cssi/SciSciGPT-SciSciNet huggingface dataset:
Endobronchial Argon Plasma Coagulation for Treatment of Hemoptysis and Neoplastic Airway Obstruction

Study objectives: To evaluate the usefulness of endobronchial argon plasma coagulation (APC) for the treatment of hemoptysis and neoplastic airway obstruction. Design: Retrospective study. Settings: Bronchoscopy unit of auniversity hospital. Patients: A total of 60 patientswith bronchogenic carcinoma (n = 43), metastatic tumors affecting thebronchi (n = 14), or benign bronchial disease (n = 3). Indicationsfor intervention were hemoptysis (n = 31), symptomatic airwayobstruction (n = 14), and both obstruction and hemoptysis (n = 25). Hemoptysis was stratified as a volume of > 200 mL/d (n = 6), > 50to 200 mL/d (n = 23), or ≤ 50 mL/d but persistence for > 1 week(n = 27). The mean (± SD) duration of hemoptysis was16.5 ± 16.1 days before intervention. Obstruction sites were thetrachea (n = 8), mainstem bronchi (n = 21), and lobar bronchi(n = 30). In 24 cases, the patient had obstructions at multiplesites. The mean size of the pretreatment obstruction was76 ± 24.9%. Interventions: APC, a noncontact formof electrocoagulation, was performed via flexible bronchoscopy. Sixtypatients underwent 70 procedures. Conscious sedation with outendotracheal intubation was used in all patients except four, who weremechanically ventilated because of underlying respiratory failure. Measurements and results All patients with hemoptysisexperienced a resolution of bleeding immediately after APC. Hemoptysisfrom treated sites did not recur during a mean follow-up duration of97 ± 91.9 days. Patients with endoluminal airway lesions had anoverall decrease in mean obstruction size to 18.4 ± 22.1%. Allpatients with obstructive lesions, except one who died of sepsis, experienced symptom improvement. In these patients, symptom control wasmaintained during a median follow-up period of 53 days (range, 18 to321 days). There were no complications related to the procedure. Conclusions: APC is effective for the treatment of endoluminal hemoptysis and airway obstruction. The procedure can beperformed in an outpatient setting or at the bedside in the ICUs. APCprovides a simpler, lower-risk alternative to other interventionalendobronchial techniques.
Individual snag detection using neighborhood attribute filtered airborne lidar data.

Abstract The ability to estimate and monitor standing dead trees (snags) has been difficult due to their irregular and sparse distribution, often requiring intensive sampling methods to obtain statistically significant estimates. This study presents a new method for estimating and monitoring snags using neighborhood attribute filtered airborne discrete-return lidar data. The method first develops and then applies an automated filtering algorithm that utilizes three dimensional neighborhood lidar point-based intensity and density statistics to remove lidar points associated with live trees and retain lidar points associated with snags. A traditional airborne lidar individual-tree detection procedure is then applied to the snag-filtered lidar point cloud, resulting in stem map of identified snags with height estimates. The filtering algorithm was developed using training datasets comprised of four different forest types in wide range of stand conditions, and then applied to independent data to determine successful snag detection rates. Detection rates ranged from 43 to 100%, increasing as the size of snags increased. The overall detection rate for snags with DBH ≥ 25 cm was 56% (± 2.9%) with low commission error rates. The method provides the ability to estimate snag density and stem map a large proportion of snags across the landscape. The resulting information can be used to analyze the spatial distribution of snags, provide a better understanding of wildlife snag use dynamics, assess achievement of stocking standard requirements, and bring more clarity to snag stocking standards.
Relationship between diabetes mellitus and obesity in the child.

Abstract Eighteen grossly obese adolescents have been investigated during a 30-day period of hospitalization. Seven were found to have asymptomatic, mild-to-moderate carbohydrate intolerance as defined by response to oral glucose administration. All subjects demonstrated marked hyperinsulinism in response to islet cell stimulants (glucose, glucagon, and arginine), when compared with children and adolescents of normal weight. However, those obese subjects with carbohydrate intolerance achieved peak insulin levels significantly below those with normal carbohydrate tolerance. Growth hormone response to arginine infusion was significantly below that of sexually mature, normal weight subjects. Weight loss was readily achieved in the hospital during caloric reduction but not on an outpatient basis. No subjects have progressed to overt diabetes.
Long-term survival after mitral valve replacement in children aged <5 years: a multi-institutional study.

Background Short- and long-term outcomes after prosthetic mitral valve replacement (MVR) in children aged <5 years are ill-defined and generally perceived as poor. The experience of the Pediatric Cardiac Care Consortium (45 centers, 1982 to 1999) was reviewed. Methods and Results MVR was performed 176 times on 139 patients. Median follow-up was 6.2 years (range 0 to 20 years, 96% complete). Age at initial MVR was 1.9±1.4 years. Complications after initial MVR included heart block requiring pacemaker (16%), endocarditis (6%), thrombosis (3%), and stroke (2%). Patient survival was as follows: 1 year, 79%; 5 years, 75%; and 10 years, 74%. The majority of deaths occurred early after initial MVR, with little late attrition despite repeat MVR and chronic anticoagulation. Among survivors, the 5-year freedom from reoperation was 81%. Age-adjusted multivariable predictors of death include the presence of complete atrioventricular canal (hazard ratio 4.76, 95% CI 1.59 to 14.30), Shone’s syndrome (hazard ratio 3.68,...
Prison, Poetry, and Polyphony in Abdilatif Abdalla's Sauti ya Dhiki

