bluuebunny/crossref_metadata_2025 huggingface dataset:
Physical and Chemical Deterioration of Reinforced Concrete Reefs in Tongyeong Reefs Coastal Waters, Korea
Authors: Kim H. S. , Kim C. G. , Na W. B. , Woo J. , Kim J. K.
Published: June 2009

As part of a marine habitat enhancement project, the physical and chemical deterioration of reinforced concrete reefs that were fully immersed in Tongyeong waters of Korea was investigated. For the investigation, marine environmental factors such as seawater, salinity, pH, dissolved
oxygen, sea-bottom materials, and water depth of the targeted sites were surveyed from 1997 to 2001. Then, four reinforced concrete reefs from four different sites were recovered and tested by using various destructive and nondestructive methods. Based on the observations and test results,
it was seen that the reinforced concrete reefs have sound physical and chemical properties, except for chloride concentration and its associated factors. However, because of the lack of dissolved oxygen in the targeted seawaters and its continuous supply, it is concluded that the originally
designed service life will be achieved, and in fact the concrete reefs will have an even longer service life than expected. By considering an extreme event such as impact loading under installation and construction, a new minimum concrete cover depth of 40 mm is introduced into practice.
Southeast Atlantic Coastal Ocean Observation System (SEACOOS) Information Management: Evolution of a Distributed Community System
Authors: Fletcher Madilyn , Cleary Jesse , Cothran Jeremy , Porter Dwayne
Published: June 2009

The Southeast Atlantic Coastal Ocean Observing System (SEACOOS) established a comprehensive information management (IM) system, comprising a distributed hardware and software applications infrastructure that enabled access to and processing of complex databases from multiple sites.
Initial focus was on the development of a set of standards for data transport mechanisms, vocabulary, and metadata. Data were organized in a relational database structure, and new developments addressed identified needs, such as more rapid aggregation and posting of near-real-time data. For
presentation of data, map-based products were developed, including both pre-generated, "report-based" maps and interactive maps generated by users at their browsers. Map development was based on parallel developments in database structure, data standards, and data transport mechanisms that
enabled aggregation and normalization of distributed data. The open source MapServer application was used, along with PostgreSQL and its extension PostGIS, as the basic mapping tool. A data animation presentation platform was created that combined maps and graphs with the capacity to select
GIS layers, scale, types of observation to graph, and time steps. Quality Assurance/Quality Control (QA/QC) issues were also addressed, with developments in automated testing of data and filtering and flagging systems. A primary concern of the IM system was to support the path towards interoperability
among national and international ocean observing system elements. Included are "lessons learned" that promote the efficiency and stability of regional systems, such as the need for appropriate redundancy and a focus on region-specific applications that demonstrate value in the relatively near
term.
A Focus on Recent Developments and Trends in Underwater Imaging
Authors: Kocak Donna M. , Dalgleish Fraser R. , Caimi Frank M. , Schechner Yoav Y.
Published: June 2009

Advances in the field of underwater optical imaging are reviewed for the years 2005 to present. A synopsis of research and technical innovations is presented, organized in much the same way as the previous report (Kocak and Caimi, 2005). Several recent applications of novel systems
are shown as examples, and trends in emerging underwater imaging research and development are briefly summarized.
2007 MTS Overview of Manned Underwater Vehicle Activity
Authors: Kohnen William
Published: June 2009

There are approximately 100 active manned submersibles in operation around the world; in this overview we refer to all non-military manned underwater vehicles that are used for scientific, research, tourism, and commercial diving applications, as well as personal leisure craft. The
Marine Technology Society committee on Manned Underwater Vehicles (MUV) maintains the only comprehensive database of active submersibles operating around the world and endeavors to continually bring together the international community of manned submersible operators, manufacturers and industry
professionals. The database is maintained through contact with manufacturers, operators and owners through the Manned Submersible program held yearly at the Underwater Intervention conference.The most comprehensive and detailed overview of this industry is given during the UI conference,
and this article cannot cover all developments within the allocated space; therefore our focus is on a compendium of activity provided from the most dynamic submersible builders, operators and research organizations that contribute to the industry and who share their latest information through
the MTS committee. This article presents a short overview of submersible activity in 2007, including new submersible construction, operation and regulatory activity of research, tourism, commercial diving and recreational applications. The scope of this article is limited to active atmospheric
submersibles, and does not include historical, ambient pressure, or laid-up submersibles, which would be an entire article on its own. For a complete overview that includes submersibles not covered in this article, readers are invited to peruse the MTS Manned Underwater Vehicle online database
at the committee's website (www.mtsmuv.org).
Underwater Acoustic Communications and Networking: Recent Advances and Future Challenges
Authors: Chitre Mandar , Shahabudeen Shiraz , Stojanovic Milica
Published: June 2009

The past 30 years have seen a growing interest in underwater acoustic communications because of its applications in marine research, oceanography, marine commercial operations, the offshore oil industry and defense. Continued research over the years has resulted in improved performance
and robustness as compared to the initial communication systems. In this paper, we aim to provide an overview of the key developments in point-to-point communication techniques as well as underwater networking protocols since the beginning of this decade. We also provide an insight into some
of the open problems and challenges facing researchers in this field in the near future.
Using Fundamental Optical Property Sensors for Characterization of Biogeochemical Materials and Processes in Marine Waters
Authors: Moore Casey
Published: June 2009

