cssi/SciSciGPT-SciSciNet huggingface dataset:
Metal-dependent allosteric activation and inhibition on the same molecular scaffold: the copper sensor CopY from Streptococcus pneumoniae

Resistance to copper (Cu) toxicity in the respiratory pathogen Streptococcus pneumoniae is regulated by the Cu-specific metallosensor CopY. CopY is structurally related to the antibiotic-resistance regulatory proteins MecI and BlaI from Staphylococcus aureus, but is otherwise poorly characterized. Here we employ a multi-pronged experimental strategy to define the Spn CopY coordination chemistry and the unique mechanism of allosteric activation by Zn(II) and allosteric inhibition by Cu(I) of cop promoter DNA binding. We show that Zn(II) is coordinated by a subunit-bridging 3S 1H2O complex formed by the same residues that coordinate Cu(I), as determined by X-ray absorption spectroscopy and ratiometric pulsed alkylation-mass spectrometry (rPA-MS). Apo- and Zn-bound CopY are homodimers by small angle X-ray scattering (SAXS); however, Zn stabilizes the dimer, narrows the conformational ensemble of the apo-state as revealed by ion mobility-mass spectroscopy (IM-MS), and activates DNA binding in vitro and in cells. In contrast, Cu(I) employs the same Cys pair to form a subunit-bridging, kinetically stable, multi-metallic Cu·S cluster (KCu ≈ 1016 M−1) that induces oligomerization beyond the dimer as revealed by SAXS, rPA-MS and NMR spectroscopy, leading to inhibition of DNA binding. These studies suggest that CopY employs conformational selection to drive Zn-activation of DNA binding, and a novel Cu(I)-mediated assembly mechanism that dissociates CopY from the DNA via ligand exchange-catalyzed metal substitution, leading to expression of Cu resistance genes. Mechanistic parallels to antibiotic resistance repressors MecI and BlaI are discussed.
Long-Term Effects of Burn Season and Frequency on Ponderosa Pine Forest Fuels and Seedlings

Prescribed fire is widely applied in western US forests to limit future fire severity by reducing tree density, fuels, and excessive seedlings. Repeated prescribed burning attempts to simulate historical fire regimes in frequent-fire forests, yet there is limited long-term information regarding optimal burn season and frequency. In addition, burns are operationally feasible only in the spring and late fall, largely outside the historical wildfire season. This study quantifies the effect of seasonal reburns on woody surface fuels, forest floor fuels, and understory tree regeneration abundance in six previously thinned ponderosa pine (Pinus ponderosa Lawson & C. Lawson) stands in the southern Blue Mountain Ecoregion of Oregon, USA. Each stand consisted of an unburned control, and four season by reburn treatments: spring 5 yr, spring 15 yr, fall 5 yr, and fall 15 yr. We evaluated season and frequency of reburn for woody surface fuel (1 hr to 1000 hr), forest floor fuel (litter and duff, undifferentiated), and understory conifer seedling density (regeneration). Burning was initiated in the fall of 1997 and spring of 1998; we present results in this paper through 2014 for fuel, and 2015 for seedlings. All reburn treatments reduced the forest floor depth compared to those areas not burned (controls). Fall burning, regardless of frequency, generated 1000 hr fuel primarily from overstory mortality resulting from the initial entry burns and subsequent snag and branch fall. But, for the other woody fuel types, reburning had minimal impact, regardless of season or frequency. All reburn treatments reduced regeneration survival, but 5 yr fall reburning was most effective in reducing excessive conifer seedlings. Repeated spring or fall reburns following thinning will reduce forest floor depth but, to achieve low woody fuel loads and control excessive conifer regeneration, it may be necessary to conduct reburns using different timing, such as during drier periods when wildfire ignitions by lightning occurred historically.
Does Celebrity Issue Advocacy Mobilize Issue Publics

Case studies and correlational evidence suggest that celebrity political advocacy leads to media coverage and public attention. With a new dataset of celebrity witnesses at congressional hearings, ...
42V PowerNet System Protection Concepts

Introduction of the 42V-PowerNet requires consideration of architecture and voltage specific fault scenarios.
Leptin and leptin receptor expression in skeletal muscle and adipose tissue in response to in vivo porcine somatotropin treatment