This article is a study of the prison poetry of Abdilatif Abdalla, one of the most talented twentieth-century Swahili poets. Abdalla penned his collection of poems Sauti ya Dhiki while serving a prison term for sedition during the Jomo Kenyatta regime in postindependence Kenya. Prison as a site for writing had tremendous influence on the form and content of his poetical productions. In this regard I suggest that, for the most part, the terribly unpleasant prison conditions that the poet experienced, enabled, and enhanced the occurrence in his poetry of a psychic or philosophical journey, which may or may not have been therapeutic, and the articulation of a whole range of "voices." I undertake a close reading of Sauti ya Dhiki , exploring the symbolic journey and the polyphony that characterizes Abdalla's reaction to his incarceration by what Achille Mbembe would call the "postcolonial potentate."
Insurance Solutions for Project Finance

Recent financial turmoil has made project and infrastructure financing in emerging markets more difficult. One helpful approach in getting deals done is the combination of insurance and project financing techniques to access capital markets. The insurance industry has years of experience addressing project risks that includes writing coverage for completion risk, operating risk, political risk, off-take risk, and residual value. When brought into the front end of the development process, insurers can help structure deals that have a higher probability of closing.
Pressure Dependence of the Refractive Index of Amorphous Lone-Pair Semiconductors

The pressure dependence of the refractive index ($\frac{\mathrm{dn}}{\mathrm{dP}}$) of several amorphous chalcogenide semiconductors is reported. $\frac{\mathrm{dn}}{\mathrm{dP}}$ is positive for materials containing group-VI elements in twofold coordination (lone-pair semiconductors), whereas it is negative for tetrahedral semiconductors. Furthermore, $\frac{\mathrm{dn}}{\mathrm{dP}}$ is the same for the amorphous and crystalline phases of a given semiconductor. Although a one-oscillator (Penn) model adequately predicts $\frac{\mathrm{dn}}{\mathrm{dP}}$ for tetrahedral semiconductors, a similar approach does not predict the positive $\frac{\mathrm{dn}}{\mathrm{dP}}$ of lone-pair semiconductors. Local-field corrections appear to be the cause of the positive $\frac{\mathrm{dn}}{\mathrm{dP}}$. The Lorenz-Lorentz description of the local field predicts $\frac{\mathrm{dn}}{\mathrm{dP}}$ in agreement with experiment for most molecular lone-pair materials. It fails, however, for materials containing large concentrations of group-IV elements. The limitations of the local-field correction in describing $\frac{\mathrm{dn}}{\mathrm{dP}}$ of partially molecular semiconductors is discussed.
Analyzing Estuarine Shoreline Change: A Case Study of Cedar Island, North Carolina

Abstract Continued climate change, sea-level rise, and coastal development have lead to concern about shoreline dynamics beyond oceanfront areas, encompassing more sheltered coastal water bodies such as estuaries. Because estuaries are critically important ecosystems, understanding coastline changes in these areas is necessary to evaluating resource risks. A transect-based approach is commonly used to quantify shoreline change on linear (i.e., ocean) shorelines; however, due to the complex morphology of the study area, a point-based approach was developed and applied in this study. Shoreline-change rates and additional parameters (i.e., wave energy and shoreline composition) were determined using 1958 and 1998 aerial photography and available datasets. From this data, the average shoreline change in the study area is −0.24 m yr−1, with 88% of the shoreline eroding. Of the parameters analyzed, shoreline composition appears to have an important control on shoreline erosion, whereas wave energy is not signif...
Cheatin' Hearts & Loaded Guns: The High Fitness Stakes of Country Music Lyrics:

Humans spend tremendous amounts of time producing and consuming narratives about people who have never existed doing things that have never been done. These narratives often concern actions that wo...
On the dispersion coefficients for poiseuille flow in a circular cylinder

For axisymmetric dispersion in laminar flow in a cylinder of circular cross section, we report the full time dependence of the first three dispersion coefficients, viz. X0, X1 and X2. We investigate the use of a variety of transverse averages. We also indicate the dependence of the dispersion coefficients on the initial solute distribution and on the chemical activity of the solute.
Application of the Okahara cyclization to the preparation of crown ethers with aromatic units

A series of crown ethers with single benzene, naphthalene, biphenyl and binaphthyl units are prepared by the intramolecular Okahara cyclization of appropriate symmetrical diols. The method is used to synthesize new crown ether compounds and to prepare previously-reported crown ethers in improved yields.
Nonlinear modeling of dynamic interactions within neuronal ensembles using Principal Dynamic Modes

