cssi/SciSciGPT-SciSciNet huggingface dataset:
Intercellular junctions of hyperplastic retinal pigment epithelium

In rats with retinopathies induced by excess fluorescent light or injections of urethane, the retinal pigment epithelium (RPE) undergoes focal hyperplasia. Neither intravascularly injected horseradish peroxidase or lanthanum nitrate penetrated the sensory retina at these hyperplastic sites. Electron microscopy revealed that this was due to the persistence of intact tight junctions among a single layer of hyperplastic cells facing the sensory retina. These junctions prevented intraocularly injected microperoxidase from passing as well. Cells within the hyperplastic foci were connected only by adherent junctions that presented no permeability barrier.
Insights into obesity and diabetes at the intersection of mouse and human genetics

Many of our insights into obesity and diabetes come from studies in mice carrying natural or induced mutations. In parallel, genome-wide association studies (GWAS) in humans have identified numerous genes that are causally associated with obesity and diabetes, but discovering the underlying mechanisms required in-depth studies in mice. We discuss the advantages of studying natural variation in mice and summarize several examples where the combination of human and mouse genetics opened windows into fundamental physiological pathways. A noteworthy example is the melanocortin-4 receptor (MC4R) and its role in energy balance. The pathway was delineated by discovering the gene responsible for the Agouti mutation in mice. With more targeted phenotyping, we predict that additional pathways relevant to human pathophysiology will be discovered.
Bringing web 2.0 to government research: a case study

DASHlink is a public NASA research collaboration website. Web 2.0 style content generation and social software technologies along with a community-moderated posting policy make it easier and faster for NASA scientists and research partners to share data and knowledge with each other and the general public. Designing and building an open collaboration website tested the boundaries of government information sharing rules and policies. In this paper we describe our experiences with and solutions to government specific design challenges.
Dissociation among Ia antigen expression, accessory cell function, and antigen processing in two acute monoblastic leukemia lines.

To better understand the role of Ia antigen expression, accessory cell function, and antigen ingestion in antigen presentation and the initiation of T cell proliferation, we studied these events in two acute monoblastic leukemia (AMoL) lines. The cell lines were positive for surface Ia antigen; one stimulated proliferation of the allogeneic mononuclear cells in mixed lymphocyte culture and culture supernatants from the other line contained interleukin 1 (IL-1) when tested for comitogen activity in a standard mouse thymocyte assay. The AMoL cells also contributed accessary factors for mitogen-induced proliferative responses by T cells. High numbers of cells of one of the lines tended to suppress mitogen induced T cell proliferation. Irradiated trinitrophenylated AMoL cells were able to stimulate TNP-specific HLA-DR matched T cell blasts to proliferate. However, when irradiated AMoL cells were cultured with a protein antigen (tetanus toxoid or varicella zoster) plus antigen-specific parental T cell blasts, antigen presentation failed to occur. Diminished phagocytosis by the AMoL cells, together with reduced catabolism of labelled antigen, is a likely explanation for this finding. Our results demonstrate that the concurrent presence of a complex protein antigen and Ia-positive monocytic leukemia cells capable of accessory function is alone insufficient to maintain antigen-specific T cell proliferation. Moreover, these findings suggest that antigen processing, involving ingestion and reexpression of antigenic determinants, is an essential aspect of antigen presentation not tightly linked to Ia antigen expression or IL-1 production in these AMoL lines.
SAMBE: The New Webserver for Predicting the Effect of nssNP on the Protein-Protein Binding Free Energy

Motivation: One of the most essential properties of all living organisms is the ability to conduct comprehensive “communication” between its individual components. At the molecular level, the communications are achieved via macromolecular binding. The corresponding protein complexes are involved in diverse processes including information transfer, immune system operation, inhibition or activation of particular functions, assembly of macromolecular structures into molecular machines, and much more. Any disruption of the biologically essential network (for example, due to protein missense mutations) may lead to pathological conditions resulting in diseases. Thus, the ability to model protein-protein interactions is essential for a wide range of biomedical applications.Results: Here we report a new webserver, SAMBE (Single Amino acid Mutation related change of Binding Energy) webserver, which addresses the demand for computational tools of predicting the effect of single amino acid substitution on the binding free energy of protein complexes. It is based on the fast modified MM-PBSA protocol that is successfully tested and optimized for more than thousand experimental data points. The SAMBE is intuitive and easy to use webserver which requires only coordinate file to be inputted and the user is provided with various, but easy to navigate, options. The output information including the change in hydrogen bonds network and binding energy due to amino acid substitution is displayed on the output and is available for download.
A Finite Element Analysis of a Viscoplastic Plate Subjected to Rapid Heating

Abstract This paper models the response of a thin metallic plate that is subjected to a rapid heat input. In order to accurately model plate response, both the dynamic mechanical and transient heat transfer problems must be solved. The solution is complicated by nonlinearities due to radiation boundary conditions and material inelasticity. Furthermore, the viscoplastic constitutive equations that model the mechanical material behavior are numerically stiff. Nonlinear finite element algorithms are developed for both heat transfer and mechanical analyses. The algorithms are both stable and efficient for solving the problems considered herein. Example problems presented in the paper demonstrate the importance of including material nonlinearity in the model
A cutaneous case of giant cell angiofibroma occurring with dermatofibrosarcoma protuberans and showing bimodal CD34+ fibroblastic and FXIIIa+ histiocytic immunophenotype

