bluuebunny/crossref_metadata_2025 huggingface dataset:
Nutrient composition and physicochemical characteristics in the destination sites of migratory water birds: a case study at the selected locations of seashores and lakes in southern India
Authors: Augustine Cyril , George James Baben , Cyril Neethu , Mary MC
Published: February 2014

The biodiversity in aquatic systems are indirectly controlled by their nutrient dynamics. The abundance of phytoplanktons and zooplanktons depends on the availability of nutrients such as nitrates, phosphates and silicates since these are the building blocks for their further growth. The phytoplanktons act as prey for the next higher trophic level including various fishes and other small organisms. One of the factors that enchant the migratory birds at some particular locations is the availability of the species of organisms that they prey on. In this paper a preliminary analysis is done to explore the nutrient dynamics of selected tropical aquatic systems in order to correlate the arrival of migratory birds at those locations. Water samples are collected from coastal region of Aleppey, Purakkad and Koonthankulam Bird Sancturay. The latter two sites are the important destination of many migratory water birds including Pallus Gull, Heuglins Gull, Bar-headed goose, Comb Duck and Spot Billed Pelican. The samples are analyzed chemically to trace the nutrient compositions and the related chemical parameters such as temperature, pH, conductivity, primary productivity, chloride, salinity, turbidity, nitrate, phosphate, dissolved oxygen and biochemical oxygen demand. Remarkable differences are observed mainly in the composition of phosphate, organic matter content and salinity. Finally, an attempt has been done to correlate the biodiversity of these locations with the chemical parameters and the prevailing nutrient compositions. DOI: http://dx.doi.org/10.3126/ije.v3i1.9943 International Journal of Environment Vol.3(1) 2014: 68-77
Occurrence of zooplanktons at Sacred Palustrine Habitat, Central Gujarat, India, with conservation and management strategies
Authors: Soni Hiren B , Thomas Sheju
Published: February 2014

The aim of the present study was to represent the zooplankton composition of Sacred Palustrine Habitat (SPH), Anand District, Central Gujarat, India. Collections of zooplanktons were carried out at three permanent sampling stations at fortnight intervals over one year period covering three consecutive seasons from June 2012 to May 2013. The zooplankton population was represented by a total of 29 genera and 31 species bestowed by 12 species of Ciliophora, followed by Rhizopoda (6), Zooflagellata (5), Rotifera (4), Cladocera (2), Copepoda and Ostracoda (1) each. Of the total 31 species of zooplanktons, nine species were abundant, 11 were common, and 12 were rare. The present paper discusses the population profile of zooplanktons in waters of SPH with suggested conservation and management strategies. DOI: http://dx.doi.org/10.3126/ije.v3i1.9948 International Journal of Environment Vol.3(1) 2014: 111-121
Inventory of threatened plants of Bangladesh and their conservation management
Authors: Harun-ur-Rashid M , Rashid M Enamur , Rahman M Atiqur
Published: February 2014

The study aimed at inventorying of threatened plant species of Bangladesh to determine their status of occurrence for emphasizing the setting-up of national conservation strategies and sustainable management. Complete inventory of two families, the Apocynaceae and Vitaceae, has been made and recognized 28 threatened species facing environmental threats, and need sustainable conservation management. The study was based on long-term field investigation, survey of relevant floristic literature and examination of herbarium specimens. An enumeration of threatened taxa is prepared with updated field data on conservation status to include into Red Data Book of Bangladesh. DOI: http://dx.doi.org/10.3126/ije.v3i1.9951 International Journal of Environment Vol.3(1) 2014: 141-167
Enhancements to the Freeway Facilities Method in the Highway Capacity Manual to Enable Reliability Analysis
Authors: Sajjadi Soheil , Schroeder Bastian , Rouphail Nagui M.
Published: February 2014

The Highway Capacity Manual (HCM) methodology provides a fast and reliable approach for the analysis of freeway traffic operations; research is ongoing to add a reliability analysis component to the method. Several key methodological enhancements are needed to make the method ready for reliability analysis; these enhancements are described and illustrated in this paper and include (a) the incorporation of the drop in capacity in the queue discharge flow compared with the prebreakdown flow; (b) the addition of a speed adjustment factor (SAF) as a new calibration factor for the modeling of nonrecurrent congestion sources, such as weather and incidents; (c) the explicit incorporation of SAFs and capacity adjustment factors (CAFs) into the HCM methodologies for merge, diverge, and weave segments; (d) the development of new SAF and CAF default values for freeways; and (e) the addition of new congestion performance measures. The enhancements overcome key limitations in the existing HCM 2010 freeway facility method, which assumes a fixed capacity throughout undersaturated and congested regimes, ignores the free-flow speed–reducing effects of inclement weather, and treats weave and merge–diverge segments as basic freeway segments for CAFs less than 1.0. In addition to the existing performance measures generated by the computational engine, some new output variables are proposed: the travel time index and a denied entry queue length measure. The various enhancements are illustrated with computational examples, and a discussion is offered as to the effects of the enhancements on conventional freeway facilities analysis, even without the evaluation of reliability.
Complete Enough for Complete Streets?
Authors: Carter Peter , Martin Francisco , Núñez Miguel , Peters Sarah , Raykin Leon , Salinas Julia , Milam Ronald
Published: February 2014