A methodology for nonlinear modeling of multi-input multi-output (MIMO) neuronal systems is presented that utilizes the concept of Principal Dynamic Modes (PDM). The efficacy of this new methodology is demonstrated in the study of the dynamic interactions between neuronal ensembles in the Pre-Frontal Cortex (PFC) of a behaving non-human primate (NHP) performing a Delayed Match-to-Sample task. Recorded spike trains from Layer-2 and Layer-5 neurons were viewed as the "inputs" and "outputs", respectively, of a putative MIMO system/model that quantifies the dynamic transformation of multi-unit neuronal activity between Layer-2 and Layer-5 of the PFC. Model prediction performance was evaluated by means of computed Receiver Operating Characteristic (ROC) curves. The PDM-based approach seeks to reduce the complexity of MIMO models of neuronal ensembles in order to enable the practicable modeling of large-scale neural systems incorporating hundreds or thousands of neurons, which is emerging as a preeminent issue in the study of neural function. The "scaling-up" issue has attained critical importance as multi-electrode recordings are increasingly used to probe neural systems and advance our understanding of integrated neural function. The initial results indicate that the PDM-based modeling methodology may greatly reduce the complexity of the MIMO model without significant degradation of performance. Furthermore, the PDM-based approach offers the prospect of improved biological/physiological interpretation of the obtained MIMO models.
Do as I do: authorial leadership in wikipedia

In seemingly egalitarian collaborative on-line communities, like Wikipedia, there is often a paradoxical, or perhaps merely playful, use of the title "Benevolent Dictator" for leaders. I explore discourse around the use of this title so as to address how leadership works in open content communities. I first review existing literature on "emergent leadership" and then relate excerpts from community discourse on how leadership is understood, performed, and discussed by Wikipedians. I conclude by integrating concepts from existing literature and my own findings into a theory of "authorial" leadership.
Radiation dosimetry predicts IQ after conformal radiation therapy in pediatric patients with localized ependymoma.

Purpose: To assess the effects of radiation dose–volume distribution on the trajectory of IQ development after conformal radiation therapy (CRT) in pediatric patients with ependymoma. Methods and Materials: The study included 88 patients (median age, 2.8 years ± 4.5 years) with localized ependymoma who received CRT (54–59.4 Gy) that used a 1-cm margin on the postoperative tumor bed. Patients were evaluated with tests that included IQ measures at baseline (before CRT) and at 6, 12, 24, 36, 48, and 60 months. Differential dose–volume histograms (DVH) were derived for total-brain, supratentorial-brain, and right and left temporal-lobe volumes. The data were partitioned into three dose intervals and integrated to create variables that represent the fractional volume that received dose over the specified intervals (e.g., V0–20 Gy, V20–40 Gy, V40–65 Gy) and modeled with clinical variables to develop a regression equation to estimate IQ after CRT. Results: A total of 327 IQ tests were performed in 66 patients with infratentorial tumors and 20 with supratentorial tumors. The median follow-up was 29.4 months. For all patients, IQ was best estimated by age (years) at CRT; percent volume of the supratentorial brain that received doses between 0 and 20 Gy, 20 and 40 Gy, and 40 and 65 Gy; and time (months) after CRT. Age contributed significantly to the intercept (p > 0.0001), and the dose–volume coefficients were statistically significant (V0–20 Gy, p = 0.01; V20–40 Gy, p Conclusion: Radiation dosimetry can be used to predict IQ after CRT in patients with localized ependymoma. The specificity of models may be enhanced by grouping according to tumor location.
Effects of background pattern on insect perception of webs spun by orb-weaving spiders

Abstract Recent studies show that many insects are able to see spider webs and avoid them. The orbspinning spiders and their close relatives are an abundant and diverse group of predators that make use of a variety of habitats and light environments. A combination of field and laboratory approaches was used to explore the effects of light environment, silk reflectance and background pattern on insect perception of spider webs. Field experiments showed that in dim visual habitats, background patterns have no significant effect on insect perception of webs but in bright visual habitats, patterns behind webs decreased the ability of insects to see and avoid them. In the laboratory Drosophila melanogaster Meigen have more difficulty seeing brightly lit webs when they are suspended close to backgrounds of high spatial frequencies than when webs are suspended in front of distant backgrounds or of low spatial frequencies. When Drosophila are confronted with webs characterized by low reflectivity, however, they are unable to see and avoid them, regardless of light level or background spatial pattern. Web visibility results from a series of complex interactions among the reflectance properties of silks, web architecture, background pattern, ambient light level and the peculiar visual physiology of the approaching insect.
MARINE RESERVES EXPLOIT POPULATION STRUCTURE AND LIFE HISTORY IN POTENTIALLY IMPROVING FISHERIES YIELDS

The collapse of many of the world's fisheries has induced a reevaluation of existing fisheries management strategies. This has fueled interest in the establishment of networks of no-take marine reserves as an additional form of protection. Proponents of marine reserves have suggested that reserves can provide a number of advantages over other, more traditional, methods. However, concerns have also persisted that marine reserves will reduce overall catch. In a theoretical context, this concern has been only partially addressed by previous work suggesting that reserves can produce equivalent yields to those from traditional management, since this possibility is widely interpreted as a limiting case. However, an ''equivalence-at-best'' scenario is based on a highly simplified model construct that ignores all spatial pattern and size structure characterizing real populations. By contrast, when coupled effects of (1) spatial pattern in adult densities and larval dispersal, (2) population size structure, and (3) aspects of life history are considered in their most basic forms, model results suggest that reserve networks may have the potential to enhance fishery yields under a surprisingly large number of circumstances. Such enhancement is predicted to be greatest, and at times substantial, in species exhibiting postdispersal density depen- dence and that have relatively long-lived and sedentary adults, life history traits common to many harvested fishes and invertebrates. A goal of this study is to spark further theoretical attention and experimental testing on this unanticipated front.
A real-time prostate cancer detection technique using needle insertion force and patient-specific criteria during percutaneous intervention

