bluuebunny/crossref_metadata_2025 huggingface dataset:
Mental Health Response to Acute Stress Following Wilderness Disaster
Authors: Mortimer Amanda R.
Published: December 2010

Expedition physicians should be prepared to respond to traumatic stress disorders following wilderness disasters. Stress disorder symptoms include re-experiencing the traumatic event, avoiding stimuli associated with the traumatic event, and increased physical arousal. These symptoms can also be seen in healthy individuals, and should only lead to disorder diagnosis when they cause distress or impairment. Treatment options for stress disorders include observation, psychological interventions, and medication. Approximately half of those with diagnosable stress disorders will return to nondiagnosable status over time without therapeutic intervention. Psychological interventions with empirical support concentrate on providing either noninvasive support in the short term, such as psychological first aid (PFA), or more long-term controlled re-experiencing of the precipitating trauma, such as many exposure-based therapies. Exposure-based treatments can result in temporary increases in symptoms before long-term gains are realized, so they are not recommended for wilderness settings. Medications to treat stress disorders include benzodiazepines, propranolol, and antidepressant medications. Benzodiazepines are often carried in wilderness first aid kits, but they provide very limited stress disorder symptom relief. Propranolol is being explored as a method of preventing traumatic stress disorders, but the data are not currently conclusive. Antidepressant medications are a good long-term strategy for stress disorder treatment, but they are of limited utility in wilderness settings as they are unlikely to be included in expedition medical kits and require approximately 4 weeks of administration for symptom reduction. Recommendations for wilderness treatment of stress disorders focus on increasing knowledge of stress disorder diagnosis and PFA.
Rhabdomyolysis and Hyponatremia: A Cluster of Five Cases at the 161-km 2009 Western States Endurance Run
Authors: Bruso Jessica Rose , Hoffman Martin D. , Rogers Ian R. , Lee Linda , Towle Gary , Hew-Butler Tamara
Published: December 2010

Objective

Five of 400 starters of the 2009 Western States Endurance Run (WSER) were hospitalized with hyponatremia and rhabdomyolysis. This article explores the risk factors associated with development of hyponatremia and rhabdomyolysis.

Methods

Data on the 5 cases were collected retrospectively from the runners and medical records, and all race participants were invited to complete a post-race survey. Characteristics of the cases were compared with the other race participants.

Results

The 5 runners developing hyponatremia with rhabdomyloysis were men with a mean (±SD) age of 39 ± 7 years. Presenting complaints included neurological symptoms among 3 and nausea among 3. Compared with those runners not developing hyponatremia with rhabdomyolysis, the cases tended to be younger, faster, more likely to have sustained an injury which interfered with training prior to the race, and were more likely to use nonsteroidal anti-inflammatory drugs (NSAIDs) during the race. The 3 of 5 cases progressing to acute renal failure were characterized by higher initial blood urea nitrogen (BUN; 43–69 vs 18–23 mg/dL) and creatinine (2.8–4.9 vs 1.1–1.2 mg/dL) levels but were not distinguished by creatinine phosphokinase (CPK) concentrations.

Conclusions

Over 1% of participants in the 2009 WSER were hospitalized with hyponatremia in combination with rhabdomyolysis. These individuals tended to be younger, faster, more likely to have had an injury that interfered with training, and more likely to have used NSAIDs during the race. Higher initial BUN and creatinine levels, but not CPK concentrations, distinguished those 3 who progressed to acute renal failure.
Is the Puerto Rican Racer, Alsophis portoricensis, Really Harmless? A Case Report Series
Authors: García-Gubern Carlos , Bello Raúl , Rivera Victor , Rocafort Angel , Colon-Rolon Lissandra , Acosta-Tapia Hector
Published: December 2010

Puerto Rico (PR) is home to 10 indigenous species of snake. Alsophis portorricensis has traditionally been considered harmless. In 1961, Hageman classified A portorricensis as somewhere between “venomous” and “nonvenomous.” In 1966, Heatwole and Banuchi reported the only case found in the literature of a “venomous” bite from Alsophis portorricensis. Only 6 cases of snakebite were reported to the PR Department of Health from 1998 to 2007; ecchymosis, swelling, and abnormal vital signs were noted in all of the cases. In 5 of these 6 cases, the captured snake was, in fact, identified as Alsophis portorricensis of the Colubridae family; in the remaining case, the description strongly suggests that it was the same species as the others. All bites were inflicted on fingers, which were presented for evaluation from 2 to 24 hours after the event. All documented cases report that the bite lasted from 1 to 4 minutes. All of the victims presented with localized pain and ecchymosis. Localized edema extended from the hand to the elbow in 4 cases, and up to the shoulder in 2 cases. All patients were treated symptomatically, observed at the Emergency Department (ED), and discharged home within 24 hours after the ED evaluation. All patients reported the resolution of symptoms within 1 week. Traditionally, PR has not been associated with any dangerous species of snake. These cases show that the second most abundant snake on the island can inflict a venomous bite, with local and systemic symptoms that warrant adequate preparation by the medical community.
Accuracy of Internet Recommendations for Prehospital Care of Venomous Snake Bites
Authors: Barker Sarah , Charlton Nathan P. , Holstege Christopher P.
Published: December 2010

Objective

To evaluate the accuracy of Internet information regarding the prehospital care of venomous snake bites.