An increasing number of jurisdictions across the United States are exploring level of service (LOS) for multiple travel modes, in part as a result of the release of the Highway Capacity Manual 2010 (HCM 2010), as well as an increased focus on complete streets policies. One of the most important questions being asked by these jurisdictions is whether new multimodal LOS methods are sensitive enough to inform transportation investments, mitigate impacts, and prioritize future projects. For this paper, transportation professionals (public, private, and academic) were surveyed about the inputs believed to have the greatest effect on pedestrian, bicycle, transit, and auto LOS or the inputs thought to have the greatest likelihood of being changed (e.g., to mitigate an impact or to improve existing conditions). Sensitivity testing was then performed at locations in four cities to measure how the HCM 2010 multimodal LOS scores responded as these inputs were incrementally increased or decreased. Although many inputs performed as expected, the testing also found model responses that were of a questionable direction or magnitude. The results of this study are informative for agencies that are considering adopting the HCM 2010 multimodal LOS for mitigation, resource allocation, and strategic decision making. The results also provide a starting point for additional research needed to enhance multimodal LOS methods.
Development of an Oversaturated Speed–Flow Model Based on the Highway Capacity Manual
Authors: Xu Yilun , Williams Billy M. , Rouphail Nagui M. , Chase R. Thomas
Published: February 2014

Oversaturated speed, flow, and density relationships are of key importance to studies of freeway operations. The Highway Capacity Manual (HCM) oversaturated model, which is defined by a linear transition from the flow and the density at capacity to a zero flow at jam density in the flow–density space, provides a reasonable representation of this relationship but does not provide an unbiased representation for all freeway facilities with different road conditions or driver behavior. This study proposes a method for fitting the HCM model to oversaturated flow and density. Fifteen-minute aggregated flow rate and speed data were collected in 2010 from Traffic.com fixed-location sensors at three sites on North Carolina urban freeways. Density was calculated as the flow rate divided by the speed. The fitted models for these sites were compared with the default HCM model. A set of thresholds was defined to identify eligible sensor observations that represented the steady-state congested traffic conditions. The results revealed that data observations during inclement weather, lane closures, or incidents biased the model-fitting results and therefore needed to be filtered out. The steady-state congestion data identified in the manner proposed in this study fit well with the HCM-based linear flow–density oversaturated model. This method avoids possible bias caused by capacity and jam density differences between the default HCM model and the site-specific models; therefore, the fitted models represented the actual traffic characteristics relationships better than the default HCM models did. Fitting a site-specific HCM-based model is recommended for sites with sufficient speed and flow data.
Operational Effectiveness of Passing Zones Depending on Length and Traffic Volume
Authors: Moreno Ana Tsui , Llorca Carlos , García Alfredo , Pérez-Zuriaga Ana-María
Published: February 2014

Most studies on two-lane highway operations have focused on the percentage of following vehicles or the adjustment of the Highway Capacity Manual (HCM) procedure to local data. The HCM proposes the length of no-passing zones as a model parameter; however, the distribution and characteristics of passing zones are not addressed. In fact, only a few studies on the expected number of passes in a passing zone have been carried out. This research presents an analysis of the effectiveness of passing zones in terms of their length and traffic volume. Data were collected from four passing zones on a rural highway in Spain. The two-way traffic volumes ranged from 100 to 900 vehicles per hour (vph), and the passing zone lengths ranged from 265 to 1,270 m. More than 1,600 passing maneuvers were recorded. The operational effectiveness of the passing zones was obtained from the passing frequency and the passing rate. The results indicated that the longer the passing zone, the higher the passing frequency; however, the results stabilized with lengths above 1,100 m. Balanced flows with two-way traffic volumes between 600 and 700 vph optimized the number of passes. Nevertheless, the increase in the passing frequency with the traffic volume was lower than with the increase in following vehicles. The results were validated with data from another 12 passing zones. Finally, HCM adjustments based on the percentage of no-passing zones did not reliably represent the effectiveness of passing zones. Therefore, the effectiveness of every passing zone should be considered, and adjustment factors should be modified to maximize the passing opportunities for traffic volumes between 600 and 700 vph.
Revised Version of the Automobile Level-of-Service Methodology for Urban Streets in the Highway Capacity Manual 2010
Authors: Ozkul Seckin , Washburn Scott S. , McLeod Douglas S.
Published: February 2014

The Highway Capacity Manual 2010 (HCM 2010) contains a significantly revised automobile analysis and level-of-service (LOS) methodology for arterials. This study compared the arterial LOS results of the HCM 2000 and HCM 2010 methodologies for an experimental set of arterial segments and analyzed the effects of the revised methodology. In addition, existing Florida field data sets were also analyzed with arterial segments obtained from Gainesville, Tallahassee, and Tampa, all in Florida, as well as data received from the Florida Department of Transportation Districts 2 and 3. The HCM 2010 results showed that for shorter, lower-speed arterial segments [such as in central business districts (CBDs)] it was not possible to obtain LOS Ratings A or B. Therefore, many CBD arterials that had good LOS values under the HCM 2000 methodology would now have moderate to poor LOS values. Consequently, the research team tested several revisions of the HCM 2010 methodology to find an approach that would not be as punitive to arterials with shorter segment lengths and that would provide a good balance of LOS values across a range of segment lengths, posted speeds, and traffic demands. Suggested revisions to the HCM 2010 methodology that allowed this objective to be achieved consisted of the following: the use of two classes instead of one (on the basis of the posted speed); the use of the average travel speed as the service measure instead of the ratio of the average travel speed to the base free-flow speed; and the setting of the free-flow speed to equal the posted speed plus 5 mph, instead of using the free-flow speed computations in the HCM 2010 methodology.
Lane-Based Breakdown Identification at Diverge Sections for Breakdown Probability Modeling
Authors: Ma Danpeng , Nakamura Hideki , Asano Miho
Published: February 2014

