cssi/SciSciGPT-SciSciNet huggingface dataset:
Three-dimensional segmentation of luminal and adventitial borders in serial intravascular ultrasound images

Intravascular ultrasound (IVUS) provides exact anatomy of arteries, allowing accurate quantitative analysis. Automated segmentation of IVUS images is a prerequisite for routine quantitative analyses. We present a new three-dimensional (3D) segmentation technique, called active surface segmentation, which detects luminal and adventitial borders in IVUS pullback examinations of coronary arteries. The technique was validated against expert tracings by computing correlation coefficients (range 0.83-0.97) and William's index values (range 0.37-0.66). The technique was statistically accurate, robust to image artifacts, and capable of segmenting a large number of images rapidly. Active surface segmentation enabled geometrically accurate 3D reconstruction and visualization of coronary arteries and volumetric measurements.
Adaptive-Rate Digital Communication System for Imagery

We propose two methods to provide optimal image quality at a fixed image delivery rate for any given transmission channel condition. The first method, channel-controlled variable-rate (CCVR) image coding, employs adaptive-rate source coding and channel coding, while operating with a fixed modulation symbol rate. The second method, adaptive-rate coding-modulation (ARCM), extends the CCVR system by utilizing adaptive modulation. Both methods use a variable-compression-ratio image coder and variable-rate channel coding. The objective is to maximize the quality of the reconstructed image at the receiver when transmitted through Rayleigh fading and additive white Gaussian noise (AWGN). The CCVR system maximizes the reconstructed image quality through a bit-rate trade-off between the source and channel coders. The ARCM method provides a trade-off between the rates of source and channel coding, and the modulation rate. Both methods require knowledge of the channel state which is used by the receiver to inform the transmitter, via a feedback channel, of the optimal strategy for image compression, channel coding, and modulation format. The resulting system using ARCM achieves up to a 17 dB improvement over the peak signal-to-noise ratio (PSNR) performance of a system using a fixed-compression-ratio image coder and fixed-rate channel coding. We extend the adaptive image transmission system to video, and present a candidate system for wireless mobile video applications using orthogonal frequency division multiplexing (OFDM).
Anti-elastofibril monoclonal antibody NKH-1: production and application.

A new monoclonal antibody NKH-1 was developed using human subepidermal basement membrane zone substances as immunogen. NKH-1, IgG1 kappa light chain, labeled proteins in the subbasement membrane zone in a linear fashion. It also labeled oxytalan fibers and elaunin fibers in the papillary dermis. Mature elastic fibers were labeled only in their peripheral microfibrils (elastofibrils) and the center core of elastin was nonreactive. Basal lamina itself was not decorated with NKH-1 even at the immunoelectron microscopic level. Skin appendages such as eccrine and apocrine glands, arrector pili muscle, hair follicle, and sebaceous gland were surrounded with NKH-1 -positive substances. This substance was in linear fashion closely associated with the basal lamina but deposited linearly outside of it. Species specificity tests were performed only in nonprimates: mouse and guinea pig skins were nonreactive with NKH-1. NKH-1 seems to recognize a new substance in the sub- basal lamina region (subbasal lamina proteins) which cross-react with elastic fiber microfibrils.
Preparative-scale synthesis and reversed-phase purification of a gonadotropin-releasing hormone antagonist

Abstract The preparation of “Nal—Glu” antagonist (Ac— d -Nal— d -Cpa— d -Pal—Ser—Arg— d -2-amino-5-oxo-5-(4-methoxyphenyl)pentanoic acid—Leu—Arg—Pro— d -Ala—NH 2 ) was accomplished in two steps: (i) preparation of [Ac— d -Nal 1 , d -Cpa 2 , d -Pal 3 , Arg 5 , d -Glu 6 , d -Ala 10 ]-GnRH via standard solid-phase synthetic techniques and (ii) acylation of anisole (Friedel—Crafts) by the glutamic acid residue in position 6. The preparative-scale, reversed-phase high-performance liquid chromatographic (HPLC) purification of the crude “Nal—Glu” antagonist employs first a triethylammonium phosphate (TEAP) (Ph 2.25)—acetonitrile solvent system, followed by an HPLC-based desalting procedure, yielding the acetate salt of the peptide. This repetitive process of purification in TEAP—acetonitrile, followed by counter-ion exchange with 0.5% acetic acid—acetonitrile is highly reproducible and allows large amounts of a given peptide to be purified efficiently in a batchwise fashion. The procedure described for the synthesis, purification and characterization of the “Nal—Glu” antagonist is presented as a model for the multi-gram synthesis and purification of peptides to be used in clinical investigations.
Effect of pH on the accumulation kinetics of pentachlorophenol in goldfish