Methods

Two major search engines were used to identify 48 Web sites regarding 6 prehospital treatment options for snake bite (removal of constrictive devices, ice, heat, electric shock, incision, and suction). Web sites were evaluated for their quality using the Health on the Net (HON) seal and Journal of the American Medical Association ( JAMA) benchmarks.

Results

Of the 48 Web sites reviewed, 26 (54.1%) contained inappropriate recommendations. The remaining 22 Web sites were appropriate regarding all modalities addressed. Among the Web sites reviewed, inappropriate treatment recommendations included: suction (14); ice (6); incision (4); electric shock (1). Five Web sites that met all 4 JAMA benchmarks and the HON seal included 3 inappropriate treatment recommendations. Conversely, the 5 Web sites that met none of the JAMA benchmarks nor included the HON seal included only 2 inappropriate treatment measures.

Conclusion

This study highlights the variety of misinformation available on the Internet regarding prehospital care of snake bites, and the unreliability of the HON seal and JAMA benchmarks as markers of accuracy. As the Internet becomes an increasing source of medical information for both the public and clinicians, the importance of accurate Web sites becomes imperative. Clinicians and lay people should be aware of the high variability of Internet information regarding snake bite prehospital care.
Expedition Medicine—the Risk of Illness and Injury
Authors: Lyon R.M. , Wiggins C.M.
Published: December 2010

Objective

Expeditions organized by commercial companies are becoming increasingly popular. Charity expeditions take inexperienced participants on trips all over the world, with participants being sponsored to raise funds for charitable causes. The incidence of illness or injury while participating in charity expeditions is unknown. The objective of this study is to report the incidence and severity of illness and injuries occurring on worldwide charity expeditions.

Methods

Retrospective, observational study reviewing expedition medical reports from 232 expeditions organized by a single commercial expedition company for a 5-year period (January 1, 2004 through December 31, 2008).

Results

Complete expedition medical reports were available for 210 (91%) trips, involving 4077 participants over 1524 expedition days. Expeditions reported a total of 1564 incidents over 42 482 participant-days in the field, including days spent traveling to the expedition site. In 1465 (94%) cases “minor” injury or illness was recorded, 79 (5%) “moderate,” and 20 (1%) “major” in severity. No deaths were reported. Gastrointestinal upset was the commonest reported minor condition and severe acute mountain sickness the commonest major condition. Overall, the incidence per 1000 participant-days of minor illness or injury was 34.48, moderate illness or injury 1.86, and major illness or injury 0.47.

Conclusion

The risk of sustaining major injury or illness on an overseas charity expedition is low. The consequences of becoming injured or unwell in a remote environment can be serious, and appropriate medical care is required.
Postexercise Peripheral Oxygen Saturation After Completion of the 6-Minute Walk Test Predicts Successfully Reaching the Summit of Aconcagua
Authors: Lazio Matthew P. , Van Roo Jon D. , Pesce Carlos , Malik Sanjeev , Courtney D. Mark
Published: December 2010

Objective

The 6-minute walk test (6MWT) is a single measurement of functional status in patients with cardiovascular disease. It has not been studied at high altitude. We investigate the screening value of 6-minute walk distance (6MWD) and postexercise vital sign (VS) measurements as predictors of successfully reaching the summit or development of acute mountain sickness (AMS) on Aconcagua (6962 m).

Methods

Prospective observational cohort in Aconcagua Provincial Park, Argentina. Adults climbing the normal route who registered with base camp physicians were included. There were no exclusion criteria. VSs were measured before (resting) and after (postexercise) completion of 6MWT while volunteers acclimatized at Plaza de Mulas base camp (4365 m). Volunteers proceeded towards the summit at their own pace and upon descent returned a questionnaire with maximum altitude reached and Lake Louise AMS Self-report Score (LLSelf).

Results

One hundred twenty-four volunteers completed the 6MWT. Sixty-four volunteers (51.6%) completed questionnaires; 56% summited. Median LLSelf was 4 (IQR: 3.0–6.5). There was no association between any resting or postexercise VS measurements and AMS. However, mean postexercise SpO2 was 80.8% in summiters and 76.4% in nonsummiters, a difference of −4.4% (95% CI: −6.7 to −2.0, p = 0.0005). Postexercise SpO2 < 75% had 97.2% sensitivity and negative likelihood ratio of 0.086 in predicting the outcome of successfully reaching the summit: only one climber with SpO2 < 75% successfully reached the summit.