Dei Tos and colleagues in 1995 reported a series of seven distinctive orbital tumors in adults which they named giant cell angiofibroma (GCA). The morphologic features are intermediate between giant cell fibroblastoma and solitary fibrous tumor with a richly vascularized, patternless spindle cell proliferation forming a collagenous or myxoid stroma with pseudovascular angiectoid spaces. The spindled tumor cells have large, rounded nuclei, sometimes with complex folded shape and pseudoinclusions. There also are multi- or mononuclear giant cells, and these tumor cells partly line so-called angiectoid spaces. Cells express human progenitor cell antigen CD34 and vimentin. One case in the buccinator fascia was also noted by the authors, but similar cutaneous lesions are thus far unknown. We report our experience with a polypoid tumor that ocurred on the thigh of a 49-year-old woman that conforms to the description of GCA. The tumor has variegated vessels admixed with patternless spindle and giant cell stroma with angiectoid spaces as well as areas of dermatofibrosarcoma protuberans (DFSP). Most tumor cells express vimentin and CD34, including giant and spindle cells lining angiectoid spaces. Focally up to 40% of the lesional cells express coagulation factor XIIIa with histiocytoid to highly dendritic cytosomes. The DFSP component is composed of admixed CD34+ and FXIIIa+ dendritic cells arranged in a storiform pattern. Tumor cells are negative for actin, desmin, S-100, and cytokeratin. The Ki67 proliferation index is 1% in GCA areas and 3% in DFSP areas; Ki 67 stains mainly fibroblasts. We conclude that this cutaneous GCA is a fibrohistiocytic tumor closely related to and representing a more organoid angioformative analog of GCF, with both being related histogenetically also to DFSP. These lesions represent part of a greater spectrum of fibrovascular tissue patterns, all probably derived from proliferations of interactive microvascular CD34+ fibroblasts and FXIIIa+ histiocytes.
The determination of dendrite morphology on lateral rectus motoneurons in cat.

Previously developed morphometric analysis of motoneurons (Ulfhake and Kellerth, '81, J. Comp. Neurol 202: 571-583) was applied to lateral rectus motoneurons (LRMs). Total dendrite size was approximated from a single stem dendrite measurement. Fifteen dendrites from nine LRMs of the principal abducens nucleus intracellularly stained with HRP were morphometrically analyzed. The diameters and lengths along the extent of the dendrite were measured to calculate the surface area, volume, and combined length of the process. Linear correlation of stem dendrite diameter to these size parameters produced r values of .80, .84, and .61, respectively. Although the regression lines could be used to estimate dendrite size from the stem dendrite diameter, two morphologically distinct types were found among the 83 dendrites of the nine cells. Six dendrites differed from the other 77. Therefore, these six and a representative sample of the more common dendrite (nine) were included in the measurements. The rare dendrites consistently branched at about 40 μm from the soma into a rostrally and a caudally directed secondary dendrite. The secondary dendrites branched less and reduced more in diameter by tapering. Also, these dendrites exhibited a higher than expected total dendrite size to stem diameter ratio compared to “regular” dendrites. Statistical correlations of the stem diameter to surface area or volume within each dendrite type showed clear increases in r values from those of all 15. Significant differences were found between the size parameters of the two types. These qualitative and quantitative differences should be considered in accurate motoneuron size determinations in the abducens nucleus.
Naming dynamic and static actions: neuropsychological evidence.

Abstract There has been considerable interest in identifying the neural correlates of action naming, but the bulk of previous work on this topic has utilized static stimuli. Recent research comparing the visual processing of dynamic versus static actions suggests that these two types of stimuli engage largely overlapping neural systems, raising the possibility that the higher-order processing requirements for naming dynamic and static actions might not be very different. To explore this issue in greater depth, we developed the Dynamic Action Naming Test (DANT), which consists of 158 video clips 3–5 s in length, for each of which the participant is asked to produce the most appropriate verb. We administered the DANT to 78 brain-damaged patients drawn from our Patient Registry, and to a demographically matched group of 50 normal participants. Out of the 16 patients who performed defectively on the DANT, nearly all (15/16) had damage in the left hemisphere. Lesion analysis indicated that the frontal operculum was the most frequent area of damage in the 15 patients; also, damage to the posterolateral temporal-occipital sector (in and near MT) was specifically related to defective dynamic action naming. Most of the brain-damaged participants (n = 71) also received our Static Action Naming Test (SANT), and we found that performances on verb items that were common across the DANT and SANT were highly correlated (R = .91). Moreover, patients who failed the DANT almost invariably also failed the SANT. These findings lend further support to the hypothesis that there is considerable commonality in the neural systems underlying the use of verbs to orally name dynamic and static actions, a conclusion that is in turn compatible with the concept of “representational momentum”. Our results also contribute more generally to the rapidly growing field of research on embodied cognition.
A Multiplex Approach to the Molecular Diagnosis of β-Thalassemia

