bluuebunny/crossref_metadata_2025 huggingface dataset:
Mortality and morbidity in Cushing’s syndrome in New Zealand
Authors: Bolland Mark J. , Holdaway Ian M. , Berkeley Juliet E. , Lim Sarina , Dransfield Will J. , Conaglen John V. , Croxson Michael S. , Gamble Greg D. , Hunt Penny J. , Toomath Robyn J.
Published: May 2011

Objective  Untreated Cushing’s syndrome (CS) is associated with significant morbidity and mortality. However, recent operative series suggest low morbidity and mortality for CS, whereas population‐based surveys report elevated mortality rates. We investigated the mortality and morbidity of CS in New Zealand.

Design  A nationwide retrospective survey of patients with CS between 1960 and 2005 managed at the four main endocrinology services.

Patients  A total of 253 patients with CS were identified, excluding adrenal carcinoma and malignant ectopic CS.

Measurements  The primary outcome was the standardized mortality ratio (SMR), comparing the observed number of deaths with the expected number for the population matched for age, sex and duration of follow‐up. Secondary outcomes were the change in prevalence of co‐morbidities at presentation and at final follow‐up.

Results  The approximate prevalence and incidence of CS was 79/million and 1·8/million/y. The mean age at presentation was 39 year, and median duration of follow‐up was 6·4 year (range 0–46). Overall, 89% achieved biochemical cure at last follow‐up, with >90% achieving biochemical cure for CS from adrenal adenoma and pituitary causes. Thirty‐six patients died during follow‐up compared with 8·8 expected deaths (SMR 4·1, 95%CI 2·9–5·6). While hypertension, sexual dysfunction, myopathy and mild psychiatric illness were significantly reduced after treatment, hypertension, diabetes mellitus, moderate or major psychiatric illness, and osteoporosis were common at final follow‐up.

Conclusion  CS is associated with both high mortality and a high prevalence of co‐morbidities, even when biochemical cure rates are between 80% and 90%.
Effect of saponins from Enterolobium cyclocarpum on in vitro microbial fermentation of the tropical grass Pennisetum purpureum
Authors: Rodríguez R. , Fondevila M.
Published: May 2011

The effect of Enterolobium cyclocarpum saponins on the fermentation of Pennisetum purpureum was studied in vitro, with P. purpureum incubated alone (PP), in combination with E. cyclocarpum (EC), E. cyclocarpum without saponins (ER) or with saponins extracted from the same amount of E. cyclocarpum (SP). Gas production was monitored and contents sampled after 24 h for short‐chain fatty acid (SCFA) and total microbial mass analyses. SCFA and microbial attachment to P. purpureum using 15N as marker were determined from different bottles at 6, 12 and 24 h. Up to 8 h, gas production was highest for SP and lowest for ER (p < 0.05), probably because highly fermentable solubles were also extracted. Gas from PP was highest from 16 h (p < 0.05). Treatments including saponins (SP and EC) increased propionate (p < 0.001) and decreased acetate and butyrate (p < 0.01) proportions. Stoichiometrically estimated methane concentration was lowest for SP and EC (p < 0.01). Microbial attachment after 24 h was lower for EC and SP than for ER (p < 0.05). Saponins from E. cyclocarpum are responsible for the reduction in gas production when supplemented with P. purpureum and modify the fermentation pattern by increasing propionate proportion and decreasing methane production. Besides, saponins increase total microbial mass, although microbial attachment to the grass substrate was reduced.
Vitamin D deficiency: Implications for acute care in the elderly and in patients with chronic illness
Authors: Youssef Dima A , El Abbassi Adel M , Cutchins Della C , Chhabra Shalini , Peiris Alan N
Published: May 2011

There is evidence that the vast majority of hospitalized patients have vitamin D deficiency. Vitamin D deficiency is a poorly recognized pandemic with evidence to indicate inadequate testing and monitoring of response to treatment in high‐risk populations. Vitamin D receptors are ubiquitous in the human body and while the endocrine effects of vitamin D are well recognized, the autocrine and paracrine effects of this steroid hormone are less well appreciated. These functions include antimicrobial and immunomodulation effects as well benefits on cardiovascular health, autoimmune disease, cancer and metabolism. Vitamin D deficiency increases mortality and even a modest amount of vitamin D may enhance longevity. Emerging evidence suggests that a vitamin D replete state carries significant health benefits in acute illness. In this review, we discuss the role of vitamin D deficiency and potential benefits in treating this deficiency focusing on the implications for managing acute illness in elderly patients and those with an underlying chronic illness. Geriatr Gerontol Int 2011; 11: 395–407.
Minority Report: Reconsidering Jürgen Moltmann's Turn to a Theology of the Cross
Authors: NEAL RYAN
Published: May 2011