Conclusions

This study provides the first published data on 6MWD recorded in the field at high altitude. Postexercise SpO2 < 75% may be a useful screening test for predicting the outcome of successfully reaching the summit of Aconcagua.
Coati (Nasua nasua) Attacks on Humans: Case Report
Authors: Bittner Guilherme Canho , Ritter Hans Nelise , Hans Neto Günter , Morais Monique Oliveira , Hans Filho Günter , Haddad Vidal
Published: December 2010

Coatis [including Nasua nasua, the ring-tailed coati], are medium-sized mammals widely distributed in the Americas. They are social animals, whose normal diet includes insects, fruits, and small vertebrates, and rarely prey on larger sized animals. There are, to our knowledge, no reports in the medical literature of attacks on humans. This report describes a coati attack on 2 children in their home. The children sustained deep scratches and bites. The animal may have injured the humans in a defensive strike, but motivation for attack was uncertain. Coati attacks may occur in places where there is interaction between these mammals and humans.
Complications of Steroid Use on Mt Everest
Authors: Subedi Bishnu Hari , Pokharel Jhapindra , Goodman Torrey L. , Amatya Sanuraja , Freer Luanne , Banskota Nalin , Johnson Eric , Basnyat Buddha
Published: December 2010

Steroids are used for the prevention and treatment of high-altitude illnesses. However, these agents can cause significant side effects. We report a case of altered mental status, gastrointestinal bleeding, skin rash, and avascular necrosis in a climber taking prophylactic dexamethasone prior to an attempt to climb Mt Everest. High-altitude cerebral edema (HACE), steroid toxicity, and acute adrenal crisis can have similar clinical presentations. Differentiating between these life-threatening conditions at high altitude is essential for successful treatment.
10% Povidone-Iodine May Be a Practical Field Water Disinfectant
Authors: Heiner Jason D. , Hile David C. , Demons Samandra T. , Wedmore Ian S.
Published: December 2010

Objective

A paucity of data exists regarding the use of iodophores such as povidone-iodine (PVI) to disinfect water. We sought to determine a practical minimal disinfecting concentration of 10% PVI over different contact times and temperatures when added to water inoculated with E. coli.

Methods

1:100, 1:1,000, and 1:10,000 dilutions of 10% PVI were created. Escherichia coli was exposed to these dilutions for 5, 15, and 30 minutes at 10, 20, and 30°C. Bactericidal activity was neutralized with 0.5% sodium thiosulfate. Mean viable colony forming units (CFUs) was determined after triplicate plating on Luria-bertani agar and 24 hours of incubation at 37°C. Effective bactericidal activity was defined as a 5-log reduction.

Results

Of the 200,000 E. coli plated, no CFUs were observed after exposure to the 1:100 dilution. After 5 minutes of contact time with the 1:1,000 dilution, at 10°C CFUs were too numerous to count (TNTC), at 20°C the mean CFU count was 92 (standard error ±11), and at 30°C the mean CFU count was 25 (standard error ±8). No CFUs were observed after 15 minutes of exposure to the 1:1,000 dilution across experimental temperatures. The 1:10,000 dilution always yielded CFU growth that was TNTC.

Conclusions

The lowest disinfecting concentration of 10% PVI was the 1:1,000 dilution at 15 minutes of contact time. This supports the use of PVI for water disinfection against E. coli, the organism most commonly responsible for traveler's diarrhea. Further studies may assess its effectiveness against more virulent water borne pathogens.
Response-Retrieval and Negative Priming
Authors: Ihrke Matthias , Behrendt Jörg , Schrobsdorff Hecke , Michael Herrmann J. , Hasselhorn Marcus
Published: December 2010

In a recent debate concerning the origin of the negative priming (NP) effect, evidence for the involvement of retrieval processes during the prime episode has accumulated. Rothermund, Wentura, and De Houwer (2005) explain the effect as a product of a conflict between retrieved and current response. Since specific properties of the involved encoding and retrieval mechanisms were not investigated so far, we extend the response-retrieval framework by asking if encoding during prime processing and retrieval-specific processes during probe processing have a modulating influence on the priming effects. In an overlapping-picture task experiment with an explicit variation of the role of the objects in prime and probe, we reproduce the response-retrieval-specific Response-retrieval × Priming interaction but find a modulation caused by the role of the repeated object in the probe trial. This modulation manifests in a vanishing interaction when the repeated object is a distractor in the probe. We interpret these findings in support of the response-retrieval theory of NP and conclude that the retrieval mechanism is more flexible than previously believed since it is sensitive to relevance of the repeated object regarding the experimental task.
Holistic Representation of Unit Fractions
Authors: Ganor-Stern Dana , Karasik-Rivkin Irina , Tzelgov Joseph
Published: December 2010

The present study examined the processing of unit fractions and the extent to which it is affected by context. Using a numerical comparison task we found evidence for a holistic representation of unit fractions when the immediate context of the fractions was emphasized, that is when the stimuli set included in addition to the unit fractions also the numbers 0 and 1. The holistic representation was indicated by the semantic congruity effect for comparisons of pairs of fractions and by the distance effect in comparisons of a fraction and 0 and 1. Consistent with previous results (Bonato, Fabbri, Umilta, & Zorzi, 2007) there was no evidence for a holistic representation of unit fractions when the stimulus set included only fractions. These findings suggest that fraction processing is context-dependent. Finally, the present results are discussed in the context of processing other complex numbers beyond the first decade.
Warnings Reduce False Memories for Missing Aspects of Events
Authors: Gerrie Matthew P. , Garry Maryanne
Published: December 2010