This Commentary discusses a new method for detecting B-thalassemia mutation as described by Xiong et al (J Mol Diagn 13:427-435).
Does Neuroscience Undermine Deontological Theory

Joshua Greene has argued that several lines of empirical research, including his own fMRI studies of brain activity during moral decision-making, comprise strong evidence against the legitimacy of deontology as a moral theory. This is because, Greene maintains, the empirical studies establish that “characteristically deontological” moral thinking is driven by prepotent emotional reactions which are not a sound basis for morality in the contemporary world, while “characteristically consequentialist” thinking is a more reliable moral guide because it is characterized by greater cognitive command and control. In this essay, I argue that Greene does not succeed in drawing a strong statistical or causal connection between prepotent emotional reactions and deontological theory, and so does not undermine the legitimacy of deontological moral theories. The results that Greene relies on from neuroscience and social psychology do not establish his conclusion that consequentialism is superior to deontology.
Pashtunwali—Law for the lawless, defense for the stateless

Abstract Despite a large and growing literature on systems of law without coercive central authority, the overwhelmingly dominant view remains that law, as a public good, must be produced by the state. Defense against attempts to subjugate a community is even more widely viewed as a public good and therefore a necessary function of the state. This case study of the Pashtunwali – the customary law followed by the ethnic Pashtun tribes in Afghanistan and Pakistan – illustrates that both law and community defense can be effectively produced without the institutions of a state. The incentives created under Pashtunwali have provided the Pashtun with a decentralized system for maintaining order within and between the tribes for several centuries without the authority of a coercive state. In addition, they have generated a system of spontaneous decentralized defense that has allowed the Pashtun to retain/regain their independence from the states that have tried to colonize or subjugate them for centuries.
Effect of monofunctional and trifunctional modifiers on a phase mixed polyurethane system

The dynamic mechanical behavior of a phase mixed polyurethane system modified with trifunctional and monofunctional alcohols was investigated and compared with a typical polyurethane system with a difunctional alcohol. Of interest was verifying that the average functionality of the alcohol would determine the dynamic mechanical properties and not whether that functionality was achieved by an equimolar blend of trifunctional and monofunctional alcohols or by a purely difunctional alcohol. The base system consisted of poly(tetramethylene ether)glycol (PTMG) cured with 4,4'-diphenylmethane diisocyanate (MDI). The trifunctional alcohol was trimethylol propane (TMP). The monofunctional alcohol was decyl alcohol (DA). Samples with a typical difunctional alcohol, 2,2-dimethyl-1,3-propanediol (DMPD), were prepared and their properties compared with those of the above samples. To a first approximation, the properties of TMP-DA modified polymers are identical to those of DMPD polymers of the same hard segment concentration. These results confirm our hypothesis that the dynamic properties obtained from a combination of a trifunctional alcohol with a monofunctional alcohol are essentially equivalent to those of a difunctional alcohol.
Pioneer 10 ultraviolet photometer observations of the Jovian hydrogen torus: The angular distribution

The Pioneer 10 ultraviolet photometer observations of the Jovian hydrogen torus are analyzed to obtain the angular distribution. The cloud is asymmetric about Io, where the atoms presumably originate, with the greater density occurring in the trailing portion. A simple model which assumes Jeans escape from the atmosphere of Io is developed and compared to the observations. The results suggest that the exospheric temperature is high (approximately 3000 K) and that the ionization lifetime of the cloud atoms is approximately 100,000 sec.
Mass spectrometry‐based proteomics: qualitative identification to activity‐based protein profiling

Mass spectrometry has become the method of choice for proteome characterization, including multicomponent protein complexes (typically tens to hundreds of proteins) and total protein expression (up to tens of thousands of proteins), in biological samples. Qualitative sequence assignment based on MS/MS spectra is relatively well-defined, while statistical metrics for relative quantification have not completely stabilized. Nonetheless, proteomics studies have progressed to the point whereby various gene-, pathway-, or network-oriented computational frameworks may be used to place mass spectrometry data into biological context. Despite this progress, the dynamic range of protein expression remains a significant hurdle, and impedes comprehensive proteome analysis. Methods designed to enrich specific protein classes have emerged as an effective means to characterize enzymes or other catalytically active proteins that are otherwise difficult to detect in typical discovery mode proteomics experiments. Collectively, these approaches will facilitate identification of biomarkers and pathways relevant to diagnosis and treatment of human disease.
Accuracy of a laser doppler velocimeter for instantaneous velocity measurements on rotating solid surfaces

