An improved approach for predicting the distribution of rare and endangered species from occurrence and pseudo-absence data

1. Few examples of habitat-modelling studies of rare and endangered species exist in the literature, although from a conservation perspective predicting their distribution would prove particularly useful. Paucity of data and lack of valid absences are the probable reasons for this shortcoming. Analytic solutions to accommodate the lack of absence include the ecological niche factor analysis (ENFA) and the use of generalized linear models (GLM) with simulated pseudo-absences. 2. In this study we tested a new approach to generating pseudo-absences, based on a preliminary ENFA habitat suitability (HS) map, for the endangered species Eryngium alpinum. This method of generating pseudo-absences was compared with two others: (i) use of a GLM with pseudo-absences generated totally at random, and (ii) use of an ENFA only. 3. The influence of two different spatial resolutions (i.e. grain) was also assessed for tackling the dilemma of quality (grain) vs. quantity (number of occurrences). Each combination of the three above-mentioned methods with the two grains generated a distinct HS map. 4. Four evaluation measures were used for comparing these HS maps: total deviance explained, best kappa, Gini coefficient and minimal predicted area (MPA). The last is a new evaluation criterion proposed in this study. 5. Results showed that (i) GLM models using ENFA-weighted pseudo-absence provide better results, except for the MPA value, and that (ii) quality (spatial resolution and locational accuracy) of the data appears to be more important than quantity (number of occurrences). Furthermore, the proposed MPA value is suggested as a useful measure of model evaluation when used to complement classical statistical measures. 6. Synthesis and applications. We suggest that the use of ENFA-weighted pseudo-absence is a possible way to enhance the quality of GLM-based potential distribution maps and that data quality (i.e. spatial resolution) prevails over quantity (i.e. number of data). Increased accuracy of potential distribution maps could help to define better suitable areas for species protection and reintroduction.

Improved diagnosis of periprosthetic joint infection by multiplex PCR of sonication fluid from removed implants.

The microbiological diagnosis of periprosthetic joint infection (PJI) is crucial for successful antimicrobial treatment. Cultures have limited sensitivity, especially in patients receiving antibiotics. We evaluated the value of multiplex PCR for detection of microbial DNA in sonication fluid from removed orthopedic prostheses. Cases of PJI in which the prosthesis (or part of it) was removed were prospectively included. The removed implant was sonicated, and the resulting sonication fluid was cultured and subjected to multiplex PCR. Of 37 PJI cases (17 hip prostheses, 14 knee prostheses, 4 shoulder prostheses, 1 elbow prosthesis, and 1 ankle prosthesis), pathogens were identified in periprosthetic tissue in 24 (65%) cases, in sonication fluid in 23 (62%) cases, and by multiplex PCR in 29 (78%) cases. The pathogen was detected in 5 cases in sonication fluid only (Propionibacterium acnes in all cases; none of these patients had previously received antibiotics) and in 11 cases by multiplex PCR only (all of these patients had previously received antibiotics). After exclusion of 8 cases caused by P. acnes or Corynebacterium species, which cannot be detected due to the absence of specific primers in the PCR kit, sonication cultures were positive in 17 cases and multiplex PCR sonication cultures were positive in 29 cases (59% versus 100%, respectively; P < 0.01). Among 19 cases (51%) receiving antibiotics, multiplex PCR was positive in all 19 (100%), whereas sonication cultures grew the organism in 8 (42%) (P < 0.01). Multiplex PCR of sonication fluid is a promising test for diagnosis of PJI, particularly in patients who previously received antibiotics. With modified primer sets, multiplex PCR has the potential for further improvement of the diagnosis of PJI.

Improved three-dimensional free-breathing coronary magnetic resonance angiography using gadocoletic acid (B-22956) for intravascular contrast enhancement.

