water, and nonisothermal effects. Depressurization of rising CO 2 is found to produce strong cooling. Conductive heat transfer from the impermeable wall rocks is an important aspect of system evolution. Pressure and temperature conditions are drawn towards the critical point of CO 2 and the CO 2 saturation line. The interplay between multiphase flow in the fracture zone and heat conduction perpendicular to it may produce nonmonotonic, quasi-periodic variations in thermodynamic conditions and CO 2 discharges across the land surface.
Mitogen-activated Protein (MAP) Kinase Is Regulated by the MAP Kinase Phosphatase (MKP-1) in Vascular Smooth Muscle Cells EFFECT OF ACTINOMYCIN D AND ANTISENSE OLIGONUCLEOTIDES

Angiotensin II stimulates hypertrophic growth of vascular smooth muscle cells (VSMC) and activates many growth-promoting kinases such as mitogen-activated protein (MAP) kinase. A novel transcriptionally regulated phosphatase, MAP kinase phosphatase-1 (MKP-1), is induced by angiotensin II in VSMC and selectively dephosphorylates MAP kinase in vitro. Using actinomycin D and antisense oligonucleotides targeted to MKP-1, we demonstrate that MKP-1 regulates MAP kinase in VSMC. Both actinomycin D and MKP-1 antisense oligonucleotides inhibited MKP-1 mRNA expression and caused prolonged activation of the p42 and p44 MAP kinases as measured by in-gel-kinase assays and Western blot. For example, MAP kinase activity 120 min after angiotensin II treatment was 30% (range 25-35%), 79%, and 74% of maximum in control, actinomycin D-treated (3 μg/ml, 30 min), and antisense oligonucleotide-treated (300 nM, 6 h) cells, respectively. A sense oligonucleotide was without effect (34%). MKP-1 antisense oligonucleotides did not affect the activity of MEK indicating that sustained activation of MAP kinase was due to inhibition of MKP-1 expression. These findings demonstrate that inactivation of MAP kinase by angiotensin II is mediated predominantly by MKP-1, suggesting an important role for MKP-1 and other related phosphatases in the regulation of MAP kinases in VSMC.
Ferromagnetic shape memory alloys: where might they be useful?

In this paper, ferromagnetic shape memory alloys, most notably NiMnGa have received considerable attention because of the remarkable 6% to 10% field induced strains they have exhibited at room temperature in the magnetic fields of order 0.5 T. In order to address this question, the important technical properties that these materials exhibit will be reviewed and compared with those of competing active materials.
Beef customer satisfaction: cooking method and degree of doneness effects on the top round steak.

The objective of this research was to evaluate the consumer-controlled factors of cooking method and degree of doneness on Top Choice, Low Choice, High Select, and Low Select top sirloin steaks. The in-home product test was conducted in Chicago, Houston, Philadelphia, and San Francisco. Consumers (n = 2,212) evaluated each top sirloin steak for overall like (OLIKE), tenderness (TEND), juiciness (JUIC), flavor desirability (DFLAV), and flavor intensity (IFLAV) using 23-point hedonic scales. Top sirloin steaks, regardless of city, were consistently cooked to well done or higher degrees of doneness. Dry-heat methods such as outdoor grilling, broiling, and indoor grilling were the most frequent cooking methods used. Four significant interactions existed for OLIKE: USDA quality grade x cooking method (P = .02), city x cooking method (P = .0001), city x degree of doneness (P = .01), and cooking method x degree of doneness (P = .009). Greater differences were found between cooking methods within USDA quality grade than between USDA quality grades within cooking method. Consumers in Houston rated steaks cooked by outdoor grilling higher than those from the other cities, and steaks cooked by indoor grilling were rated the highest among all cooking methods by consumers in Chicago. In Chicago, steaks cooked to more advanced degrees of doneness tended to receive higher ratings, but few differences between degrees of doneness in the other three cities were detected. For outdoor grilling, broiling, and pan-frying, the trend was for OLIKE ratings to decline as degree of doneness increased. The lowest customer satisfaction ratings tended to be given to top sirloin steaks cooked to more advanced degrees of doneness, and consumers most frequently cooked steaks to at least the well done stage. Consumer information programs or the development of postmortem techniques that would ensure acceptable palatability of top sirloin steaks may need to be developed.
Three-Dimensional Baselines for Perceived Self-Motion During Acceleration and Deceleration in a Centrifuge