In this article, the authors present a novel real-time cancer detection technique by using needle insertion forces in conjunction with patient-specific criteria during percutaneous interventions. Needle insertion experiments and pathological analysis were performed for developing a computer-aided detection (CAD) model. Backward stepwise regression method was performed to identify the statistically significant patient-specific factors. A baseline force model was then developed using these significant factors. The threshold force model that estimated the lower bound of the cancerous tissue forces was formulated by adding an adjustable classifier to the baseline force model. Trade-off between sensitivity and specificity was obtained by varying the threshold value of the classifier, from which the receiver-operating characteristic (ROC) curve was generated. Sequential quadratic programming was used to optimize the CAD model by maximizing the area under the ROC curve (AUC) using a set of model-training patient data. When the CAD model was evaluated using an independent set of model-validation patient data, an AUC of 0.90 was achieved. The feasibility of cancer detection in real time during percutaneous interventions was established.
De novo pyrimidine biosynthesis is required for virulence of Toxoplasma gondii

Toxoplasma gondii is a ubiquitous protozoan parasite that is responsible for severe congenital birth defects and fatal toxoplasmic encephalitis in immunocompromized people. Fundamental aspects of obligate intracellular replication and pathogenesis are only now beginning to emerge for protozoan parasites. T. gondii has a fragmented pathway for salvaging pyrimidine nucleobases derived from the parasite or host cell, and this limited pyrimidine salvage capacity is funnelled exclusively through uracil phosphoribosyltransferase. Disrupting the function of this enzyme does not affect the growth of T. gondii tachyzoites, which suggests that the de novo pyrimidine biosynthesis pathway may be necessary for growth. We have examined the virulence of T. gondii mutants that lack carbamoyl phosphate synthetase II (uracil auxotrophs) to determine whether de novo pyrimidine biosynthesis is required in vivo. Here we show that T. gondii uracil auxotrophs are completely avirulent not only in immune-competent BALB/c mice but also in mice that lack interferon-gamma. A single injection of the uracil auxotroph into BALB/c mice induces long-term protective immunity to toxoplasmosis. Our findings indicate the significance of the de novo pyrimidine biosynthesis pathway for the virulence of parasitic protozoa, and suggest routes for developing vaccines and chemotherapy.
Two measures of sample entropy

Abstract In many statistical studies the entropy of a distribution function is of prime interest. This paper proposes two estimators of the entropy. Both estimators are obtained by modifying the estimator proposed by Vasicek (1976). Consistency of both estimators is proved, and comparisons have been made with Vasicek's estimator and its generalization proposed by Dudewicz and Van der Meulen (1987). The results indicate that the proposed estimators have less bias and have less mean squared error than Vasicek's estimator and its generalization
BRANCHING COEFFICIENT ("AREA RATIO") OF THE HUMAN AORTIC BIFURCATION DETERMINED IN DISTENDED SPECIMENS

Abstract Branching coefficient or “area ratio” is the ratio of the sum of the cross-sectional areas of the daughter vessels of a bifurcation to that of the parent stem. The value of area ratio is important for the assessment of flow patterns in the bifurcation and, consequently, of its functional load. In this series of cases, the area ratio was determined in aortic bifurcations of 19 young persons who died suddenly. The specimens were distended during fixation. The area ratio found in this study (1.18 ± 0.6 SE) corresponded to the optimal value (1.15) predicted on a theoretical basis for an equibifurcation. Our ratio demonstrates an increase of 1.18 in size of the vascular bed of the human aortic bifurcation. We found a significant difference between the aortic circumference measured at the level of the divider compared with the circumference 2–2.5 cm above the bifurcation. The precise level of measurement is therefore critical for a correct determination of the area ratio of the aortic bifurcation and may explain varying values reported in the literature. Deviation from optimal value, e.g. with age, may be accompanied by increased mechanical stress and could favor the prominent involvement of aortic bifurcation by atherosclerotic lesions in man.
Phonotaxis in female Ormia ochracea (Diptera: Tachinidae), a parasitoid of field crickets