The present study was performed to examine the response of leptin and leptin receptor (Rb) genes to porcine somatotropin (pST) stimuli in finishing pigs. Twelve crossbred barrows (Yorkshire x Landrace) were used in this study. Animals were individually fed a basal diet containing 18% CP, 1.2% lysine, and 3.5 Mcal of DE/kg ad libitum (as-fed basis). At 90 kg, six pigs were treated with daily injections of recombinant pST (10 mg) in sterile bicarbonate buffer, whereas the other six pigs were injected with sterile bicarbonate buffer (controls). With initiation of pST treatment, the quantity of feed offered was 85% of calculated ad libitum intake based on BW and adjusted every 3 d. Diet restriction was designed to correct for the effects of the known inhibition in feed intake because of pST treatment in swine. Animals were maintained on treatment for 2 wk. A blood sample was obtained from each pig on d 14 of treatment, 6 h after pST injection. Tissue samples were collected on d 15, frozen in liquid N2, and stored at -80 degrees C before analysis for mRNA abundance. Total RNA was amplified by reverse transcription (RT) PCR with subsequent quantification of transcripts by capillary electrophoresis with laser-induced fluorescence detection. Samples included outer subcutaneous adipose tissue (OSQ), middle subcutaneous adipose tissue (MSQ), leaf fat (LF), liver, latissimus dorsi (LD), and biceps femoris (BF). Restricted feeding resulted in no change in BW of control pigs, whereas pST treatment increased BW by 6.9 +/- 0.5 kg (P < 0.001). Treatment with pST produced a 12-fold increase in serum ST concentration relative to control pigs (P < 0.002). Serum leptin concentration was increased by 17% in swine treated with pST relative to control pigs (P < 0.011). Leptin mRNA abundance was increased in liver by pST treatment (P < 0.05). Administration of pST decreased leptin Rb (Ob-Rb) mRNA abundance by 27% in liver (P < 0.044) and by 49.5% in OSQ (P < 0.025) relative to controls. The present data suggest that pST does not affect leptin expression independent of dietary intake because the restricted feeding regimen used in the present study precluded detection of major change in leptin gene expression. Changes in Ob-Rb mRNA abundance by pST treatment indicate that ST or the metabolic adaptations to ST have a role in regulating Ob-Rb expression.
Automatic static feature generation for compiler optimization problems

Modern compilers have many optimization passes which help to get a better binary code for a given program. These optimizations are NP-hard. People use different heuristics to get a near optimal solution. These heuristics are designed by a compiler expert after examining sample programs. This is a challenging task. Recently, people have used machine learning techniques instead of heuristics for compiler optimizations. Machine learning techniques have not only eliminated the human efforts but have also out-performed human made huristics. However, the human efforts have now been moved from creating heuristics to selecting good features. Selecting right set of features is important for machine learning techniques since no machine learning tool will work well with poorly choosen features. This paper introduces a noval approach to generate features for machine learning for compiler optimization problems with out any human involvement.
Multimedia data handling and integration for rehabilitation research

With advances in data acquisition devices, current rehabilitation research involves extensive experimental trials to identify the underlying cause or long-term consequences of certain pathologies and to improve motor functions by examining the movement patterns of affected individuals. For research focused on movement analysis, high volume of multimedia data such as high-speed video is acquired with other data types such as surveys, spreadsheets, force data recordings from instrumented surfaces etc. These datasets are recorded from various standalone sources however multimedia data in rehabilitation research is often requires analysis in context with subject’s medical history, treatment plan or progress. But in current research workflow, no pathways and data handling protocols are defined to successfully achieve comprehensive integration of multimedia data, for various data types collected at various stages in a clinical trial, different data handling protocols needs to be defined and designed. In this presentation, we will be focusing on multimedia data only such as high-speed video files collected during a clinical trial. Multimedia data collected during a rehabilitation research often end up residing in an isolated space. Our aim for this presentation is to design and evaluate data handling steps for successful integration, storage and retrieval of multimedia data. This presentation focuses on establishing tools that can be used between data acquisition step to data storage for media files. We will present method for metadata creation for multimedia data based on the electronic patient data (ePR) model design as well as two common standards of medical imaging, DICOM and PACS to form an effective data handling protocol. For evaluation, data set collected for wheelchair movement analysis study at Rancho Los Amigos National Rehabilitation Center in Downey, California will be used. The broader aim of this paper is to present development of standards and protocols for multimedia data handling in a clinical workflow based on medical imaging informatics.
Finite-Time Estimation and Control for Multi-Aircraft Systems Under Wind and Dynamic Obstacles

In this paper, the problem of generating safe trajectories for multi-agent systems in the presence of wind and dynamic obstacles is considered. A robust controller is designed to counteract a class...
A Practical Discussion of Buyer Supplier Relationship Development

Every organization engages in buyer-supplier transactions to obtain materials and services to operate its business. Each pair of buyers and suppliers involved in such transactions develops a relationship between the two parties. This paper provides a framework for understanding how these relationships develop and for developing relationship strategies. Key variables are defined and a temporal relationship process model is provided. The findings of theoretical papers are translated into a form that practitioners will find useful. Using practical scenarios, the model framework is put into a practical perspective that can be applied at any stage of the buyer-supplier relationship process.
Assessing the hemodynamic contribution of capillaries, arterioles, and collateral arteries to vascular adaptations in arterial insufficiency.

