cssi/SciSciGPT-SciSciNet huggingface dataset:
Possible role of cell cycle-dependent morphology, geometry, and mechanical properties in tumor cell metastasis.

Studies that examine the shear- and abrasion-sensitivity of proliferating cells are important in order to understand the behavior of hybridoma cells in bioreactor culture and metastasizing cancer cells in the bloodstream. Little is known about the link between morphology, structure, and mechanical properties of a given cell line, especially with respect to variations throughout the cell cycle. In our experiments with GAP A3 hybridoma cells, distinct cell morphologies were identified and correlated with phases of the cell cycle by video microscopic observation of synchronized cells, and of individual cells that were followed throughout their cell cycle. Micropipet manipulation was used to measure the geometrical (cell volume) and mechanical (apparent cell viscosity) properties of single cells. As the cell cycle progressed at 37°C, an increase in cell volume from 1400 μm3 to 5700 μm3 was accompanied by an increase in apparent cell viscosity from 430 poise to 12,000 poise, consistent with an accumulation of more cytoplasmic material in the “older” cells. Hybridomas are representative of the various leukemias derived from hemopoietic cells, and even though as a whole, they appeared to be rather shear-insensitive, the wide range of property values demonstrates that a given cell line cannot be characterized by a single value for any one property, and that properties must be related to the cell cycle when considering proliferating cells. It is interesting to see if distinct stages in the metastatic sequence of events might correlate with any of these physical features of the cell cycle, irrespective of cell type or cell line. For example, the cytokinetic doublet could represent a fragile structure that may fail and produce cell death under fluid-shear conditions that would not affect the cells at any other stage in the cell cycle. Identifying such cell cycle-dependent features in metastasizing cancer cells could lead to a better understanding of the metastatic process and to possible clinical treatments directed at making cells more shear- and abrasion-sensitive, and therefore, more likely to be killed by the natural hydrodynamic forces of the circulatory system.
Constant-slowdown simulations of normal hypercube algorithms on the butterfly network

Abstract The hypercube is both a powerful and a popular interconnection scheme for parallel computation. One of its drawbacks from a practical perspective is its logarithmic node degree. This has motivated the study of bounded-degree networks that can efficiently simulate hypercube computations. Two such networks that have received much attention are the butterfly network and the shuffle-exchange graph. While there exist simple constant-slowdown simulations of normal hypercube algorithms—algorithms that use only one dimension of hypercube edges at a time, and use adjacent dimensions at consecutive time steps—on the shuffle-exchange graph, the only such simulations known for the butterfly require a much more powerful model of network simulation. In this paper we present a simple algorithm for the simulation of normal hypercube algorithms on the butterfly network with constant slowdown, matching the best known result for the shuffle-exchange graph in terms of both slowdown and computational model.
Dynamics of Spatial Beam Collapse in Nonlinear Medium with Nonlocal Response

We study wave collapse in a nonlinear self-focusing medium with nonlocal response. The nonlocality arrests catastrophic collapse and creates focusing-defocusing oscillations. Right before maximum collapse, we observe a transverse peakon-like profile with exponentially-decaying tails.
Analysis of Mutations in the Copper B Binding Region Associated With Type I (Tyrosinase-Related) Oculocutaneous Albinism

Mutations of the tyrosinase gene are responsible for type I (tyrosinase-related) oculocutaneous albinism (OCA), an autosomal recessive genetic syndrome with a broad phenotypic spectrum. Mutant tyrosinase alleles can be associated with no melanin synthesis (I-A, tyrosinase-negative OCA), small to moderate amounts of melanin (I-B, yellow OCA) or unusual pigment patterns (I-TS, temperature-sensitive OCA). A total of 26 mutations of this gene have been described in type I OCA. Analysis of all known missense mutations (n = 17) shows that most cluster in three areas of the coding region. Two clusters involve the copper A or copper B binding sites and may disrupt the metal ion-protein interaction necessary for enzyme function and the third cluster is located in exon I. Computer modeling of the secondary structure of the copper binding regions based on homology with the known crystal structure of hemocyanin show that they both consist of two a helicies containing three histidine ligands that complex to a single copper atom. Mutations in the copper B binding region lie in the region between the two a helices that consists of a loop structure. These mutations may affect tyrosinase activity by either altering the position of the a helical domains and thus preventing proper copper binding to the histidine ligands, or affecting a catalytic or substrate binding site located between the two a helical domains.
The impact of nanoscale chemical features on micron-scale adhesion: crossover from heterogeneity-dominated to mean-field behavior.

