cssi/SciSciGPT-SciSciNet huggingface dataset:
Regression analysis of multiple protein structures

ABSTRACT A general framework is presented for analyzing multiple protein structures using statistical regression methods. The regression approach can superimpose protein structures rigidly or with shear. Also, this approach can superimpose multiple structures explicitly, without resorting to pairwise superpositions. The algorithm alternates between matching corresponding landmarks among the protein structures and superimposing these landmarks. Matching is performed using a robust dynamic programming technique that uses gap penalties that adapt to the given data. Superposition is performed using either orthogonal transformations, which impose the rigid-body assumption, or affine transformations, which allow shear. The resulting regression model of a protein family measures the amount of structural variability at each landmark. A variation of our algorithm permits a separate weight for each landmark, thereby allowing one to emphasize particular segments of a protein structure or to compensate for variances ...
The Bacterial Brain: Structure and Dynamics of a Bacterial Chemoreceptor Array

The ability of all living things, from single cells to large multicellular organisms, to sense and interpret environmental signals is central to life. Bacteria, though relatively simple unicellular organisms, have evolved exquisite protein networks, which they use to detect gradients in certain chemicals in their surroundings and alter their swimming behavior. The head of this protein circuit, a chemoreceptor array, is a remarkably ordered supramolecular complex composed of the histidine kinase, CheA; adaptor protein, CheW; and various methyl-accepting chemotaxis proteins (MCPs). These proteins cluster together by the thousands at the cell pole. The clustering of receptors within the chemoreceptor array gives rise to systems-level network properties of bacterial chemotaxis such as signal amplification, ultrasensitivity, and precise adaptation. We present an all-atom structure, roughly twelve million atoms in size, of a patch of the chemoreceptor array from the thermophile Thermotoga maritima, refined by electron cryotomography data. Molecular Dynamics simulations reveal inter-protein interactions essential to receptor communication. Based on insight into the natural structural mobility of the array from normal modes of the trajectories, steered molecular dynamics was employed to perturb the lattice at multiple sites mimicking chemoreceptor activation. The results suggest a molecular mechanism for signal transduction through the array.
Use of negative pressure dressings in head and neck reconstruction

Background. Head and neck microvascular surgery commonly requires management of complex wounds of the upper aerodigestive tract and donor sites. Negative pressure dressings have been reported to promote healing in compromised wounds. Methods. Between February 2001 and June 2004, data were collected in a retrospective manner on 23 patients who underwent treatment with negative pressure dressings at two tertiary care institutions. Results. Twenty-three patients underwent negative pressure wound treatment for donor site complications (n = 9) or head and neck wounds (n = 14) with a minimum of 5 months follow-up. Average duration of treatment was 6.5 days. Indications for use in wound complications included wound breakdown (n = 3), fistula with carotid exposure (n = 4), tendon exposure of donor site (n = 6), and others (n = 3). On average, granulation tissue was promoted in across 93% of the wound bed over the course of treatment. Two patients with anterior mandibular hardware exposure were managed successfully with negative pressure dressings. Large split-thickness skin grafts (average size, 135 cm2) at mobile sites were bolstered with negative pressure dressings in seven patients with an overall take rate of 74%. Conclusion. Although of limited use as a bolster for split-thickness skin grafts, negative pressure dressings are safe and effective in the management of complex head and neck wounds and in the treatment of donor site complications. © 2005 Wiley Periodicals, Inc. Head Neck27: XXX–XXX, 2005
Inhibition of tumor metastasis: Functional immune modulation of the CUB Domain Containing Protein 1

Despite significant progress and notable successes in tumor therapy, malignant disease remains an extremely difficult problem in today's health care setting. There is, however, an increasing application of new therapies targeting proteins specifically upregulated on tumor cells. These innovative therapeutic approaches are aimed at molecules that contribute to malignant development and progression but spare normal tissues. The CUB Domain Containing Protein 1 (CDCP1) is such a tumor-associated protein and thus, a potential candidate for targeted cancer immunotherapy. Herein, we describe the generation of function-blocking human antibodies against CDCP1 that were obtained from human scFv phage display libraries using subtractive panning protocols on CDCP1 expressing cancer cells and immunopurified CDCP1 protein. One of the isolated anti-CDCP1 antibodies, namely C20Fc, efficiently blocked experimental metastasis of human carcinoma cells, including HeLa cells stably transfected with CDCP1 and prostate carcinoma cells PC-hi/diss naturally expressing CDCP1, in both chick embryo and mouse model systems. The C20Fc antibody also reduced colony formation of CDCP1 expressing cells in a soft agar assay for anchorage-independent cell growth. Specific targeting of CDCP1 by C20Fc mediated the delivery of a toxin-conjugated antibody complex, thus, providing evidence for antibody internalization and specific killing of CDCP1-positive tumor cells. Our findings indicate a functional role for CDCP1 in human cancer and underscore the therapeutic potential of function-blocking anti-CDCP1 antibodies targeting both primary and metastatic carcinoma cells.
Investigation of Some Transparent Metal Oxides as Damp Heat Protective Coating for CIGS Solar Cells