Three-dimensional motion trajectories were computed, representing the motions that would be perceived by a perfect processor of acceleration information during the acceleration and deceleration stages of a centrifuge run. These motions serve as "baselines" for perceived self-motion in a centrifuge, and depend on the initial perception of orientation and velocity immediately preceding the acceleration and immediately preceding the deceleration. The baselines show that a perfect processor of acceleration information perceives self-motion during centrifuge deceleration significantly differently from self-motion during centrifuge acceleration, despite the fact that the angular accelerations have equal magnitude (with opposite direction). At the same time, the baselines can be compared with subjects' reported perceptions to highlight limitations of the nervous system; limitations and peculiarities of the nervous system are identified as deviations from a baseline. As a result, peculiarities of the nervous system are held responsible for any perception of pitch or roll angular velocity or change in tilt of the body-horizontal plane of motion during the centrifuge run. On the other hand, baselines explain perception of tilt position during deceleration, linear velocity, possible lack of significant linear velocity during deceleration, and yaw angular velocity, including on-axis angular velocity during centrifuge deceleration. The results lead to several experimental questions.
Alkaline cooking (nixtamalisation) and the reduction in the in vivo toxicity of fumonisin-contaminated corn in a rat feeding bioassay.

Nixtamalisation is a widely used food processing method in which whole kernel corn is cooked and steeped in alkaline water. It reduces the amount of fumonisin B1 (FB1) that can be detected after cooking. However, the fate of FB1 during nixtamalisation is not fully understood and potentially toxic reaction products, including matrix-associated “masked” FB1 forms that are not detected by routine analytical methods might remain in nixtamalised corn. To assess how nixtamalisation of whole kernel corn affects fumonisin toxicity, male rats were fed diets containing low, mid or high levels of uncooked (LU, MU, HU) or alkaline cooked (LC, MC, HC) FB1-contaminated corn for 3 weeks. The control diet contained uncontaminated corn only. Apoptotic kidney lesions of the type caused by FB1 were not found in the LC or MC groups. Lesions in the group fed HC were minimal and less severe than those found in the rats fed LU, MU or HU. Furthermore, significantly increased sphinganine and sphingosine concentrations indicative ...
Visceral fat quantification in asymptomatic adults using abdominal CT: is it predictive of future cardiac events?

The purpose of this study was to determine if quantifying visceral adipose tissue (VAT) at CT in asymptomatic adults can predict the likelihood of future cardiac events. Subcutaneous and visceral fat volumes were obtained from abdominal CT utilizing a validated semi-automated software tool in 663 asymptomatic adults (mean age 57.3 years, 379F/284M) undergoing colorectal screening. Patients were followed for subsequent cardiac events, defined as myocardial infarction or coronary intervention for a mean follow-up interval of 7.0 ± 1.4 years. Relevant clinical data including Framingham risk score (FRS) were also collected. Statistical analysis included logistic regression, Pearson correlation coefficients, and Welch and Wilcoxon rank sum tests. Cardiac events were documented in 32 subjects (4.8%) an average 3.0 years after index CT. FRS was predictive of future cardiac events, signified by a higher score (mean score 11.9 vs. 7.4; p < 0.001). HDL levels were significantly lower in the cardiac event cohort (mean 52.2 vs. 61.0; p < 0.01). None of the other clinical variables were predictive and none of the CT-based fat measurements (visceral, subcutaneous, and total adipose tissue; visceral fat %) correlated with future cardiac events (p = 0.561–0.886). Mean visceral fat % in the cardiac event cohort was 38.1% vs. 39.1% for the non-event group. Quantification of VAT at abdominal CT was not predictive of future cardiac events in this asymptomatic cohort, whereas HDL levels and FRSs correlated well with risk.
Actin filaments in human skin fibroblasts are similar in normal persons and patients with Huntington's disease