Abstract This work explores the impact of nanoscale surface heterogeneity, small relative to the effective contact area between two surfaces, on pairwise colloid-scale interactions. Polycation-based positive patches, of order 10 nm in diameter, arranged randomly and lying flat on otherwise negative substrates, were used to create surfaces whose competing attractive and repulsive features determined the net interactions with opposing surfaces. Lab experiments and simulations of the adhesion of gently flowing dilute negative microparticles varied particle size (0.5–2 μm), ionic strength (κ−1 = 1–12 nm) and the density of heterogeneity on the collectors. Limiting behaviors from heterogeneity-controlled at high ionic strength to mean-field-like interactions at low ionic strength are reported. When heterogeneities are important, pairwise interactions are more attractive than predicted by average surface properties (e.g. per DLVO), and an adhesion threshold, describing the minimum average density of cationic features needed for single particle capture (adhesion), depends strongly on Debye length. In the opposite limit, the threshold becomes insensitive to the Debye length, and the average surface character approximates the interactions. An analytical treatment, reduced to a simple scaling argument predicts a −1/2 power-law dependence of the adhesion threshold on Debye length and particle size. A slightly stronger particle size dependence in experiments and simulations results from hydrodynamic contributions along with slight scaling differences in electrostatic, van der Waals, and hydrodynamic forces. An analogy to biological ligands is made for the heterogeneity-dominated limit: it is discovered, for this particular system, that engagement of as few as 20–100 cationic patches dictates particle adhesion (with details depending on flow, particle size, and ionic strength), similar to reports for selectin-mediated rolling of white blood cells during the inflammatory pathway. Also discovered is a heterogeneity-dependent crossover in the effect of ionic strength on particle capture, where added salt promotes particle adhesion in most cases but stabilizes the particles when the heterogeneity becomes relatively dense.
How accurately can NRM/ SIRM determine the ancient planetary magnetic field intensity?

Abstract The present study tested grain-size dependence of thermoremanent magnetization (TRM)/saturation isothermal remanent magnetization (SIRM) as well as its stability against demagnetization. The TRM/SIRM ratio is dependent on the grain-size of magnetite, suggesting that a strong constraint on grain-size characterization is necessary to be used as a paleointensity proxy in planetary magnetism. In addition, the TRM/SIRM ratio increases as the alternating-field increases for fine-grained magnetite. Accuracy of TRM/SIRM was investigated using historic Showa lava erupted in 1946. It was observed that the natural remanent magnetization (NRM)/SIRM ratio of 0.032 is comparable to the field intensity of 46.80 μT. However, the uncertainty of NRM/SIRM was an order of magnitude larger than that of the companion Thellier estimation. Therefore, the NRM/SIRM ratio can only provide crude estimations on the absolute planetary magnetic field intensity. In practice, anisotropy correction is advisable to reduce the scatter of NRM/SIRM.
A modeling framework for the analysis of HPV incidence and persistence: a semi-parametric approach for clustered binary longitudinal data analysis

Human papillomavirus (HPV) infection is a common sexually transmitted disease of growing public health importance, and over 40 genotypes have been identified in genital infections. Current HPV cohort studies often follow participants at pre-determined visits, such as every 6 months, and data generated from such epidemiology studies can be described as clustered longitudinal binary data where correlation arises in two ways: the directionless clustering due to the multiple genotypes tested within an individual, and the temporal correlation among the repeated measurements on the same genotype along time. Current analyses for identification of risk factors associated with HPV incidence and persistence often either do not fully utilize information in the data set or ignore the correlation between the multiple genotypes. Given the scientific definition of incidence and persistence, conditional probability modeling provides us a natural mathematical tool. We thus present a semi-parametric regression model for such data where full specification of the joint multivariate binary distribution is avoided by using conditioning argument to handle the temporal correlation and GEE to account for the correlation between the multiple genotypes. The model is applied to the HPV data from the Rakai male circumcision (MC) trial to evaluate the as-treated efficacy of MC and also identify modifiable risk factors for incidence and persistence of oncogenic HPV types in men. A simulation study is performed to provide empirical information on the number of individuals that is needed for satisfactory power and estimation accuracy of the association parameter estimates in future studies.
An assistive navigation system for wheelchairs based upon mobile robot obstacle avoidance

The NavChair assistive navigation system is being developed to meet the needs of multiply handicapped people who are unable to operate available wheelchair systems. The NavChair Project was conceived as an application of mobile robot obstacle avoidance to a power wheelchair. During the course of this project, the vector field histogram (VFH) method has been adapted for use in human-machine systems and the shortcomings of the wheelchair platform have been overcome. This paper briefly reviews the VFH method, describes interesting aspects of its application to a power wheelchair, and presents an experimental evaluation of system performance. Finally, unresolved problems of obstacle avoidance in human-operated vehicles are discussed. >
Microbial cell modeling via reacting diffusive particles

We describe a particle-based simulator called ChemCell that we are developing with the goal of modeling the protein chemistry of biological cells for phenomena where spatial effects are important. Membranes and organelle structure are represented by triangulated surfaces. Diffusing particles represent proteins, complexes, or other biomolecules of interest. Particles interact with their neighbors in accord with Monte Carlo rules to perform biochemical reactions which can represent protein complex formation and dissociation, ligand binding, etc. In this brief paper we give the motivation for such a model, describe a few of the code's features, and highlight interesting computational issues that arise in particle-based cell modeling.
Engineering a Bacterial Tape Recorder

A method has been developed to produce and integrate single-stranded DNA into genomic locations in bacteria in response to exogenous signals. The system functions similarly to a cellular tape recorder by writing information into DNA and reading it at a later time. Much like other cellular memory platforms, its operation is based on DNA recombinase function. However, the scalability and recording capacity have been improved over previous designs. In addition, memory storage was reversible and could be recorded in response to analogue inputs, such as light exposure. This modular memory writing system is an important addition to the genomic editing toolbox available for synthetic biology.
Modeling of current crowding for on-chip multi turn differential -spiral inductors