The kinetics of accumulation of pentachlorophenol (PCP) at various pH values were investigated to explore how pH-dependent accumulation might influence PCP toxicity. Goldfish (Carassius auratus) were exposed to 5 micrograms PCP/L in a static system buffered with 7.5 mM bicine or N,N-bis(2-hydroxyethyl)-2-aminoethane sulfonic acid (BES) at pH 7.0, 8.0, or 9.0. The amount of PCP in the fish, concentration of PCP in water, and the total amount of metabolites in the system were measured after exposure of fish from 1 to 96 hr. Equations for these variables based on a two compartment pharmacokinetic model were fitted simultaneously to the data using NONLIN, which uses an iterative nonlinear least squares technique. Uptake clearance, metabolic clearance, and apparent volume of distribution of PCP decreased as pH increased. The decrease in PCP accumulation with increased pH was not due solely to a pH-induced decrease in uptake. In addition, the distribution of PCP within the fish was altered by changes in the external pH. The pH-associated changes in distribution may have altered access of PCP to sites of metabolism, thereby altering the metabolic clearance. The pH-related changes in the pharmacokinetics of PCP resulted in a decrease in its bioconcentration factor with an increase in pH and account both for the decreased capacity of the fish to accumulate PCP and for its reduced LC50.
A scenario generation-based lower bounding approach for stochastic scheduling problems

In this paper, we investigate scenario generation methods to establish lower bounds on the optimal objective value for stochastic scheduling problems that contain random parameters with continuous distributions. In contrast to the Sample Average Approximation (SAA) approach, which yields probabilistic bound values, we use an alternative bounding method that relies on the ideas of discrete bounding and recursive stratified sampling. Theoretical support is provided for deriving exact lower bounds for both expectation and conditional value-at-risk objectives. We illustrate the use of our method on the single machine total weighted tardiness problem. The results of our numerical investigation demonstrate good properties of our bounding method, compared with the SAA method and an earlier discrete bounding method.
A Survey of Evaluation Practices for Hospice Social Workers

Hospice social workers make distinct contributions to the care of terminally ill persons and their loved ones. This study contributes to social work's professional knowledge base by examining methods by which hospice social workers are evaluated by their supervisors as well as their clients. This article reports on a survey of 109 hospices' evaluative methods for social workers. Implications for patient care and hospice operations are discussed.
Photobiology and behavior of the water mite genus unionicola: A minireview☆

Abstract 1. Water mites of the genus Unionicola occur in often highly species-specific associations with freshwater bivalve molluscs. 2. Mite photobehavior includes phototaxis with differential spectral sensitivity. 3. Positive phototaxis by some mite species changes to negative phototaxis in the presence of specific chemical signals from host mussels. 4. Chemically mediated behavior involving host-recognition is consistent with the species-specificity of some mussel-mite symbioses. 5. The mechanisms effecting these mite behaviors are largely unknown.
A cutting-date estimation technique for ponderosa pine and Douglas fir wood specimens

The interpretation of noncutting tree-ring dates from archaeological sites often proves problematic, and many sites in the Southwest may be more securely dated if cutting dates can be reliably estimated. Analysis of 54 ponderosa pine and 46 Douglas fir specimens reveals that the relationship between heartwood and sapwood in these species is sufficiently structured that regression analysis can be used to estimate the number of sapwood rings, and by extension the tree's cutting date, on the basis of the number of heartwood rings present on wood specimens. The efficacy of this estimation technique is evaluated on samples from localized and well-dated proveniences at Walpi Pueblo, as well as in light of the aggregate date distribution curve for that site. Results suggest that uncritical acceptance of estimated cutting dates is ill advised, but that when cutting-date estimates (and their associated confidence intervals) are considered in light of contextualizing architectural and archaeological data, they may suggest alternative room construction and repair hypotheses. When considered as part of the aggregate date distribution for a site, estimated cutting dates may identify and augment date concentrations, thereby helping secure the chronometric placement of prehistoric sites in the Southwest.
Toll-like receptors and TLR-mediated signaling: more questions than answers.

pathogen-associated molecular patterns (PAMPs), bacterial components or products, are powerful activators of the immune system. These include lipopolysaccharide (LPS) from gram-negative bacteria; peptidoglycan and lipoteichoic acid (LTA) from gram-positive bacteria; formylated peptides from both
Aortic Intussusception Complicating Diagnostic Angiography: Recognition and Management

During the diagnostic evaluation of a 31-year-old male with Marfan syndrome, an acute type B aortic dissection, and rising creatinine, the retrograde loop of our selective catheter inadvertently engaged the entry tear of the dissection in the mid-descending aorta. Traction on the catheter led to a full circumferential dehiscence of the remaining lumen, causing an intimointimal intussusception down to the level of the celiac artery with complete collapse of the true lumen and visceral and renal artery obstruction. Balloon fenestration and supramesenteric stenting of the true lumen decompressed the intussuscepted intimal flap and restored normal perfusion pressures.
Different Signaling Pathways Control Acute Induction versus Long-Term Repression of LHβ Transcription by GnRH