According to virtually any set of criteria, Jürgen Moltmann's first two programmatic books, Theology of Hope and The Crucified God, are strikingly different. The differences are due to his turn to a theology of the cross in the intervening years. Yet Moltmann, with the vast majority of scholars concurring, argues that the two works form a continuous argument. This article investigates the problems with the consensus judgement and calls for a revision of the relationship between the two works, based on the nature of the cross–resurrection dialectic inherent to his programme and also on both the necessity and timing of the turn.
Entrepreneurial Orientation and Organizational Learning: The Impact of Network Range and Network Closure
Authors: Kreiser Patrick M.
Published: May 2011

This study develops theoretical propositions regarding the role that entrepreneurial orientation (EO) plays in enhancing an organization's level of acquisitive and experimental learning. It also develops propositions concerning the manner in which a firm's ability to directly link itself to disparate sources of knowledge (network range) impacts the relationship between EO and acquisitive learning, as well as how a firm's ability to maintain a series of strong ties within a network (network closure) impacts the relationship between EO and experimental learning. Finally, propositions are developed regarding how firms can most effectively utilize EO and network participation to maximize levels of organizational learning while conserving their limited resources.
Paliperidone in the treatment of delirium: results of a prospective open-label pilot trial
Authors: Yoon Ho-Kyoung , Kim Yong-Ku , Han Changsu , Ko Young-Hoon , Lee Heon-Jeong , Kwon Do-Young , Kim Leen
Published: May 2011

Yoon H-K, Kim Y-K, Han C, Ko Y-H, Lee H-J, Kwon D-Y, Kim L. Paliperidone in the treatment of delirium: results of a prospective open-label pilot trial.

Objective: Delirium is a life-threatening neuropsychiatric syndrome characterised by disturbances in consciousness, attention, cognition and perception. Antipsychotics are considered the drugs of choice in managing the symptoms of delirium. Paliperidone is a benzisoxazole derivative and the principal active metabolite of risperidone. In this study, we aimed to evaluate the efficacy of paliperidone for the treatment of delirium.

Methods: A prospective open-label study of paliperidone for delirium treatment was performed with 6-day follow-up. Fifteen patients who met Diagnostic and Statistical Manual of Mental disorders, Fourth Edition criteria for delirium and had a score of 13 on the Delirium Rating Scale were recruited. The starting dose was 3 mg once a day and the dose was adjusted depending on the status of delirium. Daily assessments of the severity of delirium were evaluated using Memorial Delirium Assessment Scale (MDAS).

Results: The mean daily maintenance dose of paliperidone was 3.75 ± 1.06. The MDAS scores before and after treatment (day 7) were 23.60 ± 6.31 and 11.33 ± 5.45 (t = 6.78, p < 0.001), respectively. The intensity of delirium showed a statistically significant reduction in MDAS scores from the first day of treatment. No serious adverse effects were observed, and none of the patients discontinued paliperidone because of adverse effects.

Conclusions: This study shows that low-dose paliperidone is effective in reducing behavioural disturbances and symptoms in delirium and is well tolerated in delirious patients. This trial is an open-label study with a small sample size, and further controlled studies will be necessary.
KCa3.1 channels facilitate K+ secretion or Na+ absorption depending on apical or basolateral P2Y receptor stimulation
Authors: Palmer Melissa L. , Peitzman Elizabeth R. , Maniak Peter J. , Sieck Gary C. , Prakash Y. S. , O’Grady Scott M.
Published: May 2011

Non‐technical summary  The epithelial cells lining the ducts of the human mammary gland are responsible for modifying sodium and potassium concentrations in milk by actively absorbing sodium from and secreting potassium into the ductal fluid. In the present study we show that adenosine triphosphate (ATP) and uridine triphosphate (UTP) can stimulate sodium absorption and potassium secretion by a mechanism that involves increasing intracellular calcium and activation of calcium‐dependent potassium channels. We discovered that addition of ATP or UTP to the luminal surface stimulates potassium secretion, whereas addition of the same concentrations to the epithelial surface normally exposed to the blood produces an increase in sodium absorption. These results provide a better understanding of the signalling mechanisms that control the concentrations of sodium and potassium present in milk.
Rotor Interaction Noise in Counter-Rotating Propfan Propulsion Systems
Authors: Peters Andreas , Spakovszky Zoltán S.
Published: May 2011