Current crowding severely degrades the quality factor (Q) of CMOS on-chip multi-turn spiral inductors. It needs to be considered in the lumped equivalent circuit models of inductors. Therefore its impact on RF circuit's performance can be captured at circuit simulation phase. Such models have been established for multi-turn single-ended inductors. However they have not been well developed for differential inductors. In this paper, a wideband lumped equivalent circuit model for multi-turn differential inductors is proposed. It contains both resistance and inductance variations due to current crowding. The measurement results agree with the proposed model.
Numerical Simulation of Sea Surface Directional Wave Spectra under Hurricane Wind Forcing

Numerical simulation of sea surface directional wave spectra under hurricane wind forcing was carried out using a high-resolution wave model. The simulation was run for four days as Hurricane Bonnie (1998) approached the U.S. East Coast. The results are compared with buoy observations and NASA Scanning Radar Altimeter (SRA) data, which were obtained on 24 August 1998 in the open ocean and on 26 August when the storm was approaching the shore. The simulated significant wave height in the open ocean reached 14 m, agreeing well with the SRA and buoy observations. It gradually decreased as the hurricane approached the shore. In the open ocean, the dominant wavelength and wave direction in all four quadrants relative to the storm center were simulated very accurately. For the landfall case, however, the simulated dominant wavelength displays noticeable overestimation because the wave model cannot properly simulate shoaling processes. Direct comparison of the model and SRA directional spectra in all four quadrants of the hurricane shows excellent agreement in general. In some cases, the model produces smoother spectra with narrower directional spreading than do the observations. The spatial characteristics of the spectra depend on the relative position from the hurricane center, the hurricane translation speed, and bathymetry. Attempts are made to provide simple explanations for the misalignment between local wind and wave directions and for the effect of hurricane translation speed on wave spectra.
Applications of coding in network communications

This thesis uses the tool of network coding to investigate fast peer-to-peer file distribution, anonymous communication, robust network construction under uncertainty, and prioritized transmission. In a peer-to-peer file distribution system, we use a linear optimization approach to show that the network coding framework significantly simplifies analysis even in scenarios where the optimal solution does not require coding. We also study the effect of requiring reciprocity and the impact of dynamically changing network scenarios. Second, we investigate anonymous routing in peer-to-peer networks. The goal is to design and analyze a peer-to-peer system that hides the identities of source and sink pairs against adversarial nodes. We first propose a protocol for subgraph construction signaling. The protocol uses path diversity rather than cryptographic keys. We prove information theoretic security of the proposed protocol. We investigate a variety of deterministic and randomized subgraph designs. We also give a reverse path construction mechanism, with which a sink can reply to the source without knowing the source identity. We next investigate anonymous data transmission using network coding. Again, path diversity (with network coding) is used to hide the identities of source and sink pairs. We investigate the effect of subgraph shape on anonymity and congestion arising from traffic shaping constraints, demonstrating the tradeoff between the two through simulations. Third, we study the problem of network construction under uncertainty about link-loss rates. We prove that both maximizing throughput and minimizing cost are coNP-hard problems. We find polynomial time-solvable solutions that outperform other deterministic approaches. Lastly, we investigate strategies for communication under a system that prioritizes data based on the worth of data and the probability of successful transmission. Only the highest priority data is transmitted when communication is very limited.
A Note on the Seismicity of the Ross Sea Region

summary Although the aseismicity of Antarctica has been confirmed by IGY observations, small local disturbances, up to magnitude 3, are almost a daily feature of seismograms at Scott Base. S—P intervals of these shocks range from 3 to 38s but half of the shocks recorded have S-P differences of 4-6s, values appropriate to the distance of Mt Erebus. An unusual low-velocity phase (V?0.6km/s) is present on many seismograms.
Commentary to "Lower radiation burden in state of the art fluoroscopic cystography compared to direct isotope cystography in children".

Most pediatric radiology centers worldwide prefer radiographic cystographies because of the inaccuracies inherent to sonographic cystography. Contemporary teachings state that nuclear cystography exposes patients to less radiation than fluoroscopic cystography. Thus, the ideal candidates for nuclear cystographies for the evaluation of vesicoureteral reflux (VUR) were thought to be girls, postoperative patients, and patients on active surveillance. This study provides evidence that newer technologies and techniques employed in fluoroscopic cystography can reduce its radiation burden to approximately one-third of that of nuclear studies. If one were to argue that nuclear cystography is more sensitive in detecting VUR, this study concludes that a cyclic (three cycles) fluoroscopic cystography would accrue approximately the same effective radiation dose. Assuming that indications, invasiveness, radiation exposure, and possibly cost are similar for both, then should one choose nuclear or fluoroscopic cystography? There is mounting evidence that fluoroscopic cystography provides additional clues in regard to the competency of the ureterovesical junction and therefore the clinical course of VUR. These findings include bladder volume and timing of reflux, ureteral diameter, upper
Analysis of postural perturbation responses

