bluuebunny/crossref_metadata_2025 huggingface dataset:
Sampling design and statistical considerations for the commercial groundfish fishery of Oregon
Authors: Crone Paul R.
Published: August 2009

Fisheries management is often based on data collected through various sample survey programs. At a minimum, commercial fisheries must be monitored to determine the species and age compositions of the landings; this provides the baseline data on which to assess the stocks. An equally important objective, which is often ignored, is the determination of the variability associated with derived estimates. This paper presents measures of dispersion for landing estimates generated from a two-stage sampling design used for commercially harvested groundfish species landed at Oregon ports; particular attention is given to the relative magnitudes of variability at the first and second stages of sampling designs used for estimating species and age compositions. At least two-thirds of the total amount of rockfish landed in each port/quarter stratum consisted of estimates of species composition that had small coefficients of variation (CV < 10%). For each species sampled for age composition, at least three-fourths of the total landings included estimates for individual ages with CVs < 25%. For the majority of the landings, the variation at the first stage of sampling contributed at least 63 and 90% to the variance of the estimates for the species and age compositions, respectively.
Genetic similarity among zebra mussel populations within North America and Europe
Authors: Marsden J. Ellen , Spidle Adrian , May Bernie
Published: August 2009

The zebra mussel Dreissena polymorpha has rapidly established both contiguous and disjunct populations during its spread through eastern North America. If new colonies are founded by small numbers of individuals, populations with markedly different genetic and phenotypic characters could arise (founder effect); this possibility could confound ecological comparisons of populations from different geographic locations. We analyzed genetic differentiation among 18 populations of mussels from the Great Lakes and seven populations from Europe using starch-gel electrophoresis. Analysis of 27 proteins yielded data from 15 polymorphic loci and one monomorphic locus. The data indicated that zebra mussels in North America have the same high genetic variability (Ho = 0.30–0.43) that is found in European populations (Ho = 0.27–0.35) and is typical of molluscs. Little variation appears to have been lost when zebra mussel were transported to North America. Nei's genetic distances between populations were small (0.004–0.028) compared with distances among populations of other mollusc species (0.023–0.184). Like populations from Europe, populations within North America were not highly differentiated, which suggests that founder populations have not been small and (or) frequent genetic mixing has occurred. European populations clustered seperately from North American populations (Nei's distance = 0.058).
Measurement of dissolved carbon dioxide
Authors: Alford Jr. J. S.
Published: August 2009

Several probes for measuring dissolved carbon dioxide (CO2) concentration were installed in a 68-litre fermentor and their effectiveness compared. Submerged silastic rubber tubing gave reproducible results over a wide range of operating conditions and was generally superior to all other probes evaluated.The silastic rubber probe was used to compare the partial pressure of CO2 in viscous fermentation media with that in the fermentor exhaust gas. No significant difference was found.Results show that determination of the CO2 partial pressure in the exhaust gas gives an excellent approximation of the partial pressure of dissolved CO2 in the liquid medium, eliminating the need for measurement of CO2 concentration in the broth.
Two-dimensional SDS–polyacrylamide gel electrophoresis of heat-modifiable outer-membrane proteins
Authors: Russell R. R. B.
Published: August 2009

An examination has been made of the effect which temperature of solubilization has upon the subsequent migration in SDS–polyacrylamide gel electrophoresis of proteins from the cell envelopes of Escherichia coli K12 and Neisseria sicca ATCC 9913. Conventional electrophoresis in tubes revealed substantial differences in the staining patterns of gels, depending upon whether the envelope samples were solubilized at 37 °C or 100 °C; in the case of N. sicca at least 6 of 13 discernible bands displayed heat-modifiable behavior. The relationship of the bands produced by each of the two temperatures was investigated by a two-dimensional electrophoresis procedure, in which a sample was solubilized at 37 °C and run in a usual cylindrical gel; the entire gel was then resolubilized at 100 °C, and laid along an acrylamide slab for electrophoresis in the second dimension.It was found that "free endotoxin" of both organisms examined contained the same major proteins as the total envelope fraction, and that these free endotoxin proteins showed the same heat-modifiable properties as when present in total envelopes.
Electron-microscopic study of Herpesvirus macaca in human fibroblasts
Authors: Graze Peter R. , McGrath Phillip , Washington Glenelle C. , Royston Ivor
Published: August 2009

An electron microscopic study of the morphology of Herpesvirus macaca, a serologically distinct infectious agent isolated from the leukocytes of rhesus monkeys, was performed. WI-38 fibroblast monolayers were infected with the virus and examined 18 days later. The morphology of Herpesvirus macaca was, in general, typical of the herpesvirus group. Enveloped virus particles observed via negative-stain technique had a diameter of 145–155 nm. An inner capsid composed of hexagonal capsomeres had a diameter of 100–110 nm and surrounded a central core. While enveloped forms appeared to be present within the nuclei of infected cells, they were not found in the cytoplasm except within vacuolar structures. Associated changes were found in the morphology of infected cells, including intracytoplasmic myelin figures.
The effect of cooling and warming rates on the survival of a variety of bacteria
Authors: Calcott P. H. , Lee S. K. , MacLeod R. A.
Published: August 2009