Due to their inherent noise challenge and potential for significant reductions in fuel burn, counter-rotating propfans (CRPs) are currently being investigated as potential alternatives to high-bypass turbofan engines. This paper introduces an integrated noise and performance assessment methodology for advanced propfan powered aircraft configurations. The approach is based on first principles and combines a coupled aircraft and propulsion system mission and performance analysis tool with 3D unsteady, full-wheel CRP computational fluid dynamics computations and aeroacoustic simulations. Special emphasis is put on computing CRP noise due to interaction tones. The method is capable of dealing with parametric studies and exploring noise reduction technologies. An aircraft performance, weight and balance, and mission analysis was first conducted on a candidate CRP powered aircraft configuration. Guided by data available in the literature, a detailed aerodynamic design of a pusher CRP was carried out. Full-wheel unsteady 3D Reynolds-averaged Navier-Stokes (RANS) simulations were then used to determine the time varying blade surface pressures and unsteady flow features necessary to define the acoustic source terms. A frequency domain approach based on Goldstein’s formulation of the acoustic analogy for moving media and Hanson’s single rotor noise method was extended to counter-rotating configurations. The far field noise predictions were compared to measured data of a similar CRP configuration and demonstrated good agreement between the computed and measured interaction tones. The underlying noise mechanisms have previously been described in literature but, to the authors’ knowledge, this is the first time that the individual contributions of front-rotor wake interaction, aft-rotor upstream influence, hub-endwall secondary flows, and front-rotor tip-vortices to interaction tone noise are dissected and quantified. Based on this investigation, the CRP was redesigned for reduced noise incorporating a clipped rear-rotor and increased rotor-rotor spacing to reduce upstream influence, tip-vortex, and wake interaction effects. Maintaining the thrust and propulsive efficiency at takeoff conditions, the noise was calculated for both designs. At the interaction tone frequencies, the redesigned CRP demonstrated an average reduction of 7.25 dB in mean sound pressure level computed over the forward and aft polar angle arcs. On the engine/aircraft system level, the redesigned CRP demonstrated a reduction of 9.2 dB in effective perceived noise (EPNdB) and 8.6 EPNdB at the Federal Aviation Regulations (FAR) 36 flyover and sideline observer locations, respectively. The results suggest that advanced open rotor designs can possibly meet Stage 4 noise requirements.
Science Signaling
Podcast: 24 May 2011
Authors: Martin James F. , Vasioukhin Valeri , Silvis Mark R. , VanHook Annalisa M.
Published: May 2011

Recent research reveals details about the regulation and activity of the Hippo signaling mediator Yap.
Anxiety Control
Authors: Foley John F.
Published: May 2011

Stress induces the proteolysis of the receptor tyrosine kinase EphB2 in the amygdala to promote anxiety.
Protect the Stem Cells
Authors: Wong Wei
Published: May 2011

CLAVATA3 peptide acts as a “vaccination” to activate pathogen defense pathways in plant shoot apical meristems.
The Recording of Student Performance in the Microbiology Laboratory as a Training, Tutorial, and Motivational Tool
Authors: Lipson Steven M. , Gair Marina
Published: May 2011

The laboratory component of a microbiology course consists of exercises which mandate a level of proficiency and manual dexterity equal to and often beyond that recognized among other biology courses. Bacterial growth, maintenance, identification (e.g., Gram stain, biochemical tests, genomics), as well as the continuous need to maintain laboratory safety and sterile technique, are only a few skills/responsibilities critical to the discipline of microbiology. Performance of the Gram stain remains one of the most basic and pivotal skills that must be mastered in the microbiology laboratory. However, a number of students continually have difficulty executing the Gram stain and preparative procedures associated with the test. In order to address this issue, we incorporated real-time digital recording as a supplemental teaching aid in the microbiology laboratory. Our use of the digital movie camera in the teaching setting served to enhance interest, motivate students, and in general, improve student performance.
The Use of Current Events as Assessment Tools
Authors: Miller Amy
Published: May 2011

An important student learning outcome for students in biology courses is the ability to apply the information attained to “real life” situations. Newspaper articles covering course-related material provide an avenue for students to see how the material discussed in the course relates to life outside of the course. Assessment of students’ understanding of the articles provides an opportunity to measure how well students are able to apply information to situations outside of traditional coursework.
The MicroSafari: A Journey into Microbiology, an Expedition into Engagement
Authors: Vrentas Catherine Eva , Zinnen Thomas , Huebert Lima Dana J.
Published: May 2011

In the area of hands-on science with the public, microbiology poses particular challenges in offering activities that are safe and cheap, as well as intriguing and engaging. We developed MicroSafari as part of our work with the UW–Madison Biology Outreach Club (BOC), an all-volunteer organization of biology graduate students. During the period 2005–2009, we led over a dozen MicroSafaris at venues on campus and in communities, for groups of families and youth, with group size ranging from 30 to 100. The MicroSafari is a hands-on version of Dyer’s Field Guide, using theater-based elements to share examples of these macroscopic characteristics of microscopic organisms.
Collaborative Creation of a Lab Rubric
Authors: Miller-DeBoer Carrie , Eodice Michele
Published: May 2011

While there are a number of tested rubrics in circulation, our task was to intervene in a particular situation: the lead professor was concerned because her graduate teaching assistants held negative views about student performance on the lab reports. GTAs found poor products frustrating, and admitted that their grading was thus superficial and provided no feedback to students. Specifically, GTAs did not feel equipped to evaluate writing and, as a result, simply graded on steps completed in the lab process.