We investigated the protective effectiveness of some transparent metal oxides (TMO) on CIGS solar cell coupons against damp heat (DH) exposure at 85°C and 85% relative humidity (RH). Sputter-deposited bilayer ZnO (BZO) with up to 0.5- μm Al-doped ZnO (AZO) layer and 0.2-μm bilayer InZnO were used as “inherent” part of device structure on CdS/CIGS/Mo/SLG. Sputter-deposited 0.2-μm ZnSnO and atomic layer deposited (ALD) 0.1-μm Al2O3 were used as overcoat on typical BZO/CdS/CIGS/Mo/SLG solar cells. The results were all negative — all TMO-coated CIGS cells exhibited substantial degradation in DH. Combining the optical photographs, PL and EL imaging, SEM surface micromorphology, coupled with XRD, I-V and QE measurements, the causes of the device degradations are attributed to hydrolytic corrosion, flaking, micro-cracking, and delamination induced by the DH moisture. Mechanical stress and decrease in crystallinity (grain size effect) could be additional degrading factors for thicker AZO grown on CdS/CIGS.
Carbon storage and greenhouse gases emission from a fluvial reservoir in an agricultural landscape

Abstract The significance of organic carbon (C) burial in fluvial reservoirs on the global C cycle and atmosphere composition remains debatable. While the entrapment of eroded C in these systems could represent an important C sequestration mechanism, this must be weighed against the emission of greenhouse gases (GHG) that may evolve in anoxic reservoir sediment. Over a 4-year period (2005–2008), dissolved concentrations and fluxes of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) were monitored at a Central Indiana fluvial reservoir (built in 1967) fed by streams draining a predominantly agricultural watershed. Analysis of sediment cores revealed an annual sedimentation rate of 1.6 cm and C burial rate of 2.3–2.9 Mg C ha− 1. Reservoir waters were supersaturated with CO2 (mean: 2.55 mg CO2 L− 1) and CH4 (9.44 μg CO2 L− 1). In the sediment, concentrations were 4–250 times higher reaching values up to 14,533 μg CH4 L− 1. The δ 13C profile of CH4 (− 57.7‰ at the bottom, − 48.26‰ near the surface) indicated active CH4 oxidation during diffusive transport through the water column. Instances of N2O under-saturation were occasionally noted in mid-summers when NO3− level was
Mad Men, Meth Moms, Moral Panic: Gendering Meth Crimes in the Midwest

This research examines the content of a sample of newspaper articles from the Midwestern states. The analyses find highly gendered accounts of methamphetamine related crimes. Media depictions suggest women use meth for reasons drawn from conventional notions of motherhood, sexuality, and subordination. Alternately, motives of men appear constructed around dominant notions of male criminal virility and the viability of the drug trade. The findings offer a contextual framework to consider how this sort of mediated dichotomy emerges from and reinforces popular notions of gendered crime and drug users in non-urban spaces.
Functional high efficiency expression of cloned leucocyte chemoattractant receptor cDNAs

Human kidney 293 TSA cells were transfected by a calcium phosphate method with human formylpeptide and C5a receptor cDNAs with high efficiency. Formylpeptide receptor positive transfectants expressed a total of 968,000 +/- 34,000 receptors per cell with two affinity states (Kds of ca. 0.43 nM and 39 nM), which in the presence of 100 microM GTP gamma S decreased by ca. 4-fold the number of high-affinity sites. The ligand binding pharmacology of cloned and expressed formylpeptide receptors were indistinguishable from endogenous receptors on human neutrophils. Expressed formylpeptide and C5a receptors were functionally active in mobilizing intracellular calcium via a pertussis toxin sensitive mechanism with an ED50 for formylpeptide of ca. 0.5-1.0 nM. This expression system, in which receptor expression can be monitored by flow cytometric methods and in which intracellular calcium responses are measurable, unlike in the more popular COS-7 cell expression system, will provide a useful basis for the analysis of chemoattractant receptor structure-function relationships.
Structural Aspects of Reversible Molecular Oxygen Uptake

The system IrX(CO)[P(C(6)H(5))(3)](2) in benzene solution adds mo lecular oxygen reversibly if X is chlorine and irreversibly if X is iodine. The crystal structure of the complex IrIO(2)(CO)[P(C(6)H(5))(3)](2) * CH(2)Cl(2) is reported here and compared with a previous study of the structure of IrClO(2)(CO)[P(C(6)H(5))(3)](2). The O-O bond length is 1.47 +/- 0.02 angstroms in the irreversibly oxygenated iodo-compound and 1.30 +/- 0.03 angstroms in the reversibly oxygenated chloro compound.
Exxon Valdez to Deepwater Horizon: comparable toxicity of both crude oils to fish early life stages.