When the breakdown probability on expressways is being modeled, the identification of breakdowns is a decisive issue. To date, most identification methods have treated all lanes of the main line as one unit; these methods have been conducted mainly by checking the aggregated data of the cross section. However, this cross section–based method oversimplifies breakdown identification for expressway facilities, such as diverge sections, on which preferences for lane usage differ significantly. Therefore, a lane-based method is proposed to identify breakdowns in each lane; the timing of the breakdown is determined by a critical speed, which is optimized by obtaining the most significant speed reductions that accompany the breakdown. The proposed lane-based method is applied to four bottlenecks at diverge sections on intercity expressways in Japan. The superiorities of the lane-based method are as follows. First, the method can identify and exclude semicongested cases, in which some lanes are congested and others are not. At a diverge section of the Toyota junction in Japan, 15 semicongested cases were identified by the lane-based method from the 198 breakdowns identified by the cross section–based method. Second, the timing of a breakdown can be appropriately determined, as it was for 34 cases on this diverge section. These superiorities significantly improve the accuracy of extracted breakdown flow rates, which are underestimated by the existing cross section–based method. The breakdown probability is modeled with the lane-based method on the extracted breakdown flow rates, and the impacts of traffic condition characteristics are discussed. The diverge rate and the lane utilization rate are found to have significant impacts on the breakdown probability at diverge sections.
Volume-to-Capacity Estimation of Signalized Road Networks for Metropolitan Transportation Planning
Authors: Xu Hao , Liu Hongchao , Fernando Hiron , Senadheera Sanjaya
Published: February 2014

Transportation planning plays a critical role in shaping economic health and quality of life. Transportation planning not only provides insight into the mobility of people and goods but also influences patterns of growth and economic activity. Metropolitan transportation planning is a challenging topic because of the lack of future traffic information, such as evaluations of capacity sufficiency on large metropolitan road networks with signalized intersections. The Highway Capacity Manual provides methods for the analysis of signalized intersections and urban streets for planning; however, these methods need detailed traffic volume inputs and lane configurations at signalized intersections, which are not normally available in metropolitan transportation planning. The conventional four-step planning process is widely used to forecast directional traffic volumes on road segments, but the projected volumes are not enough for the analysis of the capacity sufficiency of future road networks through existing methods. This paper discusses a proposed method developed through the integration of available transportation planning data and the characteristics of signalized intersections. The paper links traffic assignment results from conventional transportation planning procedures to the estimation of capacity sufficiency. With the proposed method, transportation planners can estimate the capacity sufficiency of future metropolitan road networks through the use of data that are readily available in transportation planning. This method will dramatically decrease the effort required for the capacity evaluation of large signalized metropolitan road networks.
Quantifying Measurement Error in Arterial Travel Times Measured by Bluetooth Detectors
Authors: Moghaddam Soroush Salek , Hellinga Bruce
Published: February 2014

Travel time is viewed by travelers and road managers as one of the key indicators of quality of service. Bluetooth detectors have recently emerged as a viable technology for the acquisition of vehicle travel times. Several studies have described the application of the technology to freeways and compared the measured travel times with the travel times obtained through other technologies. This paper examines the application of Bluetooth detectors to the acquisition of arterial travel times. The arterial environment is substantially more challenging than the freeway environment because of the frequent interruptions in the traffic flow caused by traffic signals. This paper examines the magnitude of errors in detection time and travel time measurement. It is not feasible to use field data to examine the measurement error because the error is inherent within the observations and cannot be separated. Consequently, a simulation framework is proposed to synthesize measurement errors for a range of arterial traffic conditions. The results show that the mean travel time error is essentially zero for all traffic conditions. However, the variance of the error varies as a function of the traffic conditions. Through multiple regression, the standard deviation of the travel time measurement error is modeled, and it is shown that under some conditions, the 95% confidence interval of this error may reach 25% of the true mean travel time. These results can be used to assess Bluetooth detector deployment plans and provide more insight into the reliability of arterial travel time measurements obtained from Bluetooth detectors.
Toward a Capacity Analysis Procedure for Nonstandard Two-Way Stop-Controlled Intersections
Authors: Bogdanovic Vuk , Ruskic Nenad , Kulovic Mirsad , Han Lee D.
Published: February 2014

