TRECVid 2005 experiments at Dublin City University

In this paper we describe our experiments in the automatic and interactive search tasks and the BBC rushes pilot task of TRECVid 2005. Our approach this year is somewhat different than previous submissions in that we have implemented a multi-user search system using a DiamondTouch tabletop device from Mitsubishi Electric Research Labs (MERL).We developed two versions of oursystem one with emphasis on efficient completion of the search task (Físchlár-DT Efficiency) and the other with more emphasis on increasing awareness among searchers (Físchlár-DT Awareness). We supplemented these runs with a further two runs one for each of the two systems, in which we augmented the initial results with results from an automatic run. In addition to these interactive submissions we also submitted three fully automatic runs. We also took part in the BBC rushes pilot task where we indexed the video by semi-automatic segmentation of objects appearing in the video and our search/browsing system allows full keyframe and/or object-based searching. In the interactive search experiments we found that the awareness system outperformed the efficiency system. We also found that supplementing the interactive results with results of an automatic run improves both the Mean Average Precision and Recall values for both system variants. Our results suggest that providing awareness cues in a collaborative search setting improves retrieval performance. We also learned that multi-user searching is a viable alternative to the traditional single searcher paradigm, provided the system is designed to effectively support collaboration

Assessing the impact of acid rain and forest harvest intensity with the HD-MINTEQ model – soil chemistry of three Swedish conifer sites from 1880 to 2080

Forest soils are susceptible to anthropogenic acidification. In the past, acid rain was a major contributor to soil acidification, but, now that atmospheric levels of S have dramatically declined, concern has shifted towards biomass-induced acidification, i.e. decreasing soil solution pH due to tree growth and harvesting events that permanently remove base cations (BCs) from forest stands. We use a novel dynamic model, HD-MINTEQ (Husby Dynamic MINTEQ), to investigate possible long-term impacts of two theoretical future harvesting scenarios in the year 2020, a conventional harvest (CH, which removes stems only), and a whole-tree harvest (WTH, which removes 100&thinsp;% of the above-ground biomass except for stumps) on soil chemistry and weathering rates at three different Swedish forest sites (Aneboda, Gårdsjön, and Kindla). Furthermore, acidification following the harvesting events is compared to the historical acidification that took place during the 20th century due to acid rain. Our results show that historical acidification due to acid rain had a larger impact on pore water chemistry and mineral weathering than tree growth and harvesting, at least if nitrification remained at a low level. However, compared to a no-harvest baseline, WTH and CH significantly impacted soil chemistry. Directly after a harvesting event (CH or WTH), the soil solution pH sharply increased for 5 to 10 years before slowly declining over the remainder of the simulation (until year 2080). WTH acidified soils slightly more than CH, but in certain soil horizons there was practically no difference by the year 2080. Even though the pH in the WTH and CH scenario decreased with time as compared to the no-harvest scenario (NH), they did not drop to the levels observed around the peak of historic acidification (1980–1990), indicating that the pH decrease due to tree growth and harvesting would be less impactful than that of historic atmospheric acidification. Weathering rates differed across locations and horizons in response to historic acidification. In general, the predicted changes in weathering rates were very small, which can be explained by the net effect of decreased pH and increased Al3+, which affected the weathering rate in opposite ways. Similarly, weathering rates after the harvesting scenarios in 2020 remained largely unchanged according to the model.</p

Magnetic resonance fingerprinting review part 2: Technique and directions

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154317/1/jmri26877.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154317/2/jmri26877_am.pd

Aluminium and base cation chemistry in dynamic acidification models – need for a reappraisal?

Long-term simulations of the water composition in acid forest soils require that accurate descriptions of aluminium and base cation chemistry are used. Both weathering rates and soil nutrient availability depend on the concentrations of Al3+, of H+, and of base cations (Ca2+, Mg2+, Na+, and K+) . Assessments of the acidification status and base cation availability will depend on the model being used. Here we review in what ways different dynamic soil chemistry models describe the processes governing aluminium and base cation concentrations in the soil water. Furthermore, scenario simulations with the HD-MINTEQ model are used to illustrate the difference between model approaches. The results show that all investigated models provide the same type of response to changes in input water chemistry. Still, for base cations we show that the differences in the magnitude of the response may be considerable depending on whether a cation-exchange equation (Gaines–Thomas, Gapon) or an organic complexation model is used. The former approach, which is used in many currently used models (e.g. MAGIC, ForSAFE), causes stronger pH buffering over a relatively narrow pH range, as compared to state-of-the-art models relying on more advanced descriptions in which organic complexation is important (CHUM, HD-MINTEQ). As for aluminium, a fixed gibbsite constant, as used in MAGIC, SMART/VSD, and ForSAFE, leads to slightly more pH buffering than in the more advanced models that consider both organic complexation and Al(OH)3(s) precipitation, but in this case the effect is small. We conclude that the descriptions of acid–base chemistry and base cation binding in models such as MAGIC, SMART/VSD, and ForSAFE are only likely to work satisfactorily in a narrow pH range. If the pH varies greatly over time, the use of modern organic complexation models is preferred over cation-exchange equations.</p