GnRH regulates pituitary gonadotropin gene expression through GnRH receptor activation of the protein kinase C (PKC) and calcium signaling cascades. The pulsatile pattern of GnRH release is crucial for induction of LHβ-subunit (LHβ) gene expression; however, continuous prolonged GnRH exposure leads to repression of LHβ gene transcription. Although in part, long-term repression may be due to receptor down-regulation, the molecular mechanisms of this differential regulation of LHβ transcription are unknown. Using transfection into the LH-secreting immortalized mouse gonadotrope cell line (LβT4), we have demonstrated that LHβ gene transcription is increased by acute activation (6 h) of GnRH receptor or PKC but not calcium influx; in contrast long-term activation (24 h) of GnRH receptor, PKC, or calcium influx each repress LHβ transcription. Whereas blockade of PKC prevented the acute action of GnRH and unmasked an acute repression of LHβ transcription by calcium, it did not prevent long-term repression by GnRH or calcium. Removal of calcium resulted in potentiation of acute GnRH and PKC induction of LHβ gene expression but prevented long-term repression by GnRH and reduced long-term repression by either calcium or 12-O-tetradecanoyl-phorbol-13-acetate (TPA). We conclude that GnRH uses PKC for acute induction, and calcium signaling is responsible for long-term repression of LHβ gene expression by GnRH. Furthermore, analysis of the responsiveness of truncated and mutated LHβ promoter regions demonstrated that not only do acute induction and long-term repression use different signaling systems, but they also use different target sequences for regulating the LHβ gene.
Effects of imprint training procedure at birth on the reactions of foals at age six months

Summary Reasons for performing study: While imprint training procedures have been promoted in popular magazines, they have received limited scientific investigation. Objectives: To determine the effects of a neonatal imprint training procedure on 6-month-old foals and to determine if any one session had a greater effect than others. Methods: Foals (n = 131) were divided into the following treatments: no imprint training, imprint training at birth, 12, 24 and 48 h after birth orimprint training only at birth, 12, 24, 48, or 72 h after birth. Foals then received minimal human handling until they were tested at 6 months. Results: During training, time to complete exposure to the stimulus was significant for only 2 of 6 stimuli. Percentage change in baseline heart rate was significant for only 2 of 10 stimuli. These 4 effects were randomly spread across treatments. Conclusions: Neither the number of imprint training sessions (0, 1, or 4) nor the timing of imprint training sessions (none, birth, 12, 24, 48, or 72 h after birth) influenced the foal's behaviour at 6 months of age. Potential clinical relevance: In this study, imprint training did not result in better behaved, less reactive foals.
A general program to calculate atomic continuum processes using the NIEM method

Abstract This paper describes a set of computer program packages NIEM which enable electron-atom and electron-ion collision cross sections to be calculated for a general atomic system described by LS -coupling. The calculations are based on a non-iterative integral equation method.
Tentative T cells: memory cells are quick to respond, but slow to divide.

T cell memory is a cornerstone of protective immunity, and is the key element in successful vaccination. Upon encountering the relevant pathogen, memory T cells are thought to initiate cell division much more rapidly than their naive counterparts, and this is thought to confer a significant biological advantage upon an immune host. Here, we use traceable TCR-transgenic T cells to evaluate this proposed characteristic in CD4+ and CD8+ memory T cells. We find that, even in the presence of abundant antigen that was sufficient to induce in vivo IFNγ production by memory T cells, both memory and naive T cells show an extended, and indistinguishable, delay in the onset of proliferation. Although memory cells can detect, and respond to, virus infection within a few hours, their proliferation did not begin until ∼3 days after infection, and occurred simultaneously in all anatomical compartments. Thereafter, cell division was extraordinarily rapid for both naive and memory cells, with the latter showing a somewhat accelerated accumulation. We propose that, by permitting memory T cells to rapidly exert their effector functions while delaying the onset of their proliferation, evolution has provided a safeguard that balances the risk of infection against the consequences of severe T cell–mediated immunopathology.
2011 Special Issue: Neural network modeling of central auditory dysfunction in Alzheimer's disease

Background: Many reports have described that individuals with Alzheimer's disease show neural breakdown in the brainstem nuclei, hippocampus and auditory cortex in the temporal lobe of the brain. However, it is still unclear whether auditory skills mediated by these areas differ across individuals with and without Alzheimer's disease and how these auditory skills are further confounded by reduction in cognitive function in individuals with AD. Aim: The aim of this study is to discover the hidden and nonlinear associations among higher-order auditory and cognitive processes in individuals with and without Alzheimer's disease through artificial neural network analysis. Methods: The analyses were based on auditory test data obtained from nine clinically confirmed Alzheimer's disease cases and nine age-matched controls. Hearing threshold sensitivity was equivalent across groups, indicating similar peripheral auditory function. Auditory function was evaluated by standardized tests of auditory closure, auditory attention, and auditory figure ground in listeners with and without Alzheimer's disease. The inputs used for analyses were cognitive status and auditory function. The dependent variables were RAU scores computed from scores of auditory tests. Results: Artificial neural networks showed a complex relationship between the input variables (cognitive status and auditory function) that cannot be predicted simply on the basis of cognition differences between individuals with and without Alzheimer's disease. Conclusion: The results of this study suggest that central auditory function declines with age, regardless of changes in cognitive function.
Adsorption of O, OH, and H2O on Pt-Based Bimetallic Clusters Alloyed with Co, Cr, and Ni

Binding energies and preferred adsorption sites of O, OH, and H2O to bimetallic clusters PtX, Pt2X, and PtX2 (X ) Pt, Co, Cr, Ni) are determined using density functional theory. The second metal element in the alloy has stronger affinity for OH than the Pt sites, and it is able to adsorb up to two OH radicals per site in oxygenated clusters. The highest binding strength of atomic oxygen is found in the hollow sites of Ni 3 and Co3, followed by adsorption in hollow or bridge sites of Pt 2 Xo r PtX 2, in all cases significantly stronger than that found in Pt3 .H 2O adsorbs on top sites of pure and alloy clusters with much weaker energies compared with those of OH and O; however, the H2O binding strength in the Co, Cr, and Ni atoms is enhanced with respect to that on the Pt site, whereas the binding strength of H 2O on the top of Pt sites of the alloy clusters is much reduced with respect to that in the pure cluster.
Binary addition of peak times for electroencephalic audiometric responses.