Cooling and warming rates affect bacterial survival profoundly with all bacteria tested (Azotobacter chroococcum, Klebsiella aerogenes, Salmonella typhimurium, Pseudomonas aeruginosa, Streptococcus faecalis) behaving similarly. Most bacteria were sensitive to salt on freezing and thawing. Viabilities of population frozen and thawed in saline were always less (by at least 20%) than comparable ones frozen in water alone. Under these conditions, S. faecalis was resistant to the presence of sodium chloride; viabilities of populations frozen in the presence or absence of sodium chloride were always less than 5% different. The implications of these results in light of the organisms' shape, Gram stain, and respiration are discussed.
PROCESSING AND VISUALIZATION OF LIGHT MICROSCOPE IMAGES
Authors: MAURER MAURICIO RAFAEL , PEDRINI HELIO , RANDI MARCO ANTONIO FERREIRA
Published: August 2009

The analysis of three-dimensional structures of tissues and cellular constituents is a fundamental task in Biology and Medicine. Although three-dimensional images, acquired by light microscopes, play an important role in such knowledge domains, their analysis has not been much exploited compared to other imaging technologies, such as X-ray radiography, computerized tomography or magnetic resonance. In light microscopy, the majority of the activities involved in the image analysis (for instance, detection, counting, quantification) is still performed manually. The main difficulties among the others include the fact that the objects under investigation usually have complex structures, large number of cellular elements, shape variations and presence of noise in the acquired images. This paper describes a method for processing and visualization of images obtained with light microscopes. An effective transfer function based on the optical density of the cellular constituents is employed to generate the volumetric visualization. Several real data sets are used to demonstrate the effectiveness of the proposed method.
ROBUST REFERENCE-WATERMARKING SCHEME USING WAVELET PACKET TRANSFORM AND BIDIAGONAL-SINGULAR VALUE DECOMPOSITION
Authors: BHATNAGAR GAURAV , RAMAN BALASUBRAMANIAN
Published: August 2009

This paper presents a new robust reference watermarking scheme based on wavelet packet transform (WPT) and bidiagonal singular value decomposition (bSVD) for copyright protection and authenticity. A small gray scale logo is used as watermark instead of randomly generated Gaussian noise type watermark. A reference watermark is generated by original watermark and the process of embedding is done in wavelet packet domain by modifying the bidiagonal singular values. For the robustness and imperceptibly, watermark is embedded in the selected sub-bands, which are selected by taking into account the variance of the sub-bands, which serves as a measure of the watermark magnitude that could be imperceptibly embedded in each block. For this purpose, the variance is calculated in a small moving square window of size Sp× Sp(typically 3 × 3 or 5 × 5 window) centered at the pixel. A reliable watermark extraction is developed, in which the watermark bidiagonal singular values are extracted by considering the distortion caused by the attacks in neighboring bidiagonal singular values. Experimental evaluation demonstrates that the proposed scheme is able to withstand a variety of attacks and the superiority of the proposed method is carried out by the comparison which is made by us with the existing methods.
SWT-BASED FORCE SENSOR DE-NOISING FOR THE NEUROSURGICAL ROBOT
Authors: SHEN WEIMIN , GU JASON
Published: August 2009

When our proposed neurosurgical robot is applied, the neurosurgeon usually wants to sense the force on the remote site to operate on patients. The force signal analysis is of critical importance for neurosurgeons to perform stable, reliable, and safe operations. In this paper, based on the stationary wavelet transform (SWT), force information analysis and process is designed. Since force sampled by the JR3 sensor contains noise from the sensor and mechanical vibration when drilling, to smooth the force signal sent to the operator, SWT-based force information de-noising is proposed to reduce the noise significantly, especially for the force along the x and y axes. Simulations and experiments further verified the proposed research.
AN ENERGY-EFFICIENT ADAPTIVE CLUSTERING ALGORITHM FOR WIRELESS SENSOR NETWORKS
Authors: SHANG FENGJUN , ABOLHASAN MEHRAN , WYSOCKI TADEUSZ
Published: August 2009

In this paper, we consider a network of energy constrained sensors deployed over a region. Each sensor node in such a network is systematically gathering and transmitting sensed data to a base station (via clusterheads). This paper focuses on reducing the power consumption of wireless sensor networks. We first extend LEACH's stochastic clusterhead selection algorithm by an average energy-based (LEACH-AE) deterministic component to reduce energy consumption. And then an unequal clustering idea is introduced to further reduce energy consumption of clusterheads. Simulation results show that our modified scheme can extend the network life by up to 38% before the first node dies in the network. Through both theoretical analysis and numerical results, it is shown that the proposed algorithm achieves better performance than the existing clustering algorithms such as LEACH, DCHS, LEACH-C.
Increased Susceptibility to Skin Carcinogenesis in TREX2 Knockout Mice
Authors: Parra David , Manils Joan , Castellana Bàrbara , Viña-Vilaseca Arnau , Morán-Salvador Eva , Vázquez-Villoldo Nuria , Tarancón Gemma , Borràs Miquel , Sancho Sara , Benito Carmen , Ortega Sagrario , Soler Concepció
Published: August 2009