Two-way stop-controlled (TWSC) intersections are one of the most common forms of at-grade roadway junctions in the world. These intersections are typically located where a minor road intersects or joins a major roadway and stop signs are placed on the minor approaches. When the major roadway and the traffic that it carries go straight through the intersection, it is a standard TWSC intersection. In many places, however, the prevailing traffic and the major roadway do not continue straight through the intersection. In such cases, the major roadway bends at an angle at the intersection, and the stop signs on the minor streets are placed on adjacent legs of the intersection. These intersections are nonstandard TWSC intersections. Nonstandard TWSC intersections are found frequently in some countries and exist in most. These intersections are officially recognized in traffic codes and manuals in Europe, Australia, and the United States, yet the Highway Capacity Manual (HCM) TWSC procedure does not specifically handle these intersections. In fact, a literature review yielded no established procedure for the calculation of capacity at nonstandard TWSC intersections that would consider the specificities related to the layout of the approaching roadways and the characteristics of the traffic flow, such as the critical headway and the follow-up headway. This paper demonstrates the uniqueness of nonstandard TWSC intersections, reports analysis results from field data collected at several similar nonstandard TWSC T-intersections, identifies discrepancy in critical headway figures and level-of-service ratings that can result from the use of the HCM procedure for TWSC intersections, and calls for further research on the subject in other locales.
The Role of Cycle Rickshaws in Urban Transport
Authors: Tiwari Geetam
Published: February 2014

Cycle rickshaws continue to play an important role in meeting the mobility demands in South Asian cities. Current transport policies, however, do not support their use. Rickshaws are viewed as a cause of congestion and a profession in which rickshaw owners exploit poor people. This article presents data from published studies to argue against those views. Data from Delhi metro users suggests that as cities expand their public transport services, rickshaws will continue as an important feeder mode in the future. Recent studies also suggest that if separate lanes are created for non-motorized vehicles (which can be used by bicycles as well), then rickshaws and motorized vehicles will experience less congestion and non-motorized vehicles will be exposed to lower traffic crash risk. This article advocates the collection of relevant data concerning rickshaw trips and the number of rickshaws in future travel surveys and that appropriate infrastructures should be designed to facilitate their movement.
Cinema's Journey into Homelessness Leos Carax's Holy Motors
Authors: Pause Johannes
Published: February 2014

Holy Motors, France and Germany, 2012, Pierre Grise Productions, directed
and written by Leos Carax, starring Denis Lavant, Edith Scob, Eva Mendes,
Kylie Minogue, and Michel Piccoli.
Prospective natural history study of central nervous system hemangioblastomas in von Hippel-Lindau disease
Authors: Lonser Russell R. , Butman John A. , Huntoon Kristin , Asthagiri Ashok R. , Wu Tianxia , Bakhtian Kamran D. , Chew Emily Y. , Zhuang Zhengping , Linehan W. Marston , Oldfield Edward H.
Published: February 2014

Object

The tumors most frequently associated with von Hippel-Lindau (VHL) disease are hemangioblastomas. While they are associated with significant neurological impairment and mortality, their natural history and optimal management have not been fully defined.

Methods

Patients with VHL were enrolled in a prospective study designed to define the natural history of CNS hemangioblastomas. In the present analysis, serial imaging, laboratory, genetic, and clinical data were evaluated in those with at least 2 years of follow-up data.

Results

At study entrance 225 patients (111 males, 114 females) harbored 1921 CNS hemangioblastomas in the supratentorial compartment (21 tumors [1%]), cerebellum (865 [45%]), brainstem (129 [7%]), spinal cord (689 [36%]), cauda equina (212 [11%]), and nerve roots (5 [0.3%]; follow-up 15,819 hemangioblastoma-years). Increased tumor burden was associated with partial deletions in the VHL gene (p = 0.005) and male sex (p = 0.002). Hemangioblastoma development (median 0.3 new tumors/year) was associated with younger age (p < 0.0001) and more tumors at study entrance (p < 0.0001). While 1278 hemangioblastomas (51%) did not grow, 1227 hemangioblastomas (49%) grew in a saltatory (886 [72%]), linear (76 [6%]), or exponential (264 [22%]) pattern. Faster tumor growth was associated with male sex (p = 0.001), symptomatic tumors (p < 0.0001), and tumors associated with cysts (p < 0.0001). Location-dependent tumor size was the primary predictor of eventual symptom formation (159 symptomatic tumors [6.3%]; area under the curve > 0.9).

Conclusions

Central nervous system hemangioblastoma burden in VHL is associated with partial germline deletions and male sex. Unpredictable growth of hemangioblastomas compromises assessment of nonsurgical therapies. The judicious treatment of symptom-producing hemangioblastomas, while avoiding unnecessary treatment of asymptomatic tumors that may not progress, can provide clinical stability. Clinical trial registration no.: NCT00005902 (ClinicalTrials.gov).
J. Norman Collie, the Inventive Chemist
Authors: Davies Alwyn G.
Published: February 2014

Norman Collie was Professor of Organic Chemistry and Director of Laboratories at University College London between 1902 and 1928. He was a pioneering mountaineer but was also a prolific inventor; this review focuses on that little-known latter aspect of his activities.
Chemical Synthetic Biology
Authors: Chiarabelli Cristiano , Luisi Pier Luigi
Published: February 2014