A graphic binary addition technique for the detection of evoked responses in conventional sleep EEG audiometry is described. The method displays the number of peaks of waves from all samples that m...
Determination of Equilibrium Constants and Binding Capacities Using a Modified Scatchard Method in Drug-Protein Binding Studies

Abstract The equilibrium constants and the number of binding sites for the binding of l-aniIinonaphthalene-8-sulfonate to human and bovine serum albumin, studied by a fluorescent method, were determined by an equation derived from the Scatchard multiple- equilibrium treatment. The results and the equation are discussed and compared with other equations used in drug-protein binding studies. Treatment of data by the modified method allows a clear determination of the number of binding sites.
Response of Smooth Muscle from Proximal and Distal Human Colon

Regional differences in colonic motility may be responsible for the orderly transit of intraluminal contents through the colon. The aims of this study were to compare the effect of stretch on active and passive stress development in colonic muscle from the proximal and distal colon and to compare the responses of these tissues to KC1 or bethanechol stimulation. Strips of taenia or circular smooth muscle were obtained from the disease-free segment of the colon removed for adenocarcinoma. Passive, active, and total isometric stress were measured on full-thickness strips of circular or longitudinal taenial muscle stimulated with bethanechol (10−4 M) as the muscles were stretched to 120% of the length of optimum tension (Lo.) The tissues then were stimulated with increasing concentrations of KCI and bethanechol while being stretched at Lo. The active stress in the proximal circular muscle was greater at all levels of stretch than in distal circular or longitudinal muscle (p <.001). The resting and passive stress were greater in distal circular and longitudinal taenial muscle than in proximal circular muscle (p < .05). There was a dose-dependent increase in stress development to bethanechol and KCl in each type of muscle. Proximal circular muscle had the greatest response. The EDSO was shifted to the right in distal circular muscle (2.6 ± 0.1 × 10−5 M) compared to proximal circular muscle (1.1 ± 0.1 × 10−5 M) (p < .001). These studies suggest that muscle stress differs in different locations of the colon and the role of active and passive stress development must be considered in models explaining in vivo colonic motility disturbances.
Strong electronic and counterion effects on geminal digold formation and reactivity as revealed by gold(I)-aryl model complexes.

Gold(I) cations have emerged as efficient and often times uniquely effective catalysts for the formation of C–X (X=C, O, N) bonds.[1] Its use as a soft π-acid for the activation of C–C multiple bonds has led to proposed intermediates that include π–gold, Au–vinyl, Au–alkyl, and Au–carbene structures.[2] In many instances a transient Au–C σ-bond is converted into a C–E bond through its reaction with an E+ electrophile.[3] Recently, we provided evidence that the intramolecular hydroarylation of allenes proceeded through two different gold–vinyl intermediates, one mononuclear (A), and one dinuclear (B), with the latter acting as the catalyst’s resting state. The digold structure was proposed to result from the reaction of LAu+ with monogold–vinyl A [Eq. (1)].[4]
Reductase gene sequences and protein structures: p-cymene methyl hydroxylase.

Abstract Oxygenases are critical to cycling carbon in the biosphere and dependent on reductase action, principally from flavoprotein enzymes. Oxygenase diversity among organisms and strains carries a common theme of protein sequence and folding. p -Cymene ( para -isopropyl toluene) was chosen as a point of convergence in terpene-aromatic mineralization to characterize a methyl hydroxylase electron transport system with the aerobe Pseudomonas aureofaciens. The cymA hydroxylase reductase gene was isolated and sequenced and the protein primary structure deduced. Optimized amino acid sequence alignments of flavoprotein reductases revealed major similarities over protein length, in the binding domains for NAD(P)H, and the flavine centers of pro- and eukaryote systems.
Outer surface protein A protects Lyme disease spirochetes from acquired host immunity in the tick vector.

The Lyme disease spirochete Borrelia burgdorferi alters the expression of outer surface protein (osp) genes as the bacterium cycles between ticks and mammals. OspA is produced as borreliae enter the tick vector and remains a major surface antigen during midgut colonization. To elucidate the role of OspA in the vector, we created an insertional deletion of ospA in strain B31-A3. The ospA mutant infects mice when it is injected intradermally and is acquired by larval ticks fed on these mice, where it persists through the molt to the nymph stage. Bacterial survival rates in artificially infected tick larvae fed on naive mice were compared with those in the vector fed on immune mice. The ospA mutant proliferates in larvae if it is exposed to blood from naive mice, but it declines in density after larval feeding if the blood is from immune mice. When uninfected larvae are fed on B-cell-deficient mice infected with the ospA mutant, larvae show borrelial densities and persistence that are significantly greater than those fed on infected, immunocompetent mice. We conclude that OspA serves a critical antibody-shielding role during vector blood meal uptake from immune hosts and is not required for persistence in the tick vector.
AN ACID- AND BASE-STABLE O-NITROBENZYL PHOTOLABILE LINKER FOR SOLID PHASE ORGANIC SYNTHESIS