Objective There is currently a lack of clarity regarding which vascular segments contribute most significantly to flow compensation following a major arterial occlusion. This study uses hemodynamic principles and computational modeling to demonstrate the relative contributions of capillaries, arterioles, and collateral arteries at rest or exercise following an abrupt, total, and sustained femoral arterial occlusion. Methods The vascular network of the simulated rat hindlimb is based on robust measurements of blood flow and pressure in healthy rats from exercise and training studies. The sensitivity of calf blood flow to acute or chronic vascular adaptations in distinct vessel segments is assessed. Results The model demonstrates that decreasing the distal microcirculation resistance has almost no effect on flow compensation, while decreasing collateral arterial resistance is necessary to restore resting calf flow following occlusion. Full restoration of non-occluded flow is predicted under resting conditions given all chronic adaptations, but only 75% of non-occluded flow is restored under exercise conditions. Conclusion This computational method establishes the hemodynamic significance of acute and chronic adaptations in the microvasculature and collateral arteries under rest and exercise conditions. Regardless of the metabolic level being simulated, this study consistently shows the dominating significance of collateral vessels following an occlusion.
A retreat critique: Deliberations on design and ethics in the flood zone

Climate change is increasingly making areas of our planet difficult or dangerous to inhabit. ‘Managed retreat’, the intentional relocation of settlements away from hazardous zones, is growing as a ...
On the effects of selection and mutation on species tree inference

A common question that arises when inferring species-level phylogenies from genome-scale data is whether selection acting on certain parts of the genome could create a bias in the inferred phylogeny. While most methods for species tree inference currently assume the multispecies coalescent (MSC), all methods that we are aware of utilize only the neutral coalescent process. If selection is in fact present, failure to adequately model it could introduce substantial bias. We work toward rigorously addressing this question using mathematical theory by deriving a version of the coalescent including selection and mutation as a limiting approximation of the Wright-Fisher model with selection and mutation, and showing that it can be used to closely approximate the distribution of coalescent times in the presence of selection and mutation. We confirm the adequacy of the approximation with a simulation study, and discuss its implications for species tree inference. Our results show that in a general class containing many cases of interest, selection has only a small impact on the coalescent process, and ignoring selection when it is present does not have a substantial negative impact on inference of the species tree topology.
Complex Sampling Designs in Large-Scale Education Surveys: A Two-Level Sample Distribution Approach

Large-scale education data are collected via complex sampling designs that incorporate clustering and unequal probability of selection. Multilevel models are often utilized to account for clusterin...
Lantern: an integrative repository of functional annotations for lncRNAs in the human genome

With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation resources. Although, there are a plethora of resources for annotating genes, despite the extensive corpus of lncRNA literature, the available resources with lncRNA ontology annotations are rare. We present a lncRNA annotation extractor and repository (Lantern), developed using PubMed’s abstract retrieval engine and NCBO’s recommender annotation system. Lantern’s annotations were benchmarked against lncRNAdb’s manually curated free text. Benchmarking analysis suggested that Lantern has a recall of 0.62 against lncRNAdb for 182 lncRNAs and precision of 0.8. Additionally, we also annotated lncRNAs with multiple omics annotations, including predicted cis-regulatory TFs, interactions with RBPs, tissue-specific expression profiles, protein co-expression networks, coding potential, sub-cellular localization, and SNPs for ~ 11,000 lncRNAs in the human genome, providing a one-stop dynamic visualization platform. Lantern integrates a novel, accurate semi-automatic ontology annotation engine derived annotations combined with a variety of multi-omics annotations for lncRNAs, to provide a central web resource for dissecting the functional dynamics of long non-coding RNAs and to facilitate future hypothesis-driven experiments. The annotation pipeline and a web resource with current annotations for human lncRNAs are freely available on sysbio.lab.iupui.edu/lantern.
Traveling Wave Relays for Distribution Feeder Protection with High Penetrations of Distributed Energy Resources

Increased penetration of power electronics interfaced Distributed Energy Resources (DER) like PV, electric vehicle and battery storage in the distribution system (both in numbers and sizes) may cause bi-directional power flows under normal operation. In addition, they contribute low fault current under short circuit conditions. These two changes can impact the proper operation of legacy protection systems. This can add additional challenges during weak grid and islanded operation. In this research, traveling wave (high frequency) signature based protection scheme is proposed for future distribution systems. Simulations are performed under different transient scenarios to provide insight into the high frequency signatures to show the traveling wave behavior. Finally, this paper discusses the importance of sensing and digital processing requirements for traveling-wave protection in distribution system.
Outcomes of Radial Head Fractures Treated With the "Tripod Technique".

Purpose For fractures requiring operative fixation, the “tripod technique” using headless compression screws has recently been described as a less invasive alternative to open reduction and internal fixation with plate and screws. The purpose of this study was to evaluate the clinical and radiographic outcomes of the tripod technique for the treatment of radial head and neck fractures. Methods We performed a retrospective chart review of all radial head and neck fractures treated with the tripod technique at our institution over a 10-year period. Patients with less than 6 months of follow-up were excluded. Outcomes were evaluated at the latest follow-up using range of motion measurements and the Quick Disabilities of the Arm, Shoulder and Hand questionnaire. Results We evaluated 13 patients with a mean age of 48 years and average follow-up of 72 months (range, 21–153 months). All the patients achieved union by 12 weeks after surgery. The average postoperative Quick Disabilities of the Arm, Shoulder and Hand score was 5.9 (range, 0–23). The mean flexion was 139°, and the mean extension was −8°. There were no major postoperative complications . Five patients had minor complications. No patients required a reoperation . Conclusions The tripod technique is a useful alternative to the traditional method of plate and screw fixation for unstable radial head and neck fractures. Type of study/level of evidence Therapeutic IV.
A modernized PDL approach for Ada software development