PURPOSE: To evaluate gadocoletic acid (B-22956), a gadolinium-based paramagnetic blood pool agent, for contrast-enhanced coronary magnetic resonance angiography (MRA) in a Phase I clinical trial, and to compare the findings with those obtained using a standard noncontrast T2 preparation sequence. MATERIALS AND METHODS: The left coronary system was imaged in 12 healthy volunteers before B-22956 application and 5 (N = 11) and 45 (N = 7) minutes after application of 0.075 mmol/kg of body weight (BW) of B-22956. Additionally, imaging of the right coronary system was performed 23 minutes after B-22956 application (N = 6). A three-dimensional gradient echo sequence with T2 preparation (precontrast) or inversion recovery (IR) pulse (postcontrast) with real-time navigator correction was used. Assessment of the left and right coronary systems was performed qualitatively (a 4-point visual score for image quality) and quantitatively in terms of signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), vessel sharpness, visible vessel length, maximal luminal diameter, and the number of visible side branches. RESULTS: Significant (P < 0.01) increases in SNR (+42%) and CNR (+86%) were noted five minutes after B-22956 application, compared to precontrast T2 preparation values. A significant increase in CNR (+40%, P < 0.05) was also noted 45 minutes postcontrast. Vessels (left anterior descending artery (LAD), left coronary circumflex (LCx), and right coronary artery (RCA)) were also significantly (P < 0.05) sharper on postcontrast images. Significant increases in vessel length were noted for the LAD (P < 0.05) and LCx and RCA (both P < 0.01), while significantly more side branches were noted for the LAD and RCA (both P < 0.05) when compared to precontrast T2 preparation values. CONCLUSION: The use of the intravascular contrast agent B-22956 substantially improves both objective and subjective parameters of image quality on high-resolution three-dimensional coronary MRA. The increase in SNR, CNR, and vessel sharpness minimizes current limitations of coronary artery visualization with high-resolution coronary MRA.

Improved NYVAC-based vaccine vectors.

While as yet there is no vaccine against HIV/AIDS, the results of the phase III Thai trial (RV144) have been encouraging and suggest that further improvements of the prime/boost vaccine combination of a poxvirus and protein are needed. With this aim, in this investigation we have generated derivatives of the candidate vaccinia virus vaccine vector NYVAC with potentially improved functions. This has been achieved by the re-incorporation into the virus genome of two host range genes, K1L and C7L, in conjunction with the removal of the immunomodulatory viral molecule B19, an antagonist of type I interferon action. These novel virus vectors, referred to as NYVAC-C-KC and NYVAC-C-KC-ΔB19R, have acquired relevant biological characteristics, giving higher levels of antigen expression in infected cells, replication-competency in human keratinocytes and dermal fibroblasts, activation of selective host cell signal transduction pathways, and limited virus spread in tissues. Importantly, these replication-competent viruses have been demonstrated to maintain a highly attenuated phenotype.

Traffic Signal Inventory Project, 2001

The Center for Transportation Research and Education performed a traffic signal inventory study for the Iowa Department of Transportation. The purpose of this study was to determine the level of compliance with the Manual on Uniform Traffic Control Devices (MUTCD) and other industry standards of traffic signals on the state highway system. Signals were randomly selected throughout the State of Iowa. Only signals in cities with a population less than 5,000 were considered. Several intersections need to be addressed immediately to correct clearance timing settings. Red clearance intervals were frequently too short. A handful of intersections had inadequate pedestrian clearance times. Six intersections had at least one yellow clearance interval that did not meet Institute of Transportation Engineers standards. Some of the intersections likely would not meet traffic signal warrants and should be investigated for possible removal. The most common problem found with traffic signals was a lack of maintenance. Many of the signals had at least one of the following problems: burned out lights (signals and/or pedestrian heads), pedestrian lenses in need of replacement, dirty cabinet/missing or poor filter, missing visors, or inoperative pedestrian push buttons. Timing sheets were frequently missing or out of date. Another frequent noncompliance issue was the use of backplates. The MUTCD states that backplates should be used on signals viewed against a bright sky. The majority of signals inventoried did not have backplates on the mast-arm mounted signals. The timing at some intersections could likely be improved by reducing the cycle length. Where there were multiple signals in close proximity rarely was there any attempt at signal coordination. Finally, a number of intersections had equipment that by today’s standards would be considered obsolete.

FY2015 Equipment and Vehicle Revolving Fund report

The Equipment and Vehicle Revolving Fund report covers all equipment and vehicle purchases through the highway materials and equipment revolving fund during FY 2015.

Assessment of Channelizing Device Effectiveness on High Speed/High Volume Roadways, 2007