TREX2 is a proofreading 3′-5′ exonuclease that can be involved in genome maintenance; however, its biological role remains undefined. To better understand the function and physiologic relevance of TREX2, we generated mice deficient in TREX2 by targeted disruption of its unique coding exon. The knockout mice are viable and do not show relevant differences in growth, survival, lymphocyte development, or spontaneous tumor incidence compared with their wild-type counterparts over a period of up to 2 years. Also, we did not observe chromosomal instability or defects in cell proliferation and cell cycle upon loss of TREX2. We have observed that TREX2 expression is not ubiquitous, being expressed preferentially in tissues with stratified squamous epithelia, such as the skin or esophagus, and specifically in keratinocytes. Interestingly, TREX2-null mice are more susceptible to skin carcinogenesis induced by 7,12-dimethylbenz(a)anthracene (DMBA) compared with wild-type mice. This phenotype correlates with a reduction of DMBA-induced apoptosis in both the epidermis and keratinocytes of TREX2-null mice. Altogether, our results suggest a tumor suppressor role for TREX2 in skin carcinogenesis through which it contributes to keratinocyte apoptosis under conditions of genotoxic stress. [Cancer Res 2009;69(16):6676–84]
Unwelcome Complement
Authors: Markiewski Maciej M. , Lambris John D.
Published: August 2009

For decades, the complement system has been recognized as an effector arm of the innate immunity system that contributes to the destruction of tumor cells. However, recent studies have challenged this paradigm by demonstrating that a complement component, the anaphylatoxin C5a, promotes the growth of malignant tumors in a mouse model of cervical carcinoma. The effect of C5a on tumor growth was associated with the recruitment of myeloid-derived suppressor cells to tumors, followed by the activation of these cells. These unexpected findings identify the complement system as a potential new target for anticancer immunotherapy. [Cancer Res 2009;69(16):6367–70]
Long-Term Improvement in Tinnitus after Modified Tinnitus Retraining Therapy Enhanced by a Variety of Psychological Approaches
Authors: Seydel Claudia , Haupt Heidemarie , Szczepek Agnieszka J. , Klapp Burghard F. , Mazurek Birgit
Published: August 2009

This work evaluates an enhanced tinnitus retraining therapy (TRT) for patients with chronic tinnitus based on different group therapeutic interventions in a day hospital setting. Therapy for chronic tinnitus is intended to improve the way patients cope with tinnitus by learning how to reduce tinnitus-induced impairments. Short-term and long-term changes in stress variables and tinnitus-related distress were investigated using 3 psychometric instruments. Patients received 7 consecutive days of a multidisciplinary therapy at the Charité University Hospital in Berlin. The data were assessed before and after therapy, either immediately or after 3, 6 or 12 months. As a control, we used scores of tinnitus patients from the waiting list, and compared these to the scores of the therapy group 3 months after the end of treatment. The main factors of the modified TRT were Jacobson’s progressive muscle relaxation, physiotherapy, education via lectures and training of selective attention, as well as changes of appraisal, mental attitude and behavior towards tinnitus. The therapy resulted in a significant reduction in both short-term and long-term tinnitus-related distress and psychometric stress variables, with the latter being more reduced in patients with higher initial scores. Moreover, our study revealed differences in psychometric parameters concerning duration of tinnitus, age and gender, which may explain the different outcomes of therapy. The outpatient setting enables the patients to test, practice and transfer strategies into their everyday life.
Latencies of Auditory Steady-State Responses Recorded in Early Infancy
Authors: Alaerts Jane , Luts Heleen , Van Dun Bram , Desloovere Christian , Wouters Jan
Published: August 2009

Multiple-stimulus auditory steady-state responses (ASSRs) were assessed in 111 ears of 70 infants between –4 and 19 weeks of age at risk for hearing loss. ASSR thresholds obtained in infants with normal hearing (n = 69 ears) were compared with normal adult ASSR thresholds (n = 32 ears), and the linear relation between ASSR thresholds and behavioral thresholds (BHTs) was investigated in normal-hearing and hearing-impaired infants (n = 79 ears). Furthermore, latency estimates of significant responses to stimuli of 50 dB SPL were compared between the normal-hearing infants (n = 171 data points) and adults (n = 124 data points) and developmental changes in latency were evaluated within the infant group. Normal ASSR thresholds were on average 12 dB higher in infants compared with adults. Correlations between ASSR thresholds and BHTs were 0.75, 0.87, 0.87 and 0.79 for 500, 1000, 2000 and 4000 Hz, respectively. There was a significant effect of carrier frequency on ASSR latency, with higher carrier frequencies evoking shorter latencies in both infants and adults. Mean latencies in adults were 24.3 ± 1.5, 22.3 ± 1.1, 19.4 ± 1.0 and 18.0 ± 1.1 ms for 500, 1000, 2000 and 4000 Hz, respectively. Depending on the data fit of the infant latency estimates, mean latencies were 1.0 ms shorter or 9.5 ms longer in infants compared with adults. In infants, latencies were on average 2.0 ms longer in the youngest infant group (≤0 weeks) relative to the oldest infant group (3–8 weeks). These age-related trends, together with other arguments, point to longer latencies in infants compared with adults. The results of this study are valuable as a clinical reference for interpreting ASSR results obtained in high-risk infants within their first months of life and indicate that developmental changes occur regarding ASSR latency.
Risk Factors and Management of Presacral Abscess following Total Mesorectal Excision for Rectal Cancer
Authors: Veenhof A.A.F.A. , Brosens R. , Engel A.F. , van der Peet D.L. , Cuesta M.A.
Published: August 2009