The 2010 Deepwater Horizon disaster in the Gulf of Mexico was the largest oil spill in United States history. Crude oils are highly toxic to developing fish embryos, and many pelagic fish species were spawning in the northern Gulf in the months before containment of the damaged Mississippi Canyon 252 (MC252) wellhead (April–July). The largest prior U.S. spill was the 1989 grounding of the Exxon Valdez that released 11 million gallons of Alaska North Slope crude oil (ANSCO) into Prince William Sound. Numerous studies in the aftermath of the Exxon Valdez spill defined a conventional crude oil injury phenotype in fish early life stages, mediated primarily by toxicity to the developing heart. To determine whether this type of injury extends to fishes exposed to crude oil from the Deepwater Horizon – MC252 incident, we used zebrafish to compare the embryotoxicity of ANSCO alongside unweathered and weathered MC252 oil. We also developed a standardized protocol for generating dispersed oil water-accommodated fractions containing microdroplets of crude oil in the size range of those detected in subsurface plumes in the Gulf. We show here that MC252 oil and ANSCO cause similar cardiotoxicity and photo-induced toxicity in zebrafish embryos. Morphological defects and patterns of cytochrome P450 induction were largely indistinguishable and generally correlated with polycyclic aromatic compound (PAC) composition of each oil type. Analyses of embryos exposed during different developmental windows provided additional insight into mechanisms of crude oil cardiotoxicity. These findings indicate that the impacts of MC252 crude oil on fish embryos and larvae are consistent with the canonical ANSCO cardiac injury phenotype. For those marine fish species that spawned in the northern Gulf of Mexico during and after the Deepwater Horizon incident, the established literature can therefore inform the assessment of natural resource injury in the form of potential year-class losses.
Auditory and Visual Perception Processes and Reading Ability: A Quantitative Reanalysis and Historical Reinterpretation.

Meta-analysis was used to integrate statistically the literature assessing the relationship between auditory and visual perception and reading achievement. From 267 studies conducted between 1950–1...
Mechanical stimulation activates beating in calcium-arrested lateral cilia of Mytilus edulis gill.

Lateral cilia ofMytilus edulis gill arrest upon mechanical stimulation, the result of calcium influx. A mechanical stimulus that deflects these cilia toward the effective stroke, and is normally sufficient to cause transient arrest in beating lateral cilia or transient movement into the recovery stroke in quiescent cilia, initiates beating in Ca2+ ionophore-arrested cilia at 9–15 Hz, for periods as long as 30 S. This movement is restricted to the stimulated cilia and the beat pattern appears constrained in the first half of the beat cycle. Application of dopamine causes ciliary arrest in the presence (but not absence) of Ca2+ and mechanical stimulation will also activate such cilia to beat. In the presence of ATP, mechanical stimulation of detergent-permeabilized lateral cell models arrested in the presence of 50 μm Ca2+ will also cause activation comparable in frequency, duration, and beat pattern to that seen in Ca2+-arrested cells, but the initiation is more difficult. Upon application of ionophore in Ca2+-free (EGTA) seawater, the cilia become quiescent, stopped at the end of the recovery stroke. Mechanical stimulation will cause activation of beat, with a similar range of frequencies and duration as in Ca2+-arrested lateral cilia, but the beat pattern is normal and cilia of adjacent cells may also beat, presumably initiated by mechanical coupling. Gently lifting cilia at their basal ends, using small, slow movements of a mechanical probe, will initiate several beat cycles in quiescent lateral cilia but will cause Ca2+-arrested cilia to‘snap’ into the effective stroke and back. These data indicate that Ca2+-arrest does not involve permanent, rigor-like dynein crossbridges since such cilia are quite capable of beating, if given sufficient momentum. This would also suggest that ionic control must act at the level of crossbridge initiation, timing or coordination.
Kinetics of Tc-99m hexakis t-butyl isonitrile in normal and ischemic canine myocardium.

Hexakis 99mTc-tertiary butyl isonitrile (99mTc-TBI) was studied as a cardiac perfusion imaging agent in nine dogs with partial occlusion of the LAD. Thirty min after applying the stenosis, 99mTc-TBI was injected into the right atrium (RA) in five dogs and left atrium (LA) in four dogs. Normal and ischemic zone regional myocardial 99mTc-TBI activites were monitored continuously for 4 h. Dogs with LA injections had minimal and equivalent 4 h fractional clearance from the normal and ischemic zones. Dogs with RA injections had minimal, but significantly lower 4 h fractional 99mTc clearances in the ischemic zone (0.08±0.08) compared to the normal zone (0.16±0.07, P<0.05). The delayed ischemic zone clearance is probably due to the high initial lung uptake observed after RA injection. Despite the differences in clearance, this minimal amount of redistribution could not be detected on gamma camera images. The minimal myocardial washout and redistribution, and the 140 keV gamma make 99mTc-TBI a promising cardiac perfusion imaging agent.
Purification and characterization of human lysosomal membrane glycoproteins.