The desire to integrate newly available, graphically-oriented Computed Aided Software Engineering (CASE) tools with existing software design approaches is changing the way Program Design Language (PDL) or Process Description Language is used for large system development. In the approach documented here, Software Engineers use graphics tools to model the problem and to describe high level software design in diagrams. An Ada-based PDL is used to document low level design. Some results are provided along with an analysis for each of three smaller General Electric (GE) Ada development projects that utilized variations on this approach. Finally some considerations are identified for larger scale implementation.
The uptake, storage, release and metabolism of noradrenaline in sympathetic nerves

Publisher Summary This chapter describes some investigations on the uptake, release, and metabolism of noradrenaline (NA) in sympathetic nerves. The main approach to study the biochemistry of adrenergic neurons is the use of adrenergic drugs and radioactive catecholamines. NA is metabolized via two major metabolic pathways: deamination by monoamine oxidase and O -methylation by catechol- O -methyltransferase. Radioactive NA is a useful tool to study the subcellular localization of NA in a sympathetic neuron. Endogenous NA is localized in a particulate component within splenic nerves. The uptake and binding of [ 3 H]noradrenaline by granulated vesicles of sympathetic nerves help in the temporary inactivation of a catecholamine. The storage of NA in a sympathetic neuron requires an optimal electrolyte milieu. The rate of NA synthesis varies with the rate of utilization of the catecholamine. NA is stored in sympathetic nerves in a heterogeneous fashion. It is also possible that O -methylation serves as a mechanism for the rapid removal of NA from the extraneural pool.
Biogenesis, Structure and Function of Lysosomes

Lysosomes are organelles that are surrounded by a single membrane and contain many hydrolases that are most active at an acidic pH. The pH within the lysosomal lumen is usually maintained between 5.0 and 5.5 by a multisubunit, proton-pumping ATPase in the lysosomal membrane of mammalian cells and in the vacuolar membrane of yeast. Other organelles having some of the properties of lysosomes include late endosomes and multivesicular bodies. However, these organelles have protein and lipid constituents at least partially distinct from lysosomes. Enzymes in the lysosomal lumen are targeted to that location by mannose 6-phosphate (M6P) carbohydrate modifications in the case of mammalian cell lysosomes or by linear peptide sequences for the yeast vacuole. Integral membrane proteins within the lysosomal and vacuolar membranes are targeted to that location due to critical tyrosine or dileucine peptide motifs in cytosolic regions of the proteins. These motifs interact with vesicle coat protein complexes that concentrate the proteins into vesicles destined for fusion with lysosomes. Peripheral lysosomal membrane proteins generally interact strongly with one or more integral membrane proteins and/or lipids. Lysosomes account for 1 to 15% of cell volume and of cell protein in mammalian cells and 30 to 90% of cell volume in fungal and plant cells. This variability depends on cell type and physiological status. The morphological appearance of lysosomes also varies from vesicular to a more complex tubular lattice. Lysosomes are responsible for degrading both extracellular and intracellular proteins as well as other macromolecules. The role of lysosomes in overall intracellular protein degradation depends on the cell type and nutritional conditions. Lysosomes are responsible for most protein degradation in liver and kidney, and certain lysosomal pathways of proteolysis are activated in response to nutritional deprivation. On the other hand, lysosomes play a minor role in protein degradation in skeletal muscle and lymphocytes, where the ubiquitin-proteasome proteolytic pathway predominates. Lysosomal pathways of proteolysis operate to some extent in all eukaryotic cells except in mature red blood cells that do not contain organelles, and there are at least six different pathways by which proteins can be delivered to lysosomes for digestion. Keywords: Lysosome; Vacuole; Mannose 6-Phosphate Receptor; Phosphoinositides; Lysosomal Storage Disease
Magnetic and transport properties of single crystal LnRu2Al10 (Ln = Pr, Gd, Yb)

Single crystals of LnRu2Al10 (Ln = Pr, Gd, Yb) have been grown using the self-flux method, their structure has been determined by single crystal x-ray diffraction, and their magnetic and electronic transport properties have been studied. LnRu2Al10 are members of the Y bFe2Al10 structure type with space group Cmcm. PrRu2Al10 displays paramagnetic behaviour down to 13.2 K, at which temperature it enters a non-magnetic singlet ground state, with a large paramagnetic Curie–Weiss temperature of − 49.8(14) K. GdRu2Al10 orders antiferromagnetically at 15.5 K. Y bRu2Al10 is a Pauli paramagnet indicating that the Yb is divalent. The properties of these three analogues are compared with LnM2Al10 (M=Fe, Ru, Os).
Laboratory Activities to Support Student Understanding of the Molecular Mechanisms of Mutation & Natural Selection