Gravid females of Ormia ochracealocate their hosts by homing on their hosts' calling songs. At Gainesville, Florida, O. ochraceafemales were attracted in greatest numbers to broadcast sounds that simulated the calling song of Gryllus rubens.Other candidate hosts and the attractiveness of their songs relative to the simultaneous song of G. rubenswere G. fultoni(9%), G. integer(4%), G. firmus(3%), Orocharis luteolira(1%), Scapteriscus borellii(1%), and S. vicinus(0%). The response of female O. ochraceato simulated G. rubenssongs that have different pulse rates changes with temperature in parallel with temperature-induced changes in the pulse rate of natural songs. Speaker stations ≤ 16 m apart in an apparently uniform environment produced strikingly different fly counts (e.g., 852 and 2163). The song of G. rubensat 21 °C approximates a continuous sequence of 4.6-kHz pulses at a rate of 45 s−1and with a duty cycle of 50%. When two of these parameters were held constant and the third systematically varied in steps of 0.4kHz, 10s−1,and 10–20%, maximum attraction occurred at 4.4 kHz, 45 s−1,and 20–80%. Omitting as many as half the pulses in a rubenssimulation (e.g., 1, 2, 4, or 16 pulses followed by an equivalent silence, and repeat) did not significantly reduce the counts of O. ochracea,proving that chirping (producing pulses in brief groups) is no safeguard from call-seeking O. ochracea.Phase shifting of pulses in successive chirps sometimes decreased fly counts. When songs were first broadcast, flies came within seconds. Flies that landed at sound often stayed for minutes, even when the sound was turned off.
Androgen receptor gene amplification and protein expression in recurrent prostate cancer.

ABSTRACTPurpose: The androgen receptor (AR) is highly expressed in androgen dependent and recurrent prostate cancer, suggesting that it has a role in tumor growth and progression after androgen deprivation. AR amplification may contribute to androgen receptor activation in relative androgen absence.Materials and Methods: Formalin fixed and frozen specimens of recurrent prostate cancer were obtained by transurethral resection from men with increasing serum level of prostate specific antigen in whom urinary retention developed. AR amplification and X-chromosome number were determined by 2-color fluorescence in situ hybridization, and AR protein expression was determined by automated image analysis. We compared clinical characteristics and survival of patients with recurrent prostate cancer whose tumors did or did not exhibit AR amplification and X-chromosome polysomy.Results: Thirty-three percent of the 24 recurrent prostate cancer specimens 8 (33%) showed AR amplification. AR was more intensely immunostain...
Donor graft steatosis influences immunity to hepatitis C virus and allograft outcome after liver transplantation.

BACKGROUND Hepatitis C virus (HCV) recurrence after orthotopic liver transplantation (OLT) is universal, often with accelerated allograft fibrosis. Donor liver steatosis is frequently encountered and often associated with poor early postoperative outcome. The aim of this study was to test the hypothesis that allograft steatosis alters immune responses to HCV and self-antigens promoting allograft fibrosis. METHODS Forty-eight HCV OLT recipients (OLTr) were enrolled and classified based on amount of allograft macrovesicular steatosis at time of OLT. Group 1: no steatosis (0%-5% steatosis, n=21), group 2: mild (5%-35%, n=16), and group 3: moderate (>35%, n=11). Cells secreting interleukin (IL)-17, IL-10, and interferon gamma (IFN-γ) in response to HCV antigens were enumerated by Enzyme Linked Immunospot Assay. Serum cytokines were measured by Luminex, antibodies to Collagen I, II, III, IV, and V by ELISA. RESULTS OLTr of moderate steatotic grafts had the highest incidence of advanced fibrosis in protocol 1 year post-OLT biopsy (10.8% vs. 15.8% vs. 36.6%, r=0.157, P<0.05). OLTr from groups 2 and 3 had increased HCV-specific IL-17 (P<0.05) and IL-10 (P<0.05) with reduced IFN-γ (P<0.05) secreting cells when compared with group 1. This was associated with increase in serum IL-17, IL-10, IL-1β, IL-6, IL-5, and decreased IFN-γ. In addition, there was development of antibodies to Collagen I, II, III and V in OLTr with increased steatosis (P<0.05). CONCLUSION The results demonstrate that allograft steatosis influences post-OLT HCV-specific immune responses leading to an IL-17 T-helper response and activation of humoral immune responses to liver-associated self-antigens that may contribute to allograft fibrosis and poor outcome.
Binding of Munc18-1 to synaptobrevin and to the SNARE four-helix bundle.

Sec1/Munc18 (SM) proteins and soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNAREs) form part of the core intracellular membrane fusion machinery, but it is unclear how they cooperate in membrane fusion. The synaptic vesicle SNARE synaptobrevin and the plasma membrane SNAREs syntaxin-1 and SNAP-25 assemble into a tight SNARE complex that includes a four-helix bundle formed by their SNARE motifs and is key for fusion. The neuronal SM protein Munc18-1 binds to syntaxin-1 and to the SNARE complex through interactions with the syntaxin-1 N-terminal region that are critical for neurotransmitter release. It has been proposed that Munc18-1 also binds to synaptobrevin and to the SNARE four-helix bundle and that such interactions might be crucial for membrane fusion, but definitive, direct evidence of these interactions has not been described. Using diverse biophysical approaches, we now demonstrate that Munc18-1 indeed binds to synaptobrevin and to the SNARE four-helix bundle. Both inter...
Transmission dynamics of an insect-specific flavivirus in a naturally infected Culex pipiens laboratory colony and effects of co-infection on vector competence for West Nile virus

We established a laboratory colony of Culex pipiens mosquitoes from eggs collected in Colorado and discovered that mosquitoes in the colony are naturally infected with Culex flavivirus (CxFV), an insect-specific flavivirus. In this study we examined transmission dynamics of CxFV and effects of persistent CxFV infection on vector competence for West Nile virus (WNV). We found that vertical transmission is the primary mechanism for persistence of CxFV in Cx. pipiens, with venereal transmission potentially playing a minor role. Vector competence experiments indicated possible early suppression of WNV replication by persistent CxFV infection in Cx. pipiens. This is the first description of insect-specific flavivirus transmission dynamics in a naturally infected mosquito colony and the observation of delayed dissemination of superinfecting WNV suggests that the presence of CxFV may impact the intensity of enzootic transmission of WNV and the risk of human exposure to this important pathogen.
Reticular and thalamic multiple unit activity during wakefulness, sleep and anesthesia

