bluuebunny/crossref_metadata_2025 huggingface dataset:
Space savings and design considerations in variable length deduplication
Authors: Appaji Nag Yasa Giridhar , Nagesh P. C.
Published: January 2013

Explosion of data growth and duplication of data in enterprises has led to the deployment of a variety of deduplication technologies. However not all deduplication technologies serve the needs of every workload. Most prior research in deduplication concentrates on fixed block size (or variable block size at a fixed block boundary) deduplication which provides sub-optimal space efficiency in workloads where the duplicate data is not block aligned. Workloads also differ in the nature of operations and their priorities thereby affecting the choice of the right flavor of deduplication. Object workloads for instance, hold multiple versions of archived documents that have a high degree of duplicate data. They are also write-once read-many in nature and follow a whole object GET, PUT and DELETE model and would be better served by a deduplication strategy that takes care of nonblock aligned changes to data.

In this paper, we describe and evaluate a hybrid of a variable length and block based deduplication that is hierarchical in nature. We are motivated by the following insights from real world data: (a) object workload applications do not do in-place modification of data and hence new versions of objects are written again as a whole (b) significant amount of data among different versions of the same object is shareable but the changes are usually not block aligned. While the second point is the basis for variable length technique, both the above insights motivate our hierarchical deduplication strategy.

We show through experiments with production data-sets from enterprise environments that this provides up to twice the space savings compared to a fixed block deduplication.
Panel on use of proprietary data
Authors: Callan Jamie , Moffat Alistair
Published: January 2013

A panel discussion on the use of proprietary data was held at SIGIR 2012 in Portland. This report summarizes the positions put forward by the six panelists and the points that arose during the wider discussion that followed.
Report on INEX 2012
Authors: Bellot P. , Chappell T. , Doucet A. , Geva S. , Gurajada S. , Kamps J. , Kazai G. , Koolen M. , Landoni M. , Marx M. , Mishra A. , Moriceau V. , Mothe J. , Preminger M. , Ramírez G. , Sanderson M. , Sanjuan E. , Scholer F. , Schuh A. , Tannier X. , Theobald M. , Trappett M. , Trotman A. , Wang Q.
Published: January 2013

INEX investigates focused retrieval from structured documents by providing large test collections of structured documents, uniform evaluation measures, and a forum for organizations to compare their results. This paper reports on the INEX'12 evaluation campaign, which consisted of a five tracks: Linked Data, Relevance Feedback, Snippet Retrieval, Social Book Search, and Tweet Contextualization. INEX'12 was an exciting year for INEX in which we joined forces with CLEF and for the first time ran our workshop as part of the CLEF labs in order to facilitate knowledge transfer between the evaluation forums.
PROMISE retreat report prospects and opportunities for information access evaluation
Authors: Agosti Maristella , Berendsen Richard , Bogers Toine , Braschler Martin , Buitelaar Paul , Choukri Khalid , Maria Di Nunzio Giorgio , Ferro Nicola , Forner Pamela , Hanbury Allan , Heppin Karin Friberg , Hansen Preben , Järvelin Anni , Larsen Birger , Lupu Mihai , Masiero Ivano , Müller Henning , Peruzzo Simone , Petras Vivien , Piroi Florina , de Rijke Maarten , Santucci Giuseppe , Silvello Gianmaria , Toms Elaine
Published: January 2013

The PROMISE network of excellence organized a two-days brainstorming workshop on 30th and 31st May 2012 in Padua, Italy, to discuss and envisage future directions and perspectives for the evaluation of information access and retrieval systems in multiple languages and multiple media. This document reports on the outcomes of this event and provides details about the six envisaged research lines: search applications; contextual evaluation; challenges in test collection design and exploitation; component-based evaluation; ongoing evaluation; and signal-aware evaluation. The ultimate goal of the PROMISE retreat is to stimulate and involve the research community along these research lines and to provide funding agencies with effective and scientifically sound ideas for coordinating and supporting information access research.
Open source information retrieval
Authors: Trotman Andrew , Clarke Charles L.A. , Ounis Iadh , Culpepper Shane , Cartright Marc-Allen , Geva Shlomo
Published: January 2013

On August 16, 2012 the SIGIR 2012 Workshop on Open Source Information Retrieval was held as part of the SIGIR 2012 conference in Portland, Oregon, USA. There were 2 invited talks, one from industry and one from academia. There were 6 full papers and 6 short papers presented as well as demonstrations of 4 open source tools. Finally there was a lively discussion on future directions for the open source Information Retrieval community. This contribution discusses the events of the workshop and outlines future directions for the community.
#TAIA2012
Authors: Diaz Fernando , Dumais Susan , Radinsky Kira , de Rijke Maarten , Shokouhi Milad
Published: January 2013