Over the past ten years, efforts to characterize the optical properties of Earth's natural waters have largely merged with the need to better understand underlying biological and chemical processes. Fundamental optical properties such as light level, absorption, scattering and fluorescence
are now being utilized with increasing effectiveness to specify particulate and dissolved in-water components in a wide range of applications, including detection of harmful algal blooms, studying ecosystem dynamics, monitoring the effect of industrial and agricultural pollutants, and understanding
carbon sequestration processes in the oceans. A diverse offering of commercial optical sensing products capable for research, routine measurements, and in some cases, operational monitoring are now available. These technologies have provided the scientific community with a set of tools for
developing, testing, and placing into practice analytical and semi-analytical methods to infer specific biogeochemical parameters and processes. As a result, new, more specialized sensors are now emerging. New sensors couple basic optical property measurements with processing algorithms to
provide specific indicators for Harmful Algal Bloom (HAB) identification, carbon products, nutrients, and particle size distributions. The basic measurement methods are described and examples of devices incorporating them are provided to illustrate their use in modern oceanographic research
and monitoring.
Observations of the Middle Island Sinkhole in Lake Huron – A Unique Hydrogeologic and Glacial Creation of 400 Million Years
Authors: Ruberg Steven A. , Kendall Scott T. , Biddanda Bopaiah A. , Black Tyrone , Nold Stephen C. , Lusardi Wayne R. , Green Russ , Casserley Tane , Smith Elliott , Sanders Garrison T. , Lang Gregory A. , Constant Stephen A.
Published: June 2009

In the northern Great Lakes region, limestone sediments deposited some 400 million ybp during the Devonian era have experienced erosion, creating karst features such as caves and sinkholes. The groundwater chemical constituents of the shallow seas that produced these rock formations
now contribute to the formation of a unique physical (sharp density gradients), chemical (dissolved oxygen-depleted, sulfate-rich) and biological (microbe-dominated) environment in a submerged sinkhole near Middle Island in freshwater Lake Huron. A variety of methods including aerial photography,
physico-chemical mapping, time series measurements, remotely operated vehicle (ROV) survey, diver observations and bathymetric mapping were employed to obtain a preliminary understanding of sinkhole features and to observe physical interactions of the system's groundwater with Lake Huron.
High conductivity ground water of relatively constant temperature hugs the sinkhole floor creating a distinct sub-ecosystem within this Great Lakes ecosystem. Extensive photosynthetic purple cyanobacterial benthic mats that characterize the benthos of this shallow sinkhole were strictly limited
to the zone of ground water influence.
Patterns in the Local Distribution of the Sea Whip, Halipteris willemoesi, in an Area Impacted by Mobile Fishing Gear
Authors: Lindholm James , Kelly Megan , Kline Donna , de Marignac Jean
Published: June 2009

While conducting a larger project along the continental shelf off central California in June 2006, we encountered a large patch of sea whips (Halipteris willemoesi) in an area that was actively fished by vessels using otter trawls. A total of 10 transects were conducted using
a remotely operated vehicle (ROV) to collect video imagery of seafloor communities. Video records allowed us to quantify sea whip density and to calculate the densities of upright and damaged or broken sea whips. Though the transects were sited within a dense aggregation of trawl tracks, we
recorded significant variability in sea whip densities across transects. While subtle differences in water depth among transects may have contributed to the variability in sea whip density, we suggest that the distribution of trawling effort is a more likely explanation.
Search for the Bonhomme Richard Using Computer Modeling and Submarine Technologies
Authors: Ryan Melissa S. , McGrath John P.
Published: June 2009

The Ocean Technology Foundation and Naval Historical Center have been searching for the remains of the Bonhomme Richard, which sank in the western North Sea as a casualty of the American Revolution. Historical information about the ship's final resting place is lacking, but its
activities up until the sinking are well documented. The results of many years of historical research have been incorporated into computer modeling programs, and a Geographic Information System (GIS) map was created to document all known information on shipwreck locations, seabed geology,
and other pertinent information to enable the most effective survey. A recent survey expedition utilized the U.S. Navy's nuclear research submarine NR-1 to search nearly 400 square nautical miles of the North Sea. This paper focuses on the technological tools used in the search for
the Bonhomme Richard: computer modeling, GIS, and submarine technologies. It also discusses the benefits and drawbacks of using a submarine to conduct marine archaeological surveys. The expedition yielded insights into the strengths and limitations of computerized drift modeling, especially
when used to reconcile empiric environmental data with conflicting eyewitness accounts.
Estimation of Chlorophyll-a Concentrations in the Pearl River Estuary Using In Situ Hyperspectral Data: A Case Study
Authors: Xing Qianguo , Chen Chuqun , Shi Heyin , Shi Ping , Zhang Yuanzhi
Published: June 2009