Actin filaments in skin fibroblasts from patients with Huntington's disease (HD) were examined using immunofluorescent methods. Actin filaments were seen along the axis of cell elongation (stress or sheath filaments) as well as in areas of membrane ruffling (lattice filaments). In some cases, filaments appeared to radiate from foci within the cell. Bundles of these filaments radiated in various directions at different depths within a cell. These structures are similar, in cells from both normal individuals and HD patients, to actin filaments observed in other cell types. The higher-than-normal confluent densities achieved in culture by fibroblasts from patients with Huntington's chorea do not involve alterations in the ultrastructure of actin filaments.
Friendship Networks in Transitions: Married Mothers Return to School

The present study uses a combination of qualitative and quantitative data on forty-four married mothers and 231 of their non-familial associates to investigate changes in the mothers' friendship networks during their first year of enrolment in a university. Drawing upon theories of status similarity and reference groups, it was anticipated that the women's friendship networks would be affected both by changes in status similarity to their associates, and by the women's degree of involvement in the new focus of activity. It was found that (1) the women and their husbands reported that well-educated friends held predominantly positive attitudes towards the enrolment, while less educated friends held predominantly negative attitudes towards it; and (2) full-time students' closeness and frequency of interaction with less educated friends declined notably over the year, while a similar pattern did not emerge among part-time students. Explanations for these patterns are discussed.
Climatological Variations in North Atlantic Tropical Cyclone Tracks

AbstractThis study investigates the relationship between tropical cyclone (TC) tracks and climatological variations in large-scale environmental parameters associated with the TC steering flow. By using the Atlantic Ocean hurricane database for 1950–2010, TCs that form in the main development region (MDR) are categorized into one of three track types: straight moving, recurving landfall, or recurving ocean. As expected, the straight-moving storms are associated with a westward extension and strengthening of the subtropical high, whereas the recurving ocean storms are associated with a weakening of the high. The presence of El Nino conditions in the tropical Pacific Ocean is shown to be associated with a weakening of the high, an increase in the percentage of recurving ocean TCs, and a decrease in the percentage of recurving landfall TCs. Positive phases of the Atlantic Meridional Mode are associated with an increase in the percentage of recurving ocean TCs and a decrease in the percentage of straight-movi...
Neuronal degeneration in the brain of the brindled mouse

Brindled mutant mouse (MObr) is clinically closely similar to kinky hair syndrome (KHS) in humans. Hemizygous males (MObr/Y) of this mutant usually cannot survive beyond the 15th–16th postnatal day. However, some were found to survive into the adult life. Extensive neuronal degeneration in the cerebral cortex was a prominent neuropathological feature of MObr/Y (Yajima and Suzuki, 1979a). In the long-surviving ones, however, such neuronal degeneration gradually disappeared and cortical neuronal loss and axonal degeneration of the underlying white matter were the predominant neuropathological features. which are closely similar to those of KHS, in particular in those patients who survive for more than 1 year. On the basis of our observations on the brain of MObr/Y mice, we hypothesized the possible chronological events on the development of neuropathological lesions in KHS in humans.
Turbine operation with nonsteady flow-analysis and experiments

Abstract The paper describes a theoretical and experimental study of the internal flows in single-stage, axial-flow pulse turbine. In the theoretical analysis, based on the method of characteristics, special attention was given to the boundary condition governing the flow from the nozzles into the rotor blades under off-design conditions. The analysis showed a momentum exchange occurring across the nozzle-rotor boundary, leading to entropy generation in the rotor passages, and corresponding energy dissipation. Experiments conducted on a test turbine, in which turbine internal work was calculated from speed change data, showed remarkably high performance figures. A comparison of predicted performance with test measurements showed good agreement in the range of turbine speeds for which the analysis was written. It was concluded that substantial improvements in pulse turbine performance through design changes involving nozzle and rotor blades are not to be expected.
Nuclear mutations and mitotic recombination in Saccharomyces by light-activated ethidium azides.