The SIGIR 2012Workshop on Time-aware Information Access (#TAIA2012)1 was held in Portland on Thursday, 16 August 2012. The workshop brought together about 50 researchers from academia and industry for a full-day programme on time-sensitive information access that involved three keynotes and nine paper presentations.
Learning to Predict the Future using Web Knowledge and Dynamics
Authors: Radinsky Kira
Published: January 2013

Mark Twain famously said that "the past does not repeat itself, but it rhymes." In the spirit of this reflection, we present novel algorithms and methods for leveraging large-scale digital histories and human knowledge mined from the Web to make real-time predictions about the likelihoods of future human and natural events of interest.

The Web is a dynamic being, with constantly updating content, which is entangled with sophisticated user behaviors and interactions. Some of these behaviors have the ability to convey current trends in the present, e.g., economical growth (predicting automobile sales based on query volume [6]), popular movies [4], and political unrest [1, 3, 5]. We mine the ever-changing Web content and user Web behavior. We show that, not only the dynamics itself can be predicted, but also that it can be used for future real-world event prediction. We mine decades of news reports (1851 - 2010) from the New York Times (NYT), and describe how we can learn to predict the future by generalizing sets of concrete transitions in sequences of reported news events. In addition to the news corpora, we leverage data from freely available Web resources, including Wikipedia, FreeBase, OpenCyc, and GeoNames, via the LinkedData platform [2]. The goal is to build predictive models that generalize from specific sets of sequences of events to provide likelihoods of future outcomes, based on patterns of evidence observed in near-term Web activities. We propose the methods as a means of generating actionable forecasts in advance of the occurrence of target events in the world.

This thesis is one of the first works to demonstrate general, unrestricted artificial-intelligence prediction capacity. We present methods derived from heterogeneous Web sources to make knowledge-intensive reasoning about causality and future event prediction, using both automatic feature extraction and novel algorithms for generalizing over historical examples.
Analysis of Convective Thunderstorm Split Cells in South-Eastern Romania
Authors: Carbunaru Daniel , Stefan Sabina , Sasu Monica , Stefanescu Victor
Published: January 2013

The mesoscale configurations are analysed associated withthesplitting process of convective cells responsible for severe weather phenomena in the south-eastern part of Romania. The analysis was performed using products from the S-band Doppler weather radar located in Medgidia. The cases studied were chosen to cover various synoptic configurations when the cell splitting process occurs. To detect the presence and intensity of the tropospheric jet, the Doppler velocity field and vertical wind profiles derived from radar algorithms were used. The relative Doppler velocity field was used to study relative flow associated with convective cells. Trajectories and rotational characteristics associated with convective cells were obtained from reflectivity and relative Doppler velocity fields at various elevations. This analysis highlights the main dynamic features associated with the splitting process of convective cells: the tropospheric jet and vertical moisture flow associated with the configuration of the flow relative to the convective cells for the lower and upper tropospheric layers. These dynamic characteristics seen in the Doppler based velocity field and in the relative Doppler velocity field to the storm can indicate further evolution of convective developments, with direct implications to very short range forecast (nowcasting).
Endoscopic Treatment of Intrasheath Peroneal Tendon Subluxation
Authors: Michels Frederick , Jambou Stéphane , Guillo Stéphane , Van Der Bauwhede Jan
Published: January 2013

Intrasheath subluxation of the peroneal tendons within the peroneal groove is an uncommon problem. Open exploration combined with a peroneal groove-deepening procedure and retinacular reefing is the recommended treatment. This extensive lateral approach needs incision of the intact superior peroneal retinaculum and repair afterwards. We treated three patients with a painful intrasheath subluxation using an endoscopic approach. During this tendoscopy both tendons were inspected. The distal muscle fibers of the peroneus brevis tendon were resected in two patients. A partial tear was debrided in the third patient. All patients had a good result. No wound-healing problems or other complications occurred. Early return to work and sports was possible. An endoscopic approach was successful in treatment of an intrasheath subluxation of the peroneal tendons.
Artificial-Intelligence-Based Techniques to Evaluate Switching Overvoltages during Power System Restoration
Authors: Sadeghkhani Iman , Ketabi Abbas , Feuillet Rene
Published: January 2013