Abstract Two human cell lysosomal membrane glycoproteins of ∼120 kDa, hLAMP-1 and hLAMP-2, were identified by use of monoclonal antibodies prepared against U937 myelomonocytic leukemia cells or blood mononuclear cells. The two glycoproteins were purified by antibody affinity chromatography and each was found to be a major constituent of human spleen cells, representing ∼0.05% of the total detergent-extractable protein. Both molecules were highly glycosylated, being synthesized as polypeptides of 40 to 45 kDa and cotranslationally modified by the addition of Asn-linked oligosaccharides. NH2-terminal sequence analysis indicated that each was ∼50% identical to the corresponding mLAMP-1 or mLAMP-2 of mouse cells. Electron microscopic studies of human blood monocytes, HL-60, and U937 cells demonstrated that the principal location of these glycoproteins was intracellular, in vacuoles and lysosomal structures but not in the peroxidase-positive granules of monocytes. Transport of the proteins between organelles was evidenced by their marked accumulation in the membranes of phagolysosomes. A fraction of each glycoprotein was also detected on the plasma membrane of U937 and HL-60 cells but not on a variety of other tissue culture cells. This cell-surface expression may be differentiation related, since the proteins were not detected in the plasma membrane of normal blood monocytes and their expression on U937 and HL-60 cells was reduced when the cells were treated with differentiating agents. Cell-surface expression of both glycoproteins was markedly increased in blood monocytes but not in U937 cells after exposure to the lysosomotropic reagent methylamine HCl, indicating differences in LAMP-associated membrane flow in these cell types.
THE HISTOGENESIS OF BLOOD PLATELETS

1. Under normal circumstances blood platelets are largely derived from the megakaryocyte of the blood-forming organs. 2. The transitional leucocyte, representing a persistent form of the embryonic premegakaryocyte, is a circulating homologue of the megakaryocyte and probably plays some part in normal platelet formation. 3. Under conditions of excessive demand for platelet production, there may be a greater or less reversion to an embryonic mode of platelet formation in which less highly specialized cells than the megakaryocyte participate in platelet production. 4. In addition to the megakaryocyte, the cells that have been observed to take part in platelet formation are hyperplastic endothelial cells in the marrow, and mononuclear and transitional cells (premegakaryocytes) in the marrow, spleen, and blood.
General infrared and ultraviolet properties of the gluon propagator in the axial gauge

Some general properties of the gluon propagator are studied in the axial gauge with emphasis on its infrared and ultraviolet behavior. In spacelike gauges we derive a Lehmann representation and consequently a K\"all\'en sum rule for ${Z}_{3}$. We investigate in some detail the apparent inconsistency between ${Z}_{3}g1$ (antiscreening and the origin of asymptotic freedom) and the positivity of the Hilbert space due to the absence of ghosts which suggests ${Z}_{3}l1$. We show that in timelike gauges there is no Lehmann representation so that the propagator is no longer analytic in its virtual mass parameter. General positivity coupled with these results restricts certain IR singularities from being any worse than they are in QED, so consequently it is not possible to use the IR behavior of the propagator in this gauge (whether timelike or spacelike) as a signal for confinement if the Wilson loop is used as the criterion. We also show that a judicious use of the renormalization group involving a variation of the axial-gauge parameter allows one to drive the theory into the IR in such a way that the effective coupling constant is the asymptotically free one. We use this result to show that the presence of nonperturbative contributions of the generic form ${e}^{\ensuremath{-}\frac{c}{{g}^{2}}}$ associated with instantons leads to a power-law correction to the IR behavior of the propagator.
A model of strength.

In her AAAS News & Notes piece “Can the Southwest manage its thirst?” (26 July, p. [362][1]), K. Wren quotes Ajay Kalra, who advocates a particular method for predicting Colorado River streamflow “because it eschews complex physical climate models for a statistical data-driven modeling
Risk of rising sea level to population and land area

Low-elevation land areas and their populations are at risk globally from rising sea level. Global sea level has risen by about 2 millimeters per year over the past century. About half of this rise may be attributed to thermal expansion of the ocean and the melting of temperate-latitude glaciers [Dyurgerov and Meier, 1997]. The remainder of the rise is believed to come from a net loss of mass from the Antarctic and Greenland ice sheets, although the exact contribution is unknown.
Radiologically placed tunneled hemodialysis catheters: a single pediatric institutional experience of 120 patients.

Abstract Purpose To report the outcome of tunneled dialysis catheter insertion in 120 patients. Materials and Methods A retrospective review of the interventional radiology database and electronic medical records of 120 patients who had tunneled dialysis catheters inserted from April 1997 to July 2010 was performed with institutional review board approval. There were 61 female patients and 59 male patients, with a mean age of 13.3 years (range, 0.2–28.5 y). A total of 193 primary insertions and 330 salvage procedures were performed. Results The technical success rate for primary catheter insertions was 100%. Immediate complications included self-limiting tract bleeding and air embolism in two of 193 insertions each (1.03%). Mean indwell duration for primary insertions was 66 catheter-days (range, 1–765 d), compared with a total mean of 159.4 catheter-days (range, 1–1,034 d). Rates of infection and mechanical complications were 0.21 and 0.9 per 100 total catheter-days, respectively. Mechanical and infections complications were increased in children younger than 9 years of age and weighing less than 20 kg. The catheter removal rates for infection and mechanical complications were 0.084 and 0.081 per 100 catheter-days, respectively. Medical salvage procedures, ie, intracatheter thrombolytic agent use or antibiotic therapy (52.1%) and interventional radiologic catheter salvage procedures (47.1%), increased catheter survival by an average of 54.8 days (range, 0–959 d). Conclusions Radiologic placement of tunneled hemodialysis catheters is a safe and technically successful procedure in pediatric patients. However, there is a high rate of infectious and mechanical complications, particularly in younger and smaller patients.
Mutational analysis of G-protein coupled receptor – FFA2