Abstract Ethidium mono- and diazide analogs have been used as photoaffinity probes to study the mechanism of the ethidium-induced petite mutation in yeast [7,10,14]. The azide moiety when exposed to light is converted to a reactive nitrine intermediate. The diradical nitrene effects a covalent attachment to sites of interaction bound reversibly by the drug. Ethidium azide photoaffinity labeling has been used to verify the prerequisite covalent attachment of ethidium to mitochondrial DNA to bring about the petite mutation in yeast [6]. Bastos has also reported a specific photoattachment of ethidium azide to a polypeptide (subunit 9) of the membrane bound ATPase in yeast mitochondria [1]. Isolated DNA from yeast cells treated in vivo with [14C]ethidium monoazide plus light contained covalent adducts on both nuclear and mitochondrial DNA, although the specific radioactivity of mitochondrial DNA was more than 10 times higher than nuclear DNA [11]. Drug distribution studies of [14C]ethidium monoazide have indicated that greater than 50% of the covalent adducts in the nuclear centrifugation fraction (2000 × g) reside on nuclear proteins [3]. Nuclear damage in yeast by the photolysis of ethidium azides is apparent from the increased killing effect in cells treated with ethidium azide derivatives plus light as opposed to dark-treated cells [7,10,11]. This communication reports a concomitant increase in nuclear mutations and genetic activity from the photoactivated covalent attachment of ethidium azides to nuclear components.
Radioprotection of the rat small intestine with topical WR‐2721

BACKGROUND The classic radioprotectant WR-2721 has been shown to reduce the severity of small bowel injury when administered systemically shortly before irradiation is delivered. This study tested the possibility that WR-2721 could provide protection when applied topically to intestinal mucosa. The second question addressed was the influence of pH on the effectiveness of this agent. METHODS The model used involved irradiation of exteriorized rat small bowel. A length of intestine was compartmentalized. The various individual segments were filled with a lumenal Tris buffer (pH 9), WR-2721, or a combination of these two, then irradiated with 1100 cGy. The animals were sacrificed 5 days later. Surviving crypt cells and mucosal height were the criteria used to quantitate mucosal injury. RESULTS The pH 9 buffer alone provided a small (16%) but significant preservation of crypt cell numbers. WR-2721 improved crypt survival by 54% at neutral pH, 83% at pH 9. CONCLUSIONS These data indicate that WR-2721, when applied topically to the small bowel mucosa of the rat before irradiation, provides substantial protection against radiation damage. The degree of benefit is amplified greatly when the drug is in an alkaline medium.
Positron-impact ionization, positronium formation, and electronic excitation cross sections for diatomic molecules

Absolute measurements are presented for the positron-impact cross sections for positronium formation, direct ionization, and total ionization of the diatomic molecules ${\mathrm{N}}_{2}$, CO, and ${\mathrm{O}}_{2}$, in the range of energies from threshold to $90\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$. Cross sections for the electronic excitation of the $a\phantom{\rule{0.2em}{0ex}}^{1}\ensuremath{\Pi}$ and ${a}^{\ensuremath{'}}\phantom{\rule{0.2em}{0ex}}^{1}\ensuremath{\Sigma}$ state in ${\mathrm{N}}_{2}$ and the $A\phantom{\rule{0.2em}{0ex}}^{1}\ensuremath{\Pi}$ state in CO near threshold are also presented. The experiment uses a cold, trap-based positron beam and the technique of studying positron scattering in a strong magnetic field. In ${\mathrm{O}}_{2}$, a feature previously seen in the total ionization cross section is observed in both the positronium formation and total ionization cross sections. The possible origin of this feature and its relationship to positron-induced dissociation is discussed. In ${\mathrm{N}}_{2}$, the near-threshold electronic excitation cross section is larger than that for positronium formation. This likely explains the relatively high efficiency of this molecule when used for buffer-gas positron trapping.
Robust capacity expansion of network flows