We have a rubric now for an Introduction to Zoology lab that could be submitted here as a pretty darn good rubric for other instructors to use. But the intent of our “Tips and Tools” is to describe the actual creation of the rubric. We believe the active “real time” development of the rubric carried as much or more value than the finished product.
Implementation of a Service-learning Module in Medical Microbiology and Cell Biology Classes at an Undergraduate Liberal Arts University
Authors: Larios-Sanz Maia , Simmons Alexandra D. , Bagnall Ruth Ann , Rosell Rosemarie C.
Published: May 2011

Here we discuss the implementation of a service-learning module in two upper-division biology classes, Medical Microbiology and Cell Biology. This exciting hands-on learning experience provided our students with an opportunity to extend their learning of in-class topics to a real-life scenario. Students were required to volunteer their time (a minimum of 10 hours in a semester) at an under-served clinic in Houston, Texas. As they interacted with the personnel at the clinic, they were asked to identify the most prevalent disease (infectious for Medical Microbiology, and cellular-based for Cell) seen at the clinic and, working in groups, come up with educational material in the form of a display or brochure to be distributed to patients. The material was meant to educate patients about the disease in general terms, as well as how to recognize (symptoms), prevent and treat it. Students were required to keep a reflective journal in the form of a blog throughout the semester, and present their final materials to the class orally. Students were surveyed about their opinion of the experience at the end of the semester. The vast majority of student participants felt that the project was a positive experience and that it helped them develop additional skills beyond what they learn in the classroom and understand how lecture topics relate to every day life.
Suggested Resources for Scholarly Teaching and for the Scholarship of Teaching and Learning
Authors: Nelson Craig E.
Published: May 2011

These are some of my favorite resources of informing scholarly teaching (ST) and the scholarship of teaching and learning (SOTL). This list is focused on the needs of college biology faculty. It is highly selective and somewhat idiosyncratic in that many more items are relevant and could have been included.
Still waiting for predictive biomarkers in Barrett's oesophagus
Authors: Moyes L H , Going J J
Published: May 2011

Barrett's oesophagus is important as a precursor of oesophageal adenocarcinoma via a metaplasia-dysplasia-carcinoma sequence. It is often detected on upper gastrointestinal endoscopy. In the absence of glandular dysplasia the risk of progression to cancer is low but ascertainment of dysplasia is not always straightforward. Sparse mucosal sampling may miss dysplasia, or reactive changes may be overinterpreted due to inter and intraobserver variation. Low-grade and even high-grade dysplasia do not necessarily progress, provided prevalent cancer has been rigorously excluded. This indeterminacy motivates an ongoing search for clinically useful predictive biomarkers. Although many genetic and epigenetic abnormalities have been associated with neoplastic progression in Barrett's mucosa no molecular tests have as yet been accepted into routine pathology practice. Challenges of assay definition remain and many marker studies lack statistical power or have other methodological flaws. Even where strong evidence of clinically relevant predictive value does exist (in the case of ploidy analysis by flow or image cytometry) adoption has been minimal, likely reflecting technological and possible reimbursement obstacles. Well designed multicentre studies are likely to be required to translate improved knowledge of Barrett's carcinogenesis into clinically significant progress on predictive testing, and will require a degree of cooperation not so far widely seen in the field.
TRANSIENT ELECTRIC RESPONSE OF CHARGE DENSITY WAVES IN BLUE BRONZE
Authors: YUE SONG
Published: May 2011

The transient voltage response of the charge density wave (CDW) to current pulses in Tl 0.3 MoO 3 and K 0.15 Tl 0.15 MoO 3 have been studied. Contrasted with the data reported previously for other blue bronze systems, a kind of superimposed (overshoot and sluggish) response waveform is observed for the first time. These results are discussed in analogy with the coexisting of "inductive" and "capacitive" effects at the onset of the CDW depinning.
THE SPECTRUM OF CHAOTIC TIME SERIES (I): FOURIER ANALYSIS
Authors: CHEN GOONG , HSU SZE-BI , HUANG YU , ROQUE-SOL MARCO A.
Published: May 2011

The question of spectral analysis for deterministic chaos is not well understood in the literature. In this paper, using iterates of chaotic interval maps as time series, we analyze the mathematical properties of the Fourier series of these iterates. The key idea is the connection between the total variation and the topological entropy of the iterates of the interval map, from where special properties of the Fourier coefficients are obtained. Various examples are given to illustrate the applications of the main theorems.
SIMPLE SELF-INSTRUCTIONAL MODULES BASED ON CHAOTIC OSCILLATORS: FEW BLOCKS GENERATING MANY PATTERNS
Authors: KLOMKARN KITDAKORN , SOORAKSA PITIKHATE
Published: May 2011

Chaotic circuits have been widely used in the teaching of nonlinear dynamics disciplines, where a common practice is pedagogically based on the circuit point of view. Chua's circuit is the most popular platform for the demonstration of its components with rich dynamical patterns. However, engineering students majoring in control systems are more familiar with feedback systems rather than physical electronics with nonlinear components. This may lead to some difficulty in understanding the nonlinear properties of Chua's circuit, at least on first sight. This paper provides an alternative approach to teaching and learning chaotic oscillators by using the inherent understanding of feedback systems with simple modules at the undergraduate level. Utilizing the idea of chaotification, which means to make a nonchaotic module chaotic, the modules consist of only four blocks yet can generate more than thirty types of chaotic patterns via their various combinations. Conceptually, the blocks can be assembled as various mixed-mode chaotic circuits. Functionally, the blocks are easy-to-use in a Simulink-like fashion. Structurally, they are a LEGO-like educational kit. With low-cost implementation employing a few op-amps for each block, the newly proposed modules are simple, self-instructional and suitable for teaching and training students in school laboratories and in experimental environments.
CROSS-CULTURAL PERCEPTIONS ON KNOWLEDGE SHARING IN HETEROGENEOUS COLLABORATIONS
Authors: NIEDERGASSEL BENJAMIN , KANZLER STEFFEN , ALVIDREZ SALVADOR , LEKER JENS
Published: May 2011