Part 6 of the Manual on Uniform Traffic Control Devices (MUTCD) describes several types of channelizing devices that can be used to warn road users and guide them through work zones; these devices include cones, tubular markers, vertical panels, drums, barricades, and temporary raised islands. On higher speed/volume roadways, drums and/or vertical panels have been popular choices in many states, due to their formidable appearance and the enhanced visibility they provide when compared to standard cones. However, due to their larger size, drums also require more effort and storage space to transport, deploy and retrieve. Recent editions of the MUTCD have introduced new devices for channelizing; specifically of interest for this study is a taller (>36 inches) but thinner cone. While this new device does not offer a comparable target value to that of drums, the new devices are significantly larger than standard cones and they offer improved stability as well. In addition, these devices are more easily deployed and stored than drums and they cost less. Further, for applications previously using both drums and tall cones, the use of tall cones only provides the ability for delivery and setup by a single vehicle. An investigation of the effectiveness of the new channelizing devices provides a reference for states to use in selecting appropriate traffic control for high speed, high volume applications, especially for short term or limited duration exposures. This study includes a synthesis of common practices by state DOTs, as well as daytime and nighttime field observations of driver reactions using video detection equipment. The results of this study are promising for the day and night performance of the new tall cones, comparing favorably to the performance of drums when used for channelizing in tapers. The evaluation showed no statistical difference in merge distance and location, shy distance, or operating speed in either daytime or nighttime conditions. The study should provide a valuable resource for state DOTs to utilize in selecting the most effective channelizing device for use on high speed/high volume roadways where timely merging by drivers is critical to safety and mobility.

Improved detection of Rhodococcus coprophilus with a new quantitative PCR assay.

Agricultural practices, such as spreading liquid manure or the utilisation of land as animal pastures, can result in faecal contamination of water resources. Rhodococcus coprophilus is used in microbial source tracking to indicate animal faecal contamination in water. Methods previously described for detecting of R. coprophilus in water were neither sensitive nor specific. Therefore, the aim of this study was to design and validate a new quantitative polymerase chain reaction (qPCR) to improve the detection of R. coprophilus in water. The new PCR assay was based on the R. coprophilus 16S rRNA gene. The validation showed that the new approach was specific and sensitive for deoxyribunucleic acid from target host species. Compared with other PCR assays tested in this study, the detection limit of the new qPCR was between 1 and 3 log lower. The method, including a filtration step, was further validated and successfully used in a field investigation in Switzerland. Our work demonstrated that the new detection method is sensitive and robust to detect R. coprophilus in surface and spring water. Compared with PCR assays that are available in the literature or to the culture-dependent method, the new molecular approach improves the detection of R. coprophilus.

Improved Employment Data for Transportation Planning, 1998

Transportation planners typically use census data or small sample surveys to help estimate work trips in metropolitan areas. Census data are cheap to use but are only collected every 10 years and may not provide the answers that a planner is seeking. On the other hand, small sample survey data are fresh but can be very expensive to collect. This project involved using database and geographic information systems (GIS) technology to relate several administrative data sources that are not usually employed by transportation planners. These data sources included data collected by state agencies for unemployment insurance purposes and for drivers licensing. Together, these data sources could allow better estimates of the following information for a metropolitan area or planning region: · Locations of employers (work sites); · Locations of employees; · Travel flows between employees’ homes and their work locations. The required new employment database was created for a large, multi-county region in central Iowa. When evaluated against the estimates of a metropolitan planning organization, the new database did allow for a one to four percent improvement in estimates over the traditional approach. While this does not sound highly significant, the approach using improved employment data to synthesize home-based work (HBW) trip tables was particularly beneficial in improving estimated traffic on high-capacity routes. These are precisely the routes that transportation planners are most interested in modeling accurately. Therefore, the concept of using improved employment data for transportation planning was considered valuable and worthy of follow-up research.

Improved SNR efficiency in gradient echo coronary MRA with high temporal resolution using parallel imaging.

Contemporary coronary magnetic resonance angiography techniques suffer from signal-to-noise ratio (SNR) constraints. We propose a method to enhance SNR in gradient echo coronary magnetic resonance angiography by using sensitivity encoding (SENSE). While the use of sensitivity encoding to improve SNR seems counterintuitive, it can be exploited by reducing the number of radiofrequency excitations during the acquisition window while lowering the signal readout bandwidth, therefore improving the radiofrequency receive to radiofrequency transmit duty cycle. Under certain conditions, this leads to improved SNR. The use of sensitivity encoding for improved SNR in three-dimensional coronary magnetic resonance angiography is investigated using numerical simulations and an in vitro and an in vivo study. A maximum 55% SNR enhancement for coronary magnetic resonance angiography was found both in vitro and in vivo, which is well consistent with the numerical simulations. This method is most suitable for spoiled gradient echo coronary magnetic resonance angiography in which a high temporal and spatial resolution is required.