We consider the problem of expanding arc capacities in a network subject to demand and travel time uncertainty. We propose a robust optimization approach to obtain capacity expansion solutions that are insensitive to this uncertainty. Our results show that, under reasonable assumptions for network flow applications, such robust solutions can be computed by solving tractable conic linear problems. For example, the robust solution for a multicommodity flow problem is obtained by solving a linear program if the problem has a single source and sink per commodity and the uncertainty in demand and travel time is given by independent bounded polyhedral sets. Preliminary computational results show that the robust solution is attractive, as it can reduce the worst case cost by more than 20%, while incurring a 5% loss in optimality when compared to the optimal solution of a representative scenario. © 2007 Wiley Periodicals, Inc. NETWORKS, Vol. 50(2), 136145 2007
Structural Defects Induced by Malignant Mutations in the Regulatory Light Chain of Myosin

The current study is aimed at providing insight into the structural defects underlying the development of malignant phenotypes induced by D166V and R58Q mutations in the regulatory light chain (RLC) of myosin. X-ray diffraction studies were carried out on the freshly skinned papillary muscle fibers from transgenic mutant vs. wild-type mice using the small angle instrument on the BioCAT beamline 18-D at the Advanced Photon Source. The fiber was immersed in relaxing solution and the X-ray measurements were made at two sarcomere lengths (SL), short (∼2.3 μm) and long (∼2.5 μm). At the short SL, we observed that the R58Q mutation caused a significant increase in the interfilament lattice spacing (d1,0) compared to Tg-WT while no change was observed for the D166V mutation. Interestingly, upon stretch to long SL, WT and R58Q showed a significantly decreased lattice spacing (by ∼1.5 nm) while the d1,0 in the D166V myocardium remained the same as measured at short SL. The lack of structural response to stretch observed for D166V may indicate a mutation induced increase in fiber stiffness. In support of this notion, measurements of passive force performed in glycerinated skinned papillary Tg-D166V fibers demonstrated significantly increased levels of passive tension at all points of stretch (10%, 20%, 30% and 40% of fiber length) indicating an elevated resistance to stretch in Tg-D166V compared to Tg-WT fibers. Our results suggest that the mutant-induced structural changes that most likely trigger pathological remodeling of the heart leading to FHC are different for both studied RLC mutations. Supported by AHA-10POST3420009 (PM), NIH- HL071778 (DSC), HL090786 (DSC), P41 GM103622-17 (TI)
APG UXO discrimination studies using advanced EMI models and TEMTADS data

Recently, new generation, relatively sophisticated, ultra wideband EMI sensors with novel waveforms and multi-axis or vector receivers, have been developed which operate either in the time domain or in the frequency domain. Among these emerging technologies is the Time-domain Electromagnetic Multi-sensor Tower Array Detection System (TEMTADS). The system consists of 25 transmit/receive pairs arranged in a 5 × 5 grid, each with a square 35-cm diameter transmitter coil and a concentric square 25-cm receiver coil. The sensor activates the transmitter loops in sequence, and for each transmitter all receivers receive, measuring the complete transient response over a wide dynamic time range going approximately from 100 μs to 25 ms and distributed in 123 time gates. Thus it provides 625 data points at each location, without the need for a relative positioning system due to its fixed geometry. The combination of spatial diversity in the measurements and well-located sensor positions offers unprecedented data quality for discrimination processing algorithms. To take advantage of the data diversity that this instrument provides, we will use both of the following in an analysis of data acquired with the TEMTADS at Aberdeen Proving Ground (APG) in 2008: (1) advanced, physically complete EMI forward models such as the normalized surface magnetic source (NSMS) model and (2) a data-inversion scheme that uses the newly developed HAP method to estimate the location of a target. Initially the applicability of the NSMS and HAP algorithms to TEMTADS data sets are demonstrated by comparing the modeled data to test-stand and calibration data, and then the APG blind discrimination studies are conducted using as discrimination parameters the total NSMS and principal axes of the induced magnetic polarizability tensor for each target. The classification is done on the extracted feature vector via statistical classification tools.
Photoannulation of 4,4-Dimethylcyclohex-2-en-1-one To 1,1-Diphenylethylene