When people see movies with some parts missing, they falsely recognize many of the missing parts later. In two experiments, we examined the effect of warnings on people’s false memories for these parts. In Experiment 1, warning subjects about false recognition before the movie (forewarnings) reduced false recognition, but warning them after the movie (postwarnings) reduced false recognition to a lesser extent. In Experiment 2, the effect of the warnings depended on the nature of the missing parts. Forewarnings were more effective than postwarnings in reducing false recognition of missing noncrucial parts, but forewarnings and postwarnings were similarly effective in reducing false recognition of crucial missing parts. We use the source monitoring framework to explain our results.
The Multinomial Model of Prospective Memory
Authors: Horn Sebastian S. , Bayen Ute J. , Smith Rebekah E. , Boywitt C. Dennis
Published: December 2010

The objective of this research was to provide additional experimental validation of the multinomial processing tree (MPT) model of event-based prospective memory ( Smith & Bayen, 2004 ). In particular, the parameters that measure trial-type detection in the ongoing task were examined. In three experiments with different response instructions, event-based prospective memory tasks were embedded in ongoing color-matching tasks. The results support the validity of the MPT model, that is, manipulations of ongoing-task difficulty affected the ongoing-task parameters of the MPT model, while leaving the estimates for the prospective and the retrospective components of prospective memory unaffected.
Response Interference in Compatibility Tasks
Authors: Berthet Vincent , Kop Jean-Luc , Kouider Sid
Published: December 2010

Affective priming (AP) is a well-established phenomenon in which performance to a valenced target is typically better when it is preceded by an affectively congruent prime than when it is preceded by an incongruent prime. Several studies have emphasized a strong similarity between AP and Stroop suggesting that both are driven by response interference. The present study investigated this hypothesis by testing whether a general prediction of the response interference model was verified in the two tasks. This prediction refers to target strength and states that the size of compatibility effects should increase as the strength of the relevant information decreases. In four experiments, we show that this general prediction of the response interference model was verified in AP and Stroop when the strength of the relevant information was manipulated at the perceptual level (Experiments 1 and 2), while the opposite pattern was observed when this variable was manipulated at the semantic level (Experiments 3 and 4). While the results do not undermine the hypothesis that AP and Stroop effects are governed by response interference, they suggest that the model should be refined in order to account for differential effects of target strength in compatibility tasks.
Does the Name-Race Implicit Association Test Measure Racial Prejudice?
Authors: van Ravenzwaaij Don , van der Maas Han L. J. , Wagenmakers Eric-Jan
Published: December 2010

Research using the Implicit Association Test (IAT) has shown that names labeled as Caucasian elicit more positive associations than names labeled as non-Caucasian. One interpretation of this result is that the IAT measures latent racial prejudice. An alternative explanation is that the result is due to differences in in-group/out-group membership. In this study, we conducted three different IATs: one with same-race Dutch names versus racially charged Moroccan names; one with same-race Dutch names versus racially neutral Finnish names; and one with Moroccan names versus Finnish names. Results showed equivalent effects for the Dutch-Moroccan and Dutch-Finnish IATs, but no effect for the Finnish-Moroccan IAT. This suggests that the name-race IAT-effect is not due to racial prejudice. A diffusion model decomposition indicated that the IAT-effects were caused by changes in speed of information accumulation, response conservativeness, and non-decision time.
The effectiveness of personal development planning
Authors: Bullock Kate , Jamieson Ian
Published: December 2010

Over recent years, the development of strategies in schools and colleges to support individual student needs and encourage autonomous learning has influenced the work of most teachers and tutors. Personal Development Plans (PDPs) draw on good practice in careers guidance and on many of the educational initiatives introduced over the past decade, particularly, Records of Achievement (RoAs) and the Technical and Vocational Education Initiative (TVEI). The focus of PDPs is a dialogue between student and tutor which clarifies choices, identifies goals and plans appropriate actions. This process aims to raise personal understanding and motivation and, ultimately, school effectiveness. This article arises from an evaluation of the Personal Development Plans (PDP) project in Wiltshire.

The Wiltshire project was initiated in January 1992, and was a joint venture by the Careers Guidance Service, the local authority advisory service, TVEI and Wiltshire Training and Enterprise Council (TEC). These agencies perceived PDPs as a co‐operative project which, first, could make a highly positive contribution to the TEC's aim of promoting and sustaining a lifelong learning culture in the county; second, could provide the impetus to attain the National Targets for Education and Training (NTETs) which have been articulated for the year 2000 (DES, 1991) and hence, increase school effectiveness; and third, would ease the introduction of youth credits in the county by enabling 16‐year‐olds to make well‐informed decisions (Ruthven and Pike, 1993). Findings from the evaluation of Wiltshire PDPs are discussed. Positive strategies for supporting PDPs are suggested, the nature of the one‐to‐one dialogue is probed, and a hierarchy of concerns for practitioners is suggested.
Constitutive activated Cdc42-associated kinase (Ack) phosphorylation at arrested endocytic clathrin-coated pits of cells that lack dynamin
Authors: Shen Hongying , Ferguson Shawn M. , Dephoure Noah , Park Ryan , Yang Yan , Volpicelli-Daley Laura , Gygi Steven , Schlessinger Joseph , De Camilli Pietro
Published: December 2010