Abstract Recordings of multiple unit activity from reticular and thalamic sites were analyzed during wakefulness, sleep, and anesthesia. All anesthetics studied caused a decrease in averaged multiple unit activity and a variable pattern of multiple unit bursts. There were considerable differences in averaged activity associated with assessed anesthetic depth among the various anesthetics. The decline in averaged activity with ether and cyclopropane during light anesthesia was not greater than the decline that occurred during slow-ware sleep. With cyclopropane, even deep anesthesia was associated with averaged activity not lower than that occurring with slow-wave sleep. Furthermore, the multiple unit bursts that appeared during anesthesia were similar to the bursts occurring during slow-wave or paradoxical sleep. Thus different anesthetics have quantitatively different effects on the spontaneous discharge of reticular and thalamic units. In addition, there is neither a uniquely diminished level of spontaneous spike activity nor a unique pattern of spike activity that characterizes the anesthetic state. The characteristics of spontaneous unit firing at reticular and thalamic sites cannot be used to differentiate between wakefulness, sleep and anesthesia.
Nonlinear modulation characteristics of white LEDs in visible light communications

The nonlinear dependence of the modulation bandwidth and electrical to optical conversion on the drive current of white LEDs were investigated by comparing novel analytical modeling and experimental measurement for visible light communications.
The terminology and classification of steles: Historical perspective and the outlines of a system

Discussion focuses on the history of classification of the steles of vascular plants, from Jeffrey (1898) to the present. Recent stelar classifications are largely based (1) on Jeffrey’s system (protostele vs. siphonostele, the latter with ectophloic vs. amphiphloic types), (2) on the system developed by the early British morphologists, notably Brebner (1902), Gwynne-Vaughan (1901), Tansley (1907-08), and Tansley and Lulham (1902) (protostele vs. medullated protostele vs. solenostele vs. dictyostele vs. eustele, with various subtypes), or (3) on a combination of the preceding two systems, the British usually superimposed upon the Jeffreyian, although generally erratically so. An extended classification of three main stelar types and 25 stelar subtypes derived from Brebner (1902), Gwynne-Vaughan (1901), Jeffrey (1898), Tansley (1907-08), and others is presented in outline form with accompanying etymology, synonymy, examples, and with detailed notes on controversial taxa, classificatory rationale, and historical aspects. Recognized are (1) “protostele” (divided into “ectophloic,” “endophloic,” and “amphiphloic,” with 7, 1, and 1 subtypes respectively), (2) “siphonostele” (divided into “ectophloic” with 2 subtypes and “amphiphloic,” the latter divided into “solenostele” and “dictyostele” with 3 subtypes each, plus “siphonostele incertae sedis”), and (3) “eustele” (divided into “eustele sensu stricto” with 4 subtypes, “pseudosiphonostele,” “reduced eustele,” and “polycyclic eustele”).
DNA methylation and evolution of duplicate genes

The evolutionary mechanisms underlying duplicate gene maintenance and divergence remain highly debated. Epigenetic modifications, such as DNA methylation, may contribute to duplicate gene evolution by facilitating tissue-specific regulation. However, the role of epigenetic divergence on duplicate gene evolution remains little understood. Here we show, using comprehensive data across 10 diverse human tissues, that DNA methylation plays critical roles in several aspects of duplicate gene evolution. We first demonstrate that duplicate genes are initially heavily methylated, before gradually losing DNA methylation as they age. Within each pair, DNA methylation divergence between duplicate partners increases with evolutionary age. Importantly, tissue-specific DNA methylation of duplicates correlates with tissue-specific expression, implicating DNA methylation as a causative factor for functional divergence of duplicate genes. These patterns are apparent in promoters but not in gene bodies, in accord with the complex relationship between gene-body DNA methylation and transcription. Remarkably, many duplicate gene pairs exhibit consistent division of DNA methylation across multiple, divergent tissues: For the majority (73%) of duplicate gene pairs, one partner is always hypermethylated compared with the other. This is indicative of a common underlying determinant of DNA methylation. The division of DNA methylation is also consistent with their chromatin accessibility profiles. Moreover, at least two sequence motifs known to interact with the Sp1 transcription factor mark promoters of more hypomethylated duplicate partners. These results demonstrate critical roles of DNA methylation, as well as complex interaction between genome and epigenome, on duplicate gene evolution.
Generalized rotating-compensator ellipsometry

Abstract The extension of rotating-compensator ellipsometry (RCE) to measurements of the system Jones matrix J of optical systems is reported. The similarities and differences of generalized RCE as compared to other methods are noted. Measurements of several anisotropic materials, as well as of “standard” optical systems having one, two and three essential (complex) elements of J are described. Finally, a completely automated procedure for the measurement and analysis of a uniaxially anisotropic surface with the optic axis in the plane of the surface is presented.
Comparison of Clinical and Administrative Data Sources for Hospital Coronary Artery Bypass Graft Surgery Report Cards