This qualitative study investigates different perceptions of knowledge sharing in a cross-cultural research collaboration between German and Chinese scientists. Special emphasis is placed on the in-group and out-group orientation of partners, different communication styles and personal and organizational influence factors. Data was obtained by conducting six focus groups in Germany and China. All ideas expressed in these focus groups were categorized and thoroughly evaluated. Our analysis reveals that the in- and out-group orientation of collectivistic and individualistic cultures might not be as pronounced as theory would suggest. In fact, members of the more collectivistic Chinese culture even showed a higher out-group orientation than members of the more individualistic German culture in our study. The resulting theoretical and practical implications for managing cross-cultural collaboration projects are discussed in detail in the paper.
Host-Based P2P Flow Identification and Use in Real-Time
Authors: Hurley John , Garcia-Palacios Emi , Sezer Sakir
Published: May 2011

Data identification and classification is a key task for any Internet Service Provider (ISP) or network administrator. As port fluctuation and encryption become more common in P2P applications wishing to avoid identification, new strategies must be developed to detect and classify their flows. This article introduces a method of separating P2P and standard web traffic that can be applied as part of an offline data analysis process, based on the activity of the hosts on the network. Heuristics are analyzed and a classification system proposed that focuses on classifying those “long” flows that transfer most of the bytes across a network. The accuracy of the system is then tested using real network traffic from a core Internet router showing misclassification rates as low as 0.54% of flows in some cases. We expand on this proposed strategy to investigate its relevance to real-time, early classification problems. New proposals are made and the results of real-time experiments are compared to those obtained in the offline analysis. It is shown that classification accuracies in the real-time strategy are similar to those achieved in offline analysis with a large portion of the total web and P2P flows correctly identified.
Characterizing Web-Based Video Sharing Workloads
Authors: Mitra Siddharth , Agrawal Mayank , Yadav Amit , Carlsson Niklas , Eager Derek , Mahanti Anirban
Published: May 2011

Video sharing services that allow ordinary Web users to upload video clips of their choice and watch video clips uploaded by others have recently become very popular. This article identifies
invariants
in video sharing workloads, through comparison of the workload characteristics of four popular video sharing services. Our traces contain metadata on approximately 1.8 million videos which together have been viewed approximately 6 billion times. Using these traces, we study the similarities and differences in use of several Web 2.0 features such as ratings, comments, favorites, and propensity of uploading content. In general, we find that active contribution, such as video uploading and rating of videos, is much less prevalent than passive use. While uploaders in general are skewed with respect to the number of videos they upload, the fraction of multi-time uploaders is found to differ by a factor of two between two of the sites. The distributions of lifetime measures of video popularity are found to have heavy-tailed forms that are similar across the four sites. Finally, we consider implications for system design of the identified invariants. To gain further insight into caching in video sharing systems, and the relevance to caching of lifetime popularity measures, we gathered an additional dataset tracking views to a set of approximately 1.3 million videos from one of the services, over a twelve-week period. We find that lifetime popularity measures have some relevance for large cache (hot set) sizes (i.e., a hot set defined according to one of these measures is indeed relatively “hot”), but that this relevance substantially decreases as cache size decreases, owing to churn in video popularity.
Image-guided weathering
Authors: Bosch Carles , Laffont Pierre-Yves , Rushmeier Holly , Dorsey Julie , Drettakis George
Published: May 2011

The simulation of weathered appearance is essential in the realistic modeling of urban environments. A representative and particularly difficult effect to produce on a large scale is the effect of fluid flow. Changes in appearance due to flow are the result of both the global effect of large-scale shape, and local effects, such as the detailed roughness of a surface. With digital photography and Internet image collections, visual examples of flow effects are readily available. These images, however, mix the appearance of flows with the specific local context. We present a methodology to extract parameters and detail maps from existing imagery in a form that allows new target-specific flow effects to be produced, with natural variations in the effects as they are applied in different locations in a new scene. In this article, we focus on producing a library of parameters and detail maps for generating flow patterns; and this methodology can be used to extend the library with additional image exemplars. To illustrate our methodology, we show a rich collection of patterns applied to urban models.
Dynamo
Authors: Bala Vasanth , Duesterwald Evelyn , Banerjia Sanjeev
Published: May 2011