Introduction:There is scant information regarding the incidence, risk factors and management of presacral abscesses following total mesorectal excision (TME) for rectal cancer. Methods:Gender, age, body mass index (BMI), neoadjuvant radiation therapy, ASA classification, tumor size, tumor localization and fecal diversion were investigated as independent risk factors for the development of a presacral abscess. Results: 261 patients were included, 26 patients (10%) developed a presacral abscess. Twenty-two patients (14.8%) with and 4 patients (3.6%) without neoadjuvant radiation therapy developed a presacral abscess (p = 0.003), respectively. Nine ASA 1 patients (5.7%), 8 ASA 2 patients (8.5%) and 3 ASA 3 patients (70%) developed a presacral abscess (p = 0.001). More presacral abscesses were observed after resection of larger tumors: 38 versus 30 mm (p = 0.041). No correlation between gender, age, BMI, tumor localization and the development of a prescaral abscess was found. Management of the presacral abscess, without overt leakage, was initially performed by drainage through the anastomosis following anterior resections and through the perineal suture line following abdominoperineal resections. Conclusion: Presacral abscess is a frequent (10%) complication following TME for rectal cancer. Patients in poor general condition, neoadjuvant radiation therapy and large tumors are at risks for developing a presacral abscess. Management, without overt leakage, is in our experience best executed by drainage through the anastomosis or perineal suture line.
Cost-Effectiveness of Therapeutic Hypothermia After Cardiac Arrest
Authors: Merchant Raina M. , Becker Lance B. , Abella Benjamin S. , Asch David A. , Groeneveld Peter W.
Published: August 2009

Background—

Therapeutic hypothermia can improve survival and neurological outcomes in cardiac arrest survivors, but its cost-effectiveness is uncertain. We sought to evaluate the cost-effectiveness of treating comatose cardiac arrest survivors with therapeutic hypothermia.

Methods and Results—

A decision model was developed to capture costs and outcomes for patients with witnessed out-of-hospital ventricular fibrillation arrest who received conventional care or therapeutic hypothermia. The Hypothermia After Cardiac Arrest (HACA) trial inclusion criteria were assumed. Model inputs were determined from published data, cooling device companies, and consultation with resuscitation experts. Sensitivity analyses and Monte Carlo simulations were performed to identify influential variables and uncertainty in cost-effectiveness estimates. The main outcome measures were quality-adjusted survival after cardiac arrest, cost of hypothermia implementation, cost of posthospital discharge care, and incremental cost-effectiveness ratios. In our model, postarrest patients receiving therapeutic hypothermia gained an average of 0.66 quality-adjusted life years compared with conventional care, at an incremental cost of $31 254. This yielded an incremental cost-effectiveness ratio of $47 168 per quality-adjusted life year. Sensitivity analyses demonstrated that poor neurological outcome postcooling and costs associated with posthypothermia care (in-hospital and long term) were the most influential variables in the model. Even at extreme estimates for costs, the cost-effectiveness of hypothermia remained less than $100 000 per quality-adjusted life year. In 91% of 10 000 Monte Carlo simulations, the incremental cost-effectiveness ratio was less than $100 000 per quality-adjusted life year.

Conclusions—

In cardiac arrest survivors who meet HACA criteria, therapeutic hypothermia with a cooling blanket improves clinical outcomes with cost-effectiveness that is comparable to many economically acceptable health care interventions in the United States.
Folk Literature among Sephardic Bourgeois Women at the Beginning of the Twentieth Century
Authors: Díaz-Mas Paloma
Published: August 2009

Folklorists, philologists and ethnomusicologists have emphasized the important role of women for the preservation of Sephardic folklore and traditional literature in the twentieth century. Many scholars accept that Sephardic women who knew and performed folklore where almost illiterate and belonged to lower classes. This article intends to show that at the beginning of the twentieth century, some bourgeois, middle-class Sephardic women, although they had a very Western, modern life style, knew and appreciated the intangible heritage of Sephardic folklore that they had received handed down from their mothers and grandmothers. Those considerations are based on the information and comments about folklore and folksongs contained in the letters of affluent Sephardic Jews who maintained correspondence with Angel Pulido, a Spanish doctor and senator who in 1904 started a political campaign to strenghten ties and relations between Spain and the Sephardic Jews.
Personal Historical Narrative Shaping the Past and the Present
Authors: Rosen Ilana
Published: August 2009

The twentieth century proved to be a fateful era for the majority of European Jewry, who experienced prosperity and emancipation, persecution and destruction, and rehabilitation in their newly founded state or in the West. Based on several research projects, the present essay examines the narrative responses of formerly Austro-Hungarian Jews (presently Israelis and Hungarians) to these events and processes. In addition to telling their personal experiences, some of them also wish to confront generally accepted views and images of their past lives and communities in the inter-war period and—more acutely—in WWII and the Holocaust. The essay reads their contentions on the background of historical and literary-cultural research and vice-versa, thus enabling these narrators to voice disagreements and grievances that are otherwise rarely heard. The essay likewise highlights the function of personal narrative, as part of folkloric repertoire, and its study in enriching research and public awareness with less known and exposed people and experiences.
Torah and Magic: The Torah Scroll and Its Appurtenances as Magical Objects in Traditional Jewish Culture
Authors: Sabar Shalom
Published: August 2009