This paper presents the results of an analytical and experimental investigation of the accuracy of a laser Doppler velocimeter (LDV) for solid surface velocity measurements made over very short averaging times (less than a millisecond). Fundamental limitations exist on the accuracy of such “instantaneous” measurements. For frequency domain signal processing (spectrum analysis) the accuracy is limited by finite transit time broadening and, in the case of a rotating surface, tangential velocity gradient broadening. For time domain processing (time period measurement) the accuracy is limited by stochastic phase variations in the nominally sinusoidal signal. Experiments were conducted using both signal processing techniques to determine the conditions needed to minimize the error in instantaneous measurements using the LDV. An analysis of the relative performance of a laser speckle velocimeter is also included.This paper presents the results of an analytical and experimental investigation of the accuracy of a laser Doppler velocimeter (LDV) for solid surface velocity measurements made over very short averaging times (less than a millisecond). Fundamental limitations exist on the accuracy of such “instantaneous” measurements. For frequency domain signal processing (spectrum analysis) the accuracy is limited by finite transit time broadening and, in the case of a rotating surface, tangential velocity gradient broadening. For time domain processing (time period measurement) the accuracy is limited by stochastic phase variations in the nominally sinusoidal signal. Experiments were conducted using both signal processing techniques to determine the conditions needed to minimize the error in instantaneous measurements using the LDV. An analysis of the relative performance of a laser speckle velocimeter is also included.
Computational investigation of surface reactivity of functionalized silicon surfaces in deposition processes

Recent advances in chemical vapor deposition and atomic layer deposition coupled with the ever-increasing demand for better control over the interface formation driven by practical applications require understanding and controlling chemical reactions, leading to the deposition of metal-based films onto semiconductor substrates at a truly atomic level. Computational investigation of possible surface-mediated reactions of metalorganic precursors used to deposit thin films used in practical applications allows for an efficient screening of the parameters needed to optimize the process of interface formation. Here, we will use a simple frontier orbital analysis coupled with cluster calculations to explore the surface reactions of functionalized silicon surfaces with test metalorganic precursor molecules. Two molecular precursors are investigated. Trimethylaluminum allows us to investigate the contribution of relatively simple C–Al and C–H dissociation processes in determining the mechanism of surface reaction with a silicon surface either terminated with hydrogen or modified with several nitrogen- or oxygen-containing functional groups. Following similar processes with tetrakis(dimethylamido)titanium provides an opportunity to expand the type of processes investigated and to decouple electronic and steric factors determining surface reactivity.
Effects of exogenous glucagon on lipids in lipoproteins and liver of lactating dairy cows.

Abstract Decreased concentrations of phospholipids, free cholesterol, and cholesteryl ester in plasma and liver are associated with fatty liver, a major metabolic disease of dairy cows in early lactation. The objective was to test whether daily subcutaneous injections of 7.5 and 15mg of glucagon, which can decrease concentrations of liver triacylglycerol, affect concentrations of plasma lipoprotein components and liver lipids other than triacylglycerol. Multiparous Holstein cows (n = 32) were grouped on the basis of liver triacylglycerol concentrations at d 8 postpartum into "normal" (n = 8; triacylglycerol 1% liver wet wt) cows. Susceptible cows were assigned randomly to three groups and beginning at d 8 postpartum received 0 (same for Normal cows), 2.5, or 5mg of glucagon by subcutaneous injections every 8h for 14 d. In comparison to saline injections, subcutaneous injections of glucagon either increased or tended to increase concentrations of phospholipids and free cholesterol in liver, with greater increases of the latter during ambient temperatures below 35°C. Glucagon injections decreased or tended to decrease concentrations of very low-density lipoprotein-triacylglycerol, high-density lipoprotein 1 -phospholipids, and high-density lipoprotein 2 -free cholesterol in plasma, with no changes of the latter two during ambient temperatures below 35°C. The results indicate that subcutaneously administered glucagon has only minor effects on the lipid transport in plasma of dairy cows in early lactation with more beneficial effects occurring during ambient temperatures below 35°C and, most importantly, no indications that glucagon has negative effects.
Autophagosomes and lipid droplets: no longer just chewing the fat

Autophagosomes are organelles capable of sequestering and degrading diverse cytoplasmic cargo for nutritional and quality control purposes. Targeted are also lipid droplets (LDs), the cytoplasmic stores of neutral lipids. In this issue of The EMBO Journal, Shpilka et al (2015) show that the relationship between LDs and autophagosomes is far more intricate and that LDs regulate autophagosome biogenesis.
Plasma molding over surface topography: Simulation of ion flow, and energy and angular distributions over steps in RF high-density plasmas

A two-dimensional fluid/Monte Carlo (MC) simulation model was developed to study plasma "molding" over surface topography. The radio frequency (RF) sheath potential evolution, ion density, and flux profiles over the surface were predicted with a self-consistent fluid simulation. The trajectories of ions and energetic neutrals (resulting by ion neutralization on surfaces or charge exchange collisions in the gas phase) were then followed with a MC simulation. In this paper, ion flow, energy and angular distributions of ions, and energetic neutrals bombarding an otherwise planar surface with a step are reported. The step height was comparable to the sheath thickness for the RF high-density plasma considered. As one approaches the step sidewall, the ion flux decreases, the ion energy distribution narrows, and the ion impact angle increases drastically. The ion impact angle at the foot of the step scales with the ratio of sheath thickness to step height. The energetic neutral flux is found to be comparable to the ion flux on the horizontal surface near the step sidewall. Simulation results are in good agreement with experimental data on ion flux and ion energy and angular distributions near the step.
POD-based Aeroelastic Analysis of a Complete F-16 Configuration: ROM Adaptation and Demonstration