Abstract The molecular basis of evolution is an important and challenging concept for students to understand. In a previous article, we provided some of the scientific background necessary to teach this topic. This article features a series of laboratory activities demonstrating that molecular events can alter the genomes of organisms. These activities are most appropriate for undergraduate students in Honors Biology, Genetics, or Molecular Biology courses. Student laboratory instructions are included to allow students to conduct the activities, make observations, interpret the results, and draw conclusions.
Evidence for a fruit fly hemangioblast and similarities between lymph-gland hematopoiesis in fruit fly and mammal aorta-gonadal-mesonephros mesoderm

The Drosophila melanogaster lymph gland is a hematopoietic organ1 and, together with prospective vascular cells (cardioblasts) and excretory cells (pericardial nephrocytes), arises from the cardiogenic mesoderm. Clonal analysis provided evidence for a hemangioblast2,3 that can give rise to two daughter cells: one that differentiates into heart or aorta and another that differentiates into blood. In addition, the GATA factor gene pannier (pnr) and the homeobox gene tinman (tin), which are controlled by the convergence of Decapentaplegic (Dpp), fibroblast growth factor (FGF), Wingless (Wg) and Notch signaling, are required for the development of all cardiogenic mesoderm, including the lymph gland. Here we show that an essential genetic switch that differentiates between the blood or nephrocyte and vascular lineages involves the Notch pathway. Further specification occurs through specific expression of the GATA factor Serpent (Srp) in the lymph-gland primordium. Our findings suggest that there is a close parallel between the molecular mechanisms functioning in the D. melanogaster cardiogenic mesoderm and those functioning in the mammalian aorta-gonadal-mesonephros mesoderm4.
Nuclear physics and detection of solar neutrinos and dark matter

Abstract Nuclear physics of a solar neutrino detector based on 127I is described first. It is shown that an iodine detector could be a relatively high-statistics 8B ve detector, and possibly an excellent detector of 7Be neutrinos. The nuclear physics issues of direct detection of neutralinos are discussed next. For light nuclei and/or relatively light neutralinos the nuclear structure aspects can be handled easily, and quite accurately. For heavier targets and heavier neutralinos, the momentum transfer dependence of the scalar and axial-vector structure functions must be evaluated. This is a nontrivial problem, particularly for the spin-dependent (axial-vector) scattering. Examples of different approaches are discussed.
Orthogonal matrices as linear combinations of permulation matrices

Abstract The paper deals with those orthogonal matrices which can be expressed as linear combinations of permutation matrices. A necessary condition for such a linear combination to be an orthogonal matrix is that the sum of the coefficients in the linear combination be ±1.
Metabolic fate of hydrazine.

Studies of the disposition of hydrazine administered to mammals have not succeeded in accounting for more than a modest fraction of the dose, nor have the excretory products been completely identified. We have utilized 15N‐labeled hydrazine and conventional methods to account for about 75% of single doses of about 0.5 LD50 (1 mmol/ kg). In 48 h, about 30% appeared in urine as hydrazine and about 20% emerged as a derivative that is acid‐hydrolyzable to hydrazine. About 25% was converted to N2 gas, most of which appeared less than 30 min after administration. The percentage converted to N2 at 4 h increased only slightly with dose between 0.5 and 2.0 mmol /kg. Disappearance of hydrazine from blood was biphasic with half‐times of 0.74 and 26.9 h.
Conservation versus cluster subdivisions and implications for habitat connectivity

Cluster Subdivisions are intended to create open space in proximity to residential areas, but there is growing recognition that they do little to ensure connectivity between these areas. Conservation Subdivisions, in which open space is designed around proactively identified areas of high ecological value, have been proposed as a means to ensure a connected network of undeveloped land. In this paper we produce and compare buildout scenarios for a focal town under Cluster and Conservation Subdivision regulations and with varying levels of open space requirements. We explicitly model the location of houses and open space in each subdivision. As a comparison of the potential outcomes, we assess the connectivity resulting from the various policies using a landscape permeability model for wood frogs (Rana sylvatica), a vernal pool-breeding species. The results suggest that higher levels of open space tend to enhance connectivity, but that careful subdivision design may to some extent be a substitute for either policy. Conservation Zoning produces a more permeable landscape than Cluster Zoning under most scenarios, suggesting that the design of open space may be at least as important as the quantity. An important implication is the existence of a tradeoff between the amount and design of open space, suggesting the possibility for policies that benefit both wildlife and developers.
A cationic hydroxo-bridged dinuclear gallium complex.