This paper presents an approach to the study of switching overvoltages during power equipment energization. Switching action is one of the most important issues in the power system restoration schemes. This action may lead to overvoltages which can damage some equipment and delay power system restoration. In this work, switching overvoltages caused by power equipment energization are evaluated using artificial-neural-network- (ANN-) based approach. Both multilayer perceptron (MLP) trained with Levenberg-Marquardt (LM) algorithm and radial basis function (RBF) structure have been analyzed. In the cases of transformer and shunt reactor energization, the worst case of switching angle and remanent flux has been considered to reduce the number of required simulations for training ANN. Also, for achieving good generalization capability for developed ANN, equivalent parameters of the network are used as ANN inputs. Developed ANN is tested for a partial of 39-bus New England test system, and results show the effectiveness of the proposed method to evaluate switching overvoltages.
Determination of As, Cd, and Pb in Tap Water and Bottled Water Samples by Using Optimized GFAAS System with Pd-Mg and Ni as Matrix Modifiers
Authors: Bakırdere Sezgin , Yaroğlu Tolga , Tırık Nihan , Demiröz Mehmet , Fidan A. Kemal , Maruldalı Onur , Karaca Abdullah
Published: January 2013

Arsenic, lead, and cadmium were determined in tap and bottled water samples consumed in the west part of Turkey at trace levels. Graphite furnace atomic absorption spectrometry (GFAAS) was used in all detections. All of the system parameters for each element were optimized to increase sensitivity. Pd-Mg mixture was selected as the best matrix modifier for As, while the highest signals were obtained for Pb and Cd in the case of Ni used as matrix modifier. Detection limits for As, Cd, and Pb were found to be 2.0, 0.036, and 0.25 ng/mL, respectively. 78 tap water and 17 different brands of bottled water samples were analyzed for their As, Cd, and Pb contents under the optimized conditions. In all water samples, concentration of cadmium was found to be lower than detection limits. Lead concentration in the samples analyzed varied between N.D. and 12.66 ± 0.68 ng/mL. The highest concentration of arsenic was determined as 11.54 ± 2.79 ng/mL. Accuracy of the methods was verified by using a certified reference material, namely, Trace Element in Water, 1643e. Results found for As, Cd, and Pb in reference materials were in satisfactory agreement with the certified values.
High Frequency Jet Ventilation during Initial Management, Stabilization, and Transport of Newborn Infants with Congenital Diaphragmatic Hernia: A Case Series
Authors: Zhang Qianshen , Macartney Jason , Sampaio Lita , O'Brien Karel
Published: January 2013

Objective. To review experience of the transport and stabilization of infants with CDH who were treated with high frequency jet ventilation (HFJV).Study Design. Retrospective chart review was performed of infants with antenatal diagnosis of CDH born between 2004 and 2009, at Mount Sinai Hospital Toronto, Ontario, Canada. Detailed information was abstracted from the charts of all infants who received HFJV.Results. Of the 55 infants, 25 were managed with HFJV at some point during resuscitation and stabilization prior to transport. HFJV was the initial ventilation mode in six cases and nineteen infants were placed on HFJV as rescue therapy. Blood gases procured from the umbilical artery before and/or after the initiation of HFJV. There was a significant difference detected for both PaCO2(P=0.0002) and pH (P<0.0001). The pre- and posttransport vital signs remained stable and no transport related deaths or significant complications occurred.Conclusion. HFJV appears to be safe and effective providing high frequency rescue therapy for infants with CDH failing conventional mechanical ventilation. This paper supports the decision to utilize HFJV as it likely contributed to safe transport of many infants that would not otherwise have tolerated transport to a surgical centre.
A Trillion Tons
Authors: Harvey Hal , Orr Franklin M. , Vondrich Clara
Published: January 2013

There is a consensus among scientists that stark dangers await in a world where the global mean temperature rises by more than about 2 degrees Celsius. That threshold corresponds to a collective human carbon emissions “budget” of around a trillion tons, of which half has been spent. This paper uses a new simulation model to look at strategies to stay within that budget, specifically assessing the impact of improvements in energy efficiency, aggressive deployment of renewables, and energy technology innovation. The simulations examine the timing of investments, turnover of capital stock, and the effect of learning on costs, among other factors. The results indicate that efficiency, renewables, and technology innovation are all required to keep humanity within the trillion-ton budget. Even so, these measures are not by themselves sufficient: changes in land use and a price on carbon emissions are also needed.
Does the American Public Support Legislation to Reduce Greenhouse Gas Emissions?
Authors: Krosnick Jon A. , MacInnis Bo
Published: January 2013