Abstract The synthesis of an o-nitrobenzyl photolabile linker (1) from o-nitrobenzaldehyde is described, and the efficiency of its light-mediated (365 nm) cleavage is found to be comparable to related, previously developed systems. In contrast, 1 is shown to be stable to acid, base, and Lewis acid/amine combinations while the previously developed linker 2 is shown to degrade under the latter two conditions.
Review: Proton-pump inhibitors are associated with increased risk for Clostridium difficile infection

Source Citation Kwok CS, Arthur AK, Anibueze CI, et al. Risk of Clostridium difficile infection with acid suppressing drugs and antibiotics: meta-analysis. Am J Gastroenterol. 2012;107:1011-9. 22525304
Total phenolics and individual phenolic acids vary with light environment in Lindera benzoin

The understory shrub Lindera benzoin L. experiences lower rates of herbivory in sun environments than in shade environments. The production of secondary metabolites (e.g., phenolic compounds with k...
Control Theory And Transformation Methods In Classical Mechanics

Within the framework of the Hamiltonian description of dynamical systems, canonical transformations and Hamilton-Jacobi theory are examined from the control perspective. For canonical transformations, conditions on the transformation Jacobian matrices are derived such that an equivalent linear (Brunovsky form) representation of nonlinear systems is obtained. Hamilton-Jacobi theory is used to parametrize the solution of the equations of motion in terms of the control variable.
Development of a Compact and High-Throughput Laser Trap Raman System for Fully Automated Single Cell Analysis

The translation of laser tweezers Raman spectroscopy is impeded by several instrumentation limitations. This paper presents our latest work in developing a faster (< 10s acquisition time), compact system for fully automated single cell analysis.
Synaptic connections of DB3 diffuse bipolar cell axons in macaque retina.

In primate retinas, the dendrites of DB3 diffuse bipolar cells are known to receive inputs from cones. The goal of this study was to describe the synaptic connections of DB3 bipolar cell axons in the inner plexiform layer. DB3 bipolar cells in midperipheral retina were labeled with antibodies to calbindin, and their axons were analyzed in serial, ultrathin sections by electron microscopy. Synapses were found almost exclusively at the axonal varicosities of DB3 axon terminals. There were 2.14 synaptic ribbons per varicosity. There were 33 varicosities per DB3 cell, giving an average of 71 ribbons per axon terminal. Because there were 1.5 postsynaptic ganglion cell dendrites per DB3 axonal varicosity, we estimate that there is at least 1 synapse per varicosity onto a parasol ganglion cell dendrite. There were 3.4 input synapses from amacrine cells per axonal varicosity. Among these were feedback synapses to the DB3 bipolar cell axon varicosities, which were made by 47% of the postsynaptic amacrine cell processes. Some of the feedback synapses could be from amacrine cells immunoreactive for cholecystokinin precursor or choline acetyltransferase, because both types of amacrine cells costratify with parasol cells and are known to be presynaptic to bipolar cells. AII amacrine cells were both presynaptic and postsynaptic to DB3 axons, a finding consistent with the large rod input to parasol ganglion cells reported in physiological experiments. DB3 bipolar cell axons also made frequent contacts with neighboring DB3 axons, and gap junctions were always found at these sites.
Design of an introductory engineering course

The design of an introductory engineering course at the University of Minnesota is described. The course, How to Model It: Building Models to Solve Engineering Problems, is a first quarter first year course that focuses on problem formulation, design and construction of models, and drawing conclusions from modeling results. Students work in small teams an several problems selected from various engineering contexts. They learn how to use computer based modeling tools, including spreadsheets and equation solvers. The entire course is problem based, that is, the emphasis is on formulating and solving problems. Our procedures for integrating modeling and design in the course are described. The text for the course is A.M. Starfield, K.A. Smith and A.L. Bleloch's (1994) How to model it: Problem solving for the computer age. Problems such as the 10 problems in How to Model It (ping-pong, purging a gas storage tank, the student's dilemma, tennis, etc.) are given to help students learn engineering and modeling concepts.
Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions

Motivation: Structural variations and in particular copy number variations (CNVs) have dramatic effects of disease and traits. Technologies for identifying CNVs have been an active area of research for over 10 years. The current generation of high-throughput sequencing techniques presents new opportunities for identification of CNVs. Methods that utilize these technologies map sequencing reads to a reference genome and look for signatures which might indicate the presence of a CNV. These methods work well when CNVs lie within unique genomic regions. However, the problem of CNV identification and reconstruction becomes much more challenging when CNVs are in repeat-rich regions, due to the multiple mapping positions of the reads. Results: In this study, we propose an efficient algorithm to handle these multi-mapping reads such that the CNVs can be reconstructed with high accuracy even for repeat-rich regions. To our knowledge, this is the first attempt to both identify and reconstruct CNVs in repeat-rich regions. Our experiments show that our method is not only computationally efficient but also accurate. Contact: eeskin@cs.ucla.edu
Computer simulations of a wide-bandwidth ferrite-loaded high-power waveguide termination