T he proper orthogonal decomposition method (POD) is applied to the computational fluid dynamics (CFD)-based reduced-order aeroelastic modeling of a complete F-16 fighter configuration, in order to assess its potential for the solution of realistic aeroelastic problems. The limitation of such a computational approach to a fixed free-stream Mach number is addressed by a Mach-adaptation strategy that interpolates the angle between two POD subspaces rather than the POD basis vectors directly. The predicted aeroelastic frequencies and damping ratio coefficients are compared with counterparts obtained from full-order nonlinear simulations and from flight test data. The results of these comparisons, including in the transonic regime, reveal a good potential of POD-based reduced-order modeling for the near real-time prediction of aircraft flutter using CFD technology.
Role of nitric oxide and endothelin-1 in monocrotaline-induced pulmonary hypertension in rats

Objective: Nitric oxide (NO) and endothelin-1 (ET-1) have both been implicated in the pathogenesis of pulmonary hypertension (PH). Therefore, we examined NO-related relaxation and ET-1 levels in rat hilar pulmonary arteries (PA) during the progression of monocrotaline (MCT)-induced PH. Methods: Rats were studied 1 and 2 weeks after a single subcutaneous injection of MCT (80 mg/kg). Pulmonary artery pressure (PAP), right ventricular hypertrophy (RVH), NO-related relaxation and tissue ET-1 levels in PA were evaluated and compared with control (C). Results: One week post-MCT, endothelium (E)-dependent relaxation to 10−5 M adenosine diphosphate (ADP), 10−5 M A23187 and 10−5 M acetylcholine (ACh) and tissue ET-1 levels in PA were normal. Rats in this group did not develop PH or RVH. Two weeks post-MCT, E-dependent relaxation was impaired (ADP, 7 ± 3% vs. C, 62 ± 5%; A23187, 2 ± 7% vs. C, 58 ± 2%; ACh, 33 ± 7% vs. C, 86 ± 2%; P < 0.05) and ET-1 levels were elevated (1925 ± 244 pg/g wwt vs. C, 469 ± 59 pg/g wwt, P < 0.05). In addition, significant PH and RVH were present (PAP 33 ± 4 mmHg vs. C 18 ± 0.8 mmHg, P < 0.05; RVH index 0.40 ± 0.006 vs. C, 0.25 ± 0.01, P < 0.05). Incubation with 10 μM indomethacin, 150 U/ml superoxide dismutase or 300 μM l-arginine failed to restore impaired relaxation to ACh. In E-intact rings, relaxation to 10−6 M glyceryl trinitrate (GTN) was inhibited at 1 week post-MCT (72 ± 2% vs. C, 87 ± 3%, P < 0.05) with further inhibition at 2 weeks (39 ± 4%). Response to GTN in E-denuded rings was normal in MCT groups. Conclusions: These results indicate that MCT injection in rats results in delayed but progressive endothelial injury and PH. Despite mild endothelial dysfunction 1 week post-MCT, NO-related relaxation and ET-1 levels are normal. At 2 weeks post-MCT, inhibition of E-dependent NO-related relaxation and elevation of ET-1 levels are associated with PH and RVH. Thus, inhibition of NO production associated with elevated ET-1 levels may play an important role in the pathophysiology of MCT-induced PH.
Dynamic Behavior of Steel Deck Tension-Tied Arch Bridges

The dynamic responses of a steel deck tension-tied arch bridge subjected to earthquake excitations were investigated. The Birmingham Bridge with span of 189 m (620 ft) located in Pittsburgh, PA was selected as an analytical model for the study. Two analytical models were considered for representing the bridge deck system: in one the bridge deck was replaced by a series of simple beams connected to the tension-ties at panel points; in the other the deck was modeled by using substructures. To evaluate the seismic resistance of the bridge, a comparative study has been conducted. Three orthogonal records of the El Centro 1940 earthquake were used as support excitation for the seismic response analysis. Based on the study, it was found that the simple beam model would be inadequate for representing the bridge deck system in the seismic response analysis of the bridge. The accuracy of the analytical models may be improved by applying a method of parameter estimation. A schematic diagram of the identification process is presented, which controls on the accuracy of the data processing and parameter estimation checked by an expert system program.
Mathematical formulation of cognitive and learning processes in neural networks

Recent results in modeling the processes of recognition of complex patterns and learning performed by an artificial neural network as a nonlinear mapping from a data vector space into a space of binary strings are presented. By the construction of a suitable nonlinear functional space for this mapping. an optimal solution in terms of a closed-form description of the neural net model can be obtained. A learning algorithm for this model, which is aimed at reducing the redundancy and complexity of the net by the extraction of a minimal set of prototypes from the training set, is described. >
A Proteomic Study of Pectin Degrading Enzymes Secreted by Botrytis cinerea Grown in Liquid Culture