We describe the design and implementation of Dynamo, a software dynamic optimization system that is capable of transparently improving the performance of a native instruction stream as it executes on the processor. The input native instruction stream to Dynamo can be dynamically generated (by a JIT for example), or it can come from the execution of a statically compiled native binary. This paper evaluates the Dynamo system in the latter, more challenging situation, in order to emphasize the limits, rather than the potential, of the system. Our experiments demonstrate that even statically optimized native binaries can be accelerated Dynamo, and often by a significant degree. For example, the average performance of --O optimized SpecInt95 benchmark binaries created by the HP product C compiler is improved to a level comparable to their --O4 optimized version running without Dynamo. Dynamo achieves this by focusing its efforts on optimization opportunities that tend to manifest only at runtime, and hence opportunities that might be difficult for a static compiler to exploit. Dynamo's operation is transparent in the sense that it does not depend on any user annotations or binary instrumentation, and does not require multiple runs, or any special compiler, operating system or hardware support. The Dynamo prototype presented here is a realistic implementation running on an HP PA-8000 workstation under the HPUX 10.20 operating system.
Cost-Effectiveness of Dabigatran for Stroke Prophylaxis in Atrial Fibrillation
Authors: Shah Shimoli V. , Gage Brian F.
Published: May 2011

Background—

Recent studies have investigated alternatives to warfarin for stroke prophylaxis in patients with atrial fibrillation (AF), but whether these alternatives are cost-effective is unknown.

Methods and Results—

On the basis of the results from Randomized Evaluation of Long Term Anticoagulation Therapy (RE-LY) and other trials, we developed a decision-analysis model to compare the cost and quality-adjusted survival of various antithrombotic therapies. We ran our Markov model in a hypothetical cohort of 70-year-old patients with AF using a cost-effectiveness threshold of $50 000/quality-adjusted life-year. We estimated the cost of dabigatran as US $9 a day. For a patient with an average risk of major hemorrhage (≈3%/y), the most cost-effective therapy depended on stroke risk. For patients with the lowest stroke rate (CHADS
2
stroke score of 0), only aspirin was cost-effective. For patients with a moderate stroke rate (CHADS
2
score of 1 or 2), warfarin was cost-effective unless the risk of hemorrhage was high or quality of international normalized ratio control was poor (time in the therapeutic range <57.1%). For patients with a high stroke risk (CHADS
2
stroke score ≥3), dabigatran 150 mg (twice daily) was cost-effective unless international normalized ratio control was excellent (time in the therapeutic range >72.6%). Neither dabigatran 110 mg nor dual therapy (aspirin and clopidogrel) was cost-effective.

Conclusions—

Dabigatran 150 mg (twice daily) was cost-effective in AF populations at high risk of hemorrhage or high risk of stroke unless international normalized ratio control with warfarin was excellent. Warfarin was cost-effective in moderate-risk AF populations unless international normalized ratio control was poor.
Guns for Cotton? Aid, Trade, and the Soviet Quest for Base Rights in Egypt, 1964–1966
Authors: Ferris Jesse
Published: May 2011

This article reexamines the economic and strategic aspects of Soviet-Egyptian relations in the mid-1960s based on recently declassified documents from Russian archives and recently published memoirs in Arabic. The article explores the tensions that developed between the Soviet Union and Egypt as the Soviet government exploited Egypt's economic difficulties to press for basing rights that would help to offset the U.S. Sixth Fleet in the Mediterranean. In addition to offering a corrective to scholarly understanding of the Soviet-Egyptian relationship at this time, the article provides a fascinating glimpse into the mechanics of Soviet foreign economic policy and carries revisionist implications for students of the origins of the Six-Day Mideast War.
MINE: Module Identification in Networks
Authors: Rhrissorrakrai Kahn , Gunsalus Kristin C
Published: May 2011

Background

Graphical models of network associations are useful for both visualizing and integrating multiple types of association data. Identifying modules, or groups of functionally related gene products, is an important challenge in analyzing biological networks. However, existing tools to identify modules are insufficient when applied to dense networks of experimentally derived interaction data. To address this problem, we have developed an agglomerative clustering method that is able to identify highly modular sets of gene products within highly interconnected molecular interaction networks.

Results

MINE outperforms MCODE, CFinder, NEMO, SPICi, and MCL in identifying non-exclusive, high modularity clusters when applied to the C. elegans protein-protein interaction network. The algorithm generally achieves superior geometric accuracy and modularity for annotated functional categories. In comparison with the most closely related algorithm, MCODE, the top clusters identified by MINE are consistently of higher density and MINE is less likely to designate overlapping modules as a single unit. MINE offers a high level of granularity with a small number of adjustable parameters, enabling users to fine-tune cluster results for input networks with differing topological properties.