Background— Regardless of statistical methodology, public performance report cards must use the highest-quality validated data, preferably from a prospectively maintained clinical database. Using logistic regression and hierarchical models, we compared hospital cardiac surgery profiling results based on clinical data with those derived from contemporaneous administrative data. Methods and Results— Fiscal year 2003 isolated coronary artery bypass grafting surgery results based on an audited and validated Massachusetts clinical registry were compared with those derived from a contemporaneous state administrative database, the latter using the inclusion/exclusion criteria and risk model of the Agency for Healthcare Research and Quality. There was a 27.4% disparity in isolated coronary artery bypass grafting surgery volume (4440 clinical, 5657 administrative), a 0.83% difference in observed in-hospital mortality (2.05% versus 2.88%), corresponding differences in risk-adjusted mortality calculated by various s...
A comparison of machine learning algorithms for chemical toxicity classification using a simulated multi-scale data model

Bioactivity profiling using high-throughput in vitro assays can reduce the cost and time required for toxicological screening of environmental chemicals and can also reduce the need for animal testing. Several public efforts are aimed at discovering patterns or classifiers in high-dimensional bioactivity space that predict tissue, organ or whole animal toxicological endpoints. Supervised machine learning is a powerful approach to discover combinatorial relationships in complex in vitro/in vivo datasets. We present a novel model to simulate complex chemical-toxicology data sets and use this model to evaluate the relative performance of different machine learning (ML) methods. The classification performance of Artificial Neural Networks (ANN), K-Nearest Neighbors (KNN), Linear Discriminant Analysis (LDA), Naive Bayes (NB), Recursive Partitioning and Regression Trees (RPART), and Support Vector Machines (SVM) in the presence and absence of filter-based feature selection was analyzed using K-way cross-validation testing and independent validation on simulated in vitro assay data sets with varying levels of model complexity, number of irrelevant features and measurement noise. While the prediction accuracy of all ML methods decreased as non-causal (irrelevant) features were added, some ML methods performed better than others. In the limit of using a large number of features, ANN and SVM were always in the top performing set of methods while RPART and KNN (k = 5) were always in the poorest performing set. The addition of measurement noise and irrelevant features decreased the classification accuracy of all ML methods, with LDA suffering the greatest performance degradation. LDA performance is especially sensitive to the use of feature selection. Filter-based feature selection generally improved performance, most strikingly for LDA. We have developed a novel simulation model to evaluate machine learning methods for the analysis of data sets in which in vitro bioassay data is being used to predict in vivo chemical toxicology. From our analysis, we can recommend that several ML methods, most notably SVM and ANN, are good candidates for use in real world applications in this area.
Evolving non-autonomous neuromorphic flight control for a flapping-wing mechanical insect

In the previous work, it was demonstrated that one can effectively employ CTRNN-EH (a neuromorphic variant of EH method) methodology to evolve autonomous neuromorphic flight controllers for a flapping wing robot. This paper further explores the similar prospective by evolving non-autonomous neuromorphic controllers, which would render them potentially deployable controllers in a realistic micro-scale flapping wing robot. A summary of the previous work related to evolving Autonomous flight controllers for a flapping-wing mechanical insect is provided along with the incentives towards evolving the non-autonomous controllers for the same. Further, the details of the experimental design and the outcomes of experiments to evolve non-autonomous flight controllers are provided with appropriate discussion and implications for possible future work.
Analysis of sequences and predicted structures required for viral satellite RNA accumulation by in vivo genetic selection

In vivo genetic selection was used to study the sequences and structures required for accumulation of subviral sat-RNA C associated with turnip crinkle virus (TCV). This technique is advantageous over site-specific mutagenesis by allowing side-by-side selection from numerous sequence possibilities as well as sequence evolution. A 22 base hairpin and 6 base single-stranded tail located at the 3'-terminus of sat-RNA C were previously identified as the promoter for minus strand synthesis. Approximately 50% of plants co-inoculated with TCV and sat-RNA C containing randomized sequence in place of the 22 base hairpin accumulated sat-RNA in uninoculated leaves. The 22 base region differed in sat-RNA accumulating in all infected plants, but nearly all were predicted to fold into a hairpin structure that maintained the 6 base tail as a single-stranded sequence. Two additional rounds of sat-RNA amplification led to four sequence family 'winners', with three families containing multiple variants, indicating that evolution of these sequences was occurring in plants. Three of the four sequence family winners had the same 3 bp at the base of the stem as wild-type sat-RNA C. Two of the winners shared 15 of 22 identical bases, including the entire stem region and extending two bases into the loop. These results demonstrate the utility of the in vivo selection approach by showing that both sequence and structure contribute to a more active 3'-end region for accumulation of sat-RNA C.
Sample size and power: how big is big enough?