This essay deals with a little noticed aspect of the Torah scroll in Jewish life and practice—namely, the usage of the scroll and its accessories in the context of sympathetic magic. The Torah is undoubtedly the holiest text in the Jewish tradition, and early on rabbinical authorities set a code that determined the fitting rules of conduct towards the scroll upon which it is written. In the course of time, the Torah scroll and the appurtenances associated with it emerged as the most sacred tangible objects in Jewish tradition and folk culture. Select Torah scrolls in various communities, especially in the lands of Islam, were elevated to a special position and were considered as possessing extraordinary protective powers. Aside from miraculous stories told about such scrolls, the popular beliefs in the power of the Torah scroll in general are best reflected in the ornamental appurtenances which enhanced the physical appearance of the sacred object. Thus, costly ceremonial objects such as the tik (Torah case) or rimonim (Torah finials) were decorated in several communities with magical designs and carefully selected texts, which reflect ideas of Jewish magic in general and are reminiscent of Hebrew amulets in particular.
Towards a Contemporary View of Islamic Criminal Procedures: A Focus on the Testimony of Witnesses
Authors: Badawy Tarek
Published: August 2009

This paper challenges the traditional conception of Islamic criminal law and provides alternatives to the rules of criminal procedures that are both compatible with modern life and the sprit of Shari'ah. The first part of the article provides a brief explanation of the four main sources of Islamic law. The second part focuses on the different classifications of crimes in Islamic law and explains Shari'ah's classical rules of evidence. It gives answers to some complicated legal questions by examining the law's underlying rationales. For example, the author challenges the conservative view that calls for the imposition of the death penalty onto apostates and clarifies that such punishment has no foundation in Shari'ah. He also explains why, from an evidentiary standpoint, the crime of rape should be qualified as haraba as opposed to zina, which both entails a harsher penalty for the perpetrator and more lenient evidentiary requirements from prosecutors. Finally, the author contests the traditional stream of Islamic thinking by arguing that in criminal matters, the testimony of female witnesses should be equal to that of males and that in hudūd crimes, scientific evidence should be given the same status as the testimony of eye witnesses.
Estimates of the Water Vapor Climate Feedback during El Niño–Southern Oscillation
Authors: Dessler A. E. , Wong S.
Published: August 2009

The strength of the water vapor feedback has been estimated by analyzing the changes in tropospheric specific humidity during El Niño–Southern Oscillation (ENSO) cycles. This analysis is done in climate models driven by observed sea surface temperatures [Atmospheric Model Intercomparison Project (AMIP) runs], preindustrial runs of fully coupled climate models, and in two reanalysis products, the 40-yr European Centre for Medium-Range Weather Forecasts Re-Analysis (ERA-40) and the NASA Modern Era Retrospective-Analysis for Research and Applications (MERRA). The water vapor feedback during ENSO-driven climate variations in the AMIP models ranges from 1.9 to 3.7 W m−2 K−1, in the control runs it ranges from 1.4 to 3.9 W m−2 K−1, and in the ERA-40 and MERRA it is 3.7 and 4.7 W m−2 K−1, respectively. Taken as a group, these values are higher than previous estimates of the water vapor feedback in response to century-long global warming. Also examined is the reason for the large spread in the ENSO-driven water vapor feedback among the models and between the models and the reanalyses. The models and the reanalyses show a consistent relationship between the variations in the tropical surface temperature over an ENSO cycle and the radiative response to the associated changes in specific humidity. However, the feedback is defined as the ratio of the radiative response to the change in the global average temperature. Differences in extratropical temperatures will, therefore, lead to different inferred feedbacks, and this is the root cause of spread in feedbacks observed here. This is also the likely reason that the feedback inferred from ENSO is larger than for long-term global warming.
Models of Privacy Preserving Traffic Tunneling
Authors: Nicol David M. , Schear Nabil
Published: August 2009

Encrypted protocols, such as Secure Socket Layer (SSL), are becoming more prevalent because of the growing use of e-commerce, anonymity services, and secure authentication. Likewise, traffic analysis is becoming more common because it is often the only way to analyze these protocols. Although there are many valid uses for traffic analysis (such as network policy enforcement and intrusion detection), it can also be used to maliciously compromise the secrecy or privacy of a user. While the payload can be strongly protected by encryption, analysis of traffic patterns can yield information about the type and nature of traffic. In this paper we use simulation and analytic models to examine the impact on user experience of a scheme that masks the behavior of real traffic by embedding it in synthetic, encrypted, cover traffic. Through simulation and an analytic model we investigate the effects on the user experience using disparate and similar traffic models. This point provides a novel context where we observe the synergy of simulation and analytic modeling. We show that a detailed simulation model of network traffic characteristics can be used to estimate the parameters of an analytic model of tunneling. We see that the accuracy of the model’s predictions is directly dependent on the accuracy of parameters we obtain from the simulation. However, the simulation model does not need to have any concept of tunneling. Using simulation and analytic modeling together, we obtain an analysis whose whole is greater than the sum of its parts.
Indigenous Movements and the Andean Dynamics of Ethnicity and Class
Authors: Pape I.S.R.
Published: August 2009