Taking Pearl River Estuary (PRE), China as an example, we explored the potential of in situ hyperspectral data in estimating chlorophyll-a concentrations of turbid waters. Two cruises were conducted on August 21, 2006 and May 18, 2004 to collect the data of water quality and
remote sensing reflectance (Rrs). The field surveys showed that: chlorophyll-a concentration ranged from 2.97μg/L to 49.97μg/L, and turbidity 13.6-128.9 NTU. The Rrs spectra were binned to 10 nm resolution, and then processed to be first-order and second-order derivatives. A linear algorithm
is developed to estimate chlorophyll-a concentrations based on second-order derivative at 670 nm; its mean relative error of estimation is less than 58%, and the root mean square error is 6.69 μg/L, which is better than other popular algorithms for turbid waters, i.e., the ratio of Rrs
at 700 nm and 670 nm. The Case-I algorithm of blue-green band ratio is also proved to be a failed application in PRE, and so does the algorithm of fluorescence line height (FLH), which is questionable for its application in waters with strong light scattering and absorption. All the above
work was done without classification of cloud conditions. This suggests that the second-order derivative at 670 nm could be effective for estimation of chlorophyll-a concentrations in turbid waters, especially in situ.
An Active Operator Guidance System for Ship Maneuvers—Prototype System
Authors: Ong M. C. , Lim Arthur T. B. , Lee Selina C. C. , Lo Edmond Y. M. , Tan S. K.
Published: June 2009

This paper presents an Active Operator Guidance System (AOGS) that has been developed as a guidance tool for operators on safe maneuvering of container ships in coastal and deep waters. The system is capable of predicting ship trajectories in surge, sway and yaw motions, accounting
for the effects of current, wind and water depth as well as ship command parameters on rudder and propeller. Operators can, in actual sea conditions, actively assess trial commands on various control-input scenarios and predicted ship trajectory responses under those ambient sea conditions.
The predicted parameters of vessel response, such as track reach, turning circle and overshoot, are displayed graphically on the system console to provide guidance on any potential dangers. The system has been validated and verified for a container ship with sea trial data from its ship manual
and actual sea voyage data. Comparisons between the predictions and data are in reasonable agreement.
Demonstration of a New Technology for Restoration of Red Mangrove (Rhizophora mangle) in High-Energy Environments
Authors: Krumholz Jason , Jadot Catherine
Published: June 2009

AbstractRestoration of red mangroves (Rhizophora mangle) in high-energy environments has proven difficult in the past, but it is a critical aspect of restoration science, since mangroves provide natural protection to shorelines and buffer sensitive near-shore tropical
ecosystems. We present here the initial field results from a pilot test of a new technique for the restoration of R. mangle in high-energy environments, using anchored armored concrete cultivator pots to stabilize the juvenile mangrove until it can establish a network of buttress roots.
Mangroves were reared in a nursery for 15 months before transplantation to fully and partially exposed field sites. Mangroves transplanted in this way on Grand Cayman Island were able to survive two direct hurricane hits shortly after transplantation during the hurricane season of 2008, with
survival rates ranging from 42% to 73% depending on the exposure of the site. We discuss the implications of these results and a proposed revision to our technique, which we hope will eliminate the work-intensive and costly nursery phase while also facilitating higher survival rates by minimizing
washout, which was a key source of mortality, accounting for 20%-50% of mortalities, depending on site.
Evaluation of Dynamic Analysis Methods for Seismic Analysis of Drydocks
Authors: Kubic Charles
Published: June 2009

AbstractThree numerical methods are used to model the structural response of Bremerton drydock no. 6 to the 2001 Nisqually earthquake. The models considered include: (1) a numerical linear-elastic soil response model, (2) a numerical non-linear time-history response model,
and (3) a non-linear finite element model. The results of the models are compared to the observed drydock response and each other in order to determine their effectiveness in modeling drydock structures. The research demonstrated that the non-linear finite element program PLAXIS is suitable
for the seismic analysis of drydocks. In addition, the research showed that the existing United States Army Corps of Engineers program CorpsWallROTATE is not suited for the dynamic analysis of drydocks; while a method developed by Wood in 1973 could be further developed
to be used as a linear approximation of the drydock’s time-history seismic response. The research is presented to assist in the development of comprehensive seismic drydock design standards.
Cluster Space Control of Autonomous Surface Vessels
Authors: Mahacek Paul , Mas Ignacio , Petrovic Ognjen , Acain Jose , Kitts Christopher
Published: June 2009

AbstractMulti-robot systems offer many advantages over a single-robot system, including redundancy, coverage and flexibility. One of the key technical considerations in fielding multi-robot systems for real-world applications is the coordination of the individual units. The
cluster space control technique promotes simplified specification and monitoring of the motion of mobile multi-robot systems. Previous work has established this approach and has experimentally verified its use for land-based systems consisting of 2-4 robots and with varying implementations
ranging from automated trajectory control to human-in-the-loop piloting. In this paper, we describe the design and fabrication of a new low-cost autonomous surface vessel (ASV). The technical system includes a multi-boat system capable of autonomous navigation using the cluster space control
technique. It also includes a centralized controller, currently implemented via a shore-based computer that wirelessly receives ASV data and relays drive commands. Using the cluster space control approach, these drive commands allow a pilot to remotely drive a two-ASV cluster or to specify
that the two ASVs maintain formation with a third boat. The resulting multi-ASV clusters can be arbitrarily translated, rotated, and resized depending on the needs of a specific application. Experimental results demonstrating these capabilities are provided, and plans for future work are discussed.
Trends in Emerging Tidal and Wave Energy Collection Technology
Authors: Price Rachel
Published: June 2009