Although both the most popular form of synthetic biology (SB) and chemical synthetic biology (CSB) share the biotechnologically useful aim of making new forms of life, SB does so by using genetic manipulation of extant microorganism, while CSB utilises classic chemical procedures in order to obtain biological structures which are non-existent in nature. The main query concerning CSB is the philosophical question: why did nature do this, and not that? The idea then is to synthesise alternative structures in order to understand why nature operated in such a particular way. We briefly present here some various examples of CSB, including those cases of nucleic acids synthesised with pyranose instead of ribose, and proteins with a reduced alphabet of amino acids; also we report the developing research on the “never born proteins” (NBP) and “never born RNA” (NBRNA), up to the minimal cell project, where the issue is the preparation of semi-synthetic cells that can perform the basic functions of biological cells.
Handover practice amongst core surgical trainees at the Oxford School of Surgery
Authors: Sadideen Hazim , Hamaoui Karim , Saadeddin Munir , Cogswell Lucy , Goodacre Tim , Jefferis Tony
Published: February 2014

Purpose: To date there are no United Kingdom (UK) studies specifically evaluating handovers amongst core surgical trainees (CSTs). The Oxford School of Surgery examined regional handover practice, aiming to assess and improve trainee perception of handover, its quality, and ultimately patient care. Methods: Based on two guidance documents ('Safe handover, safe patients' by the British Medical Association and 'Safe Surgical Practice' by the Royal College of Surgeons'), a 5-point Likert style questionnaire was designed, exploring handover practice, educational value, and satisfaction. This was given to 50 CSTs in 2010.Results: There were responses from 40 CSTs (80.0 %). The most striking findings revolved around perceived educational value, formal training, and auditing practice with regards to handover, which were all remarkably lower than expected. CST handover was thus targeted in the Department of Plastic Surgery at the University Hospital, with the suggestion and implementation of targeted changes to improve practice. Conclusion: In the EWTD era with many missed educational opportunities, daily handover represents an underused educational tool for CSTs, especially in light of competency-based and time-limited training. We recommend modifications based on our results and the literature and hope schools of surgery follow suit nationally by assessing and addressing handover practice.
Specific Inhibition of the VEGFR-3 Tyrosine Kinase by SAR131675 Reduces Peripheral and Tumor Associated Immunosuppressive Myeloid Cells
Authors: Espagnolle Nicolas , Barron Pauline , Mandron Marie , Blanc Isabelle , Bonnin Jacques , Agnel Magali , Kerbelec Erwan , Herault Jean , Savi Pierre , Bono Françoise , Alam Antoine
Published: February 2014

Myeloid derived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs) represent prominent components in cancer progression. We previously showed that inhibition of the VEGFR-3 pathway by SAR131675 leads to reduction of TAM infiltration and tumor growth. Here, we found that treatment with SAR131675 prevents the accumulation of immunosuppressive blood and splenic MDSCs which express VEGFR-3, in 4T1 tumor bearing mice. Moreover we showed that soluble factors secreted by tumor cells promote MDSCs proliferation and differentiation into M2 polarized F4/80+ macrophages. In addition, cell sorting and transcriptomic analysis of tumor infiltrating myeloid cells revealed the presence of a heterogeneous population that could be divided into 3 subpopulations: (i) immature cells with a MDSC phenotype (GR1+/CD11b+/F4/80−); (ii) “immuno-incompetent” macrophages (F4/80high/CD86neg/MHCIILow) strongly expressing M2 markers such as Legumain, CD206 and Mgl1/2 and (iii) “immuno-competent”-M1 like macrophages (F4/80Low/CD86+/MHCIIHigh). SAR131675 treatment reduced MDSCs in lymphoid organs as well as F4/80High populations in tumors. Interestingly, in the tumor SAR131675 was able to increase the immunocompetent M1 like population (F4/80low). Altogether these results demonstrate that the specific VEGFR-3 inhibitor SAR131675 exerts its anti tumoral activity by acting on different players that orchestrate immunosuppression and cancer progression in a tumoral context: MDSCs in peripheral lymphoid organs and TAMs infiltrating the tumor.
Acknowledgement to Reviewers of Diagnostics in 2013
Authors: Diagnostics Editorial Office
Published: February 2014

The editors of Diagnostics would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2013. [...]
Information Flow in Animal-Robot Interactions
Authors: Butail Sachit , Ladu Fabrizio , Spinello Davide , Porfiri Maurizio
Published: February 2014

The nonverbal transmission of information between social animals is a primary driving force behind their actions and, therefore, an important quantity to measure in animal behavior studies. Despite its key role in social behavior, the flow of information has only been inferred by correlating the actions of individuals with a simplifying assumption of linearity. In this paper, we leverage information-theoretic tools to relax this assumption. To demonstrate the feasibility of our approach, we focus on a robotics-based experimental paradigm, which affords consistent and controllable delivery of visual stimuli to zebrafish. Specifically, we use a robotic arm to maneuver a life-sized replica of a zebrafish in a predetermined trajectory as it interacts with a focal subject in a test tank. We track the fish and the replica through time and use the resulting trajectory data to measure the transfer entropy between the replica and the focal subject, which, in turn, is used to quantify one-directional information flow from the robot to the fish. In agreement with our expectations, we find that the information flow from the replica to the zebrafish is significantly more than the other way around. Notably, such information is specifically related to the response of the fish to the replica, whereby we observe that the information flow is reduced significantly if the motion of the replica is randomly delayed in a surrogate dataset. In addition, comparison with a control experiment, where the replica is replaced by a conspecific, shows that the information flow toward the focal fish is significantly more for a robotic than a live stimulus. These findings support the reliability of using transfer entropy as a measure of information flow, while providing indirect evidence for the efficacy of a robotics-based platform in animal behavioral studies.
Level and Contamination Assessment of Environmentally Sensitive Elements in Smaller than 100 μm Street Dust Particles from Xining, China
Authors: Zhao Ni , Lu Xinwei , Chao Shigang
Published: February 2014