We describe our experience of using MacNeal-Schwendler's finite element code EMAS to design a 10 kW ferrite-loaded rectangular waveguide termination. We require a VSWR of <2:1 over a bandwidth of 700 MHz to 3 GHz. We present results in the frequency domain for several distributions of ferrite tiles in the waveguide.
Down-regulation of Plasminogen Activator Inhibitor 1 Expression Promotes Myocardial Neovascularization by Bone Marrow Progenitors

Human adult bone marrow–derived endothelial progenitors, or angioblasts, induce neovascularization of infarcted myocardium via mechanisms involving both cell surface urokinase-type plasminogen activator, and interactions between β integrins and tissue vitronectin. Because each of these processes is regulated by plasminogen activator inhibitor (PAI)-1, we selectively down-regulated PAI-1 mRNA in the adult heart to examine the effects on postinfarct neovascularization and myocardial function. Sequence-specific catalytic DNA enzymes inhibited rat PAI-1 mRNA and protein expression in peri-infarct endothelium within 48 h of administration, and maintained down-regulation for at least 2 wk. PAI-1 inhibition enhanced vitronectin-dependent transendothelial migration of human bone marrow–derived CD34+ cells, and resulted in a striking augmentation of angioblast-dependent neovascularization. Development of large, thin-walled vessels at the peri-infarct region was accompanied by induction of proliferation and regeneration of endogenous cardiomyocytes and functional cardiac recovery. These results identify a causal relationship between elevated PAI-1 levels and poor outcome in patients with myocardial infarction through mechanisms that directly inhibit bone marrow–dependent neovascularization. Strategies that reduce myocardial PAI-1 expression appear capable of enhancing cardiac neovascularization, regeneration, and functional recovery after ischemic insult.
Ultrasound histotripsy and the destruction of Escherichia coli biofilms

Ultrasound histotripsy has shown great potential for replacing surgery in many applications. In this work, a modification of ultrasound histotripsy was used to destroy Escherichia coli (E. coli) biofilms that had been grown on chambered microscope slides. Biofilms are central to the pathogenesis and persistence of nosocomial (hospital-acquired) infections associated with indwelling medical devices. The slides were exposed to 9.1 μs pulses at a pulse repetition frequency of 1000 Hz. The pulses were generated by a 1.1 MHz spherically focused source with a focal length of 6.3 cm and an active diameter of 7 cm. The peak rarefactional pressure for the pulses was varied as 3.1, 4.1, 5.2, 6.2, and 7.6 MPa in addition to a sham where the biofilms were not exposed. The effectiveness of the treatment was assessed by determining the viable number of colony forming units (CFU) remaining in the biofilm. Most of the biofilms treated at the higher exposures of 6.2 and 7.6 MPa had no remaining CFU indicating that the biofilm was completely destroyed. However, the persistence of some CFU for some of the biofioms at the higher exposure settings needs to be resolved prior to implementing the treatment clinically.
Role of Apoprotein and Calcium Ions in Surfactant Function

Pulmonary surfactant isolated in the presence of calcium ions contains substantial amounts of the morphologic structure, tubular myelin. Chelation of these calcium ions results in disruption of this structure and attendant loss of surface adsorption. Reassembly studies indicate that ability of the lipids to rapidly form surface films is dependent on the presence of a specific surfactant protein in addition to the calcium ions. The formation of this surface-active complex (apoprotein-lipid-calcium ions) is accompanied by aggregation of the lipid. This increase in aggregation may have important implications in the mechanism of surfactant function.
Additive and transcript-specific effects of KPAP1 and TbRND activities on 3' non-encoded tail characteristics and mRNA stability in Trypanosoma brucei.

Short, non-encoded oligo(A), oligo(U), or A/U tails can impact mRNA stability in kinetoplastid mitochondria. However, a comprehensive picture of the relative effects of these modifications in RNA stability is lacking. Furthermore, while the Upreferring exoribonuclease TbRND acts on U-tailed gRNAs, its role in decay of uridylated mRNAs has only been cursorily investigated. Here, we analyzed the roles of mRNA 39 tail composition and TbRND in RNA decay using cells harbouring single or double knockdown of TbRND and the KPAP1 poly(A) polymerase. Analysis of mRNA abundance and tail composition reveals dramatic and transcript-specific effects of adenylation and uridylation on mitochondrial RNAs. Oligo(A) and A-rich tails can stabilize a proportion of edited and never-edited RNAs. However, non-tailed RNAs are not inherently unstable, implicating additional stability determinants and/or spatial segregation of sub-populations of a given RNA in regulation of RNA decay. Oligo(U) tails, which have been shown to contribute to decay of some never-edited RNAs, are not universally destabilizing. We also show that RNAs display very different susceptibility to uridylation in the absence of KPAP1, a factor that may contribute to regulation of decay. Finally, 39 tail composition apparently impacts the ability of an RNA to be edited.
A hybrid model for speech synthesis