People with cerebellar ataxia lack lower limb coordination and dissipate sway motion slowly and inefficiently after a posture perturbation. We report a practical and low-cost "human resonance frequency test" for both laboratory and clinical use to quantify progress in balance and cerebellar rehabilitation. We assumed that the center-of-pressure (COP) oscillation rate of decay following a standing posture perturbation is directly related to resonance frequency; a more rapidly dissipating COP oscillation about the position of equilibrium indicates, by definition, more efficient postural control. We hypothesized that following successful physical rehabilitation, people with cerebellar degeneration will have a faster rate of decay of the COP response to an external perturbation. Because the COP is modulated by a synergy of trunk and lower limb motion strategies, COP decay rate may be a useful measure of lower limb coordination in people with cerebellar ataxia. The method was applied to three subjects with cerebellar ataxia before and after rehabilitation; there was good agreement between the calculated COP decay rate and conventionally used gait stability parameters providing pilot data for this simple approach.
Refractive indices of powdered materials using attenuated total reflectance spectroscopy

The attenuated total reflectance spectroscopy method of determining the complex refractive indices of materials which occur only as small particles was applied at a 10.6-μm wavelength to numerous pressed powder samples. Fresnel relations were used to obtain best fit values for the complex refractive indices of the samples. Good fits were obtained only when the particles were small compared to the wavelength. For such samples, several effective medium theories were used to predict values of bulk material refractive indices from those of samples with different volume packing fractions. Only the Bruggeman theory produced consistent results.
Atrial Fibrosis Quantified Using Late Gadolinium Enhancement MRI is Associated With Sinus Node Dysfunction Requiring Pacemaker Implant

Atrial Fibrosis and Sinus Node Dysfunction. Introduction: Sinus node dysfunction (SND) commonly manifests with atrial arrhythmias alternating with sinus pauses and sinus bradycardia. The underlying process is thought to be because of atrial fibrosis. We assessed the value of atrial fibrosis, quantified using Late Gadolinium Enhanced-MRI (LGE-MRI), in predicting significant SND requiring pacemaker implant. Methods: Three hundred forty-four patients with atrial fibrillation (AF) presenting for catheter ablation underwent LGE-MRI. Left atrial (LA) fibrosis was quantified in all patients and right atrial (RA) fibrosis in 134 patients. All patients underwent catheter ablation with pulmonary vein isolation with posterior wall and septal debulking. Patients were followed prospectively for 329 ± 245 days. Ambulatory monitoring was instituted every 3 months. Symptomatic pauses and bradycardia were treated with pacemaker implantation per published guidelines. Results: The average patient age was 65 ± 12 years. The average wall fibrosis was 16.7 ± 11.1% in the LA, and 5.3 ± 6.4% in the RA. RA fibrosis was correlated with LA fibrosis (R2= 0.26; P 35%). Twenty-two patients (mean atrial fibrosis, 23.9%) required pacemaker implantation during follow-up. Univariate and multivariate analysis identified LA fibrosis stage (OR, 2.2) as a significant predictor for pacemaker implantation with an area under the curve of 0.704. Conclusions: In patients with AF presenting for catheter ablation, LGE-MRI quantification of atrial fibrosis demonstrates preferential LA involvement. Significant atrial fibrosis is associated with clinically significant SND requiring pacemaker implantation. (J Cardiovasc Electrophysiol, Vol. 23, pp. 44-50, January 2012)
Range and stability of cell fate determination in isolated sea urchin blastomeres

We have examined the developmental potential of blastomeres isolated from either the animal (mesomeres) or vegetal (macromeres-micromeres) half of 16-cell embryos of the sea urchin Lytechinus pictus. We have also examined the effects of two known vegetalizing agents on the development of isolated mesomeres; LiCl treatment and combination with micromeres, the small blastomeres found at the vegetal pole of the 16-cell embryo. The markers for differentiation used were both morphological (invaginations, spicules and pigment cells) and molecular (gut-specific alkaline phosphatase activity, and monoclonal antibodies against antigens specific for gut and oral ectoderm). Embryoids derived from isolated mesomeres expressed markers characteristic of vegetal differentiation only at very low levels. They did express an antigen characteristic of animal development, the oral ectoderm antigen, but with an altered pattern. Isolated macromere-micromere pairs expressed all markers characteristic of vegetal development, but did not express the marker characteristic of animal development. Increasing concentrations of LiCl caused isolated mesomeres to give rise to embryoids with an increasing tendency to express vegetal markers of differentiation, and it was found that expression of different vegetal markers begin to appear at different concentrations of LiCl. LiCl also caused the marker for oral ectoderm to be expressed in a more normal pattern. Combining micromeres with mesomeres also induced mesomere derivatives to differentiate in a vegetal manner. Micromeres were not completely effective in inducing a more normal pattern of expression of the marker for oral ectoderm. The treatment of isolated mesomeres with both LiCl and micromeres produces a synergistic effect resulting in embryoids expressing markers not induced by either treatment alone.
CXCL10 blockade protects mice from cyclophosphamide-induced cystitis