Botrytis cinerea is a pathogenic filamentous fungus, which infects more than 200 plant species. The enzymes secreted by B. cinerea play an important role in the successful colonization of a host plant. Some of the secreted enzymes are involved in the degradation of pectin, a major component of the plant cell wall. A total of 126 proteins secreted by B. cinerea were identified by growing the fungus on highly or partially esterified pectin, or on sucrose in liquid culture. Sixty-seven common proteins were identified in each of the growth conditions, of which 50 proteins exhibited a SignalP motif. Thirteen B. cinerea proteins with functions related to pectin degradation were identified in both pectin growth conditions, while only four were identified in sucrose. Our results indicate it is unlikely that the activation of B. cinerea from the dormant state to active infection is solely dependent on changes in the degree of esterification of the pectin component of the plant cell wall. Further, these results suggest that future studies of the B. cinerea secretome in infections of ripe and unripe fruits will provide important information that will describe the mechanisms that the fungus employs to access nutrients and decompose tissues.
Obesity and Breast Cancer Prognosis: Weight of the Evidence

progression is associated with prolonged overall survival in metastatic colorectal cancer: Results from a large observational cohort study (BRiTE). J Clin Oncol 26:5326-5334, 2008 17. Ellis LM, Reardon DA: Is there really a yin and yang to VEGF-targeted therapies? Lancet Oncol 11:809-811, 2010 18. Welch S, Spithoff K, Rumble RB, et al: Bevacizumab combined with chemotherapy for patients with advanced colorectal cancer: A systematic review. Ann Oncol 21:1152-1162, 2010 19. Willett CG, Boucher Y, di Tomaso E, et al: Direct evidence that the VEGF-specific antibody bevacizumab has antivascular effects in human rectal cancer. Nat Med 10:145-147, 2004 20. Van Cutsem E, Kohne CH, Hitre E, et al: Cetuximab and chemotherapy as initial treatment for metastatic colorectal cancer. N Engl J Med 360:1408-1417, 2009 21. Van Cutsem E, Labianca R, Bodoky G, et al: Randomized phase III trial comparing biweekly infusional fluorouracil/leucovorin alone or with irinotecan in the adjuvant treatment of stage III colon cancer: PETACC-3. J Clin Oncol 27:3117-3125, 2009 22. Schneider BP, Wang M, Radovich M, et al: Association of vascular endothelial growth factor and vascular endothelial growth factor receptor-2 genetic polymorphisms with outcome in a trial of paclitaxel compared with paclitaxel plus bevacizumab in advanced breast cancer: ECOG 2100. J Clin Oncol 26:4672-4678, 2008 23. Lambrechts D, Delmar P, Buysschaert I, et al: VEGFR-1 polymorphisms as potential predictors of clinical outcome in bevacizumab-treated patients with metastatic pancreatic cancer. Eur J Cancer Supplements 7:10, 2009 (abstr 16LBA) 24. Sorensen AG, Batchelor TT, Zhang WT, et al: A “vascular normalization index” as potential mechanistic biomarker to predict survival after a single dose of cediranib in recurrent glioblastoma patients. Cancer Res 69:52965300, 2009 25. Duda DG, Willett CG, Ancukiewicz M, et al: Plasma soluble VEGFR-1 is a potential dual biomarker of response and toxicity for bevacizumab with chemoradiation in locally advanced rectal cancer. Oncologist 15:577-583, 2010
Analysis of copolymerization systems involving multiple reaction pathways

A method of analysis of copolymerization systems involving multiple reaction pathways is presented. The method involves fractionation and separate analysis of the individual product populations comprising each sample. Modification of the Kelen–Tudos linearization techniques into the form necessary to deal with high conversion copolymerizations involving multiple reaction pathways is presented. The method is applied to the ionizing radiation initiated copolymerization of styrene derivatives in dichloromethane, in which case simultaneous copolymerization via cationic and free radical mechanisms is found to occur. Reactivity ratios corresponding to each mechanism are calculated and discussed.
A high-responsivity high-bandwidth asymmetric twin-waveguide coupled InGaAs-InP-InAlAs avalanche photodiode

The authors demonstrate an integratable high-responsivity high-bandwidth long wavelength InGaAs-InP-InAlAs avalanche photodiode based on an asymmetric twin-waveguide structure. The device has an external quantum efficiency of 48 /spl plusmn/ 1.5% at /spl lambda/ = 1.55 /spl mu/m, a 3-dB bandwidth of 28.5 /spl plusmn/ 0.5 GHz with gain of up to 4, and a fiber-to-waveguide misalignment tolerance of /spl plusmn/ 1.0 /spl mu/m in the vertical and /spl plusmn/ 1.3 /spl mu/m in the horizontal directions resulting in a 1-dB sensitivity penalty.
Neurodegeneration in spinal muscular atrophy: from disease phenotype and animal models to therapeutic strategies and beyond

Of the numerous inherited diseases known to afflict the pediatric population, spinal muscular atrophy (SMA) is among the most common. It has an incidence of approximately one in 10,000 newborns and a carrier frequency of one in 50. Despite its relatively high incidence, SMA remains somewhat obscure among the many neurodegenerative diseases that affect humans. Nevertheless, the last two decades have witnessed remarkable progress in our understanding of the pathology, underlying biology and especially the molecular genetics of SMA. This has led to a genuine expectation within the scientific community that a robust treatment will be available to patients before the end of the decade. The progress made in our understanding of SMA and, therefore, towards a viable therapy for affected individuals is in large measure a consequence of the simple yet fascinating genetics of the disease. Nevertheless, important questions remain. Addressing these questions promises not only to accelerate the march towards a cure for SMA, but also to uncover novel therapies for related neurodegenerative disorders. This review discusses our current understanding of SMA, considers the challenges ahead, describes existing treatment options and highlights state-of-the-art research being conducted as a means to a better, safer and more effective treatment for the disease.
Pharmacodynamic Activity of Amphotericin B Deoxycholate Is Associated with Peak Plasma Concentrations in a Neutropenic Murine Model of Invasive Pulmonary Aspergillosis