Concentrations of the environmentally sensitive elements (ESEs) As, Co, Cu, Mn, Ni, Pb, V and Zn in smaller than 100 μm street dust particles from Xining were measured using X-ray fluorescence spectrometry and their contamination levels were assessed based on enrichment factor (EF), geoaccumulation index (Igeo) and pollution load index (PLI). The concentrations of As, Co, Cu, Mn, Ni, Pb, V and Zn in smaller than 100 μm street dust particles from Xining are 0.1–0.8, 2.7–10.9, 0.7–5.2, 0.3–1.1, 0.6–2.5, 1.2–11.1, 0.7–1.3 and 0.4–2.9 times the background values of Qinghai soil, respectively. The calculated EF and Igeo values reveal the order Co > Pb > Cu > Zn > V > Ni > Mn > As. The EF and Igeo values of Co, Cu, Pb and Zn are higher indicating that there is considerable pollution by these elements in smaller than 100 μm street dust particles, especially for Co. The EF and Igeo of Mn, Ni and V are lower and the assessment results indicate an absence of distinct Mn, Ni and V pollution in the studied samples. The mean value of PLIsite is 1.14, indicating a slightly pollution in the whole city of Xining. The order of PLIarea for the five tested districts is Center District (CD) > East District (ED) > West District (WD) > North District (ND) > South District (SD), showing that ESEs pollution in the South District is the lightest while it is the highest in the Central District.
Identifying Regional Key Eco-Space to Maintain Ecological Security Using GIS
Authors: Xie Hualin , Yao Guanrong , Wang Peng
Published: February 2014

Ecological security and environmental sustainability are the foundations of sustainable development. With the acceleration of urbanization, increasing human activities have promoted greater impacts on the eco-spaces that maintain ecological security. Regional key eco-space has become the primary need to maintain environmental sustainability and can offer society with continued ecosystem services. In this paper, considering the security of water resources, biodiversity conservation, disaster avoidance and protection and natural recreation, an integrated index of eco-space importance was established and a method for identifying key eco-space was created using GIS, with Lanzhou City, China as a case study. The results show that the area of core eco-space in the Lanzhou City is approximately 50,908.7 hm2, accounting for 40% of the region’s total area. These areas mainly consist of geological hazard protection zones and the core zones of regional river systems, wetlands, nature reserves, forest parks and scenic spots. The results of this study provide some guidance for the management of ecological security, ecological restoration and environmental sustainability.
Spatial and Semantic Validation of Secondary Food Source Data
Authors: Lyseen Anders , Hansen Henning
Published: February 2014

Governmental and commercial lists of food retailers are often used to measure food environments and foodscapes for health and nutritional research. Information about the validity of such secondary food source data is relevant to understanding the potential and limitations of its application. This study assesses the validity of two government lists of food retailer locations and types by comparing them to direct field observations, including an assessment of whether pre-classification of the directories can reduce the need for field observation. Lists of food retailers were obtained from the Central Business Register (CVR) and the Smiley directory. For each directory, the positive prediction value (PPV) and sensitivity were calculated as measures of completeness and thematic accuracy, respectively. Standard deviation was calculated as a measure of geographic accuracy. The effect of the pre-classification was measured through the calculation of PPV, sensitivity and negative prediction value (NPV). The application of either CVR or Smiley as a measure of the food environment would result in a misrepresentation. The pre-classification based on the food retailer names was found to be a valid method for identifying approximately 80% of the food retailers and limiting the need for field observation.
An Overview of Poly(lactic-co-glycolic) Acid (PLGA)-Based Biomaterials for Bone Tissue Engineering
Authors: Gentile Piergiorgio , Chiono Valeria , Carmagnola Irene , Hatton Paul
Published: February 2014

Poly(lactic-co-glycolic) acid (PLGA) has attracted considerable interest as a base material for biomedical applications due to its: (i) biocompatibility; (ii) tailored biodegradation rate (depending on the molecular weight and copolymer ratio); (iii) approval for clinical use in humans by the U.S. Food and Drug Administration (FDA); (iv) potential to modify surface properties to provide better interaction with biological materials; and (v) suitability for export to countries and cultures where implantation of animal-derived products is unpopular. This paper critically reviews the scientific challenge of manufacturing PLGA-based materials with suitable properties and shapes for specific biomedical applications, with special emphasis on bone tissue engineering. The analysis of the state of the art in the field reveals the presence of current innovative techniques for scaffolds and material manufacturing that are currently opening the way to prepare biomimetic PLGA substrates able to modulate cell interaction for improved substitution, restoration, or enhancement of bone tissue function.
A Proteomic Approach of Bradyrhizobium/Aeschynomene Root and Stem Symbioses Reveals the Importance of the fixA Locus for Symbiosis
Authors: Delmotte Nathanael , Mondy Samuel , Alunni Benoit , Fardoux Joel , Chaintreuil Clémence , Vorholt Julia , Giraud Eric , Gourion Benjamin
Published: February 2014