Background: Alterations in serum CXCR3 ligand levels were examined in interstitial cystitis (IC) patients; similar expression patterns in serum as well as CXCR3, CXCR3 ligands, and cytokines expressed by peripheral and local leukocyte subpopulations were characterized during cyclophosphamide (CYP)-induced acute cystitis in mice. Results: Serum levels of monokine-induced by interferon-γ (IFN-γ) (MIG/CXCL9), IFN-γ-inducible protein-10 (IP-10/CXCL10), and IFN-γ-inducible T cell α chemoattractant (I-TAC/CXCL11) were elevated in patients with IC. These clinical features closely correlated with CYP-induced cystitis in mice. Serum levels of these CXCR3 ligands and local T helper type 1 (Th1) cytokines were also increased. We demonstrate that CXCR3 as well as CXCL9, CXCL10 and CXCL11 mRNA were significantly expressed by urinary bladder lymphocytes, while CXCR3 and CXCL9 transcripts were significantly expressed by iliac lymph node leukocytes following CYP treatment. We also show that the number of CD4+ T cells, mast cells, natural killer (NK) cells, and NKT cells were increased at systemic (spleen) and mucosal (urinary bladder and iliac lymph nodes) sites, following CYP-induced cystitis in mice. Importantly, CXCL10 blockade attenuated these increases caused by CYP. Conclusion: Antibody (Ab)-mediated inhibition of the most abundant serum CXCR3 ligand, CXCL10, in mice decreased the local production of CXCR3 ligands as well as Th1 cytokines expressed by local leukocytes, and lowered corresponding serum levels to reduce the severity of CYP-induced cystitis. The present study is among the first to demonstrate some of the cellular and molecular mechanisms of chemokines in cystitis and may represent new drug target for this disease.
Linking Public Relations Tactics to Long-Term Success: An Investigation of How Communications Contribute to Trust, Satisfaction, and Commitment in a Nonprofit Organization

This study measured the impact of communications on building trust, commitment, and satisfaction among donors of a large nonprofit organization located in Fort Worth, Texas. Donors (n = 275) responded to a mail survey that included a modified version of the Hon and Grunig (1999) organization-public relationship scale and stewardship communication tactics. Regression analyses indicate that roughly 50% of the variance in trust, satisfaction, and commitment is attributable to a combination of communication tactics; most importantly, clearly communicating to donors how their donations help those in need. Implications for nonprofit organizations and public relations relationship theory are offered.
Economic Strategies and Ethnic Alternatives

This paper examines the relationship between economic adaptation and ethnic identity change among the Otomi Indians of Central Mexico. As the Otomies are recruited into more viable economic systems they undergo a change of ethnic identity and social status. The data were gathered through personal interviews and participant observation.
Bisphenol A Inhibits Follicle Growth and Induces Atresia in Cultured Mouse Antral Follicles Independently of the Genomic Estrogenic Pathway

Bisphenol A (BPA) is an estrogenic chemical used to manufacture many commonly used plastic and epoxy resin-based products. BPA ubiquitously binds to estrogen receptors throughout the body, including estrogen receptor alpha (ESR1) in the ovary. Few studies have investigated the effects of BPA on ovarian antral follicles. Thus, we tested the hypothesis that BPA alters cell cycle regulators and induces atresia in antral follicles via the genomic estrogenic pathway, inhibiting follicle growth. To test this hypothesis, we isolated antral follicles from 32- to 35-day-old control and Esr1-overexpressing mice and cultured them with vehicle control (dimethylsulfoxide [DMSO]) or BPA (1–100 μg/ml). Additionally, antral follicles were isolated from 32- to 35-day-old FVB mice and cultured with DMSO, BPA (1–100 μg/ml), estradiol (10 nM), ICI 182,780 (ICI; 1 μM), BPA plus ICI, or BPA plus estradiol. Follicles were measured for growth every 24 h for 96–120 h and processed either for analysis of estrogen receptor, cell cycle, and/or atresia factor mRNA expression, or for histological evaluation of atresia. Results indicate that estradiol and ICI do not protect follicles from BPA-induced growth inhibition and that estradiol does not protect follicles from BPA-induced atresia. Furthermore, overexpressing Esr1 does not increase susceptibility of follicles to BPA-induced growth inhibition. Additionally, BPA up-regulates Cdk4, Ccne1, and Trp53 expression, whereas it down-regulates Ccnd2 expression. BPA also up-regulates Bax and Bcl2 expression while inducing atresia in antral follicles. These data indicate that BPA abnormally regulates cell cycle and atresia factors, and this may lead to atresia and inhibited follicle growth independently of the genomic estrogenic pathway.
Gene expression in mouse brain following chronic hypoxia : role of sarcospan in glial cell death

Hypoxia is a hallmark of respiratory, neurological, or hematological diseases as well as life at high altitude. For example, chronic constant hypoxia (CCH) occurs in chronic lung diseases or at hig...
Fast animation and control of nonrigid structures

We describe a fast method for creating physically based animation of non-rigid objects. Rapid simulation of non- rigid behavior is based on global deformations. Con- straints are used to connect non-rigid pieces to each other, forming complex models. Constraints also provide mo- tion control, allowing model points to be moved accurately along specified trajectories. The use of deformations that are linear in the state of the system causes the constraint matrices to be constant. Pre-inverting these matrices there- fore yields an enormous benefit in performance, allowing reasonably complex models to be manipulated at interac- tive speed.
Anchored Text for Software Weaving and Merging