An analysis of the Andean dynamics of ethnicity and class in historical perspective with a focus on political institutions, decision making, and organizational structure at the communal and subregional levels reveals that, in the Andean context, ethnicity and class are inextricably linked in a societal dynamic that is closely mirrored in the two main organizations representing indigenous people in the Bolivian highlands. As a result, the main differences in organization, representation, and decision-making patterns manifest themselves within organizations, between the higher and lower levels of the hierarchy, rather than between the two organizations. The two organizations cover the same social, economic, and cultural realities; they perform largely the same practical and symbolic functions and occupy the same position in relation to the state. At the communal and subregional levels, the functioning of authority, decision-making patterns, and organizational structures are highly similar in the two organizations, and so are their overarching organizational structures.
Social Service Organizations in the Era of Evidence-Based Practice
Authors: Maynard Brandy R.
Published: August 2009

• Summary: Evidence-based practice (EBP) has been gaining acceptance and momentum in the social services professions. As evidence related to specific programs and interventions mount, social service practitioners and organizations around the world have increasingly begun to implement evidence-based programs as a strategy for creating better outcomes for children, families, and adults. Unfortunately, the science of evaluating efficacious and effective programs and interventions has far outpaced the science of implementing them. A gap exists between what we know works and being able to utilize what works in practice. This article will examine the challenges facing social service organizations in implementing evidence-based programs and explore an organizational theory to address those challenges.

• Findings: The implementation of EBPs has proven to be a complex and challenging process, with organizational factors coming to the forefront as important in bridging the gap between science and service. The complexity of translating what we know from research into practice requires an organizing theory to help guide implementation efforts in the context of an organization.

• Applications : This article proposes the use of a theoretical framework, the learning organization, by social service organizations. By transforming social service organizations into learning organizations, social service organizations will be able to more effectively meet the challenges of implementing evidence-based programs and function as a bridge, rather than a barrier, between science and service.
Mesenchymal stromal cells cross-present soluble exogenous antigens as part of their antigen-presenting cell properties
Authors: François Moïra , Romieu-Mourez Raphaëlle , Stock-Martineau Sophie , Boivin Marie-Noëlle , Bramson Jonathan L. , Galipeau Jacques
Published: August 2009

Recent studies involving bone marrow mesenchymal stromal cells (MSCs) demonstrated that interferon (IFN)–γ stimulation induces major histocompatibility complex (MHC) class II–mediated antigen presentation in MSCs both in vitro and in vivo. Concordantly, we investigated the ability of MSCs to present extracellular antigen through their MHC class I molecules, a process known as cross-presentation. Using an in vitro antigen presentation assay, we demonstrated that murine MSCs can cross-present soluble ovalbumin (OVA) to naive CD8+ T cells from OT-I mice. Cross-presentation by MSC was proteasome dependent and partly dependent on transporter associated with antigen-processing molecules. Pretreatment of MSC with IFN-γ increased cross-presentation by up-regulating antigen processing and presentation. However, although the transcription of the transporter associated with antigen processing-1 molecules and the immunoproteasome subunit LMP2 induced by IFN-γ was inhibited by transforming growth factor-β, the overall cross-presentation capacity of MSCs remained unchanged after transforming growth factor-β treatment. These observations were validated in vivo by performing an immune reconstitution assay in β2-microglobulin−/− mice and show that OVA cross-presentation by MSCs induces the proliferation of naive OVA-specific CD8+ T cells. In conclusion, we demonstrate that MSCs can cross-present exogenous antigen and induce an effective CD8+ T-cell immune response, a property that could be exploited as a therapeutic cell-based immune biopharmaceutic for the treatment of cancer or infectious diseases.
Generating rate equations for complex enzyme systems by a computer-assisted systematic method
Authors: Qi Feng , Dash Ranjan K , Han Yu , Beard Daniel A
Published: August 2009

Background

While the theory of enzyme kinetics is fundamental to analyzing and simulating biochemical systems, the derivation of rate equations for complex mechanisms for enzyme-catalyzed reactions is cumbersome and error prone. Therefore, a number of algorithms and related computer programs have been developed to assist in such derivations. Yet although a number of algorithms, programs, and software packages are reported in the literature, one or more significant limitation is associated with each of these tools. Furthermore, none is freely available for download and use by the community.

Results

We have implemented an algorithm based on the schematic method of King and Altman (KA) that employs the topological theory of linear graphs for systematic generation of valid reaction patterns in a GUI-based stand-alone computer program called KAPattern. The underlying algorithm allows for the assumption steady-state, rapid equilibrium-binding, and/or irreversibility for individual steps in catalytic mechanisms. The program can automatically generate MathML and MATLAB output files that users can easily incorporate into simulation programs.