The photoannulation of 4,4-dimethylcyclohex-2-en-1-one (DMC) to 1,1-diphenylethylene (DPE) results in the [2+2] formation of cyclobutanes exhibiting regio- and stereoselectivity. Additionally, regio- and stereoisomers of substituted octahydrophenanthrenes are produced. Formally, these are derived from alpha−ortho coupling of a 1,4-biradical, followed by rearomatization. From laser flash photolysis experiments, we conclude that the temporal absorbance profile observed following excitation of DMC in the presence of DPE is a composite of multiple triplet state transients that includes triplet state 1,1-diphenylethylene and likely includes a triplet state 1,4-biradical. This analysis of the transient data reveals energy transfer and product forming interactions between 3DMC and ground-state DPE. The present work renders our earlier interpretation [J. Am. Chem. Soc. 1996, 118, 8741],1 that the transient observed in this system was a 3DMC−DPE exciplex, unnecessary and unlikely.
Phenobarbital Induction Mediated by a Distal CYP2B2 Sequence in Rat Liver Transiently Transfected in Situ

The promoter activities of the genes for cytochrome P450 2B1 (CYP2B1) and cytochrome P450 2C1 (CYP2C1) have been assayed by direct injection of promoter-luciferase chimeric genes into rat liver. Activities of minimal promoters for CYP2C1 and CYP2B1 were detectable in untreated animals but were not increased by treatment of the animals with phenobarbital. After insertion to the 5' side of the minimal promoters of one to three copies of the CYP2B2 sequence from -2318 to -2155, a phenobarbital-responsive element in primary hepatocyte cultures (Trottier, E., Belzil, A., Stoltz, C., and Anderson, A. (1995) Gene (Amst.) 158, 263-268), phenobarbital treatment induced the activity of the CYP2C1 promoter by 5-15-fold and the CYP2B1 promoter by 2.5-5-fold. Mutation of a basal transcription element-like motif and a CCAAT/enhancer binding protein element in the CYP2B1 proximal promoter region reduced expression, but 3-4-fold induction by phenobarbital was retained. Mutation of the "Barbie box," a putative phenobarbital-responsive element (He, J.-S., and Fulco, A. J. (1991) J. Biol. Chem. 266, 7864-7869) in the CYP2B1 proximal promoter did not reduce the relative response to phenobarbital. These results demonstrate that direct injection of DNA into rat liver may be used to assay phenobarbital responsiveness of cytochrome P450 genes. In this system, a distal CYP2B2 element mediates a response to phenobarbital, and proximal elements, including the Barbie box, are not required for the induction.
Epilithic periphyton and detritus studies in a subalpine stream

The accumulation of epilithic periphyton in Ward Creek, a permanent stream within the Lake Tahoe basin, California, was measured weekly at three stations from July through September, 1972. Subsamples were analyzed for total carbon and adenosine triposphate content. The mean total carbon content at three stations over the period of investigation was 0.508 ± 0.263 mg carbon cm−2. Live biomass, as estimated from ATP measurements, averaged 0.121 ± 0.115 mg carbon cm 2. It was estimated that approximately 76% of the organic carbon accumulating on rock substrates was present as detritus. Scanning electron microscopy of rock substrates suggested that much of this detrital accumulation may consist of diatom stalk materials.
Immunocompromise-dependent infection rather than opportunistic infection.

s referred to opportunistic agents or microbes and most references are to opportunistic infections. However, analyzed in this sense, “opportunistic infection” no longer is meaningful in a pathogenetic sense. Still, it is used ten times as frequently as “opportunistic microbe.” Although the former term is shorter and more euphonious, it is also incongruous. No common pathogenic microbial factors have been identified with opportunism. Because the decisive factor is the degree of immunocompromise of the host, immunocompromisedependent infection @Do is a more descriptive term. This pathogenetically and semantically compatible term is advantageous for teaching and general communication. As in politics and literature, word use conveys concepts in medicine. The medical community should strive for a scientific terminology and avoid terms that misrepresent pathogenesis. “Opportunistic microbe” and
Salivary testosterone measurements: Reliability across hours, days, and weeks