Clathrin-mediated endocytosis is a fundamental cellular process conserved from yeast to mammals and is an important endocytic route for the internalization of many specific cargos, including activated growth factor receptors. Here we examined changes in tyrosine phosphorylation, a representative output of growth factor receptor signaling, in cells in which endocytic clathrin-coated pits are frozen at a deeply invaginated state, that is, cells that lack dynamin (fibroblasts from dynamin 1, dynamin 2 double conditional knockout mice). The major change observed in these cells relative to wild-type cells was an increase in the phosphorylation state, and thus activation, of activated Cdc42-associated kinase (Ack), a nonreceptor tyrosine kinase. Ack is concentrated at clathrin-coated pits, and binds clathrin heavy chain via two clathrin boxes. RNA interference–based approaches and pharmacological manipulations further demonstrated that the phosphorylation of Ack requires both clathrin assembly into endocytic clathrin-coated pits and active Cdc42. These findings reveal a link between progression of clathrin-coated pits to endocytic vesicles and an activation–deactivation cycle of Ack.
Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq
Authors: Wu Zhengpeng , Wang Xi , Zhang Xuegong
Published: December 2010

Motivation: RNA-Seq technology based on next-generation sequencing provides the unprecedented ability of studying transcriptomes at high resolution and accuracy, and the potential of measuring expression of multiple isoforms from the same gene at high precision. Solved by maximum likelihood estimation, isoform expression can be inferred in RNA-Seq using statistical models based on the assumption that sequenced reads are distributed uniformly along transcripts. Modification of the model is needed when considering situations where RNA-Seq data do not follow uniform distribution.

Results: We proposed two curves, the global bias curve (GBC) and the local bias curves (LBCs), to describe the non-uniformity of read distributions for all genes in a transcriptome and for each gene, respectively. Incorporating the bias curves into the uniform read distribution (URD) model, we introduced non-URD (N-URD) models to infer isoform expression levels. On a series of systematic simulation studies, the proposed models outperform the original model in recovering major isoforms and the expression ratio of alternative isoforms. We also applied the new model to real RNA-Seq datasets and found that its inferences on expression ratios of alternative isoforms are more reasonable. The experiments indicate that incorporating N-URD information can improve the accuracy in modeling and inferring isoform expression in RNA-Seq.

Contact:  zhangxg@tsinghua.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Lipid Data Analyzer: unattended identification and quantitation of lipids in LC-MS data
Authors: Hartler Jürgen , Trötzmüller Martin , Chitraju Chandramohan , Spener Friedrich , Köfeler Harald C. , Thallinger Gerhard G.
Published: December 2010

Motivation: The accurate measurement of the lipidome permits insights into physiological and pathological processes. Of the present high-throughput technologies, LC-MS especially bears potential of monitoring quantitative changes in hundreds of lipids simultaneously. In order to extract valuable information from huge amount of mass spectrometry data, the aid of automated, reliable, highly sensitive and specific analysis algorithms is indispensable.

Results: We present here a novel approach for the quantitation of lipids in LC-MS data. The new algorithm obtains its analytical power by two major innovations: (i) a 3D algorithm that confines the peak borders in m/z and time direction and (ii) the use of the theoretical isotopic distribution of an analyte as selection/exclusion criterion. The algorithm is integrated in the Lipid Data Analyzer (LDA) application which additionally provides standardization, a statistics module for results analysis, a batch mode for unattended analysis of several runs and a 3D viewer for the manual verification. The statistics module offers sample grouping, tests between sample groups and export functionalities, where the results are visualized by heat maps and bar charts. The presented algorithm has been applied to data from a controlled experiment and to biological data, containing analytes distributed over an intensity range of 106. Our approach shows improved sensitivity and an extremely high positive predictive value compared with existing methods. Consequently, the novel algorithm, integrated in a user-friendly application, is a valuable improvement in the high-throughput analysis of the lipidome.

Implementation and availability: The Java application is freely available for non-commercial users at http://genome.tugraz.at/lda. Raw data associated with this manuscript may be downloaded from ProteomeCommons.org Tranche using the following hash: ZBh3nS5bXk6I/Vn32tB5Vh0qnMpVIW71HByFFQqM0RmdF4/4Hcn H3Wggh9kU2teYVOtM1JWwHIeMHqSS/bc2yYNFmyUAAAAAAACl DQ ==

Contact:  Gerhard.Thallinger@tugraz.at

Supplementary information:  Supplementary data are available from Bioinformatics online.
Multi-level mixed effects models for bead arrays
Authors: Kim Ryung S. , Lin Juan
Published: December 2010

Motivation: Bead arrays are becoming a popular platform for high-throughput expression arrays. However, the number of the beads targeting a transcript and the variation of their intensities differ from sample to sample in these arrays. This property results in different accuracy of expression intensities of a transcript across arrays.

Results: We provide evidence, with publicly available spike-in data, that the false discovery rate of differential expression is reduced by modeling bead-level variability with a multi-level mixed effects model. We compare the performance of our proposed model to existing analysis methods for bead arrays: the unweighted t-test and other weighted methods. Additionally, we provide theoretical insights into when the multi-level mixed effects model outperforms other methods. Finally, we provide a software program for differential expression analysis using the multi-level mixed effects model that analyzes tens of thousands of genes efficiently.

Availability: The software program is freely available on web at http://ephpublic.aecom.yu.edu/sites/rkim/Supplementary.