Transcriptional adaptations following exercise in Thoroughbred horse skeletal muscle highlights molecular mechanisms that lead to muscle hypertrophy

<p>Abstract</p> <p>Background</p> <p>Selection for exercise-adapted phenotypes in the Thoroughbred racehorse has provided a valuable model system to understand molecular responses to exercise in skeletal muscle. Exercise stimulates immediate early molecular responses as well as delayed responses during recovery, resulting in a return to homeostasis and enabling long term adaptation. Global mRNA expression during the immediate-response period has not previously been reported in skeletal muscle following exercise in any species. Also, global gene expression changes in equine skeletal muscle following exercise have not been reported. Therefore, to identify novel genes and key regulatory pathways responsible for exercise adaptation we have used equine-specific cDNA microarrays to examine global mRNA expression in skeletal muscle from a cohort of Thoroughbred horses (<it>n = </it>8) at three time points (before exercise, immediately post-exercise, and four hours post-exercise) following a single bout of treadmill exercise.</p> <p>Results</p> <p>Skeletal muscle biopsies were taken from the <it>gluteus medius </it>before (T₀), immediately after (T₁) and four hours after (T₂) exercise. Statistically significant differences in mRNA abundance between time points (T₀<it>vs </it>T₁and T₀<it>vs </it>T₂) were determined using the empirical Bayes moderated <it>t</it>-test in the Bioconductor package Linear Models for Microarray Data (LIMMA) and the expression of a select panel of genes was validated using real time quantitative reverse transcription PCR (qRT-PCR). While only two genes had increased expression at T₁(<it>P </it>< 0.05), by T₂932 genes had increased (<it>P </it>< 0.05) and 562 genes had decreased expression (<it>P </it>< 0.05). Functional analysis of genes differentially expressed during the recovery phase (T₂) revealed an over-representation of genes localized to the actin cytoskeleton and with functions in the MAPK signalling, focal adhesion, insulin signalling, mTOR signaling, p53 signaling and Type II diabetes mellitus pathways. At T₁, using a less stringent statistical approach, we observed an over-representation of genes involved in the stress response, metabolism and intracellular signaling. These findings suggest that protein synthesis, mechanosensation and muscle remodeling contribute to skeletal muscle adaptation towards improved integrity and hypertrophy.</p> <p>Conclusions</p> <p>This is the first study to characterize global mRNA expression profiles in equine skeletal muscle using an equine-specific microarray platform. Here we reveal novel genes and mechanisms that are temporally expressed following exercise providing new knowledge about the early and late molecular responses to exercise in the equine skeletal muscle transcriptome.</p

Practice Change in Community Pharmacy: A Case Study of Multiple Stakeholders' Perspectives

Objective: To obtain a multi-stakeholder perspective of community pharmacy practice change. Design: Qualitative study. Setting: Community pharmacy in rural Mississippi. Participants: Fourteen key stakeholders of the patient care practice including pharmacists (n=4), support staff (n=2), collaborating providers (n=4), patients (n=3), and a payer (n=1). Intervention: Semi-structured interviews and participant-observation techniques were used. Main outcome measures: Description of the community pharmacy's practice and business model and identification of practice change facilitators. Results: Change facilitators for this practice included: a positive reputation in the community, forming solid relationships with providers, and convenience of patient services. Communication in and outside of the practice, adequate reimbursement, and resource allocation were identified as challenges. Conclusions: This case study is a multi-stakeholder examination of community pharmacy practice change and readers are provided with a real-world example of a community pharmacy's successful establishment of a patient care practice. &nbsp; Type:&nbsp;Case Stud

A genome-wide SNP-association study confirms a sequence variant (g.66493737C>T) in the equine myostatin (MSTN) gene as the most powerful predictor of optimum racing distance for Thoroughbred racehorses