Rhizobia are soil bacteria that are able to form symbiosis with plant hosts of the legume family. These associations result in the formation of organs, called nodules in which bacteria fix atmospheric nitrogen to the benefit of the plant. Most of our knowledge on the metabolism and the physiology of the bacteria during symbiosis derives from studying roots nodules of terrestrial plants. Here we used a proteomics approach to investigate the bacterial physiology of photosynthetic Bradyrhizobium sp. ORS278 during the symbiotic process with the semi aquatical plant Aeschynomene indica that forms root and stem nodules. We analyzed the proteomes of bacteria extracted from each type of nodule. First, we analyzed the bacteroid proteome at two different time points and found only minor variation between the bacterial proteomes of 2-week- and 3-week-old nodules. High conservation of the bacteroid proteome was also found when comparing stem nodules and root nodules. Among the stem nodule specific proteins were those related to the phototrophic ability of Bradyrhizobium sp. ORS278. Furthermore, we compared our data with those obtained during an extensive genetic screen previously published. The symbiotic role of four candidate genes which corresponding proteins were found massively produced in the nodules but not identified during this screening was examined. Mutant analysis suggested that in addition to the EtfAB system, the fixA locus is required for symbiotic efficiency.
Nanotoxicity Overview: Nano-Threat to Susceptible Populations
Authors: Li Yang , Zhang Yi , Yan Bing
Published: February 2014

Due to the increasing applications of nanomaterials and nanotechnology, potential danger of nanoparticle exposure has become a critical issue. However, recent nanotoxicity studies have mainly focused on the health risks to healthy adult population. The nanotoxicity effects on susceptible populations (such as pregnant, neonate, diseased, and aged populations) have been overlooked. Due to the alterations in physiological structures and functions in susceptible populations, they often suffer more damage from the same exposure. Thus, it is urgent to understand the effects of nanoparticle exposure on these populations. In order to fill this gap, the potential effects of nanoparticles to pregnant females, neonate, diseased, and aged population, as well as the possible underlying mechanisms are reviewed in this article. Investigations show that responses from susceptible population to nanoparticle exposure are often more severe. Reduced protection mechanism, compromised immunity, and impaired self-repair ability in these susceptible populations may contribute to the aggravated toxicity effects. This review will help minimize adverse effects of nanoparticles to susceptible population in future nanotechnology applications.
Exposure to Diflubenzuron Results in an Up-Regulation of a Chitin Synthase 1 Gene in Citrus Red Mite, Panonychus citri (Acari: Tetranychidae)
Authors: Xia Wen-Kai , Ding Tian-Bo , Niu Jin-Zhi , Liao Chong-Yu , Zhong Rui , Yang Wen-Jia , Liu Bin , Dou Wei , Wang Jin-Jun
Published: February 2014

Chitin synthase synthesizes chitin, which is critical for the arthropod exoskeleton. In this study, we cloned the cDNA sequences of a chitin synthase 1 gene, PcCHS1, in the citrus red mite, Panonychus citri (McGregor), which is one of the most economically important pests of citrus worldwide. The full-length cDNA of PcCHS1 contains an open reading frame of 4605 bp of nucleotides, which encodes a protein of 1535 amino acid residues with a predicted molecular mass of 175.0 kDa. A phylogenetic analysis showed that PcCHS1 was most closely related to CHS1 from Tetranychus urticae. During P. citri development, PcCHS1 was constantly expressed in all stages but highly expressed in the egg stage (114.8-fold higher than in the adult). When larvae were exposed to diflubenzuron (DFB) for 6 h, the mite had a significantly high mortality rate, and the mRNA expression levels of PcCHS1 were significantly enhanced. These results indicate a promising use of DFB to control P. citri, by possibly acting as an inhibitor in chitin synthesis as indicated by the up-regulation of PcCHS1 after exposure to DFB.
Chemistry of Ammonothermal Synthesis
Authors: Richter Theresia , Niewa Rainer
Published: February 2014

Ammonothermal synthesis is a method for synthesis and crystal growth suitable for a large range of chemically different materials, such as nitrides (e.g., GaN, AlN), amides (e.g., LiNH2, Zn(NH2)2), imides (e.g., Th(NH)2), ammoniates (e.g., Ga(NH3)3F3, [Al(NH3)6]I3 · NH3) and non-nitrogen compounds like hydroxides, hydrogen sulfides and polychalcogenides (e.g., NaOH, LiHS, CaS, Cs2Te5). In particular, large scale production of high quality crystals is possible, due to comparatively simple scalability of the experimental set-up. The ammonothermal method is defined as employing a heterogeneous reaction in ammonia as one homogenous fluid close to or in supercritical state. Three types of milieus may be applied during ammonothermal synthesis: ammonobasic, ammononeutral or ammonoacidic, evoked by the used starting materials and mineralizers, strongly influencing the obtained products. There is little known about the dissolution and materials transport processes or the deposition mechanisms during ammonothermal crystal growth. However, the initial results indicate the possible nature of different intermediate species present in the respective milieus.
Identifying Potential Regions of Copy Number Variation for Bipolar Disorder
Authors: Chen Yi-Hsuan , Lu Ru-Band , Hung Hung , Kuo Po-Hsiu
Published: February 2014