A hybrid model for speech analysis/synthesis is proposed. It relies on a time-varying autoregressive moving-average (ARMA) model and the short-time Fourier transform (STFT). The model is hybrid in that the periodic (narrowband) component in speech is represented in the frequency domain by a harmonic-based STFT, while the random component in speech is represented by a random noise sequence, appropriately shaped by the ARMA model. The time-varying ARMA model has a dual function (namely, it creates a spectral envelope that fits accurately the harmonic STFT components) and provides for the spectral shaping of random noise. This hybrid model essentially incorporates the benefits of waveform coders by employing the STFT and the benefits of traditional vocoders by using an appropriately shaped noise sequence; thus, it is expected to yield robust speech synthesis at low data rates. >
A memory and computation efficient structure for MPEG polyphase synthesis

We propose a new structure for polyphase synthesis in the MPEG-1 audio standard. The algorithm is based on factorizing the DCT matrix in a way similar to FFT factorization. The proposed algorithm reduces the memory requirement significantly even with direct implementation. With optimized implementation, the computational requirement can be reduced considerably as well.
The effect of two new dressings on epidermal wound healing.

The effects of a polyethylene oxide hydrogel dressing and a co-polymer starch hydrogel dressing upon the rate of re-epithelization were evaluated in a study using Yorkshire pigs. The polyethylene oxide hydrogel dressing significantly promoted re-epithelization by 44% as compared to untreated control wounds, while the copolymer starch hydrogel dressing significantly promoted epidermal healing by 24%. A possible mechanism of action is presented for the quicker healing induced by these dressings.
2H‐2‐Hydroxy‐1,3,2‐benzodithiazole 1,1,3,3‐tetraoxide

(2H-2-Hydroxy-1,3,2-benzodithiazole 1,1,3,3-tetraoxide) [77450-62-5] C6H5NO5S2 (MW 235.24) InChI = 1S/C6H5NO5S2/c8-7-13(9,10)5-3-1-2-4-6(5)14(7,11)12/h1-4,8H InChIKey = ISMWWXXQYWXQMQ-UHFFFAOYSA-N Physical Data: mp 128–130 °C. Solubility: soluble in H2O, THF, and acetonitrile. Alternate names: N-hydroxy-o-benzenedisulfonimide; NHOBS. Form supplied in: white crystals. Preparative method: reduction of benzene o-disulphonyl chloride with Na2SO3 followed by treatment with HNO2 provides N-hydroxy-o-benzenedisulfonimide (eq 1).1 (1) Handling, Storage, and Precautions: storage in a cool, dry place is recommended.
Sensor-based motion planning for multiple mobile robots in an uncertain environment

This paper presents an approach for decentralized motion planning for multiple mobile robots operating in a common 2D environment with unknown stationary obstacles. Each robot is capable of translatory motion and is equipped with range sensors which allow it to sense surrounding objects. Each robot knows its current position, is able to distinguish a robot from an obstacle, and can assess the instantaneous motion of any robot it can sense. Other than this, the robot has no knowledge about the scene, or of the paths or objectives of other robots; there is no mutual communication among the robots. No constraints are imposed on the paths or shapes of robots and obstacles. Each robot plans its path toward its target dynamically, based on its current position and sensory feedback. Given the assumptions of incomplete information and decentralized planning, the suggested heuristic algorithm demonstrates a remarkable robustness and ability for successful decentralized real-time motion planning in an unknown complex environment. >
QUALITY OF APPLE FRUIT IN RIGID FILM CONTAINERS

The storage quality of‘Delicious’ apples individually packaged in rigid film containers was investigated. Objective quality attributes (internal and external color, firmness, soluble solids and titratable acidity) were measured as a function of storage time with and without packaging in a rigid container. Overall firmness, acidity and soluble solids content decreased over a 70-day storage period. Significant effects of rigid film packaging and storage included: superior skin color, decreased weight loss, slight decrease in soluble solids content and increased firmness loss during ripening when compared to control fruit. Upon examination of the atmosphere surrounding individual fruit in these containers, increased levels of carbon dioxide and ethylene were found. Conversely, packaged fruit contained significantly less internal carbon dioxide than control samples. It was concluded that the atmosphere modified by the rigid film container hastened ripening of‘Delicious’ apples, thus deteriorating eating quality. An adequately ventilated packaged would probably alleviate this condition.
Pancreatic cancer cachexia: a review of mechanisms and therapeutics

Over the last decade, we have gained new insight into the pathophysiology of pancreatic cancer cachexia. Unfortunately, its treatment is complex and remains a challenge. Pancreatic cancer cachexia is a multifactorial syndrome characterized by uncompensated adipose tissue and skeletal muscle loss in the setting of anorexia that leads to progressive functional impairment. This paper will review the current concepts of pancreatic cancer cachexia, its assessment and pathophysiology as well as current and future treatments. The successful management of pancreatic cancer cachexia will likely require a multimodal approach that includes nutritional support and combination pharmaceutical interventions.
Morphological corollaries and ecological implications of flightlessness in the kakapo (Psittaciformes: Strigops habroptilus)