FFA2 (GPR43) is a receptor for short-chain fatty acids (SCFAs), acetate, and propionate. FFA2 is predominantly expressed in islets, a subset of immune cells, adipocytes, and the gastrointestinal tract which suggest a possible role in inflammatory and metabolic conditions. We have previously described the identification and characterization of novel phenylacetamides as allosteric agonists of FFA2. In the current study, we have investigated the molecular determinants contributing to receptor activation with the endogenous and synthetic ligands as well as allosteric interactions between these two sites. The mutational analysis revealed previously unidentified sites that may allosterically regulate orthosteric ligand’s function as well as residues potentially important for the interactions between orthosteric and allosteric binding sites.
Social Validity: Perceptions of Check and Connect with Early Literacy Support.

Abstract This article underscores the potential advantages of qualitative methods to illustrate the depth and complexity of social validity. This investigation evaluates the social validity of Check and Connect with Early Literacy Support (CCEL) , through the perspectives of teachers and caregivers whose children participated in the intervention. Teachers from six classrooms and caregivers from six families participated in evaluating the social validity of this intervention using a combination of qualitative and quantitative methods. Participants completed the Treatment Acceptability Rating Scale—Revised ( TARF-R ; Reimers, T. M., Wacker, D. P., Cooper, L. J. & DeRaad, A. O. (1992). Clinical evaluation of the variables associated with treatment acceptability and their relation to compliance. Behavioral Disorders , 18(1), 67–76.), a quantitative measure of treatment acceptability (a component of social validity), and were interviewed using qualitative interviews and focus groups. Results were analyzed through ethnographic methodology and indicate complex, reciprocal relationships among factors related to social validity. This investigation is considered in light of recent efforts to develop a systematic approach to evaluate the adequacy of intervention research using qualitative methods.
Risk of malignancy in scleroderma: a population-based cohort study.

Objective To determine the incidence of cancer in patients with scleroderma (systemic sclerosis) and to compare those rates with cancer rates in the local population. Methods Cancer risk in scleroderma patients in the Detroit metropolitan area was assessed by linking patient identification codes of the Michigan Scleroderma Registry to the Metropolitan Detroit Cancer Surveillance System database. Patients were screened between the years 1973 and 2002, with additional followup to 2004. Standardized incidence ratios (SIRs) were calculated for selected malignancies (lung, liver, colon, breast, cervical, and prostate cancers, and non-Hodgkin's lymphomas), with stratification by sex and race. Results Of 934 patients in the Scleroderma Registry, 538 were included in the study based on tri-county residency (436 females and 102 males). Of these, 45 first malignancies were noted (37 females and 8 males). Lung cancer (10 cases) was found to be the most common cancer in scleroderma patients. However, its incidence was not significantly different from that in the general population of metropolitan Detroit (SIR 1.23). Other types of cancer were examined, and no significant differences were found as compared with the rates in the local population, with 1 exception: black females with scleroderma had significantly higher rates of liver cancer (SIR 45.8). Conclusion Contrary to previous studies, this study did not find statistical evidence of an increased incidence of cancer in scleroderma patients, except for liver cancer. One possible reason is the high background rates of certain cancers in the metropolitan Detroit area. It may be necessary to consider local cancer rates when comparing different scleroderma cohorts.
On Detecting White Space Spectra for Spectral Scavenging in Cognitive Radios

A primary task performed by a Cognitive Radio is that of spectral estimation to locate the segments in a spectral span that contain white zones, spans that contains noise only, or grey zones, spans that contain signals with significant intervals of off-time. The identification of spectral regions containing noise only spectra, as opposed to regions containing signals with low spectral density, is surprising difficult. The estimator must deal with questions of transform length, window selection, window length, window overlap, and ensemble averaging options. This paper describes the impact of each selection option and presents the architecture of the optimal spectral estimator.
Long-term change in an assemblage of North American bats: are eastern red bats declining

Abstract We examined changes in the assemblage of bats in southern Lower Michigan, USA, using results of paired netting surveys conducted with similar techniques but separated by 12–26 years. Species diversity declined by 18–35% and evenness decreased by 0–35% throughout the region and in two specific areas. Changes in diversity and evenness were attributed primarily to decreases of 44% or more in relative abundance of the foliage-roosting eastern red bat (Lasiurus borealis). Number of L. borealis captured per net-night decreased 52–85%. The decline in relative abundance of L. borealis suggested by mist netting was supported by a 10-fold decrease over 38 years in the proportion of L. borealis that were tested for rabies by the state health laboratory. The apparent decline in L. borealis is especially alarming in light of the recent upsurge in use of wind power and the large number of L. borealis that are killed at such developments. We recommend that other previously completed surveys in eastern North Ame...
Theoretical Perspectives On Correctional Structure, Evaluation, and Change:

Despite the criticisms of some sociologists that the Technical/Rational Model is too one-dimensional to capture the complexity of a social insti tution, scholars studying, evaluating, and recommend...
METHODOLOGICAL AND SPATIO‐TEMPORAL CONTEXTS FOR GEOMORPHOLOGICAL KNOWLEDGE: ANALYSIS AND IMPLICATIONS