The crystal structure of μ-hydroxo-bis{[N-isopropyl-2-(isopropylamino)troponimino-N,N'](methyl)gallium(II)} tetrakis(pentafluorophenyl)borate (troponimine is 2,4,6-cycloheptatrien-1-imine), [Ga 2 (C 14 H 22 N 2 ) 2 (OH)]B(C 6 H 5 ) 4 , is discussed. The two ( i Pr 2 -ATI)GaMe (ATI is aminotroponimime) units of the dinuclear cation are linked by a bridging hydroxo group and are both slightly twisted from planarity.
Predicting extinction or explosion in a Galton–Watson branching process

Based on observations $$X_1,\dots ,X_n$$ of successive generations of a discrete-parameter Galton–Watson branching process, one wishes to predict whether extinction or explosion will ultimately occur. This problem can be formulated as a simple hypothesis-testing problem to which the Neyman–Pearson Lemma is directly applicable if the extinction probability is known or estimable. If it is not, valid (but conservative) tests still can be obtained.
Fluvial evolution of the lower Mississippi River valley during the last 100 k.y. glacial cycle: Response to glaciation and sea-level change

The lower Mississippi valley contains multiple large braid belts for which age control has been limited. Application of the optically stimulated luminescence technique has produced a new chronology of lower Mississippi valley channel-belt formation and insight into the valley9s evolution during the last glacial cycle. Fluvial deposits range from last interglacial meander belts (85 ± 7 to 83 ± 7 ka) to multiple braid belts (64 ± 5 to 11 ± 1 ka) and record large-amplitude responses of the Mississippi River to glacially induced changes in discharge and sediment supply during the last glacial cycle. Slackwater deposits in buried tributary valleys from the middle Mississippi valley and northern lower Mississippi valley suggest that the river was flowing at a position 8–21 m below the present flood plain during the last interglacial, then rapidly aggraded and switched to a braided regime to form the highest and oldest braid belt by 64 ± 5 to 50 ± 4 ka, coincident with initial glaciation of the upper drainage basin. The Mississippi River remained braided until final meltwater withdrawal from its headwaters in the earliest Holocene. Braid-belt formation and incision was controlled by fluctuations in meltwater and sediment discharge, while glacio-eustatic sea level controlled the elevation to which the river was graded, causing late glacial braid belts to dip below the Holocene flood plain in the southern lower Mississippi valley. Moreover, avulsions in the middle Mississippi valley and northern lower Mississippi valley during the last glaciation have pinned the river over regions of shallow bedrock, preventing the modern river from incising to its last interglacial profile. The new chronology and longitudinal profiles presented here provide insight into the response of this continental-scale river system to climatic (glacial) and base-level forcing during the last 100 k.y. glacial cycle.
Observations on the Nature and Extent of Injustice in the American Prison System

The degree of civilization in a society can be judged by entering its prisons. (Fyodor Dostoevsky)Jotterand and Wangmo's (2014) reconsideration of the principle of equivalence in prison medicine co...
Use of exercise Doppler echocardiography to evaluate cardiac drugs: effects of propranolol and verapamil on aortic blood flow velocity and acceleration.

Abstract This study evaluated the ability of exercise Doppler echocardiography to identify hemodynamic changes due to cardiac medication. Twenty young healthy volunteers (mean age 30 years) underwent continuous wave Doppler examination from the suprasternal notch at rest, during each stage of a standard exercise protocol and immediately after exercise. On completion of the control test, each subject received either 60 to 80 mg of propranolol or 120 mg of verapamil orally, and the same exercise protocol was repeated after 90 min. During the control test, values for modal velocity, accelaration and flow velocity integral all increased significantly from baseline (p It is concluded that: 1) propranolol exerts a profound hemodynamic effect as measured by Doppler echocardiography at rest and during exercise; 2) despite its negative inotropic properties, propranolol results in an increased stroke volume during exercise, apparently because of increased preload; 3) verapamil, in the dosages studied, does not alter the Doppler-measured exercise response in young healthy subjects; and 4) Doppler echocardiography is a useful technique for evaluating the hemodynamic effects of medication on aortic blood flow at rest and during exercise.
Cox regression analysis of multivariate failure time data: The marginal approach

Multivariate failure time data are commonly encountered in scientific investigations because each study subject may experience multiple events or because there exists clustering of subjects such that failure times within the same cluster are correlated. In this paper, I present a general methodology for analysing such data, which is analogous to that of Liang and Zeger for longitudinal data analysis. This approach formulates the marginal distributions of multivariate failure times with the familiar Cox proportional hazards models while leaving the nature of dependence among related failure times completely unspecified. The baseline hazard functions for the marginal models may be identical or different. Simple estimating equations for the regression parameters are developed which yield consistent and asymptotically normal estimators, and robust variance-covariance estimators are constructed to account for the intra-class correlation. Simulation results demonstrate that the large-sample approximations are adequate for practical use and that ignoring the intra-class correlation could yield rather misleading variance estimators. The proposed methodology has been fully implemented in a simple computer program which also incorporates several alternative approaches. Detailed illustrations with data from four clinical or epidemiologic studies are provided.
Cohesion enhancing effect of magnesium in aluminum grain boundary: A first-principles determination