Salivary testosterone measurements would appear to be useful in behavioral research, where subjects are often reluctant to provide serum samples. The usefulness of salivary measurements depends upon their reliability, however, which was the focus of the present investigation. In four studies, 270 male and 175 female subjects collected saliva samples at times ranging from 30 min to 8 weeks apart. Subjects collected samples on at least two days, at time of awakening, midmorning, late afternoon, and late evening. Mean testosterone concentration dropped about 50% from morning to evening for both sexes, with largest drops early in the day. Mean reliability was r = .64 across two days and r = .52 across seven-eight weeks. Menstrual cycle effects were negligible. Reliability can be increased by using more than one measurement, and it is probably desirable to combine measurements taken several weeks apart. Salivary assays offer a practical way of measuring testosterone in free-ranging subjects outside the laboratory.
Interaction of Calcium with Native and Decarboxylated Human Factor X. EFFECT OF PROTEOLYSIS IN THE AUTOLYSIS LOOP ON CATALYTIC EFFICIENCY AND FACTOR Va BINDING

Abstract Human factor X is a two-chain, 58-kDa, vitamin K-dependent blood coagulation zymogen. The light chain of factor X consists of an NH2-terminal γ-carboxyglutamic acid (Gla) domain, followed by a few helical hydrophobic residues and the two epidermal growth factor-like domains, whereas the heavy chain contains the serine protease domain. In this study, native factor X was found to contain three classes of Ca2+-binding sites: two high affinity (K d 100 ± 30 μm), four intermediate affinity (K d 450 ± 70 μm), and five to six low affinity (K d2 ± 0.2 mm). Decarboxylated factor X in which the Gla residues were converted to Glu retained the two high affinity sites (K d 140 ± 20 μm). In contrast, factor X lacking the Gla domain as well as a part of the helical hydrophobic residues (des-44-X) retained only one high affinity Ca2+-binding site (K d 130 ± 20 μm). Moreover, a synthetic peptide composed of residues 238–277 (58–97 in chymotrypsinogen numbering) from the protease domain of factor X bound one Ca2+ with high affinity (K d 150 ± 20 μm). From competitive inhibition assays for binding of active site-blocked factor Xa to factor Va in the prothrombinase complex, theK d for peptide-Va interaction was calculated to be ∼10 μm as compared with 30 pm for factor Xa and ∼1.5 μm for decarboxylated factor Xa. A peptide containing residues 238–262(58–82) bound Ca2+ with reduced affinity (K d ∼600 μm) and did not inhibit Xa:Va interaction. In contrast, a peptide containing residues 253–277(73–97) inhibited Xa:Va interaction (K d ∼10 μm) but did not bind Ca2+. In additional studies, Ca2+ increased the amidolytic activity of native and des-44-Xa toward a tetrapeptide substrate (benzoyl-Ile-Glu-Gly-Arg-p-nitroanilide) by approximately 1.6-fold. The half-maximal increase was observed at ∼150 μm Ca2+ and the effect was primarily on the k cat. Ca2+ also significantly protected cleavage at Arg-332-Gln-333(150–151) in the protease domain autolysis loop. Des-44-Xa in which the autolysis loop was cleaved possessed ≤5% of the amidolytic activity of the noncleaved form; however, the S1 binding site was not affected, as determined by the p-aminobenzamidine binding. Additionally, autolysis loop-cleaved, active site-blocked native factor Xa was calculated to have ∼10-fold reduced affinity for factor Va as compared with that of the noncleaved form.
UVote: A Ubiquitous E-voting System

Traditional e-voting systems replace the paper-based process with an electronic one at official voting locations. Remote e-voting, where the voter can vote from any location, increases both participation rates in the elections and the user's satisfaction as it eases the voting process and saves time. However, having a remote e-voting system increases the security vulnerabilities. Those vulnerabilities include harder user authentication, possibility of malicious software on the user's devices, network malicious nodes, coercion, and vote-selling. We introduce UVote as a ubiquitous, convenient, verifi-able, and incoercible democratic e-voting system. UVote works as a front-end to many of the current traditional e-voting systems, providing the user with a convenient voting solution with guarantees on security, achieving the best of both worlds. The key design principal in UVote is redundancy at system architecture different components, including voting devices, vote verification, and allowing voting multiple times. We present the UVote architecture and how it leverages redundancy to achieve its goals. We also analyze the different possible attacks and how UVote combats them. Evaluation of the system performance shows that these advantages come with minimal performance overhead. This highlights that UVote is a truly ubiquitous e-voting system.
Shoreline Changes on an Urban Atoll in the Central Pacific Ocean: Majuro Atoll, Marshall Islands