Scientific statements are valid only within the confines of the approach and scale of study adopted at the outset of the inquiry. Therefore, geomorphological knowledge is considered to be valid only within the methodological and/or spatio-temporal framework adopted for study. New approaches add to understanding by changing the context within which phenomena are viewed but cannot invalidate existing concepts: these can be invalidated only if they are logically or empirically unsupported within their own frame of reference. Research programs may become self-fulfilling because it is only within their own context that hypotheses, with which they might be falsified, are generated and tested: indeed, an approach might not be capable of generating any falsifying hypotheses but be able to produce only hypotheses that are amenable to that particular mode of investigation. Therefore, contributions should be judged only within their own, stated methodological base and alternative approaches should be actively considered. Tout enonce scientifique n'est valable que dans le cadre de l'approche et de l'ehelle d'analyse adoptes au debut de la recherche. les connaissances geomorphologiques ne sont donc consideres valides que dans les limites methodologiques et ou a I'interieur des coordonnees espace-temps choisies pour l'etude. De nouvelles approches aident A la compr6hension en modifiant le contexte a l'intbrieur duquel les phenomenes sont examines, mais elles ne peuvent pas annuler les concepts existants; ces derniers ne peuvent etre invalides que s'ils ne sont pas supportes de facon logique ou empirique dans leurpropre cadre de references. Des programmes de recherche peuvent se realiser d'eux-memes, car c'est dans leur propre contexte que les hypotheses, avec lesquelles ils peuvent etre falsifies, sont creees et essayees; de fait, il se peut qu'une approche ne genere aucune hypothese falsifiante, mais puisse ne produire que des hypotheses conformes au mode particulier d'investigation. les contributions ne doivent donc etre jugees qu'a l'interieur de leur propre base methodologique, et d'autres approches doivent etre consideress de facon active.
Behavior of atoms in a compressed magneto-optical trap

We investigate the behavior of a cloud of atoms in a magneto-optical trap, which—after collection—is compressed when the field gradients of the trap magnetic field are increased. We measure sizes and shapes of the atom cloud as a function of laser detuning, magnetic field gradient, and number of trapped atoms. A transient density increase of more than an order of magnitude has been achieved. Moreover, reproducible Gaussian density distributions are observed at large detunings and intermediate magnetic-field gradients, permitting an accurate determination of density.
The Stability of a Unipolar World

The collapse of the Soviet Union produced the greatest change in world power relationships since World War II. With Moscow’s headlong fall from superpower status, the bipolar structure that had shaped the security policies of the major powers for nearly half a century vanished, and the United States emerged as the sole surviving superpower. Commentators were quick to recognize that a new “unipolar moment” of unprecedented U.S. power had arrived.1 In 1992 the Pentagon drafted a new grand strategy designed to preserve unipolarity by preventing the emergence of a global rival.2 But the draft plan soon ran into controversy, as commentators at home and abroad argued that any effort to preserve unipolarity was quixotic and dangerous.3 Ofacials quickly backed away from the idea and now eschew the language of primacy or predominance, speaking instead of the United States as a “leader” or the “indispensable nation.”4 The rise and sudden demise of an ofacial strategy for preserving primacy lends credence to the widespread belief that unipolarity is dangerous and unstable. While scholars frequently discuss unipolarity, their focus is always on its demise. For neorealists, unipolarity is the least stable of all structures because any great concentration of power threatens other states and causes them to take action to restore a balance.5 Other scholars grant that a large
A Security Middleware Model for Real-Time Applications on Grids

Real-time applications are indispensable for conducting research and business in government, industry, and academic organizations. Recently, real-time applications with security requirements increasingly emerged in large-scale distributed systems such as Grids. However, the complexities and specialties of diverse security mechanisms dissuade users from employing existing security services for their applications. To effectively tackle this problem, in this paper we propose a security middleware (SMW) model from which security-sensitive real-time applications are enabled to exploit a variety of security services to enhance the trustworthy executions of the applications. A quality of security control manager (QSCM), a centerpiece of the SMW model, has been designed and implemented to achieve a flexible trade-off between overheads caused by security services and system performance, especially under situations where available resources are dynamically changing and insufficient. A security-aware scheduling mechanism, which plays an important role in QSCM, is capable of maximizing quality of security for real-time applications running in distributed systems as large-scale as Grids. Our empirical studies based on real world traces from a supercomputing center demonstratively show that the proposed model can significantly improve the performance of Grids in terms of both security and schedulability.
Sound localization with a neural network trained with the multiple extended Kalman algorithm

A three-layer neural network is used to solve the problem of extracting relative azimuth and elevation positional information from signals detected by two spatially separate, directional receivers. This is analogous to the ability of owls to localize the position of sound based solely on the properties of the signals reaching their ears. A simple model of the acoustical environment was used to generate simulated data for training the network. The neural network was trained using the multiple extended Kalman algorithm (MEKA). MEKA enabled the network to be trained without constant user intervention for adjustment of the critical parameters of the model. >
Reversal of myeloid cell-mediated immunosuppression in patients with metastatic renal cell carcinoma.