We conducted a dose fractionation study of neutropenic, corticosteroid-immunosuppressed mice to characterize the pharmacodynamic/pharmacokinetic (PK/PD) parameter most closely associated with amphotericin B (AMB) efficacy in the treatment of invasive pulmonary aspergillosis. Pharmacokinetic parameter estimates were determined by a nonparametric population pharmacokinetic analysis of plasma drug concentrations following single intraperitoneal doses (0.25, 1.0, and 3.0 mg/kg of body weight) of amphotericin B deoxycholate. Three dosage groups (0.5, 0.75, and 1.0 mg/kg) fractionated into three dosing intervals (every 8 h [q8h], q24h, or q72h) were tested to discriminate between the PK/PD parameters (the ratio of maximum concentration of drug in serum [Cmax]/MIC, the ratio of area under the concentration-time curve/MIC, and percentage of time above MIC) most closely associated with AMB efficacy over a range of clinically achievable exposures in humans. The efficacy of each regimen was determined by quantitative PCR and survival. Reductions in pulmonary fungal burden and improvements in survival were maximized at the highest peak plasma concentrations in each of the dosage groups. Reductions in pulmonary fungal burden and increased survival were most closely associated with Cmax/MIC, with maximal activity occurring as the Cmax/MIC approached 2.4. In our model, Cmax/MIC is the PK/PD parameter most closely associated with efficacy in the treatment of invasive pulmonary aspergillosis. These data predict that less frequently administered, higher dosages of AMB would optimize efficacy.
“Draining the Sea”: Mass Killing and Guerrilla Warfare

Why do some wars result in the intentional killing of large numbers of civilians? In this article we examine the incidence of mass killing in all wars from 1945 to 2000. In the statistical analysis of our data set of 147 wars, we find strong evidence supporting our hypothesis that mass killing is often a calculated military strategy used by regimes attempting to defeat major guerrilla insurgencies. Unlike conventional military forces, guerrilla armies often rely directly on the local civilian population for logistical support. Because guerrilla forces are difficult to defeat directly, governments facing major guerrilla insurgencies have strong incentives to target the guerrillas' civilian base of support. We find that mass killing is significantly more likely during guerrilla wars than during other kinds of wars. In addition, we find that the likelihood of mass killing among guerrilla conflicts is greatly increased when the guerrillas receive high levels of active support from the local population or when the insurgency poses a major military threat to the regime.For their helpful comments on previous versions of this article the authors thank Bear Braumoeller, Alex Downes, Jim Fearon, Hazem Goborah, Stathis Kalyvas, Gary King, Will Lowe, Matthew Krain, Lisa Martin, Manus Midlarsky, Bruce Russett, Nicholas Sambanis, Naunihal Singh, Abdulkader Sinno, Allan Stam, Jeremy Weinstein, and the anonymous reviewers of International Organization. We are also grateful to Wolfgang Moehler for his research assistance. Our coauthor Dylan Balch-Lindsay was killed in an automobile accident on 1 September 2002, cutting short a promising career. He was a gifted young scholar, without whom this article would not have been possible. He is sorely missed by his friends and colleagues. Donations in his name can be sent to the Dylan Balch-Lindsay Memorial Fund for Graduate Education/Foundation of the University of New Mexico, c/o Carol Brown, Department of Political Science, University of New Mexico, Albuquerque, NM, 87131-1121.
Spin split-off transition based IR detectors operating at high temperatures

GaAs/AlGaAs based Heterojunction Interfacial Workfunction Internal Photoemission (HEIWIP) detectors were used to demonstrate experimental split-off response that is based on hole transitions between light/heavy hole bands and the split-off band (spin-orbit). Preliminary results indicate that, this detection mechanism is more efficient than free carrier mechanism for NIR operation. An unoptimized, GaAs/AlGaAs detector with a free carrier threshold wavelength of 20 lm showed a maximum operating temperature of 130 K for split-off response in the range 1.5–5 lm with a peak D * of 1.0 · 10 8 Jones. By adjusting the free carrier threshold to match the splitoff threshold, it should be feasible to further increase the operating temperature. Analysis indicates that practical devices with properly optimized parameters are capable of achieving room temperature operation with higher specific detectivity. The possible ways to tailor the threshold, for the split-off response to different wavelength rangers using different materials such as phosphides and nitrites are also discussed.
Health insurance and cervical cancer screening among older women in Latin American and Caribbean cities