AbstractTo facilitate the evaluation of the current status of tidal and wave technologies, several characteristics that would be required for them to become attractive as alternative sources of energy are defined and identified. Tidal technologies, including barrages, fences,
and turbines; and wave technologies, including the oscillating water columns, Pelamis, tapered channel, Salter Duck, and the Clam, are explained and evaluated in terms of their operating complexity, economic concerns, and environmental impact. Current implementations of each technology are
discussed. The current cost per kilowatt-hour for each technology is compared to that for coal and nuclear energy. The environmental impacts of the technologies are compared and evaluated. Finally, the technologies are compared with respect to the desirable features that were initially identified.
ICCAT: Managing or Documenting?
Authors: Straker Leslie E.
Published: June 2009

AbstractThe International Commission for the Conservation of Atlantic Tunas (ICCAT) is one of the oldest regional fisheries management organizations in the business of providing stewardship to the management of high-seas fish stocks. The Commission came into force in 1969
with eight parties and today consists of 45 contracting parties. Notwithstanding nearly 40 years of experience, this organization is also confronted with the problems of over-exploitation; over-capacity; illegal, unregulated and unreported fishing; lack of adequate scientific information;
and the continued decline in important high-seas fish stocks.Despite the moribund state of fish stocks in the ICCAT convention area, the organization has made significant progress with respect to the collection and analysis of fisheries information, recommendations to its parties and the
dissemination of this information, all key parts of its broader objective. Nonetheless, the organization has failed to make substantial progress with regard to translating a good analysis and documenting process to the effective conservation of tuna and tuna-like species in the Atlantic. That
is, the organization has failed to “close the loop” in management. The question therefore becomes, is the ICCAT merely functioning as a “documenting” organization rather than a “management” organization? This study examines the current state of fisheries
stocks in the convention area, the extent to which the Commission is meeting its own mandate, and the extent to which the management principles of the 1982 United Nations Convention on the Law of the Sea and the United Nations Fish Stocks Agreement are being followed by ICCAT.
ROV Pontus
Authors: Bragg Jake , Brockerville Leanne , Brown Trevor , Button Cait , Crewe Stephen , Doyle Gina , Flynn Mark , Follett Matthew , Follett Scott , Freeman Mikhail , Furneaux Andrew , Higdon Justin , Hillier Nancy , Hornell David , Howse Jonathan , Lewis Adam , MacNeil Pam , Minay-Goldring Matthew , Neville Chris , Pennell Joseph , Picco Wally , Quick Renee , Walsh Devin , Waterman Erin , Watson Jonathan
Published: June 2009

AbstractThis technical report describes the remotely operated vehicle (ROV) Pontus, built by the Eastern Edge Robotics Team to compete in the 2008 MATE International ROV Competition. The basis of the chassis is two fiberglass pontoons connected by high-density polyethylene
frames. The ROV uses four 24-V thrusters and a stereoscopic camera. The ROV has two pistons to hold and lift objects and a thermistor to record temperature. The control system was programmed in C# and runs using seven threads that sample data continuously. The ROV has an onboard electronics
system that is inside a polycarbonate housing connected to the surface using a custom-built tether. The topsides electronics consist of a joystick and a control unit. To build the ROV, the team learned new technical skills, like fiberglassing and programming Programmable Intelligent Computer
(PIC) controllers. Eastern Edge Robotics Team came in first place overall in the Explorer (university/college) class at the 2008 MATE Competition, winning first place in their mission tasks, first place in technical report and first place for their engineering evaluation.
Differential Association of Programmed Death-1 and CD57 with Ex Vivo Survival of CD8+ T Cells in HIV Infection
Authors: Petrovas Constantinos , Chaon Benjamin , Ambrozak David R. , Price David A. , Melenhorst J. Joseph , Hill Brenna J. , Geldmacher Christof , Casazza Joseph P. , Chattopadhyay Pratip K. , Roederer Mario , Douek Daniel C. , Mueller Yvonne M. , Jacobson Jeffrey M. , Kulkarni Viraj , Felber Barbara K. , Pavlakis George N. , Katsikis Peter D. , Koup Richard A.
Published: June 2009