<p>Abstract</p> <p>Background</p> <p>Thoroughbred horses have been selected for traits contributing to speed and stamina for centuries. It is widely recognized that inherited variation in physical and physiological characteristics is responsible for variation in individual aptitude for race distance, and that muscle phenotypes in particular are important.</p> <p>Results</p> <p>A genome-wide SNP-association study for optimum racing distance was performed using the EquineSNP50 Bead Chip genotyping array in a cohort of <it>n </it>= 118 elite Thoroughbred racehorses divergent for race distance aptitude. In a cohort-based association test we evaluated genotypic variation at 40,977 SNPs between horses suited to short distance (≤ 8 f) and middle-long distance (> 8 f) races. The most significant SNP was located on chromosome 18: BIEC2-417495 ~690 kb from the gene encoding myostatin (<it>MSTN</it>) [<it>P</it>_unadj.= 6.96 × 10^-6]. Considering best race distance as a quantitative phenotype, a peak of association on chromosome 18 (chr18:65809482-67545806) comprising eight SNPs encompassing a 1.7 Mb region was observed. Again, similar to the cohort-based analysis, the most significant SNP was BIEC2-417495 (<it>P</it>_unadj.= 1.61 × 10^-9; <it>P</it>_Bonf.= 6.58 × 10^-5). In a candidate gene study we have previously reported a SNP (g.66493737C>T) in <it>MSTN </it>associated with best race distance in Thoroughbreds; however, its functional and genome-wide relevance were uncertain. Additional re-sequencing in the flanking regions of the <it>MSTN </it>gene revealed four novel 3' UTR SNPs and a 227 bp SINE insertion polymorphism in the 5' UTR promoter sequence. Linkage disequilibrium was highest between g.66493737C>T and BIEC2-417495 (<it>r</it>²= 0.86).</p> <p>Conclusions</p> <p>Comparative association tests consistently demonstrated the g.66493737C>T SNP as the superior variant in the prediction of distance aptitude in racehorses (g.66493737C>T, <it>P </it>= 1.02 × 10^-10; BIEC2-417495, <it>P</it>_unadj.= 1.61 × 10^-9). Functional investigations will be required to determine whether this polymorphism affects putative transcription-factor binding and gives rise to variation in gene and protein expression. Nonetheless, this study demonstrates that the g.66493737C>T SNP provides the most powerful genetic marker for prediction of race distance aptitude in Thoroughbreds.</p

Fellowships in Community Pharmacy Research: Experiences of Five Schools and Colleges of Pharmacy

Objective To describe common facilitators, challenges, and lessons learned in 5 schools and colleges of pharmacy in establishing community pharmacy research fellowships. Setting: Five schools and colleges of pharmacy in the United States. Practice description: Schools and colleges of pharmacy with existing community partnerships identified a need and ability to develop opportunities for pharmacists to engage in advanced research training. Practice innovation: Community pharmacy fellowships, each structured as 2 years long and in combination with graduate coursework, have been established at the University of Pittsburgh, Purdue University, East Tennessee State University, University of North Carolina at Chapel Hill, and The Ohio State University. Evaluation: Program directors from each of the 5 community pharmacy research fellowships identified common themes pertaining to program structure, outcomes, and lessons learned to assist others planning similar programs. Results: Common characteristics across the programs include length of training, prerequisites, graduate coursework, mentoring structure, and immersion into a pharmacist patient care practice. Common facilitators have been the existence of strong community pharmacy partnerships, creating a fellowship advisory team, and networking. A common challenge has been recruitment, with many programs experiencing at least one year without filling the fellowship position. All program graduates (n = 4) have been successful in securing pharmacy faculty positions. Conclusion: Five schools and colleges of pharmacy share similar experiences in implementing community pharmacy research fellowships. Early outcomes show promise for this training pathway in growing future pharmacist-scientists focused on community pharmacy practice

Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training

<p>Abstract</p> <p>Background</p> <p>Digital gene expression profiling was used to characterize the assembly of genes expressed in equine skeletal muscle and to identify the subset of genes that were differentially expressed following a ten-month period of exercise training. The study cohort comprised seven Thoroughbred racehorses from a single training yard. Skeletal muscle biopsies were collected at rest from the <it>gluteus medius </it>at two time points: T₁- untrained, (9 ± 0.5 months old) and T₂- trained (20 ± 0.7 months old).</p> <p>Results</p> <p>The most abundant mRNA transcripts in the muscle transcriptome were those involved in muscle contraction, aerobic respiration and mitochondrial function. A previously unreported over-representation of genes related to RNA processing, the stress response and proteolysis was observed. Following training 92 tags were differentially expressed of which 74 were annotated. Sixteen genes showed increased expression, including the mitochondrial genes <it>ACADVL</it>, <it>MRPS21 </it>and <it>SLC25A29 </it>encoded by the nuclear genome. Among the 58 genes with decreased expression, <it>MSTN</it>, a negative regulator of muscle growth, had the greatest decrease.</p> <p>Functional analysis of all expressed genes using FatiScan revealed an asymmetric distribution of 482 Gene Ontology (GO) groups and 18 KEGG pathways. Functional groups displaying highly significant (<it>P </it>< 0.0001) increased expression included mitochondrion, oxidative phosphorylation and fatty acid metabolism while functional groups with decreased expression were mainly associated with structural genes and included the sarcoplasm, laminin complex and cytoskeleton.</p> <p>Conclusion</p> <p>Exercise training in Thoroughbred racehorses results in coordinate changes in the gene expression of functional groups of genes related to metabolism, oxidative phosphorylation and muscle structure.</p