Contact:  ryung.kim@einstein.yu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Ocean surface characteristics influence recruitment variability of populations of northern shrimp (Pandalus borealis) in the Northwest Atlantic
Authors: Ouellet Patrick , Fuentes-Yaco César , Savard Louise , Platt Trevor , Sathyendranath Shubha , Koeller Peter , Orr David , Siegstad Helle
Published: December 2010

Ouellet, P., Fuentes-Yaco, C., Savard, L., Platt, T., Sathyendranath, S., Koeller, P., Orr, D., and Siegstad, H. 2011. Ocean surface characteristics influence recruitment variability of populations of northern shrimp (Pandalus borealis) in the Northwest Atlantic. – ICES Journal of Marine Science, 68: 737–744. Remotely sensed data were used to derive simple ecosystem indicators for four regions of the Northwest Atlantic to test the hypothesis that sea surface temperatures (SSTs) and spring phytoplankton bloom characteristics (initiation, timing, intensity, and duration) have a significant influence on larval survival and recruitment of northern shrimp (Pandalus borealis). For all years (1998–2007) and regions, hatching was after the initiation of the bloom and before or after the bloom reached its maximum intensity. The results suggest that the best survival of larvae is associated with high warming rates of SST following hatching, but in very cold environments, warm temperatures at hatching seem to be important for larval survival. The analyses also indicate that larval survival is supported by an early, long phytoplankton bloom which attains high concentrations of chlorophyll a. The results demonstrate the potential of remotely sensed data for deriving simple population-specific ecosystem indicators for potential use in building operational recruitment models for predicting changes in northern shrimp abundance.
Ideal Permissive Hypotension to Resuscitate Uncontrolled Hemorrhagic Shock and the Tolerance Time in Rats
Authors: Li Tao , Zhu Yu , Hu Yi , Li Lijie , Diao Youfang , Tang Jing , Liu Liangming
Published: December 2010

Background

Studies have shown that permissive hypotension for uncontrolled hemorrhagic shock can result in good resuscitation outcome. The ideal target mean arterial pressure (MAP) and the tolerance time for permissive hypotension have not been determined.

Methods

To elucidate the ideal target MAP and tolerance time for permissive hypotension with uncontrolled hemorrhagic shock rats, the effects of different target MAPs (40, 50, 60, 70, 80, and 100 mmHg) and 60-, 90-, and 120-min permissive hypotension (50 mmHg) on uncontrolled hemorrhagic shock were observed.

Results

Rats in normotensive groups (80 and 100 mmHg) had increased blood loss (101%, 126% of total blood volume), decreased hematocrit, decreased vital organ (liver and kidney) and mitochondrial function, and decreased animal survival rate (1 of 10). Rats in the 50- and 60-mmHg target MAP groups had decreased blood loss (52% and 69%, respectively), good hematocrit and vital organ and mitochondrial function, stable hemodynamics, and increased animal survival (8 of 10 and 6 of 10, respectively). Rats in the 40-mmHg target MAP group, although having decreased blood loss (39%), appeared to have very inferior organ function and animal survival (2 of 10). Animal survival (1 of 10) and vital organ function in the 120-min permissive hypotension group were significantly inferior to the 60- and 90-min groups. The 60- and 90-min groups had similar animal survival (8 of 10 and 6 of 10) and vital organ function.

Conclusion

A target resuscitation pressure of 50-60 mmHg is the ideal blood pressure for uncontrolled hemorrhagic shock. Ninety minutes of permissive hypotension is the tolerance limit; 120 min of hypotensive resuscitation can cause severe organ damage and should be avoided.
Impaired Visual Hand Recognition in Preoperative Patients during Brachial Plexus Anesthesia
Authors: Silva Stein , Loubinoux Isabelle , Olivier Michel , Bataille Benoîmt , Fourcade Olivier , Samii Kamran , Jeannerod Marc , Démonet Jean-Francois
Published: December 2010

Background

Perceptual illusions described in healthy subjects undergoing regional anesthesia (RA) are probably related to short-term plastic brain changes. We addressed whether performance on an implicit mental rotation task reflects these RA-induced changes in body schema brain representations. Studying these changes in healthy volunteers may shed light on normal function and the central mechanisms of pain.

Methods

Performance pattern was studied in upper limb-anesthetized subjects on a left/right hand judgment task, which is known to involve motor imagery processes relating to hand posture. Three conditions were used: control (i.e., absence of deafferentation), RA (i.e., deafferentation), and vision (i.e., deafferentated limb exposed to view). To limit potential bias such as order effect, the control state was recorded in a randomized manner.

Results

All subjects described perceptual illusions of their anesthetized limb. They were slower and less accurate on the task during RA compared with control. Response patterns were similar in all conditions, suggesting sensitivity of performance to arm/hand biomechanical constraints. Vision was associated with an increase in the proportion of correct responses and a reduction of the response times in hand judgment and was accompanied by disappearance of the lateralization of the underlying mental representations, which was identified during RA.