Recent studies have revealed the critical role of programmed death-1 (PD-1) in exhaustion of HIV- and SIV-specific CD8+ T cells. In this study, we show that high expression of PD-1 correlates with increased ex vivo spontaneous and CD95/Fas-induced apoptosis, particularly in the “effector-memory” CD8+ T cell population from HIV+ donors. High expression of PD-1 was linked to a proapoptotic phenotype characterized by low expression of Bcl-2 and IL7-Rα, high expression of CD95/Fas and high mitochondrial mass. Expression of PD-1 and CD57 was differentially associated with the maturation status of CD8+ T cells in HIV infection. CD57 was linked to higher apoptosis resistance, with cells expressing a PD-1LCD57H phenotype exhibiting lower levels of cell death. The majority of HIV-specific CD8+ T cells were found to express a PD-1HCD57L or PD-1HCD57H phenotype. No correlation was found between PD-1 expression and ex vivo polyfunctionality of either HIV- or CMV-specific CD8+ T cells. Contrary to CD57, high expression of PD-1 was characterized by translocation of PD-1 into the area of CD95/Fas-capping, an early necessary step of CD95/Fas-induced apoptosis. Thus, our data further support the role of PD-1 as a preapoptotic factor for CD8+ T cells in HIV infection.
The Induction of IL-10 by Zymosan in Dendritic Cells Depends on CREB Activation by the Coactivators CREB-Binding Protein and TORC2 and Autocrine PGE2
Authors: Alvarez Yolanda , Municio Cristina , Alonso Sara , Sánchez Crespo Mariano , Fernández Nieves
Published: June 2009

Stimulation of human monocyte-derived dendritic cells with the yeast extract zymosan is characterized by a predominant production of IL-10 and a strong induction of cyclooxygenase-2, but the molecular mechanisms underlying this response are only partially understood. To address this issue, the activation of transcription factors that may bind to the il10 proximal promoter was studied. Binding activity to Sp1, Sp3, NF-Y, and cAMP response element (CRE) sites was detected in the nuclear extracts of dendritic cells; however these binding activities were not influenced by zymosan. No binding activity to Stat1, Stat3, and c/EBP sites was detected. Notably, zymosan activated κB-binding activity, but inhibition of NF-κB was associated with enhanced IL-10 production. In sharp contrast, treatments acting on CREB (CRE binding protein), including 8-Br-cAMP, PGE2, and inhibitors of PKA, COX, and glycogen-synthase kinase-3β showed a direct correlation between CREB activation and IL-10 production. Zymosan induced binding of both P-CREB and CREB-binding protein (CBP) to the il10 promoter as judged from chromatin immunoprecipitation assays, whereas negative results were obtained with Ab reactive to Sp1, Sp3, c-Maf, and NF-Y. Zymosan also induced nuclear translocation of the CREB coactivator transducer of regulated CREB activity 2 (TORC2) and interaction of TORC2 with P-CREB coincidental with the association of CREB to the il10 promoter. Altogether, our data show that zymosan induces il10 transcription by a CRE-dependent mechanism that involves autocrine secretion of PGE2 and a network of interactions of PKA, MAP/ERK, glycogen-synthase kinase-3β, and calcineurin, which regulate CREB transcriptional activity by binding the coactivators CBP and TORC2 and inhibiting CBP interaction with other transcription factors.
Regulation of Dendritic Cells and Macrophages by an Anti-Apoptotic Cell Natural Antibody that Suppresses TLR Responses and Inhibits Inflammatory Arthritis
Authors: Chen Yifang , Khanna Sahil , Goodyear Carl S. , Park Yong Beom , Raz Eyal , Thiel Steffen , Grönwall Caroline , Vas Jaya , Boyle David L. , Corr Maripat , Kono Dwight H. , Silverman Gregg J.
Published: June 2009

Although natural Abs (NAbs) are present from birth, little is known about what drives their selection and whether they have housekeeping functions. The prototypic T15-NAb, first identified because of its protective role in infection, is representative of a special type of NAb response that specifically recognizes and forms complexes with apoptotic cells and which promotes cell-corpse engulfment by phagocytes. We now show that this T15-NAb IgM-mediated clearance process is dependent on the recruitment of C1q and mannose-binding lectin, which have known immune modulatory activities that also provide “eat me” signals for enhancing phagocytosis. Further investigation revealed that the addition of T15-NAb significantly suppressed in vitro LPS-induced TNF-α and IL-6 secretion by the macrophage-like cell line, RAW264.7, as well as TLR3-, TLR4-, TLR7-, and TLR9-induced maturation and secretion of a range of proinflammatory cytokines and chemokines by bone marrow-derived conventional dendritic cells. Significantly, high doses of this B-1 cell produced NAb also suppressed in vivo TLR-induced proinflammatory responses. Although infusions of apoptotic cells also suppressed such in vivo inflammatory responses and this effect was associated with the induction of high levels of IgM antiapoptotic cell Abs, apoptotic cell treatment was not effective at suppressing such TLR responses in B cell-deficient mice. Moreover, infusions of T15-NAb also efficiently inhibited both collagen-induced arthritis and anti-collagen II Ab-mediated arthritis. These studies identify and characterize a previously unknown regulatory circuit by which a NAb product of innate-like B cells aids homeostasis by control of fundamental inflammatory pathways.
Squamous Cell Carcinoma of the Scrotum in a Nigerian: Case Report
Authors: Azike Jerome E. , Chukwujama N.O. , Oguike T.C.
Published: June 2009