Purpose: Tumor-induced immunosuppression remains a significant obstacle that limits the efficacy of biological therapy for renal cell carcinoma. Here we evaluate the role of CD33 myeloid-derived suppressor cells (MDSC) in the regulation of T-cell responses in renal cell carcinoma patients. We also examine effect of all-trans-retinoic acid (ATRA) on MDSC-mediated immune suppression. Experimental Design: CD33-positive myeloid cells were isolated from the peripheral blood of renal cell carcinoma patients with magnetic beads and tested in vitro for their ability to inhibit T-cell responses. T-cell function was evaluated using ELISPOT and CTL assays. Results: MDSC isolated from renal cell carcinoma patients, but not from healthy donors, were capable of suppressing antigen-specific T-cell responses in vitro through the secretion of reactive oxygen species and nitric oxide upon interaction with CTL. MDSC-mediated immune suppression and IFN-γ down-regulation was reversible in vitro by exposing cells to the reactive oxygen species inhibitors. Moreover, ATRA was capable of abrogating MDSC-mediated immunosuppression and improving T-cell function by direct differentiation into antigen-presenting cell precursors. Conclusions: These results may have significant implications regarding the future design of active immunotherapy protocols that may include differentiation agents as part of a multimodal approach to renal cell carcinoma immunotherapy.
The Status of Euhrychiopsis lecontei (Dietz) (Coleoptera: Curculionidae) in California, with Notes on Other Weevils Associated with Milfoil

As part of an ongoing survey to determine the geographic distribution of Euhrychiopsis lecontei (Dietz) in California water systems, three aquatic species from two subfamilies of Curculionidae were found associated with two species of water milfoil. An accounting of weevils associated with water milfoil is provided, as well as a brief synopsis of E. lecontei as a biological control agent, a detailed distribution map for E. lecontei in California, and diagnostic characters to distinguish E. lecontei from other aquatic and semi-aquatic weevils.
Alexandrium and Scrippsiella cyst viability and cytoplasmic fullness in a 60-cm sediment core from Sequim Bay, WA

Many marine protists produce a benthic resting stage during their life history. This non-motile cyst stage can either germinate near the sediment surface to provide the inoculum for subsequent blooms or, be buried by sediment deposits over time and entrained into the sedimentary record. Buried cysts can be resuspended into the water column by mixing events (e.g., storms) or other disturbances (e.g., dredging). It is not clear how long cysts can survive while buried in the sediments and still be capable of germinating given favorable conditions. Here, the germination success of cysts produced by the potentially toxic dinoflagellate genus Alexandrium and the non-toxic dinoflagellate genus Scrippsiella is reported from a 60-cm sediment core collected in Sequim Bay, WA, in December 2011. Cysts of Alexandrium spp. and Scrippsiella spp. were isolated from 2-cm sections of the core, placed in individual wells of a 96-well plate with growth medium, imaged, incubated at favorable conditions and monitored for germination. An image analysis program, DinoCyst, was used to quantitatively measure the amount of granular storage products, presumed energy stores, inside the cytoplasm to test the hypothesis that older cysts located deeper in the sediment core will have fewer energy stores available and will be less likely to germinate. An index of the area of the cytoplasm occupied with granular storage products relative to cyst size, termed ‘cytoplasmic fullness’, and age, based on ^(210)Pb dating of surrounding sediments, was compared with germination success or failure. This research indicates that cysts of Alexandrium spp. and Scrippsiella spp. can remain viable in sediments for 60 years or longer, show little visual evidence of cytoplasmic deterioration over this timescale (as measured by cytoplasmic fullness), and that germination success is statistically similar for cysts isolated from 0–60 cm deep in the sediment core. These results suggest that a cyst's cytoplasmic fullness is not indicative of viability and that cysts located as deep as 60 cm in the sediments are as likely to germinate as surface cysts given favorable conditions.
Detection of insect fragments in wheat flour by near-infrared spectroscopy $

Insect fragments in commercial wheat flour are a major concern to the milling industry because consumers expect high quality and wholesome products at the retail level. Thus, the US Food and Drug Administration (FDA) has established a defect action level of 75 insect fragments per 50 g of flour. Millers routinely test their wheat flour to comply with this federal requirement and to deliver sound flour to their consumers. The current standard flotation method for detecting fragments in flour is expensive and labor intensive. Therefore, we examined the possible use of a rapid, near-infrared spectroscopy (NIRS) method for detecting insect fragments in wheat flour. We also compared the sensitivity and accuracy of the NIRS method with that of the current standard flotation method. Fragment counts with both techniques were significantly correlated with the actual number of fragments present in flour samples. However, the flotation method was more sensitive than the NIRS method with fragment counts below the FDA defect action level. We were unable to predict whether the number of fragments in a sample exceeded the FDA action level with our NIRS instrumentation. However, we were able to predict accurately whether flour samples contained less than or more than 130 fragments. Although current NIRS instruments are unable to detect insect fragments at the FDA action level, this method should be re-examined in the future because NIRS technology is rapidly improving.
Epidemiology of unexplained fatigue and major depression in the community: the Baltimore ECA follow-up, 1981-1994.