Conclusions

These results suggest the following: (1) the right/left judgment task involves mental simulation of hand movements, (2) underlying mental representations and their neural substrates are subject to acute alterations after RA, and (3) the proprioceptive deficit induced by RA is influenced by the subject's ability to see the anesthetized limb.
Taxonomy, ontogeny and molecular phylogeny of Anteholosticha marimonilata spec. nov. (Ciliophora, Hypotrichida) from the Yellow Sea, China
Authors: Xu Yuan , Huang Jie , Hu Xiaozhong , Al-Rasheid Khaled A. S. , Song Weibo , Warren Alan
Published: December 2010

The morphology, morphogenesis and molecular phylogeny of the marine ciliated protozoan Anteholosticha marimonilata spec. nov., isolated from mollusc-farming waters of the Yellow Sea, Qingdao, PR China, were investigated using microscopic observations of live and protargol-impregnated specimens and by small subunit rRNA gene sequence analysis. The novel species could be distinguished by the following features: an elongated elliptical body, in vivo size 80–160 µm × 30–50 µm; an adoral zone consisting of about 36 membranelles; three frontal, one parabuccal, one buccal, two frontoterminal and usually two pretransverse ventral cirri; 10–13 transverse cirri; a midventral complex composed of 12–17 pairs of cirri only, terminating in posterior 1/5; four or five dorsal kineties; two types of colourless cortical granules; four to nine moniliform macronuclear nodules and one to three micronuclei, and a contractile vacuole positioned at mid-body. Hitherto, the ontogenesis of the genus Anteholosticha has been regarded as rather diverse, which was confirmed by the morphogenetic processes of this novel species. The most noteworthy feature of A. marimonilata was that the proter retained almost the entire parental adoral zone except for a few proximal membranelles that were renewed in situ. The SSU rRNA gene sequence information clearly discriminated this isolate from its congeners. Molecular phylogenetic analyses demonstrated, with high statistical support, that A. marimonilata branched as a sister lineage to the Nothoholosticha–Pseudokeronopsis clade and hence belongs to the core part of the order Urostylida.
Nitratireductor aquimarinus sp. nov., isolated from a culture of the diatom Skeletonema costatum, and emended description of the genus Nitratireductor
Authors: Jang Gwang Il , Hwang Chung Yeon , Cho Byung Cheol
Published: December 2010

Two Gram-negative-staining, aerobic bacterial strains, designated CL-SC21T and CL-SC22, were isolated from a culture of the diatom Skeletonema costatum (Korean Marine Microalgae Culture Center, KMMCC strain B-396) established from the East Sea, Korea. The two novel strains shared 99.9 % 16S rRNA gene sequence similarity. Analysis of the 16S rRNA gene sequences showed an affiliation with the genus Nitratireductor, with the strains sharing 96.5–97.5 % similarity with the type strains of recognized species of the genus Nitratireductor and being most closely related to Nitratireductor aquibiodomus NL21T. Phylogenetic analyses of the 16S rRNA gene sequences showed that strain CL-SC21T together with strain CL-SC22 belonged to the genus Nitratireductor and formed a robust clade among closely related Nitratireductor species. The polar lipids comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, two unidentified aminophospholipids, an unidentified aminolipid, an unidentified phospholipid and five unidentified lipids. Ubiquinone 10 was the major quinone. The major cellular fatty acids of strains CL-SC21T and CL-SC22 were C18 : 1ω7c (70.6–72.3 %) and C19 : 0ω8c cyclo (10.9–11.8 %). The genomic DNA G+C contents of strains CL-SC21T and CL-SC22 were 56.7 and 57.1 mol%, respectively. The level of DNA–DNA relatedness between strains CL-SC21T and CL-SC22 was 86 % (reciprocal 91 %), indicating that the two isolates represented a single species. However, levels of DNA–DNA relatedness between N. aquibiodomus NL21T and strains CL-SC21T and CL-SC22 were 28 % (reciprocal 45 %) and 25 % (reciprocal 50 %), respectively. Phylogenetic analysis and the results of biochemical tests showed that strains CL-SC21T and CL-SC22 were different from all recognized species of the genus Nitratireductor. Thus, strains CL-SC21T and CL-SC22 represent a novel species of the genus Nitratireductor, for which the name Nitratireductor aquimarinus sp. nov. is proposed. The type strain is CL-SC21T ( = KCCM 90090T = JCM 17288T).
Streptomyces indicus sp. nov., an actinomycete isolated from deep-sea sediment
Authors: Luo Yingxue , Xiao Jing , Wang Yin , Xu Jing , Xie Shujie , Xu Jun
Published: December 2010

The taxonomic position of an actinomycete isolated from deep-sea sediment from the Indian Ocean was determined by using a polyphasic approach. The presence of iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0 as the major cellular fatty acids, ll-diaminopimelic acid as the characteristic diamino acid, and MK-9(H4, H6 and H8) as the major menaquinones supported the affiliation of strain IH32-1T to the genus Streptomyces. Comparison of 16S rRNA gene sequences showed that strain IH32-1T exhibited highest similarities to the type strains of Streptomyces globosus (97.6 %) and Streptomyces toxytricini (97.6 %). However, DNA–DNA relatedness values between strain IH32-1T and the type strains of S. globosus and S. toxytricini were determined as 55.2±4.7 and 38.3±2.5 %, respectively. Based on its chemotaxonomic, phenotypic and genotypic characteristics, strain IH32-1T is considered to represent a novel species in the genus Streptomyces, for which the name Streptomyces indicus sp. nov. is proposed. The type strain is IH32-1T ( = DSM 42001T = CGMCC 4.5727T).
Three‐dimensional modelling of bond behaviour between concrete and FRP reinforcement
Authors: Salomoni Valentina , Mazzucco Gianluca , Pellegrino Carlo , Majorana Carmelo
Published: December 2010

Purpose

The purpose of this paper is to investigate the bond behaviour between fiber reinforced polymer (FRP) sheets and concrete elements, starting from available experimental evidences, through a calibrated and upgraded 3D mathematical‐numerical model.