Squamous cell carcinoma of the scrotum is rare and to the best of our knowledge has never been reported from Nigeria. We report on a case thought to be occupation-related in a 42-year-old Nigerian taxi driver who had previously been an automobile mechanic and later a long-haul truck driver. He presented with a stage D disease and only palliation was feasible.
Health care for under-fives in Ile-Ife, South-West Nigeria: Effect of the Integrated Management of Childhood Illnesses (IMCI) strategy on growth and development of under-fives
Authors: Ebuehi Olufunke M.
Published: June 2009

Background: The study obtained information on key growth promotion and developmental household and community health practices in Community-Integrated Management of Childhood Illnesses (C-IMCI) and non-C-IMCI in local government areas (LGAs) in Osun State, Nigeria, to determine the differences that existed, between these LGAs.Method: A cross-sectional comparative study to compare Integrated Management of Childhood Illnesses (IMCI) key growth promotion and development health practices in two LGAs in Osun State was conducted using quantitative and qualitative techniques. Data analysis was done using Epi Info version 6.0 for the quantitative survey and a content analysis method for the qualitative survey. The subjects were mothers or caregivers of children 0–59 months of age, and their index children.Results: Findings revealed that the IMCI key growth and development health practices were generally better rated in the CIMCI-compliant LGA than in the non-CIMCI compliant LGA. Breastfeeding practice was widespread in both LGAs. However, the exclusive breastfeeding (EBF) rate among children under six months was higher in the compliant LGA (66.7%) than in the non-compliant LGA (25%). More caregivers (59.7%) from the non-compliant LGA introduced complementary feeds earlier than six months. Growth monitoring activities revealed that there were more underweight children (19.1%) in the non-compliant LGA. Community Resource Persons (CORPs) and health workers were the most popular sources of information on IMCI key practices in the compliant LGA, while in the non-compliant LGA the traditional healers, elders and, to a lesser extent, health workers provided information on these key practices.Conclusion: The IMCI strategy, if well implemented, is an effective and low-cost intervention that is useful in achieving optimal growth, development and survival of Nigerian children.
Impact of demographic and psychosocial factors on hysterosalpingography pain and discomfort
Authors: Ugwu Anthony C. , Imo Augustine O. , Erondu Okey F.
Published: June 2009

Background: Hysterosalpingography (HSG) is an important diagnostic procedure in the investigation of infertility. It is the radiographic delineation of uterine and tubal cavities and is part of the diagnostic evaluation of conjugal infertility. This diagnostic procedure is associated with high levels of anxiety, pain and stress from various causes. This study was designed to investigate the impact of demographic and psychosocial factors on HSG pain and discomfort.Objective: The objective of this study was to determine the impact of demographic and psychosocial factors on hysterosalpingography pain and discomfort.Method: One hundred hysterosalpingography referrals were recruited for this study. Verbal detector scales were used to assess pain perception, Likert scales were used to assess the psychosocial variables, while visual analogue scales were used to assess discomfort. Pearson’s correlations were conducted. Tests were two-tailed, with p < 0.05 indicating statistical signifcance.Results: Some of the patients (34%) indicated that the administration of analgesics prior to the procedure reduced the pain and discomfort associated with the procedure. Mean ± standard deviation of pain and discomfort were 2.82 ± 0.77 and 6.36 ± 2.19 respectively. Age correlated signifcantly with pain perception (r = -0.22, P < 0.05), while pain correlated signifcantly with perception of discomfort (r = -0.46, P < 0.05).Conclusion: Age signifcantly correlated with pain. This is a factor that could be harnessed for clinical use.
Using NCBI BLAST
Authors: Stover Nicholas A. , Cavalcanti Andre R.O.
Published: June 2009

BLAST is the most widely used software in bioinformatics research. Its main function is to compare a sequence of interest, the query sequence, to sequences in a large database. BLAST then reports the best matches, or “hits,” found in the database. This simple program has two primary applications. First, if the function of the query sequence is unknown, it may be possible to infer its function based on the recognized functions of similar sequences. Second, if the researcher has a query sequence with a known function, it may be possible to identify sequences in the database that have similar functions. The utility of BLAST therefore depends on the researcher's choice of query sequence and database. An appreciation for the functions and limitations of BLAST are vital to using this program effectively. This unit will introduce the basic concepts behind BLAST, walk through BLAST searching protocols, and interpret common results. Curr. Protoc. Essential Lab. Tech. 1:11.1.1‐11.1.36. © 2009 by John Wiley & Sons, Inc.
Submitting a Sequence to GenBank
Authors: Chang Wei‐Jen , Coppola Thomas W.
Published: June 2009

In the post‐genomic era, more and more research projects involve the generation of molecular sequence data. How should these newly obtained DNA/protein sequences be analyzed, and how should they be prepared for submission to sequence databases? In this unit, we provide guidelines and a flow chart to help first‐time users process new sequence data using third‐party freeware programs and give a step‐by‐step demonstration on the preparation of a sequence file for submission to GenBank using the Sequin program. Curr. Protoc. Essential Lab. Tech. 1:11.2.1‐11.2.20. © 2009 by John Wiley & Sons, Inc.
Beyond Simple Homology Searches: Multiple Sequence Alignments and Phylogenetic Trees
Authors: Zufall Rebecca A.
Published: June 2009