Text-based software merge/refactoring systems are predominantly used. Anchored text, a datatype with first-class location anchors and greater commutativity of software merge operations has been proposed recently. In this paper we develop anchored text as a novel weaver for simultaneous, separate concerns. Irregular, crosscutting concerns such as porting issues are applicable simultaneously (multi-dimensional separation of multi-target porting concerns), in order to allow for choice of a desired subset for a given port. Form-checking rules can be specified with individual concerns, to verify their correct weaving. The simultaneous concerns model can be viewed as an offline, concurrent change weaving problem, according to which a direct implementation is provided. A novel wait-free implementation of an online model, wherein concurrent changes arrive in a dynamic sequence but with fixed scheduling tags is provided and a highly-concurrent version of the same described using speculative scheduling. All these implementations use minimal synchronisation primitives only, namely atomic registers.
Anthracene bioconcentration in rainbow trout during single-compound and complex-mixture exposures

Rainbow trout were exposed for 72 h to [14C]anthracene alone and [14C]anthracene in an oil shale retort water. Tissue levels of [14C]anthracene were analyzed at 24, 48 and 72 h to determine non-steady-state bioconcentration factors (BCFs), and uptake and depuration rates were calculated from anthracene disappearance in exposure waters and metabolite appearance in depuration waters. Uptake rates (14.6 to 16.9 h−1) were similar to previously reported values; however, depuration rates (0.00158 to 0.00188 h−1) were very low. Consequently, measured non-steady-state BCFs after 72 h (9,000 to 9,200) for anthracene were higher than expected, probably because fish were not fed and had low excretion rates. Measured and estimated anthracene BCFs were lower in retort water exposures than in single-compound exposures because of slower uptake and faster depuration. We attribute slower uptake during retort water exposures to either decreased bioavailability of anthracene or rate-limiting transport of contaminants from uptake sites to storage and processing sites. Induction of mixed-function oxidases may have increased depuration from fish exposed to retort water. We conclude that bioconcentration of individual compounds from complex chemical mixtures may be difficult to predict based on single-compound kinetics.
Coherent Network Interfaces for Fine-Grain Communication

Historically, processor accesses to memory-mapped device registers have been marked uncachable to insure their visibility to the device. The ubiquity of snooping cache coherence, however, makes it possible for processors and devices to interact with cachable, coherent memory operations. Using coherence can improve performance by facilitating burst transfers of whole cache blocks and reducing control overheads (e.g., for polling).This paper begins an exploration of network interfaces (NIs) that use coherence---coherent network interfaces (CNIs)---to improve communication performance. We restrict this study to NI/CNIs that reside on coherent memory or I/O buses, to NI/CNIs that are much simpler than processors, and to the performance of fine-grain messaging from user process to user process.Our first contribution is to develop and optimize two mechanisms that CNIs use to communicate with processors. A cachable device register---derived from cachable control registers [39,40]---is a coherent, cachable block of memory used to transfer status, control, or data between a device and a processor. Cachable queues generalize cachable device registers from one cachable, coherent memory block to a contiguous region of cachable, coherent blocks managed as a circular queue.Our second contribution is a taxonomy and comparison of four CNIs with a more conventional NI. Microbenchmark results show that CNIs can improve the round-trip latency and achievable bandwidth of a small 64-byte message by 37% and 125% respectively on the memory bus and 74% and 123% respectively on a coherent I/O bus. Experiments with five macrobenchmarks show that CNIs can improve the performance by 17-53% on the memory bus and 30-88% on the I/O bus.
Modeling Regional-Scale Sediment Transport and Medium-Term Morphology Change at a Dual-Inlet System Examined with the Coastal Modeling System (CMS): A Case Study at Johns Pass and Blind Pass, West-Central Florida

Abstract The Coastal Modeling System (CMS), developed by the US Army Engineer Research and Development Center's (ERDC) Coastal Inlets Research Program (CIRP), is applied to model morphology change at a dual-inlet system, the Johns Pass and Blind Pass system in West-Central Florida. The CMS combines computation of current, wave, and sediment transport, leading to the prediction of morphology change at tidal inlets and the surrounding beaches. Medium-term CMS runs, with simulated times of 1.2 to 1.6 years, were completed and compared with extensive field data. Stronger tidal flow through the dominating Johns Pass and weaker flow through the secondary Blind Pass were calculated, indicating that the model reproduced an essential aspect of this interactive two-inlet system. The complicated wave refraction and breaking over the ebb tidal deltas and along the adjacent shorelines were accurately modeled, leading to a realistic representation of the wave-current interaction. Wave-breaking induced elevated sediment...
Changes in Species Richness, Abundance, and Composition of Arboreal Twig-nesting Ants Along an Elevational Gradient in Coffee Landscapes