Background The purpose of this study is to describe the prevalence of Papanicolaou (Pap) smear use for cervical cancer screening and to estimate its association with type of health care insurance. Methods A cross-sectional study using data from the Health, Well-Being and Aging in Latin America and the Caribbean Study (SABE). The sample includes 6357 women aged 60 and older from seven cities. The outcome was reporting a Pap smear for cervical cancer screening during the previous 2 years. Main independent variable was health care insurance. Covariates were demographic or socioeconomic variables, medical conditions and functional status. Results Prevalence of Pap smear use across the seven cities ranged from 21% in Bridgetown to 45% in Mexico City. In a multivariate analysis of the combined sample, without Havana that has universal health care insurance, women with public insurance (OR 0.55, 95% CI 0.43–0.71) or with no insurance (OR 0.23, 95% CI 0.15–0.34) were less likely to have a Pap smear compared with women with private insurance. Also, women with no insurance were less likely to have a Pap smear (OR 0.40, 95% CI 0.30–0.54) compared with women with any health insurance. Conclusions In general, the prevalence of Pap smear use was lower than that reported for Hispanic populations in the United States. Overall, lack of health insurance or having public health insurance determined lower odds for having a Pap smear for cervical cancer screening.
The capital markets

The purpose of this paper is to first introduce what capital markets are and then break them down between primary and secondary markets. Secondly, we will explore and differentiate between money markets and capital markets, which together make up the financial market. The first part of the paper is designed to give a sound understanding of the capital markets, so that the latter part of the paper can explore real-time issues within the capital markets. After exploring what the capital markets look like, we will delve into what a perfect capital market would look like in theory then use that framework to explore market imperfections. In the real world, the capital markets are not perfect, so it is important to explore what the implications for an imperfect market are.
A secure integrated routing and localization scheme for broadband mission critical networks

In randomly-deployed wireless mission critical networks, the crucial steps of ad hoc route setup and node localization are vulnerable to various security breaches and attacks. In this paper, we introduce SIRLoS, a lightweight secure integrated routing and localization scheme which addresses this problem by exploiting the security benefits of link directionality in directed networks that have found popularity for multimedia networking. SIRLoS is a circuit-based algorithm that leverages the resources of the base station and the hierarchical structure of the network to reconstruct the graph of the network, and detect any security violations in the neighborhood discovery and routing schemes. We demonstrate the performance of our algorithm, and provide security and attack analysis.
Fully Coupled Three-Dimensional Train-Track-Soil Model for High-Speed Rail

With the increase of train speed, track modeling has faced great challenges as traditional static or quasi-static analyses become insufficient. Many track models have not had a train model and defined the wheel–rail interaction force as a stationary, independent, and empirical loading profile. In fact, the wheel–rail contact force is a function of train–track interaction and is difficult to predetermine. Another limitation of two-dimensional track models is the lack of sophisticated three-dimensional soil parts; this deficiency becomes critical when train speed is high enough to cause significant wave motion in the subgrade soil. A fully coupled three-dimensional train-track-soil model is developed and verified by a benchmark finite element program. Case studies are then described to demonstrate the capability of this track model.
P-selective sets, and reducing search to decision vs. self-reducibility

Several results that distinguish self-reducibility of a language L with the question of whether search reduces to decision for L are obtained. It is proved that if NE intersection co-NE not=E, then there exists a set L in NP-P such that search reduces to decision for L, search does not nonadaptively reduce to decision for L, and L is not self-reducible. Results that distinguish adaptively randomly self-reducible sets from nonadaptively randomly self-reducible sets, results concerning tradeoffs in multipower interactive proof systems, and results that distinguish checkable languages from those that are nonadaptively checkable are obtained. Many of the results depend on new techniques for constructing P-selective sets. >
A note on real-time linear prediction of speech waveforms

A well-known, real-time computational algorithm for use in adaptive linear prediction of speech waveforms is discussed and is related to known research in other fields.
Percutaneous Intervention for Recurrent Aortic Insufficiency in a Patient With a Left Ventricular Assist Device and a Centrally Oversewn Aortic Valve

76-year-old man with severe degenerative aortic stenosis, coronary artery disease, and progressive congestive heart failure with severe systolic dysfunction underwent implantation of a Heartmate II left ventricular assist device (LVAD; Thoratec Corporation, Pleasanton, CA) after developing refractory cardiogenic shock. Because there was moderate aortic insufficiency (AI), the aortic valve was closed with a pledgeted central coaptation stitch that approximated the Noduli of Arantius with minimal residual regurgitation.
Parental beliefs about emotions are associated with early adolescents’ independent and interdependent self-construals

We assessed linkages between parents’ beliefs and their children’s self-construals with 60 7th and 8th graders. Early adolescents completed an open-ended, Self-Guide Questionnaire and an independent and interdependent reaction-time measure. The self-guide responses were coded for independent and interdependent traits. Parents reported beliefs about the danger of emotions and parental guidance of emotions. When parents were high in beliefs about danger of emotions, and about parental guidance, early adolescents more rapidly responded to traits, especially interdependent traits. When parents were low in beliefs about both danger of emotions and parental guidance, daughters, but not sons, included fewer independent and interdependent traits in their self-construals. Girls responded faster to interdependent traits and included more interdependent and fewer independent traits in their self-construals than boys.