Phylogenetic trees represent hypotheses about evolutionary relationships between organisms or nucleotide or amino acid sequences. Because the best BLAST hit often does not represent the most closely related sequence, phylogenetic analyses are an essential extension of inquiry into any new protein or gene. In this unit, the reader will first learn how to create a multiple sequence alignment using ClustalX. He or she will then learn how to use that alignment to build a neighbor‐joining phylogeny using the program Geneious. Finally, the user will learn how to interpret the phylogeny in light of the research questions. Curr. Protoc. Essential Lab. Tech. 1:11.3.1‐11.3.17. © 2009 by John Wiley & Sons, Inc.
Using Model Organism Databases (MODs)
Authors: Engel Stacia R.
Published: June 2009

Model Organism Databases (MODs) represent the union of database technology and biology, and are essential to modern biological and medical research. Research communities are producing floods of new data, of increasingly different types and complexity. MODs assimilate this information from a wide variety of sources, organize it in a comprehensible manner, and make it freely available to the public via the Internet. MODs permit researchers to sort through massive amounts of data, providing access to key information that they might otherwise have overlooked. The protocols in this unit offer a general introduction to different types of data available in the growing number of MODs, and approaches for accessing, browsing, and querying these data. Curr. Protoc. Essential Lab. Tech. 1:11.4.1‐11.4.17. © 2009 by John Wiley & Sons, Inc.
Risk Assessment in the Research Laboratory
Authors: Burnett LouAnn C.
Published: June 2009

Risk assessment is a term that is applied to a process that we all use every day to make decisions. Conducting risk assessments while working in the laboratory should be integrated into the research culture. Reagents and equipment used in research laboratories can be hazardous if used improperly or without appropriate precautions. The first step in limiting risk is identifying the materials that can be hazardous. The second step is to assess the risk that they present during the experiments that will take place—a process called risk assessment. Once the hazards are identified and the risks assessed, a risk management strategy can be put in place to reduce the risks to an acceptable level. This process (hazard identification, risk assessment, risk management) must be repeated as often as new materials, new procedures, and new people are introduced into the laboratory. Curr. Protoc. Essential Lab. Tech. 1:A.1B.1‐A.1B.11. © 2009 by John Wiley & Sons, Inc.
Simulation of a slurry‐bubble column reactor for Fischer‐Tropsch synthesis using single‐event microkinetics
Authors: Lozano‐Blanco Gisela , Thybaut Joris W. , Surla Karine , Galtier Pierre , Marin Guy B.
Published: June 2009

A single‐event microkinetic model for Fischer‐Tropsch synthesis including the water‐gas shift reaction has been implemented in a one‐dimensional, two‐bubble class, heterogeneous model with axial effective diffusion to study the performance of a commercial slurry bubble column reactor. Mass balance equations are solved for every species in the reaction network in the large bubbles, small bubbles, and slurry phase, whereas the energy balance is applied to the slurry phase. The catalyst concentration profile is described by a sedimentation‐dispersion model. The combination of microkinetics that generate net production rates for the individual reaction products and hydrodynamics allows describing detailed concentration profiles along the reactor axis as a function of operating conditions and design parameters. As example, the effects of catalyst loading, syngas feed flow rate, inlet temperature, or hydrogen to carbon monoxide inlet ratio on the individual hydrocarbons are investigated. To our knowledge, no reactor model in literature is able to describe detailed compositions at the level described by the reactor model developed in this work. © 2009 American Institute of Chemical Engineers AIChE J, 2009
Scheduling multistage batch plants with sequence‐dependent changeovers
Authors: Castro Pedro M. , Novais Augusto Q.
Published: June 2009

This article deals with the optimal short‐term scheduling of multistage batch plants with parallel units and sequence‐dependent changeovers, together with the optimal selection of the number and size of batches to be produced. A new resource‐task network‐based, multiple time‐grid continuous‐time formulation is proposed that explicitly considers a virtual, shared, intermediate storage unit per stage to keep track of material transfer between processing units belonging to consecutive stages of production. Adequate material transfer is implicitly ensured through mass balances and timing constraints relating the times of event points of dissimilar grids. The new formulation is compared with a conceptually different approach from another research group. The results for several example problems show that the new formulation is tighter, typically requiring fewer event points to find the global optimal solution, and is significantly more efficient computationally. The results also show that for single batch problems other approaches are preferable. © 2009 American Institute of Chemical Engineers AIChE J, 2009
Discrete element simulation of free flowing grains in a four‐bladed mixer
Authors: Remy Brenda , Khinast Johannes G. , Glasser Benjamin J.
Published: June 2009