The distribution, diversity, and assembly of tropical insects have long intrigued ecologists, and for tropical ants, can be affected by competitive interactions, microhabitat requirements, dispersal, and availability and diversity of nesting sites. Arboreal twig-nesting ants are limited by the number of hollow twigs available, especially in intensive agricultural systems. Ant diversity and abundance may shift along elevation gradients, but no studies have examined if the proportion of occupied twigs or richness of arboreal twig-nesting ants vary with elevation. In coffee agroecosystems, there are over 40 species of arboreal twig-nesting ants. We examined communities of twig-nesting ants in coffee plants along an elevational gradient to answer the following questions: (1) Do species richness and colony abundance decline with elevation or show a mid-elevation peak? (2) Does community composition change with elevation? (3) Is elevation an important predictor of change in ant abundance, richness, and relative abundance of common species? We surveyed 42 10 9 10 m plots in 2013 from 450 to1550 m elevation across a coffee landscape in Chiapas, Mexico. We sampled a total of 2211 hollow coffee twigs, 77.1 percent of which were occupied by one of 28 species of ants. Pseudomyrmex simplex was more abundant in lower elevations, whereas Pseudomyrmex ejectus dominated in high elevations. Species richness and the percent of occupied hollow twigs both peaked at mid-elevations (800–1050 m). In sum, we found that species richness, abundance, and composition of arboreal twig-nesting ants shift with elevation. These findings may provide important insights for understanding ant communities in coffee agroecosystems.
Growth of spring camelina (Camelina sativa) under deficit irrigation in western Nebraska.

Abstract The High Plains of the U.S.A. is subject to periodic drought where low-water using crops are desired. Camelina is a potential biofuel crop that may be suitable for this region. The objective was to determine the growth, seed yield, and oil characteristic of camelina exposed to four levels of applied water in western Nebraska. The cultivar Cheyenne was exposed to rain-fed only (RF), and irrigated with 10 (LI), 20 (MI), and 30 (HI) cm water. Irrigation increased plant growth as measured by canopy height, stem length, and canopy weight. Maximum height (70–80 cm) was reached by 10 weeks after planting (WAP) with a total of 23 cm of applied water or 13 cm of irrigation. By 13 WAP, canopy and pod fresh weights were increased by 40–50% by the MI and HI irrigations. Likewise, at harvest (13 WAP), plant dry weight was increased by 50% by the two higher irrigation levels. Seed yields were increased by each incremental increase in irrigation from 890 kg/ha for RF to 2540 for HI, a 2.85-fold increase. Oil content was not affected by irrigating at the LI or MI but was increased only by the HI irrigation level. The fatty acid profile was altered by irrigation with an increase in the major constituent, linolenic acid, and a corresponding decrease in two other large constituents, oleic and linoleic acids. There also was a slight increase in the minor constituent of erucic acid. The growth pattern of camelina showed that 23 cm of applied water would be required for healthy plant growth but as much as 43 cm would be needed for maximum yield. The results indicate that camelina could be grown successfully in western Nebraska, supplying oil for fuel and cooking.
Job Authority and Support for Income Redistributive Policy

Building on substantive yet neglected foundations provided by classical sociological theorists—theorists who emphasized the experiential conditions of work in structuring ideology—we examine in this article the impact of job authority tasks on levels of support for policy to redistribute income. Such a focus contributes to a broader sociological understanding of the links between status, ideology, and political action. With data drawn from the 2010 and 2012 National Election Studies, we find that workplace experiences and tasks involving sanctioning/organizational responsibility as well as the hierarchical patterning of interactions on one’s job help structure generalized views regarding inequality and policy orientations ultimately enacted outside of the workplace. In this regard, the number of authority tasks is inversely related to support for redistributive policy. Subsequent analyses, however, reveal this general pattern does not hold on the basis of race: less variation in policy support as well as ...
Divergent overlapping transcripts at the PET122 locus in Saccharomyces cerevisiae.

Abstract PET122 is one of three nuclear genes specifically required for translation of the mitochondrial mRNA for cytochrome c oxidase subunit III in Saccharomyces cerevisiae. The nucleotide sequence of 2,862 base pairs (bp) of yeast genomic DNA encompassing the PET122 locus shows very close spacing between the PET122 gene (254 codons) and two unidentified open reading frames, termed ORF2 and ORF3. ORF2 is encoded by the same strand of DNA as PET122 and is located 53 bp downstream of PET122, while ORF3 is encoded on the opposite strand and is located 215 bp upstream of PET122. Five transcripts, with sizes of 2.9, 2.3, 2.1, 1.5, and 1.4 kilobases (kb), are produced from this locus. The 2.1- and 1.4-kb transcripts encode ORF3, the 1.5-kb transcript encodes ORF2, and the 2.9- and 2.3-kb transcripts encode PET122. A particularly interesting feature of the ORF3-PET122-ORF2 transcription unit is a 535-base overlap between the 2.3-kb PET122 transcript produced from one strand and a 2.1-kb ORF3 transcript produced from the opposite strand. Similarly, the 2.9-kb PET122 transcript overlaps the 2.1-kb ORF3 transcript by more than 900 bases and the 1.5-kb ORF3 transcript by at least 200 bases. Hence, these pairs of transcripts are antisense to one another and have the potential to regulate, in an interdependent fashion, the posttranscriptional expression of ORF3 and PET122.
δ-Opioid receptor (DOR) signaling and reactive oxygen species (ROS) mediate intermittent hypoxia induced protection of canine myocardium