Abstract FORD, M., 2012. Shoreline changes on an urban atoll in the central Pacific Ocean: Majuro atoll, Marshall Islands. Majuro is the capital and most populated atoll in the Republic of the Marshall Islands and is located approximately 3700 km W–SW of Oahu, Hawaii. Like other atolls, Majuro is considered highly vulnerable to sea level rise. One of the widely perceived impacts of sea level rise on atoll islands is widespread chronic erosion. Using a combination of aerial photos and satellite imagery, this study presents an analysis of shoreline change over a 34- to 37-year study period, characterized by rapidly increasing population, coastal development, and rising sea level (3.0 mm y−1). Results show most (93%) urban and rural villages have increased in size over the study period. Shoreline change analysis indicates the urban area has expanded both toward the lagoon and onto the ocean-facing reef flat. Shoreline change within the urban area of Majuro has been largely driven by widespread reclamation fo...
Pregnancy-associated Hypertriglyceridemia in Normal and Diabetic Women: Differences in Insulin-dependent, Non-insulin-dependent, and Gestational Diabetes

In this study longitudinal observations of plasma lipo-proteins were made in pregnant diabetic women classified according to the National Diabetes Data Group. Sequential measurements at second trimester (25–27 wk), third trimester (34–37 wk), and 3 mo postpartum (control period) were carried out in 18 diabetic and 6 normal women. In 15 diabetic and 4 normal women from this group, 24-h plasma glucose, serum C-peptide levels, and HbA 1c concentrations were measured. Another group of 15 normal and 18 diabetic women underwent determinations of fasting plasma lipoproteine and other parameters at one or more of the test periods. Insulin-dependent diabetic patients (IDDM, type I) as a group did not differ from normal controls in mean plasma levels of total cholesterol (CHOL), triglyceride (TG), very-low-density lipoprotein triglyceride (VLDL TG), low-density lipoprotein cholesterol (LDL CHOL), high-density lipoprotein cholesterol (HDL CHOL), or ratios of TG:CHOL in LDL or HDL during mid or late pregnancy or 3 mo postpartum. In marked contrast, non-insulin-dependent diabetics (NIDDM, type II) had significantly higher total fasting TG at second trimester (P These results indicate that women with IDDM diabetes do not differ from normal women with respect to pregnancy-associated changes in lipid metabolism. On the other hand, women with NIDDM and GDM exhibit a pregnancy-associated hypertriglyceridemia.
Phenology for Science, Resource Management, Decision Making, and Education

[1] Fourth USA National Phenology Network (USA-NPN) Research Coordination Network (RCN) Annual Meeting and Stakeholders Workshop; Milwaukee, Wisconsin, 21–22 September 2010; Phenology, the study of recurring plant and animal life cycle events, is rapidly emerging as a fundamental approach for understanding how ecological systems respond to environmental variation and climate change. The USA National Phenology Network (USA-NPN;http://www.usanpn.org) is a large-scale network of governmental and nongovernmental organizations, academic institutions, resource management agencies, and tribes. The network is dedicated to conducting and promoting repeated and integrated plant and animal phenological observations, identifying linkages with other relevant biological and physical data sources, and developing and distributing the tools to analyze these data at local to national scales. The primary goal of the USA-NPN is to improve the ability of decision makers to design strategies for climate adaptation.
The sectoral labor supply of married couples in Brazil: Testing the unitary model of household behavior

An assumption of the unitary model of household decision-making is that household members maximize one household utility function. This assumption implies that households pool their income and, therefore, the ownership of nonwage income has no effect on household demand. In this paper, this implication is tested by estimating multi-sector labor supply equations for men and women in Brazil. The results indicate that the unitary model is rejected in the informal and self-employment sectors for men and the formal and informal sectors for women; in these cases own nonwage income has a significantly negative effect on labor supply while spousal nonwage income has no significant effect.