Conclusions

MINE was created in response to the challenge of discovering high quality modules of gene products within highly interconnected biological networks. The algorithm allows a high degree of flexibility and user-customisation of results with few adjustable parameters. MINE outperforms several popular clustering algorithms in identifying modules with high modularity and obtains good overall recall and precision of functional annotations in protein-protein interaction networks from both S. cerevisiae and C. elegans.
Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface
Authors: Sroka Jacek , Bieniasz-Krzywiec Łukasz , Gwóźdź Szymon , Leniowski Dariusz , Łącki Jakub , Markowski Mateusz , Avignone-Rossa Claudio , Bushell Michael E , McFadden Johnjoe , Kierzek Andrzej M
Published: May 2011

Background

Constraint-based approaches facilitate the prediction of cellular metabolic capabilities, based, in turn on predictions of the repertoire of enzymes encoded in the genome. Recently, genome annotations have been used to reconstruct genome scale metabolic reaction networks for numerous species, including Homo sapiens, which allow simulations that provide valuable insights into topics, including predictions of gene essentiality of pathogens, interpretation of genetic polymorphism in metabolic disease syndromes and suggestions for novel approaches to microbial metabolic engineering. These constraint-based simulations are being integrated with the functional genomics portals, an activity that requires efficient implementation of the constraint-based simulations in the web-based environment.

Results

Here, we present Acorn, an open source (GNU GPL) grid computing system for constraint-based simulations of genome scale metabolic reaction networks within an interactive web environment. The grid-based architecture allows efficient execution of computationally intensive, iterative protocols such as Flux Variability Analysis, which can be readily scaled up as the numbers of models (and users) increase. The web interface uses AJAX, which facilitates efficient model browsing and other search functions, and intuitive implementation of appropriate simulation conditions. Research groups can install Acorn locally and create user accounts. Users can also import models in the familiar SBML format and link reaction formulas to major functional genomics portals of choice. Selected models and simulation results can be shared between different users and made publically available. Users can construct pathway map layouts and import them into the server using a desktop editor integrated within the system. Pathway maps are then used to visualise numerical results within the web environment. To illustrate these features we have deployed Acorn and created a web server allowing constraint based simulations of the genome scale metabolic reaction networks of E. coli, S. cerevisiae and M. tuberculosis.

Conclusions

Acorn is a free software package, which can be installed by research groups to create a web based environment for computer simulations of genome scale metabolic reaction networks. It facilitates shared access to models and creation of publicly available constraint based modelling resources.
Attenuated expression of HRH4 in colorectal carcinomas: a potential influence on tumor growth and progression
Authors: Fang Zhengyu , Yao Wantong , Xiong Yi , Li Jiana , Liu Li , Shi Lei , Zhang Wei , Zhang Chao , Nie Liping , Wan Jun
Published: May 2011

Background

Earlier studies have reported the production of histamine in colorectal cancers (CRCs). The effect of histamine is largely determined locally by the histamine receptor expression pattern. Recent evidence suggests that the expression level of histamine receptor H4 (HRH4) is abnormal in colorectal cancer tissues. However, the role of HRH4 in CRC progression and its clinical relevance is not well understood. The aim of this study is to evaluate the clinical and molecular phenotypes of colorectal tumors with abnormal HRH4 expression.

Methods

Immunoblotting, real-time PCR, immunofluorescence and immunohistochemistry assays were adopted to examine HRH4 expression in case-matched CRC samples (n = 107) and adjacent normal tissues (ANTs). To assess the functions of HRH4 in CRC cells, we established stable HRH4-transfected colorectal cells and examined cell proliferation, colony formation, cell cycle and apoptosis in these cells.

Results

The protein levels of HRH4 were reduced in most of the human CRC samples regardless of grade or Dukes classification. mRNA levels of HRH4 were also reduced in both early-stage and advanced CRC samples. In vitro studies showed that HRH4 over-expression caused growth arrest and induced expression of cell cycle proteins in CRC cells upon exposure to histamine through a cAMP -dependent pathway. Furthermore, HRH4 stimulation promoted the 5-Fu-induced cell apoptosis in HRH4-positive colorectal cells.

Conclusion

The results from the current study supported previous findings of HRH4 abnormalities in CRCs. Expression levels of HRH4 could influence the histamine-mediated growth regulation in CRC cells. These findings suggested a potential role of abnormal HRH4 expression in the progression of CRCs and provided some new clues for the application of HRH4-specific agonist or antagonist in the molecular therapy of CRCs.
A new in-silico method for determination of helical transmembrane domains based on the PepLook scan: application to IL-2Rβ and IL-2Rγc receptor chains
Authors: Charlois Yan , Lins Laurence , Brasseur Robert
Published: May 2011

Background

Modeling of transmembrane domains (TMDs) requires correct prediction of interfacial residues for in-silico modeling and membrane insertion studies. This implies the defining of a target sequence long enough to contain interfacial residues. However, too long sequences induce artifactual polymorphism: within tested modeling methods, the longer the target sequence, the more variable the secondary structure, as though the procedure were stopped before the end of the calculation (which may in fact be unreachable). Moreover, delimitation of these TMDs can produce variable results with sequence based two-dimensional prediction methods, especially for sequences showing polymorphism. To solve this problem, we developed a new modeling procedure using the PepLook method. We scanned the sequences by modeling peptides from the target sequence with a window of 19 residues.