Conclusion

A computer program, called KAPattern, for generating rate equations for complex enzyme system is a freely available and can be accessed at http://www.biocoda.org.
Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content
Authors: Maruyama Fumito , Kobata Mitsuhiko , Kurokawa Ken , Nishida Keishin , Sakurai Atsuo , Nakano Kazuhiko , Nomura Ryota , Kawabata Shigetada , Ooshima Takashi , Nakai Kenta , Hattori Masahira , Hamada Shigeyuki , Nakagawa Ichiro
Published: August 2009

Background

Streptococcus mutans is the major pathogen of dental caries, and it occasionally causes infective endocarditis. While the pathogenicity of this species is distinct from other human pathogenic streptococci, the species-specific evolution of the genus Streptococcus and its genomic diversity are poorly understood.

Results

We have sequenced the complete genome of S. mutans serotype c strain NN2025, and compared it with the genome of UA159. The NN2025 genome is composed of 2,013,587 bp, and the two strains show highly conserved core-genome. However, comparison of the two S. mutans strains showed a large genomic inversion across the replication axis producing an X-shaped symmetrical DNA dot plot. This phenomenon was also observed between other streptococcal species, indicating that streptococcal genetic rearrangements across the replication axis play an important role in Streptococcus genetic shuffling. We further confirmed the genomic diversity among 95 clinical isolates using long-PCR analysis. Genomic diversity in S. mutans appears to occur frequently between insertion sequence (IS) elements and transposons, and these diversity regions consist of restriction/modification systems, antimicrobial peptide synthesis systems, and transporters. S. mutans may preferentially reject the phage infection by clustered regularly interspaced short palindromic repeats (CRISPRs). In particular, the CRISPR-2 region, which is highly divergent between strains, in NN2025 has long repeated spacer sequences corresponding to the streptococcal phage genome.

Conclusion

These observations suggest that S. mutans strains evolve through chromosomal shuffling and that phage infection is not needed for gene acquisition. In contrast, S. pyogenes tolerates phage infection for acquisition of virulence determinants for niche adaptation.
Alterations of BCCIP, a BRCA2 interacting protein, in astrocytomas
Authors: Liu Jingmei , Lu Huimei , Ohgaki Hiroko , Merlo Adrian , Shen Zhiyuan
Published: August 2009

Background

Loss of heterozygosity of chromosome 10q26 has been shown to be associated with the aggressiveness of astrocytic tumors (or astrocytomas), but the responsible gene(s) residing in this region has not been fully identified. The BCCIP gene is located at chromosome 10q26. It encodes a BRCA2 and CDKN1A (p21) interacting protein. Previous studies have shown that down-regulation of BCCIP impairs recombinational DNA repair, G1/S cell cycle checkpoint, p53 trans-activation activity, cytokinesis, and chromosome stability, suggesting a potential role of BCCIP in cancer etiology. In this study, we investigated whether BCCIP is altered in astrocytomas.

Methods

Genomic DNA from 45 cases of grade IV astrocytic tumor (glioblastoma) tissues and 12 cases of normal tissues were analyzed by quantitative PCR. The BCCIP protein expression in 96 cases of grade II–IV astrocytic tumors was detected by immunohistochemistry (IHC). IHC staining of glial fibrillary acid protein (GFAP), a marker for astrocytic cells, was used to identify cells of the astrocytic lineage.

Results

We found that BCCIP protein is expressed in normal cells with positive staining of GFAP. However, BCCIP protein expression was not detectable in ~45% of all astrocytic tumors, and in > 60% in the grade IV glioblastoma. About 45% glioblastoma have significant (p < 0.01) reduction of BCCIP gene copy number when compared to normal DNA. Furthermore, the frequency of lacking BCCIP expression is associated with the aggressiveness of astrocytic tumors.

Conclusion

Our data implicate a role of BCCIP in astrocytic tumorigenesis, and lack of BCCIP may be used as a marker for astrocytomas.
Inhibition of HIV-1 entry by extracts derived from traditional Chinese medicinal herbal plants
Authors: Park In-Woo , Han Changri , Song Xiaoping , Green Linden A , Wang Ting , Liu Ying , Cen Changchun , Song Xinming , Yang Biao , Chen Guangying , He Johnny J
Published: August 2009

Background

Highly active anti-retroviral therapy (HAART) is the current HIV/AIDS treatment modality. Despite the fact that HAART is very effective in suppressing HIV-1 replication and reducing the mortality of HIV/AIDS patients, it has become increasingly clear that HAART does not offer an ultimate cure to HIV/AIDS. The high cost of the HAART regimen has impeded its delivery to over 90% of the HIV/AIDS population in the world. This reality has urgently called for the need to develop inexpensive alternative anti-HIV/AIDS therapy. This need has further manifested by recent clinical trial failures in anti-HIV-1 vaccines and microbicides. In the current study, we characterized a panel of extracts of traditional Chinese medicinal herbal plants for their activities against HIV-1 replication.

Methods

Crude and fractionated extracts were prepared from various parts of nine traditional Chinese medicinal herbal plants in Hainan Island, China. These extracts were first screened for their anti-HIV activity and cytotoxicity in human CD4+ Jurkat cells. Then, a single-round pseudotyped HIV-luciferase reporter virus system (HIV-Luc) was used to identify potential anti-HIV mechanisms of these extracts.