The morphological corollaries of flightlessness of the kakapo (Strigops habroptilus) have been studied using skin specimens, skeletons, and pectoral dissection of an anatomical specimen. These have been compared with the closely related, flighted kea (Nestor notabilis), and secondarily with other Psittaciformes and the convergent hoatzin (Cuculiformes: Opisthocomus hoazin). S. habroptilus is the most massive and sexually dimorphic psittaciform in the world, and has the smallest relative wing size of any parrot. Alar pterylography of S. habroptilus is similar to that of other parrots, but remiges of the species are shorter, comparatively rounded, show less asymmetry of vanes, and have fewer interlocking barbules distally. S. habroptilus shows peculiarities of the sternum (vestigial carina, shortened spina externa), coracoid (elongate processus lateralis, enlarged angle with scapula), and humerus (prominent tuberculum ventrale, undercut crista bicipitalis). Pectoral skeletal dimensions of S. habroptilus are smaller than those of N. notabilis, whereas the reverse is true for pelvic dimensions. Most skeletal dimensions of S. habroptilus are more variable (within sexes) than those of N. notabilis. Proximal wing elements are disproportionately long and distal elements disproportionately short in S. habroptilus. The legs of S. habroptilus are characterized by disproportionately long femora and disproportionately short tarsometatarsi. Distinctive features of the pectoral musculature of S. habroptilus include a greatly reduced Mm. pectoralis thoracica and supracoracoideus, the absence of a distinct proximal muscle belly of M. propatagialis tendo longus, an extensive M. cucullaris capitis clavicularis associated with a voluminous crop, and an essentially tendinous M. sternocoracoideus. Relative to mean body mass, all dimensions of the antebrachial, carpometacarpal, digital, and patagial muscles are smaller in S. habroptilus than in N. notabilis. These aspects are compared to those of other flightless birds. Discussed are implications of flightlessness and associated large body size of S. habroptilus for issues of thermodynamics, metabolism, activity patterns, digestive anatomy, diet, reproduction, and insularit. © 1992 Wiley-Liss, Inc.
Asymptotic and numerical study of Brusselator chaos

We investigate the Brusselator reaction–diffusion equations with periodic boundary conditions. We consider the range of values of the parameters used by Kuramoto in his study of chaotic concentration waves. We determine numerically the bifurcation diagram of the long-time travelling and standing wave solutions using a highly accurate Fourier pseudo-spectral method. For moderate values of the bifurcation parameter, we have found a sequence of instabilities leading either to periodic and quasiperiodic standing waves, or to chaotic regimes. However, for large values of the control parameter, we have found only uniform time-periodic solutions or time-periodic travelling wave solutions. Our numerical study motivates a new asymptotic analysis of the Brusselator equations for large values of the control parameter and small diffusion coefficients. This analysis explains the numerical predictions. The chaotic regime is limited to moderate values of the control parameter and periodic solutions are the only solutions for large values of the control parameter. We identify the stabilizing mechanism as the relaxation oscillations which appear when the control parameter is large. Our asymptotic result on the stability of periodic solutions is then generalized to a class of two-variable reaction-diffusion equations.
Replication-independent histone deposition by the HIR complex and Asf1.

Summary The orderly deposition of histones onto DNA is mediated by conserved assembly complexes, including chromatin assembly factor-1 (CAF-1) and the Hir proteins [1–4]. CAF-1 and the Hir proteins operate in distinct but functionally overlapping histone deposition pathways in vivo [5, 6]. The Hir proteins and CAF-1 share a common partner, the highly conserved histone H3/H4 binding protein Asf1, which binds the middle subunit of CAF-1 as well as to Hir proteins [7–11]. Asf1 binds to newly synthesized histones H3/H4 [12], and this complex stimulates histone deposition by CAF-1 [7, 11, 12]. In yeast, Asf1 is required for the contribution of the Hir proteins to gene silencing [7, 13]. Here, we demonstrate that Hir1, Hir2, Hir3, and Hpc2 comprise the HIR complex, which copurifies with the histone deposition protein Asf1. Together, the HIR complex and Asf1 deposit histones onto DNA in a replication-independent manner. Histone deposition by the HIR complex and Asf1 is impaired by a mutation in Asf1 that inhibits HIR binding. These data indicate that the HIR complex and Asf1 proteins function together as a conserved eukaryotic pathway for histone replacement throughout the cell cycle.
Efficient interference-aware TDMA link scheduling for static wireless networks

We study efficient link scheduling for a multihop wireless network to maximize its throughput. Efficient link scheduling can greatly reduce the interference effect of close-by transmissions. Unlike the previous studies that often assume a unit disk graph model, we assume that different terminals could have different transmission ranges and different interference ranges. In our model, it is also possible that a communication link may not exist due to barriers or is not used by a predetermined routing protocol, while the transmission of a node always result interference to all non-intended receivers within its interference range. Using a mathematical formulation, we develop synchronized TDMA link schedulings that optimize the networking throughput. Specifically, by assuming known link capacities and link traffic loads, we study link scheduling under the RTS/CTS interference model and the protocol interference model with fixed transmission power. For both models, we present both efficient centralized and distributed algorithms that use time slots within a constant factor of the optimum. We also present efficient distributed algorithms whose performances are still comparable with optimum, but with much less communications. Our theoretical results are corroborated by extensive simulation studies.