Numerical simulations of granular flow in a cylindrical vessel agitated by a four‐blade impeller were performed using the discrete element method. Velocity, density, and stress profiles within the mixer displayed a periodic behavior with a fluctuation frequency equal to that of the blade rotation. Blade orientation was found to affect flow patterns and mixing kinetics. For an obtuse blade pitch orientation, a three‐dimensional recirculation zone develops in‐front of the blade due to formation of heaps where the blades are present. This flow pattern promotes vertical and radial mixing. No recirculation zone was observed when the blade orientation was changed to an acute blade pitch. The system's frictional characteristics are shown to strongly influence the granular behavior within the mixer. At low friction coefficients, the 3‐D recirculation in front of the obtuse blade is not present reducing convective mixing. Higher friction coefficients lead to an increase in granular temperature which is associated with an increase in diffusive mixing. Normal and shear stresses were found to vary with mixer height with maximum values near the bottom plate. Additionally, a strong dependence between the magnitude of the shear stresses and the friction coefficient of the particles was found. The stress tensor characteristics indicate that the granular flow in our simulations occurs in the quasi‐static regime. At the same time, the averaged pressure was found to vary linearly with bed height and could be predicted by a simple hydrostatic approximation. © 2009 American Institute of Chemical Engineers AIChE J, 2009
Oscillating migration and the epidemics of silicosis, tuberculosis, and HIV infection in South African gold miners
Authors: Rees David , Murray Jill , Nelson Gill , Sonnenberg Pam
Published: June 2009

Background

Hundreds of thousands of men from rural areas of South Africa and neighboring countries have come to seek work in the gold mines. They are not immigrants in the usual sense as they work for periods in the mines, go home, and then return. This is termed oscillating or circular migration. Today we have serious interrelated epidemics of silicosis, tuberculosis, and HIV infection in the gold mining industry.

Methods

This article discusses the role of oscillating migration in fuelling these epidemics, by examining the historical, political, social, and economic contexts of these diseases.

Results

The impact of silicosis, tuberculosis, and HIV infection extends beyond individual miners to their families and communities.

Conclusion

Failure to control dust and tuberculosis has resulted in serious consequences decades later. The economic and political migrant labor system provided the foundations for the epidemics seen in southern Africa today. Am. J. Ind. Med. 53:398–404, 2010. © 2009 Wiley‐Liss, Inc.
Copeptin: A novel, independent prognostic marker in patients with ischemic stroke
Authors: Katan Mira , Fluri Felix , Morgenthaler Nils G. , Schuetz Philipp , Zweifel Christian , Bingisser Roland , Müller Klaus , Meckel Stephan , Gass Achim , Kappos Ludwig , Steck Andreas J. , Engelter Stefan T. , Müller Beat , Christ‐Crain Mirjam
Published: June 2009

Objective

Early prediction of outcome in patients with ischemic stroke is important. Vasopressin is a stress hormone. Its production rate is mirrored in circulating levels of copeptin, a fragment of provasopressin. We evaluated the prognostic value of copeptin in acute stroke patients.

Methods

In a prospective observational study, copeptin was measured using a new sandwich immunoassay on admission in plasma of 362 consecutive patients with an acute ischemic stroke. The prognostic value of copeptin to predict the functional outcome (defined as a modified Rankin Scale score of ≤2 or ≥3), mortality within 90 days, was compared with the National Institutes of Health Stroke Scale score and with other known outcome predictors.

Results

Patients with an unfavorable outcomes and nonsurvivors had significantly increased copeptin levels on admission (p <0.0001 and p <0.0001). Receiver operating characteristics to predict functional outcome and mortality demonstrated areas under the curve of copeptin of 0.73 (95% confidence interval [CI], 0.67–0.78) and 0.82 (95% CI, 0.76–0.89), which was comparable with the National Institutes of Health Stroke Scale score but superior to C‐reactive protein and glucose (p <0.01). In multivariate logistic regression analysis, copeptin was an independent predictor of functional outcome and mortality, and improved the prognostic accuracy of the National Institutes of Health Stroke Scale to predict functional outcome (combined areas under the curve, 0.79; 95% CI, 0.74–0.84; p <0.01) and mortality (combined areas under the curve, 0.89; 95% CI, 0.84–0.94; p <0.01).

Interpretation

Copeptin is a novel, independent prognostic marker improving currently used risk stratification of stroke patients. Ann Neurol 2009;66:799–808
Chronic inflammatory demyelinating polyneuropathy sera inhibit axonal growth of mouse dorsal root ganglion neurons by activation of rho‐kinase
Authors: Taniguchi Junko , Sawai Setsu , Mori Masahiro , Kubo Takekazu , Kanai Kazuaki , Misawa Sonoko , Isose Sagiri , Yamashita Toshihide , Kuwabara Satoshi
Published: June 2009

Clinical course and prognosis are variable among patients with chronic inflammatory demyelinating polyneuropathy (CIDP), whereas the extent of axonal degeneration is the major prognostic factor. We studied the effects of sera from CIDP patients on axonal growth in cultured mouse dorsal root ganglion neurons. Compared with control sera, CIDP sera prominently suppressed axonal outgrowth of dorsal root ganglion neurons and shortened axonal length. The inhibitory activity was abolished by adding Y27632, a Rho‐kinase inhibitor. These findings suggest that CIDP sera inhibit axonal elongation by Rho‐kinase activation, and some serum factors may be responsible for development of axonal degeneration in CIDP. Ann Neurol 2009;66:694–697