Bipolar disorder is a complex psychiatric disorder with high heritability, but its genetic determinants are still largely unknown. Copy number variation (CNV) is one of the sources to explain part of the heritability. However, it is a challenge to estimate discrete values of the copy numbers using continuous signals calling from a set of markers, and to simultaneously perform association testing between CNVs and phenotypic outcomes. The goal of the present study is to perform a series of data filtering and analysis procedures using a DNA pooling strategy to identify potential CNV regions that are related to bipolar disorder. A total of 200 normal controls and 200 clinically diagnosed bipolar patients were recruited in this study, and were randomly divided into eight control and eight case pools. Genome-wide genotyping was employed using Illumina Human Omni1-Quad array with approximately one million markers for CNV calling. We aimed at setting a series of criteria to filter out the signal noise of marker data and to reduce the chance of false-positive findings for CNV regions. We first defined CNV regions for each pool. Potential CNV regions were reported based on the different patterns of CNV status between cases and controls. Genes that were mapped into the potential CNV regions were examined with association testing, Gene Ontology enrichment analysis, and checked with existing literature for their associations with bipolar disorder. We reported several CNV regions that are related to bipolar disorder. Two CNV regions on chromosome 11 and 22 showed significant signal differences between cases and controls (p < 0.05). Another five CNV regions on chromosome 6, 9, and 19 were overlapped with results in previous CNV studies. Experimental validation of two CNV regions lent some support to our reported findings. Further experimental and replication studies could be designed for these selected regions.
Can Archival Tissue Reveal Answers to Modern Research Questions?: Computer-Aided Histological Assessment of Neuroblastoma Tumours Collected over 60 Years
Authors: Chetcuti Albert , Mackie Nicole , Tafavogh Siamak , Graf Nicole , Henwood Tony , Charlton Amanda , Catchpoole Daniel
Published: February 2014

Despite neuroblastoma being the most common extracranial solid cancer in childhood, it is still a rare disease. Consequently, the unavailability of tissue for research limits the statistical power of studies. Pathology archives are possible sources of rare tissue, which, if proven to remain consistent over time, could prove useful to research of rare disease types. We applied immunohistochemistry to investigate whether long term storage caused any changes to antigens used diagnostically for neuroblastoma. We constructed and quantitatively assessed a tissue microarray containing neuroblastoma archival material dating between 1950 and 2007. A total of 119 neuroblastoma tissue cores were included spanning 6 decades. Fourteen antibodies were screened across the tissue microarray (TMA). These included seven positive neuroblastoma diagnosis markers (NB84, Chromogranin A, NSE, Ki-67, INI1, Neurofilament Protein, Synaptophysin), two anticipated to be negative (S100A, CD99), and five research antibodies (IL-7, IL-7R, JAK1, JAK3, STAT5). The staining of these antibodies was evaluated using Aperio ImageScope software along with novel pattern recognition and quantification algorithms. This analysis demonstrated that marker signal intensity did not decrease over time and that storage for 60 years had little effect on antigenicity. The construction and assessment of this neuroblastoma TMA has demonstrated the feasibility of using archival samples for research.
Effect of Corn Steep Liquor (CSL) and Cassava Wastewater (CW) on Chitin and Chitosan Production by Cunninghamella elegans and Their Physicochemical Characteristics and Cytotoxicity
Authors: Berger Lúcia , Stamford Thayza , Stamford-Arnaud Thatiana , De Oliveira Franco Luciana , Do Nascimento Aline , Cavalcante Horacinna , Macedo Rui , De Campos-Takaki Galba
Published: February 2014

Microbiological processes were used for chitin and chitosan production with Cunninghamella elegans UCP/WFCC 0542 grown in different concentrations of two agro-industrial wastes, corn steep liquor (CSL) and cassava wastewater (CW) established using a 22 full factorial design. The polysaccharides were extracted by alkali-acid treatment and characterized by infrared spectroscopy, viscosity, thermal analysis, elemental analysis, scanning electron microscopy and X-ray diffraction. The cytotoxicity of chitosan was evaluated for signs of vascular change on the chorioallantoic membrane of chicken eggs. The highest biomass (9.93 g/L) was obtained in trial 3 (5% CW, 8% CSL), the greatest chitin and chitosan yields were 89.39 mg/g and 57.82 mg/g, respectively, and both were obtained in trial 2 (10% CW, 4% CSL). Chitin and chitosan showed a degree of deacetylation of 40.98% and 88.24%, and a crystalline index of 35.80% and 23.82%, respectively, and chitosan showed low molecular weight (LMW 5.2 × 103 Da). Chitin and chitosan can be considered non-irritating, due to the fact they do not promote vascular change. It was demonstrated that CSL and CW are effective renewable agroindustrial alternative substrates for the production of chitin and chitosan.
Acknowledgement to Reviewers of Nutrients in 2013
Authors: Nutrients Editorial Office
Published: February 2014

The editors of Nutrients would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2013. [...]