Questions about sample size are some of the most frequent requests that statisticians encounter in their collaborative work with investigators. Although the question can be posed in many different ways, investigators typically need to know the answer to the following question before they can embark on a scientific study: “How large should my study be?” For example, in planning a study to compare a new treatment with a standard treatment, investigators need to know how many subjects to include in the study to have some specified power to detect that the new treatment is superior to the standard. That is, investigators need to ensure that their study is in some sense “big enough” so that a treatment effect of subject matter importance can be detected by a statistical test. In principle, the answer to this question is relatively straightforward and statisticians have developed simple formulae for sample size calculations. The purpose of this column is not to show how these sample size formulae can be derived. Instead, I emphasize the main considerations in determining how large the sample size needs to be to have a specified power to detect some effect of scientific interest. Explicit formulae for sample size and power can be found in many introductory textbooks in statistics. In addition, some statistical software packages include procedures for sample size calculations and publicly available sample size and power calculators can be found on the Internet. However, sample size calculations do require that investigators possess some knowledge of the key ingredients of sample size formulae. As we shall see later in this column, there are a number of factors that influence the answer to the proverbial question: “How big is big enough?” In general, sample size calculations can be tackled from two somewhat different, but complementary, angles. One approach is to determine the sample size necessary to attain a confidence interval1 with some desired degree of precision. For example, it may be of interest to know how large the sample size must be to produce a 95% confidence interval with some prespecified width. This was the topic of an earlier column.2 An alternative approach, and the one that is more commonly encountered, is to determine the sample size required to attain some prespecified level of power of a statistical test. In this column, I focus on the latter case and highlight the key factors that play roles in sample size calculations.
Pattern recognition of marine provinces

The objective of this Letter is to introduce a concept for identifying marine provinces by applying two band ratios that are indicative of chlorophyll distribution patterns. The ratios of water‐leaving radiances 443 nm/551 nm and 678 nm/ 667 nm are close to the two absorption bands of chlorophyll; however, as photon penetration depth at the applied wavelengths varies, each ratio responds to different depths. This allows a qualitative interpretation of separated clusters in scatter diagrams. Pattern classification separates the major biogeochemical provinces as documented with the Peruvian upwelling system and the convergence zone in the Brazil–Falkland/Malvinas current system.
Transfer of social influence effects on psychophysical judgments.

Changes in psychophysical judgments of roughness due to social influence with other subjects
The Effects of Correlation and Response Bias in Alerted Monitor Displays

Many modern systems, such as advanced aircraft, are so complex that a human cannot control the system without the assistance of automation. The author performed an experiment in which a human, working in conjunction with an automated signal detection device, monitored a system for abnormal states. The human and the automated alarm monitored sets of information that were either dependent, partially independent, or independent of each other. The response criteria of the alarm and human were manipulated. The participants concurrently performed either an easy or difficult tracking task as a load task. The results indicate that system sensitivity decreases as the sets of information become increasingly dependent on each other. The benefits of the alarm did not always outweigh its costs, especially in the more dependent conditions, which are probably more characteristic of real-life situations.
Emergency Department Visits for Antibiotic- Associated Adverse Events

(See the editorial commentary by Linder on pages 744–6) Background. Drug-related adverse events are an underappreciated consequence of antibiotic use, and the national magnitude and scope of these events have not been studied. Our objective was to estimate and compare the numbers and rates of emergency department (ED) visits for drug-related adverse events associated with systemic antibiotics in the United States by drug class, individual drug, and event type. Methods. We analyzed drug-related adverse events from the National Electronic Injury Surveillance System– Cooperative Adverse Drug Event Surveillance project (2004–2006) and outpatient prescriptions from national sample surveys of ambulatory care practices, the National Ambulatory Medical Care Survey and the National Hospital Ambulatory Medical Care Survey (2004–2005). Results. On the basis of 6614 cases, an estimated 142,505 visits (95% confidence interval [CI], 116,506–168,504 visits) annually were made to US EDs for drug-related adverse events attributable to systemic antibiotics. Antibiotics were implicated in 19.3% of all ED visits for drug-related adverse events. Most ED visits for antibiotic-associated adverse events were for allergic reactions (78.7% of visits; 95% CI, 75.3%–82.1% of visits). One-half of the estimated ED visits were attributable to penicillins (36.9% of visits; 95% CI, 34.7%–39.2% of visits) and cephalosporins (12.2%; 95% CI, 10.9%–13.5%). Among commonly prescribed antibiotics, sulfonamides and clindamycin were associated with the highest rate of ED visits (18.9 ED visits per 10,000 outpatient prescription visits [95% CI, 13.1–24.7 ED visits per 10,000 outpatient prescription visits] and 18.5 ED visits per 10,000 outpatient prescription visits [95% CI, 12.1–25.0 ED visits per 10,000 outpatient prescription visits], respectively). Compared with all other antibiotic classes, sulfonamides were associated with a significantly higher rate of moderate-to-severe allergic reactions (4.3% [95% CI, 2.9%–5.8%] vs. 1.9 % [95% CI, 1.5%–2.3%]), and sulfonamides and fluoroquinolones were associated with a significantly higher rate of neurologic or psychiatric disturbances (1.4% [95% CI, 1.0%– 1.7%] vs. 0.5% [95% CI, 0.4%–0.6%]). Conclusions. Antibiotic-associated adverse events lead to many ED visits, and allergic reactions are the most common events. Minimizing unnecessary antibiotic use by even a small percentage could significantly reduce the immediate and direct risks of drug-related adverse events in individual patients.