The effect of magnesium on grain boundary cohesion in aluminum was investigated by means of first-principles calculations using the Rice-Wang model [Rice and Wang, Mater. Sci. Eng. A 107, 23 (1989)]. It is demonstrated that magnesium is a cohesion enhancer with a potency of −0.11 eV/atom. It is further determined through electronic structure and bonding character analysis that the cohesion enhancing property of magnesium is due to a charge transfer mechanism which is unusually strong and overcomes the negative result of the size effect mechanism. Consistent with experimental results, this work clarifies the controversy and establishes that Mg segregation does not contribute to stress corrosion cracking in Al alloys.
Qualitative Perspectives on the Use of Traditional and Nontraditional Food Venues among Middle- and Low-Income Women in Eastern North Carolina

The purpose of this qualitative study was to examine motivations for use of food venues among 23 urban and rural women from eastern North Carolina. Women were eligible if they cared for children, were non-Hispanic black or white, and were English speakers. Interviews elicited participants' decisions for food venue use. Reasons for use of supermarkets were low cost, convenient location, quality/availability of specific foods, and customer service. Main reasons for use of supercenters were bulk foods at low prices and one-stop shopping. Rural and urban nonworking women shopped more frequently at discount superstores compared to urban working women.
Effects of infection control procedures on the accuracy of a new mechanical torque wrench system for implant restorations

Loosening of screw components for implant restorations has been attributed to insufficient tightening. The degree of tightening may be increased and more closely controlled by use of calibrated mechanical torque wrenches. The DynaTorq wrench system has been introduced to the market and consists of three individual wrenches with torque values of 10, 20, and 30 newton-centimeters (Ncm). This study evaluated the accuracy of the DynaTorq wrench system before and after steam autoclave and Chemiclave sterilization treatment. Before sterilization treatments, the wrenches demonstrated high accuracy and precision. Autoclaving resulted in increases in torque values for the 10 Ncm torque wrench compared with baseline measurements. Except for the effect of autoclaving on the 10 Ncm torque wrench, sterilization procedures did not adversely affect the accuracy of the DynaTorq torque wrench system.
Dialogue complexity with portability?: research directions for the information state approach

We review existing types of dialogue managers (DMs), and propose that the Information State (IS) approach may allow both complexity of dialogue and ease of portability. We discuss implementational drawbacks of the only existing IS DM, and describe our work underway to develop a new DM resolving those drawbacks.
Liposarcoma of thigh presenting as deep venous thrombosis.

ObjectivesTo discuss the differential diagnosis of a case with leg swelling and pain with special emphasis on soft-tissue malignancy.MethodsSymptomatic deep vein thrombosis (DVT) of lower limb was ...
General two-dimensional theory of laminated cylindrical shells

The theory accounts for a desired degree of approximation of the displacements through the thickness, thus accounting for any discontinuities in their derivatives at the interface of laminae. Geometric nonlinearity in the sense of the von Karman strains is also included. Navier-type solutions of the linear theory are presented for simply supported boundary conditions
SU‐FF‐J‐33: Image Guided Radiotherapy in Prostate Localization: A Comparison of Ultrasound Modalities to Implanted Seed Markers and Assessment of Intrafractional Prostate Motion

Purpose: To compare 2D (BAT) and 3D (IBeam) ultrasounds with seed markers (SM) for prostate localization, and to assess intrafractional prostate motion during external beam radiotherapy(EBRT).Method and Materials: Prior to daily prostate localization with SM, patients underwent localization with two ultrasound systems for one week and with one ultrasound system for remaining treatments. Ultrasound shifts were prospectively recorded and patients were shifted as per SM alignment. The differences in lateral (LR), craniocaudal (CC) and anterior‐posterior (AP) directions were compared assuming SM revealed the true position of the prostate. Intrafraction motion of the prostate was assessed by repeating the SM after EBRT treatment on four fractions. Results: From 20 patients, 455 I‐Beam and 343 BAT ultrasound scans were compared to SM localizations. I‐Beam had a mean error ± sd of 0.6±3.3mm in the LR direction, 2.2±4.8mm (CC) and 0.2±3.8mm (AP). BAT had a mean error ± sd of 0.0±3.8mm (LR), 0.8±4.5mm (CC), and −1.5±4.3mm (AP). Deviations >5mm occurred in 11%, 32% and 18% in the LR, CC and AP directions respectively for I‐Beam, and 11%, 24% and 23% respectively for BAT. Deviations >1cm occurred in 7% in the CC direction for I‐Beam. Intrafraction prostate motion is minimal with a mean displacement ⩽1.5mm. The greatest movement is in the AP direction with 4% of patients having >5mm displacement. Conclusion: Target localization with two US systems provide different results than SM localization. Our data suggest that PTV margin guidelines for BAT and I‐Beam should be greater than those for SM. The US margin requirements may also need to be greater than if no daily localization is performed. In addition, intrafractional prostate motion is minimal with large displacements occurring in <5% of patients. We have adopted seed markers for daily prostate localization at our institution.
The Good, the Bad, and the Ugly: Demonstrating Basic Circuit Layout and Measurement Concepts [Education Column]