Results

Two extracts, one from Euphorbiaceae, Trigonostema xyphophylloides (TXE) and one from Dipterocarpaceae, Vatica astrotricha (VAD) inhibited HIV-1 replication and syncytia formation in CD4+ Jurkat cells, and had little adverse effects on host cell proliferation and survival. TXE and VAD did not show any direct inhibitory effects on the HIV-1 RT enzymatic activity. Treatment of these two extracts during the infection significantly blocked infection of the reporter virus. However, pre-treatment of the reporter virus with the extracts and treatment of the extracts post-infection had little effects on the infectivity or gene expression of the reporter virus.

Conclusion

These results demonstrate that TXE and VAD inhibit HIV-1 replication likely by blocking HIV-1 interaction with target cells, i.e., the interaction between gp120 and CD4/CCR5 or gp120 and CD4/CXCR4 and point to the potential of developing these two extracts to be HIV-1 entry inhibitors.
Comparisons of optically monitored small-scale stirred tank vessels to optically controlled disposable bag bioreactors
Authors: Hanson Michael A , Brorson Kurt A , Moreira Antonio R , Rao Govind
Published: August 2009

Background

Upstream bioprocesses are extremely complex since living organisms are used to generate active pharmaceutical ingredients (APIs). Cells in culture behave uniquely in response to their environment, thus culture conditions must be precisely defined and controlled in order for productivity and product quality to be reproducible. Thus, development culturing platforms are needed where many experiments can be carried out at once and pertinent scale-up information can be obtained.

Results

Here we have tested a High Throughput Bioreactor (HTBR) as a scale-down model for a lab-scale wave-type bioreactor (CultiBag). Mass transfer was characterized in both systems and scaling based on volumetric oxygen mass transfer coefficient (kLa) was sufficient to give similar DO trends. HTBR and CultiBag cell growth and mAb production were highly comparable in the first experiment where DO and pH were allowed to vary freely. In the second experiment, growth and mAb production rates were lower in the HTBR as compared to the CultiBag, where pH was controlled. The differences in magnitude were not considered significant for biological systems.

Conclusion

Similar oxygen delivery rates were achieved in both systems, leading to comparable culture performance (growth and mAb production) across scales and mode of mixing. HTBR model was most fitting when neither system was pH-controlled, providing an information-rich alternative to typically non-monitored mL-scale platforms.
Delaying the onset of experimental autoimmune encephalomyelitis with the microtubule-stabilizing compounds, paclitaxel and Peloruside A
Authors: Crume Kevin P , O’Sullivan David , Miller John H , Northcote Peter T , La Flamme Anne C
Published: August 2009

Microtubule-stabilizing drugs able to delay the onset of CNS disease in an MS mouse model depends on altering both the lymphoid and myeloid cell compartments.

The hallmark of autoimmunity is the activation and proliferation of autoreactive lymphocytes. Therefore, one potential strategy to treat autoimmunity is to target the proliferating autoreactive lymphocytes with antimitotic drugs. Paclitaxel and peloruside are two microtubule-stabilizing drugs that halt cell proliferation by stabilizing microtubules in the G2/M phase of the cell cycle. C57BL/6 mice treated for 5 consecutive days with paclitaxel or peloruside had a reduced incidence and significantly delayed development of EAE, a mouse model of MS. Although paclitaxel and peloruside were effective at inhibiting T cell proliferation in vitro, paclitaxel was shown to be ineffective at preventing the proliferation of autoreactive T cells in vivo during the 5-day treatment period. However, after the 5-day treatment, the ability of splenocytes or LN cells to proliferate in vitro was reduced significantly, suggesting that drug treatment targeted late but not early proliferative events in the animal. Moreover, in paclitaxel-treated, MOG-immunized mice, there was a complete inhibition of the recruitment of myeloid cells (especially macrophages) to the peripheral lymphoid organs. These results indicate that microtubule-stabilizing drugs are effective at reducing disease but require a prolonged exposure to paclitaxel in vivo to alter proliferation in the myeloid and lymphoid cell compartments.
Nup358 interacts with APC and plays a role in cell polarization
Authors: Murawala Prayag , Tripathi Mukesh Mani , Vyas Pankhuri , Salunke Aparna , Joseph Jomon
Published: August 2009

Asymmetric localization of adenomatous polyposis coli (APC) to the ends of a subset of microtubules located in the leading edges is essential for the establishment of front-rear polarity during cell migration. APC is known to associate with microtubules in three ways: through interaction with the plus-end tracking protein EB1, direct binding through a C-terminal basic region, and through interaction with the plus-end motor kinesin-2. Here we report that the middle region of APC has a previously unidentified microtubule plus-end-targeting function, suggesting an additional microtubule-binding mode for APC. Through the same region, APC interacts with Nup358 (also called RanBP2), a microtubule-binding nucleoporin. Ectopic expression of the middle region of APC is sufficient to recruit endogenous Nup358 to the plus ends of microtubules. Furthermore, our results indicate that Nup358 cooperates with kinesin-2 to regulate the localization of APC to the cell cortex through a nuclear-transport-independent mechanism. Using RNA interference and a scratch-induced wound-healing assay we demonstrate that Nup358 functions in polarized cell migration. These results reveal a more active role for structural nucleoporins in regulating fundamental cellular processes than previously anticipated.