Design/methodology/approach

The complex mechanism of debonding/peeling failure of FRP reinforcement is studied within the context of damage mechanics to appropriately catch transversal effects and developing a more realistic and comprehensive study of the delamination process. The FE ABAQUS© code has been supplemented with a numerical procedure accounting for Mazars's damage law inside the contact algorithm.

Findings

It has been shown that such an approach is able to catch the delamination evolution during loading processes as well.

Originality/value

A Drucker‐Prager constitutive law is adopted for concrete whereas FRP elements are assumed to behave in a linear‐elastic manner, possibly undertaking large strains/displacements. Surface‐to‐surface contact conditions have been applied between FRP and adjacent concrete, including the enhancement given by the strain‐softening law according to Mazars' damage model. The procedure has been introduced to describe the coupled behaviour between concrete, FRP and adhesive resulting in specific bonding‐debonding features under different load levels.
Finite element analysis of delamination of a composite component with the cohesive zone model technique
Authors: Lampani Luca
Published: December 2010

Purpose

The purpose of this paper is to assess a numerical tool to simulate and predict the onset and the propagation of the delaminations in a composite structure.

Design/methodology/approach

The approach to the work is done through the cohesive zone model technique applied to the finite element method.

Findings

Double cantilever beam, end notched flexure and mixed mode bending tests have been performed and correlated to benchmark cases, in order to validate the procedure. Numerical test campaign on specimens of the skirts with delaminations has been performed to analyze the behaviour under compressive load and the buckling.

Originality/value

This tool is applied to the study of the behaviour of some components in carbon/epoxy composite of a space structure in which one or more delaminations are eventually present following impact damage or manufacturing process. The components in particular are the booster's skirts of a small class launcher, subjected to a compressive load.
Analysis of a gravity dam considering the influence of couple‐stresses
Authors: Liu Jun , Huan Ming
Published: December 2010

Purpose

Traditional continuum theory is usually applied in analysis of a gravity dam and its foundation; as we all know, both analytic and numerical solution of traditional theory imply that stress concentration around the dam heel and toe is very severe. However, stress condition of the dam and its foundation seems better for it can work normally for decades. Since concrete masses have macroscopic inhomogeneity, a new model has been built in order to simulate the mechanics behaviour of dam and its foundation rationally as the influence of inhomogeneity of the material has been taken into consideration. The purpose of this paper is to describe the application of the Cosserat granular model to analyze the stress condition of a mass concrete structure.

Design/methodology/approach

Granular model of Cosserat theory has been built and adopted to model the gravity, considering the influence of the couple‐stresses, due to the inhomogeneity of the material.

Findings

The Cosserat results have been compared with the traditional numerical solution, and the outcome indicates that the distributions of the stresses and displacements are rational, and the stress concentration around dam hell and toe is less severe and closer to the reality when Cosserat theory adopted.

Originality/value

The granular model based on Cosserat theory has been used in modelling a dam body for the first time; because the model can reflect the influence of the inhomogeneity, it is more suitable than traditional continuum model under this condition.
Computer simulation of two‐dimensional linear‐shaped charge jet using smoothed particle hydrodynamics
Authors: Gang Yang , Xu Han , De'an Hu
Published: December 2010

Purpose

The purpose of this paper is to investigate the formation process of linear‐shaped charge jet using the smoothed particle hydrodynamics (SPH). Different material yield models are embed to test the performance of SPH method in the simulation of explosive driven metal liner. The effects of different ignition model to the formation of metal jet have also been studied.

Design/methodology/approach

The SPH method is used with the correction of artificial viscosity and penalty force to simulate the formation process of linear‐shaped charge jet, which includes the process of explosion and interaction between explosive gas and metal liner. The numerical results which got by SPH method are compared with these obtained by mesh‐based method. Different material yield models are implemented in the numerical examples to show the effect of material model to the formation process of metal jet. The single point and two point ignition models are used to study the effect of ignition models to the process of explosion and formation of metal jet.

Findings

Compared with the original mesh‐based method, the SPH method can simulate the physical process of linear‐shaped charge jet naturally, as well as the capturing of explosive wave propagation. The implementation of different material yields models to obtain the same formation tendency of metal jet, but some numerical difference exists. In two‐point ignition model the explosive pressure is superimposed at the location that two detonation waves intersect. Compared with two ignition models, the two point ignition model can form the metal jet faster and get the higher velocity metal jet.

Originality/value

There are a few references that address the application of SPH to simulate shaped charge explosion process. The feasibility of the SPH method to simulate the formation process of linear shaped charged jet is tested and verified in this paper. From the results which compared with mesh‐based method, it is shown that the SPH method has the advantage in tracking the large deformation of material and capturing the explosive wave propagation. The SPH method can be selected as a good alternative to traditional mesh‐based numerical methods in simulating similar explosively driven metal material problems which can be referenced from this paper.