Results

Using sequences whose NMR-structures are already known (GpA, EphA1 and Erb2-HER2), we first determined that the hydrophobic to hydrophilic accessible surface area ratio (ASAr) was the best criterion for delimiting the TMD sequence. The length of the helical structure and the Impala method further supported the determination of the TMD limits. This method was applied to the IL-2Rβ and IL-2Rγ TMD sequences of Homo sapiens, Rattus norvegicus, Mus musculus and Bos taurus.

Conclusions

We succeeded in reducing the variation in the TMD limits to only 2 residues and in gaining structural information.
Descriptive analysis of childbirth healthcare costs in an area with high levels of immigration in Spain
Authors: Comas Mercè , Català Laura , Sala Maria , Payà Antoni , Sala Assumpció , Del Amo Elisabeth , Castells Xavier , Cots Francesc
Published: May 2011

Background

The aim of this study was to estimate the cost of childbirth in a teaching hospital in Barcelona, Spain, including the costs of prenatal care, delivery and postnatal care (3 months). Costs were assessed by taking into account maternal origin and delivery type.

Methods

We performed a cross-sectional study of all deliveries in a teaching hospital to mothers living in its catchment area between October 2006 and September 2007. A process cost analysis based on a full cost accounting system was performed. The main information sources were the primary care program for sexual and reproductive health, and hospital care and costs records. Partial and total costs were compared according to maternal origin and delivery type. A regression model was fit to explain the total cost of the childbirth process as a function of maternal age and origin, prenatal care, delivery type, maternal and neonatal severity, and multiple delivery.

Results

The average cost of childbirth was 4,328€, with an average of 18.28 contacts between the mother or the newborn and the healthcare facilities. The delivery itself accounted for more than 75% of the overall cost: maternal admission accounted for 57% and neonatal admission for 20%. Prenatal care represented 18% of the overall cost and 75% of overall acts. The average overall cost was 5,815€ for cesarean sections, 4,064€ for vaginal instrumented deliveries and 3,682€ for vaginal non-instrumented deliveries (p < 0.001). The regression model explained 45.5% of the cost variability. The incremental cost of a delivery through cesarean section was 955€ (an increase of 31.9%) compared with an increase of 193€ (6.4%) for an instrumented vaginal delivery. The incremental cost of admitting the newborn to hospital ranged from 420€ (14.0%) to 1,951€ (65.2%) depending on the newborn's severity. Age, origin and prenatal care were not statistically significant or economically relevant.

Conclusions

Neither immigration nor prenatal care were associated with a substantial difference in costs. The most important predictors of cost were delivery type and neonatal severity. Given the impact of cesarean sections on the overall cost of childbirth, attempts should be made to take into account its higher cost in the decision of performing a cesarean section.
Monitoring trends in HIV prevalence among young people, aged 15 to 24 years, in Manicaland, Zimbabwe
Authors: Marsh Kimberly A , Nyamukapa Constance A , Donnelly Christl A , Garcia‐Calleja Jesus M , Mushati Phillis , Garnett Geoffrey P , Mpandaguta Edith , Grassly Nicholas C , Gregson Simon
Published: May 2011

Background

In June 2001, the United Nations General Assembly Special Session (UNGASS) set a target of reducing HIV prevalence among young women and men, aged 15 to 24 years, by 25% in the worst‐affected countries by 2005, and by 25% globally by 2010. We assessed progress toward this target in Manicaland, Zimbabwe, using repeated household‐based population serosurvey data. We also validated the representativeness of surveillance data from young pregnant women, aged 15 to 24 years, attending antenatal care (ANC) clinics, which UNAIDS recommends for monitoring population HIV prevalence trends in this age group. Changes in socio‐demographic characteristics and reported sexual behaviour are investigated.

Methods

Progress towards the UNGASS target was measured by calculating the proportional change in HIV prevalence among youth and young ANC attendees over three survey periods (round 1: 1998‐2000; round 2: 2001‐2003; and round 3: 2003‐2005). The Z‐score test was used to compare differences in trends between the two data sources. Characteristics of participants and trends in sexual risk behaviour were analyzed using Student's and two‐tailed Z‐score tests.

Results

HIV prevalence among youth in the general population declined by 50.7% (from 12.2% to 6.0%) from round 1 to 3. Intermediary trends showed a large decline from round 1 to 2 of 60.9% (from 12.2% to 4.8%), offset by an increase from round 2 to 3 of 26.0% (from 4.8% to 6.0%). Among young ANC attendees, the proportional decline in prevalence of 43.5% (from 17.9% to 10.1%) was similar to that in the population (test for differences in trend: p value = 0.488) although ANC data significantly underestimated the population prevalence decline from round 1 to 2 (test for difference in trend: p value = 0.003) and underestimated the increase from round 2 to 3 (test for difference in trend: p value = 0.012). Reductions in risk behaviour between rounds 1 and 2 may have been responsible for general population prevalence declines.

Conclusions

In Manicaland, Zimbabwe, the 2005 UNGASS target to reduce HIV prevalence by 25% was achieved. However, most prevention gains occurred before 2003. ANC surveillance trends overall were an adequate indicator of trends in the population, although lags were observed. Behaviour data and socio‐demographic characteristics of participants are needed to interpret ANC trends.