Circuit prototyping and layout are facts of life for many of us in the EM community. Whether we are designing amplifiers, phase shifters, or filters, or trying to diagnose a difficult electromagnetic compatibility problem, the physical construction of high-frequency circuits is a major concern. The topic of circuit layout is often overlooked in the typical undergraduate curriculum. Proper measurement practices are also important, since a poor testing configuration can lead to misleading data. This issue's column will demonstrate one way to introduce the importance of good circuit layout and measurement practices into introductory level courses.
Late Neogene paleoclimate and paleoenvironment reconstructions from the Pipe Creek Sinkhole, Indiana, USA

Abstract The Late Neogene represents warm Earth conditions immediately prior to the development of extensive northern hemisphere glaciation, and this period in Earth history may therefore provide the best available analog for the projected outcome of continued global warming. There are few interior continental sites of Late Neogene age from the eastern half of North America and subsequently very little is known about the conditions characterizing climate. The Early Pliocene (~ 5 Ma) Pipe Creek Sinkhole (PCS) includes the sediment fill of a complex karst environment that developed in north-central Indiana, USA (Lat. 40° 27′ 25.4″, Long. 85° 47′ 37.2″). The site includes more than 3 m of high-chroma, red-colored silty-clay sediment interpreted to be terra rossa. The terra rossa δ13C values average − 20 ± 0.7‰ PDB and are interpreted to represent sediment deposited in a closed cave system under high summer temperatures and with well-drained soils. An in-situ paleosol at the top of the terra rossa represents a transition from a closed cave to an open environment that eventually flooded, thereby becoming a small pond. δ13C values from lacustrine sediments with organic matter derived dominantly from algae average − 20.6‰ and suggest the pond was stagnant and enriched with bicarbonate from the underlying limestones or via aquifers. Pond sediments include abundant vertebrate fossils, which are broadly consistent with those inhabiting an open ecosystem such as a savannah or parkland. However, the PCS pollen includes low taxonomic diversity that is dominated by pine with some hickory and flowering plants, but no grass pollen. We propose two hypotheses to explain the PCS stratigraphic record: (1) The pollen assemblage may represent a local pine dominated ecosystem associated with the pond paleoenvironment, such as a riparian community, and that the greater landscape was drier and open; (2) Alternatively, the climate may have became wetter raising the elevation of the groundwater table and initiating the formation of the pond. Then in response to the wetter conditions an early succession forest ecosystem developed.
Structure of the CAC1 Gene and in Situ Characterization of Its Expression (The Arabidopsis thaliana Gene Coding for the Biotin-Containing Subunit of the Plastidic Acetyl-Coenzyme A Carboxylase)

The CAC1 gene of Arabidopsis thaliana that codes for the biotin carboxyl-carrier subunit of the heteromeric acetyl-coenzyme A carboxylase was isolated and sequenced. CAC1 is a single-copy gene interrupted by six introns. Subcellular immunogold labeling indicates that the biotin carboxyl-carrier subunit is localized in the stroma of the plastids and chloroplasts. The CAC1 mRNA accumulates throughout developing embryos and ovules of siliques at a time of rapid growth and oil accumulation (7 d after flowering), but is present at much lower levels in wall cells and central septal cells of the silique. Immunolocalization studies show that the pattern of accumulation of the biotin carboxyl-carrier subunit within the siliques and leaves is similar to that of the CAC1 mRNA. These observations indicate that the cellular pattern of biotin carboxyl-carrier protein accumulation in the developing silique may be determined by the transcriptional activity of the CAC1 gene.
Discovery of 2,8-diazaspiro[4.5]decane-based trisubstituted urea derivatives as highly potent soluble epoxide hydrolase inhibitors and orally active drug candidates for treating hypertension.

Abstract We identified 2,8-diazaspiro[4.5]decane-based trisubstituted urea derivatives as highly potent soluble epoxide hydrolase (sEH) inhibitors and orally active agents for treating hypertension. Docking studies using human and murine sEH X-ray crystal structures revealed steric hindrance around the side chain of Phe406 of murine sEH. The trifluoromethyl moiety (11) was replaced with a trifluoromethoxy moiety (12) to prevent steric clash, and improved murine sEH inhibitory activity was observed. The oral administration of 12, 20, and 37 at a dose of 30 mg/kg reduced blood pressure in spontaneously hypertensive rat, but had little effect on blood pressure in normotensive rat.
Satellite clock bias estimation for iGPS

The High Integrity GPS program seeks to provide enhanced navigation performance by combining conventional GPS with a communications and ranging broadcast from the Iridium® Communications System. Through clock and message aiding, it would enable existing GPS receivers to acquire and track in more challenging environments. As is the case for standard GPS, accurate and precise timing is key to performance. An approach is presented for estimating the bias of each Iridium satellite clock using satellite-to-ground and satellite-to-satellite measurements. The satellite clock bias estimates are based on a Kalman filter that incorporates code-type observations from the measurements at 10 s intervals. Filter parameters are set based on the expected behavior of the clocks, allowing for discontinuous bias and frequency adjustments due to ground commands. Typical results show the current filter to be accurate to within 200 ns while always meeting the initial system specification of half a microsecond.