Background. Fatigue is a common, non-specific, subjective symptom associated with several medical and psychiatric illnesses. The purpose of this investigation was to explore further the epidemiology of unexplained fatigue in the general population and the relationship between fatigue and depression. Methods. The design was a prospective population-based study. Subjects included community-dwelling adults who were participants of the Baltimore sample of the Epidemiologic Catchment Area Program in 1981 and who were reinterviewed 13 years later. Lay interviewers using the Diagnostic Interview Schedule interviewed subjects. Results. Number of somatization symptoms and history of a dysphoric episode at baseline were the two strongest predictors of both new onset of fatigue as well as recurrent/chronic fatigue over the 13-year follow-up interval. In addition, individuals who reported a history of unexplained fatigue at baseline as well as during the follow-up, were at markedly increased risk for new onset major depression as compared to those who never reported such fatigue, (RR = 28·4, 95% CI) (11·7, 68·0). Similarly, respondents who developed new fatigue or had remitted fatigue after 1981 were also at increased risk for developing major depression. Conclusions. Somatization was the strongest predictor of both new and chronic fatigue with unknown cause. In addition, fatigue was both predictive and a consequence of the depression syndrome.
Instability and chaotic behaviour in a free-surface flow

Abstract : This paper describes some experimental observations of free-surface flows arising when fluid poured over the end of a flat plate into a reservoir well below the plate. This class of flows was found to be highly unstable with over seven hundred qualitatively different flows being observed in the experiment. At very small values of the flux the liquid fell from the plate into the reservoir in the form of droplets which developed periodically at a number of sites on the underside of the plate. As the flux was increased these 'sites' were able to sustain continuous, unbroken streams and combinations of drip sites and continuous streams were possible. At still larger values of the flux there was a tendency for the liquid to fall in 'sheets' and several combinations of 'sheet flows' and continuous streams were observed, some of which flows exhibited a rather chaotic temporal behavior. At even larger flux values the flow resembled that of the classic waterfall, but here there were also some unexpected instabilities where the attachment line of the free surface of the liquid with the plate developed corrugations. Keywords: Hydrodynamic stability; Chaotic behaviour; Free-surface flows.
Complementarity framework for non‐linear dynamic analysis of skeletal structures with softening plastic hinges

In this paper, we describe an algorithm for the incremental state update of elasto-plastic systems with softening. The algorithm uses a complementary pivoting technique and is based on casting the incremental state update as a complementarity problem. In developing the algorithm, we take advantage of the special features of solid and structural mechanics problems to achieve good computational performance, and hence the ability to compute numerical solutions to practical size problems. For example, the notion of a tangent stiffness matrix arises. Numerical examples using models of skeletal structures are presented to demonstrate the practicability of the algorithm. The numerical examples also raise some interesting questions about multiplicity of the solutions. Copyright © 2010 John Wiley & Sons, Ltd.
Tissue kallikreins and kinins: regulation and roles in hypertensive and diabetic diseases.

The spectrum of cellular, or whole animal responses to kinins has expanded enormously in the last five years. The molecular basis for these consequences of kinin-kinin receptor interactions is being glimpsed as a series of cascading and parallel biochemical events occurring either in the same or adjacent, but communicating, cells of the same tissue (e.g. epithelial, endothelial, muscle, neural). Although it is likely that even more kinin-induced events remain to be discovered, like the interesting effects of the peptides on osteoclastic activity (128), a greater challenge in this field is the gathering of insights into precisely how the regulation of system component gene expression is coordinately carried out to allow component protein synthesis, transport and processing when necessary, and limitation of activities, when required. With these insights, we will be more able to understand the meaning of many observations of tissue kallikrein-kinin system abnormalities in common human diseases. This understanding will then make more obvious the drug design strategies to be used to stimulate or replace, and modulate or inhibit kallikrein-kinin system components in those diseases.
Disseminated intravascular coagulation during resection of a meningioma: case report.

Background and importance Disseminated intravascular coagulation is a relatively common complication in patients with trauma, sepsis, obstetric calamities, and certain malignancies. We report a rare case of DIC after embolization and surgery for a large meningioma. We also review the literature on coagulopathy during brain tumor surgery as well as the diagnosis and treatment of this complication. Clinical presentation A 62-year-old woman presented with a 3-week history of aphasia, difficulty with handwriting, personality change, and right-sided weakness. Magnetic resonance imaging demonstrated a 6.3 × 5.4-cm multilobe and avidly enhancing mass within the left frontal region. The patient underwent preoperative transcatheter Onyx embolization of the tumor, followed immediately by craniotomy for resection of the tumor. Surgery was complicated by coagulopathy leading to substantial blood loss. The diagnosis of disseminated intravascular coagulation was established by intraoperative thromboelastography, after which the patient was treated with replacement therapy, Amicar, and modest hypotension. One year after surgery, the patient had fully recovered and had no focal neurological deficit. Conclusion This case report adds to the few reported cases of disseminated intravascular coagulation as a complication of brain tumor surgery. This patient's successful outcome may be attributed to timely recognition of the condition and effective, prompt treatment.