Genetic diversity between improved banana diploids using canonical variables and the Ward-MLM method

The objective of this work was to estimate the genetic diversity of improved banana diploids using data from quantitative analysis and from simple sequence repeats (SSR) marker, simultaneously. The experiment was carried out with 33 diploids, in an augmented block design with 30 regular treatments and three common ones. Eighteen agronomic characteristics and 20 SSR primers were used. The agronomic characteristics and the SSR were analyzed simultaneously by the Ward-MLM, cluster, and IML procedures. The Ward clustering method considered the combined matrix obtained by the Gower algorithm. The Ward-MLM procedure identified three ideal groups (G1, G2, and G3) based on pseudo-F and pseudo-t² statistics. The dendrogram showed relative similarity between the G1 genotypes, justified by genealogy. In G2, 'Calcutta 4' appears in 62% of the genealogies. Similar behavior was observed in G3, in which the 028003-01 diploid is the male parent of the 086079-10 and 042079-06 genotypes. The method with canonical variables had greater discriminatory power than Ward-MLM. Although reduced, the genetic variability available is sufficient to be used in the development of new hybrids.

Portal Vein Embolization before Right Hepatectomy: Improved Results Using n-Butyl-Cyanoacrylate Compared to Microparticles Plus Coils.

BACKGROUND: There is currently no consensus in the literature on which embolic agent induces the greatest degree of liver hypertrophy after portal vein embolization (PVE). Only experimental results in a pig model have demonstrated an advantage of n-butyl-cyanoacrylate (NBCA) over 3 other embolic materials (hydrophilic gel, small and large polyvinyl alcohol particles) for PVE. Therefore, the aim of this human study was to retrospectively compare the results of PVE using NBCA with those using spherical microparticles plus coils. METHODS: A total of 34 patients underwent PVE using either NBCA (n = 20), or spherical microparticles plus coils (n = 14). PVE was decided according to preoperative volumetry on the basis of contrast-enhanced CT. Groups were compared for age, sex, volume of the left lobe before PVE and future remnant liver ratio (FRL) (volume of the left lobe/total liver volume - tumor volume). The primary end point was the increase in left lobe volume 1 month after PVE. Secondary end points were procedure complications and biological tolerance. RESULTS: Both groups were similar in terms of age, sex ratio, left lobe volume, and FRL before PVE. NBCA induced a greater increase in volume after PVE than did microparticles plus coils (respectively, +74 ± 69 % and +23 ± 14 %, p < 0.05). The amount of contrast medium used for the procedure was significantly larger when microparticles and coils rather than NBCA were used (respectively, 264 ± 43 ml and 162 ± 34 ml, p < 0.01). The rate of PVE complications as well as the biological tolerance was similar in both groups. CONCLUSION: NBCA seems more effective than spherical microparticles plus coils to induce left-lobe hypertrophy.

Improved flooding of broadcast messages using extended multipoint relaying

A common operation in wireless ad hoc networks is the flooding of broadcast messages to establish network topologies and routing tables. The flooding of broadcast messages is, however, a resource consuming process. It might require the retransmission of messages by most network nodes. It is, therefore, very important to optimize this operation. In this paper, we first analyze the multipoint relaying (MPR) flooding mechanism used by the Optimized Link State Routing (OLSR) protocol to distribute topology control (TC) messages among all the system nodes. We then propose a new flooding method, based on the fusion of two key concepts: distance-enabled multipoint relaying and connected dominating set (CDS) flooding. We present experimental simulationsthat show that our approach improves the performance of previous existing proposals.

Major mite allergen Der f 1 concentration is reduced in buildings with improved energy performance.

BACKGROUND: Environmental conditions play a crucial role in mite growth, and optimal environmental control is key in the prevention of airway inflammation in chronic allergic rhinoconjunctivitis or asthma. OBJECTIVE: To evaluate the relationship between building energy performance and indoor mite allergen concentration in a cross-sectional study. METHODS: Major allergen concentration (Der f 1, Der p 1, mite group 2, Fel d 1 and Bla g 2) was determined by quantitative dot blot analysis from mattress and carpet dust samples in five buildings designed for low energy use (LEB) and in six control buildings (CB). Inhabitants had received 4 weeks prior to mite measurement a personal validated questionnaire related to the perceived state of health and comfort of living. RESULTS: Cumulative mite allergen concentration (with Der f 1 as the major contributor) was significantly lower in LEB as compared with CB both in mattresses and in carpets. In contrast, the two categories of buildings did not differ in Bla g 2 and Fel d 1 concentration, in the amount of dust and airborne mould collected. Whereas temperature was higher in LEB, relative humidity was significantly lower than in CB. Perceived overall comfort was better in LEB. CONCLUSIONS: Major mite allergen Der f 1 preferentially accumulates in buildings not specifically designed for low energy use, reaching levels at risk for sensitization. We hypothesize that controlled mechanical ventilation present in all audited LEB may favour lower air humidity and hence lower mite growth and allergen concentration, while preserving optimal perceived comfort.