Intermittent, normobaric hypoxia confers robust cardioprotection against ischemia-induced myocardial infarction and lethal ventricular arrhythmias. δ-Opioid receptor (DOR) signaling and reactive oxygen species (ROS) have been implicated in cardioprotective phenomena, but their roles in intermittent hypoxia are unknown. This study examined the contributions of DOR and ROS in mediating intermittent hypoxia-induced cardioprotection. Mongrel dogs completed a 20 day program consisting of 5-8 daily, 5-10 min cycles of moderate, normobaric hypoxia (FIO2 0.095-0.10), with intervening 4 min room air exposures. Subsets of dogs received the DOR antagonist naltrindole (200 μg/kg, sc) or antioxidant N-acetylcysteine (250 mg/kg, po) before each hypoxia session. Twenty-four hours after the last session, the left anterior descending coronary artery was occluded for 60 min and then reperfused for 5 h. Arrhythmias detected by electrocardiography were scored according to the Lambeth II conventions. Left ventricles were sectioned and stained with 2,3,5-triphenyl-tetrazolium-chloride, and infarct sizes were expressed as percentages of the area at risk (IS/AAR). Intermittent hypoxia sharply decreased IS/AAR from 41 ± 5 % (n = 12) to 1.8 ± 0.9 % (n = 9; P < 0.001) and arrhythmia score from 4.1 ± 0.3 to 0.7 ± 0.2 (P < 0.001) vs. non-hypoxic controls. Naltrindole (n = 6) abrogated the cardioprotection with IS/AAR 35 ± 5 % and arrhythmia score 3.7 ± 0.7 (P < 0.001 vs. untreated intermittent hypoxia). N-acetylcysteine (n = 6) interfered to a similar degree, with IS/AAR 42 ± 3 % and arrhythmia score 4.7 ± 0.3 (P < 0.001 vs. untreated intermittent hypoxia). Without the intervening reoxygenations, hypoxia (n = 4) was not cardioprotective (IS/AAR 50 ± 8 %; arrhythmia score 4.5 ± 0.5; P < 0.001 vs. intermittent hypoxia). Thus DOR, ROS and cyclic reoxygenation were obligatory participants in the gradually evolving cardioprotection produced by intermittent hypoxia.
Gamow-state analysis of Fe 54 ( d , n ) to proton resonances in Co 55

Distorted-wave Born-approximation (DWBA) calculations are performed for $^{54}\mathrm{Fe}(d,n)$ angular distributions at 10 MeV populating five proton resonances in $^{55}\mathrm{Co}$, at 5.17, 5.54, 5.74, 5.86, and 6.07 MeV excitation, using Gamow states as form factors. Results of the calculations are compared with previous DWBA analyses in which bound-state functions were used.[NUCLEAR REACTIONS $^{54}\mathrm{Fe}(d,n)$, $E=10.0$ MeV; calculated $\ensuremath{\sigma}(\ensuremath{\theta})$; deduced proton-unbound $^{55}\mathrm{Co}$ levels, $J$, $\ensuremath{\pi}$.]
Properties of a solubilized form of the cytochrome P-450-containing mixed-function oxidase of liver microsomes.

The carbon monoxide-sensitive liver microsomal mixed-function oxiodase has recently been solubilized and resolved into three components: cytochrome P-450, TPNH-cytochrome P-450 reductase, and a heat-stable fraction. Of a variety of compounds tested as possible substrates in the reconstituted rat liver enzyme system, d -benzphetamine ( N -benzyl- N ,α-dimethylphenylethylamine) was the most active. A series of n -alkanes (hexane, heptane, octane, nonane, decane, dodecane, tetradecane, and hexadecane) were shown to serve as substrates, as well as compounds such as cyclohexane, ethylmorphine, hexobarbital, aminopyrine, and norcodeine, which are known to undergo hydroxylation in intact microsomal suspensions. Trilaurin, diolein, and triolein appeared to be active, whereas certain other lipids, including a series of fatty acids, and aniline were not. In the reconstituted rabbit liver enzyme system, hexane was the most active substrate, followed by cyclohexane and benzphetamine. A series of fatty acids front hexanoate to palmitoleate were found to undergo hydroxylation, in contrast to the results obtained in the rat liver enzyme system. An absolute requirement for the heat-stable lipid fractoin was shown for the hydroxylation of the various drugs as well as of several alkanes. A study of the stoichiometry of benzphetamine demethylation resulting from hydroxylation of the methyl group and liberation of the resulting hydroxymethyl group as formaldehyde) indicated that equimolar amounts of TPNH and molecular oxygen were consumed and of formaldehyde were produced. The results corresponded to the stoichiometry expected of a mixed-function oxidase, provided that catalase was added to the enzyme system. In the absence of catalase, a significantly greater oxygen uptake was observed. The Km of benzphetamine was 1.8 x 10-4 in the reconstituted enzyme system, and the Ks of benzphetamine, which was unaltered in the absence of the heat-stable lipid fraction, was 5.5 x 10-4 M. Aniline and octante were shown to act as competitive inhibitors with respect to benzphetamine. ACKNOWLEDGMENT We wish to acknowledge the technical assistance of Miss Joanne Heidema.