Despite efforts by some congressional legislators to pass laws to limit greenhouse gas emissions and reduce the use of fossil fuels, no such laws have yet been adopted. Is this failure to pass new laws attributable to a lack of public desire for such legislation? Data from national surveys support two answers to this question. First, large majorities of Americans have endorsed a variety of policies designed to reduce greenhouse gas emissions; second, policy support has been consistent across years and across scopes and types of policies. Popular policies include fuel economy and energy-efficiency standards, mandated use of renewable sources, and limitations on emissions by utilities and by businesses more generally. Support for policies has been price sensitive, and the American public appears to have been willing to pay enough money for these purposes to cover their costs. Consistent with these policy endorsements, surveys show that large majorities of Americans believe that global warming has been happening, that it is attributable to human activity, and that future warming will be a threat if unaddressed. Not surprisingly, these beliefs appear to have been important drivers of public support for policies designed to reform energy generation and use. Thus, it seems inappropriate to attribute lack of legislation to lack of public support in these arenas.
The Collapse of Western Civilization: A View from the Future
Authors: Oreskes Naomi , Conway Erik M.
Published: January 2013

Authors' note: Science fiction writers construct an imaginary future; historians attempt to reconstruct the past. Ultimately, both are seeking to understand the present. In this essay, we blend the two genres to imagine a future historian looking back on a past that is our present and (possible) future. The occasion is the tercentenary of the end of Western culture (1540 – 2073); the dilemma being addressed is how we – the children of the Enlightenment – failed to act on robust information about climate change and knowledge of the damaging events that were about to unfold. Our historian concludes that a second Dark Age had fallen on Western civilization, in which denial and self-deception, rooted in an ideological fixation on “free” markets, disabled the world's powerful nations in the face of tragedy. Moreover, the scientists who best understood the problem were hamstrung by their own cultural practices, which demanded an excessively stringent standard for accepting claims of any kind – even those involving imminent threats. Here, our future historian, living in the Second People's Republic of China, recounts the events of the Period of the Penumbra (1988 – 2073) that led to the Great Collapse and Mass Migration (2074).
Why & How Governments Support Renewable Energy
Authors: Gallagher Kelly Sims
Published: January 2013

Many countries have adopted comprehensive policy frameworks to support renewable energy, but the United States has not adopted any consistent and stable policies at the national level to foster the use of renewable energy. This essay explores why some nations (Germany, China, and Denmark) and certain U.S. states (Colorado, Texas, and Ohio) have developed robust policies for the deployment of renewable energy. My aim is not to evaluate the specific policy mechanisms that countries and states have chosen, but rather to shed light on the underlying societal factors that contributed to each government's decision to enact the policies in the first place. I explore four factors that could influence a government's decision to adopt favorable policies for renewable energy: (1) economic motives; (2) a high endowment of renewable resources and/or a low endowment of nonrenewable sources; (3) the political system; and (4) cultural factors and attitudes.
The Institutional Blind Spot in Environmental Economics
Authors: Burtraw Dallas
Published: January 2013

Economic approaches are expected to achieve environmental goals at less cost than traditional regulations, but they have yet to find widespread application. One reason is the way these tools interact with existing institutions. The federalist nature of governmental authority assigns to subnational governments much of the implementation of environmental policy and primary authority for planning the infrastructure that affects environmental outcomes. The federalist structure also interacts with the choice of economic instruments; a national emissions cap erodes the additionality of actions by subnational governments. Even the flagship application of sulfur dioxide emissions trading has been outperformed by the venerable Clean Air Act, and greenhouse gas emissions in the United States are on course to be less than they would have been if Congress had frozen emissions with a cap in 2009. The widespread application of economic tools requires a stronger political theory of how they interact with governing institutions.
Justice for the Innocent Job!
Authors: LaCocque André
Published: January 2013

Job's final theophany is puzzling. In fact, far from being a display of God's omnipotence, it is a confession of divine weakness: God needs Job/the human to fight evil in creation—the latter is here de-moralized, only restrained but ever threatened by inhuman forces, at times monstrous). The persistence of evil torments the innocent (Abel, Job, Jesus, the martyrs of the Shoah ...). Job's theme is highlighted from the outset in 1:8-12 where God's insecurity is manifest, depending as it is on an unpredictable human response (1:9). The central point is that there is no deus ex machina as there is no human robot. Job's insistence on this becomes subversive as it routs the principle of distributive justice and promotes one of disinterested righteousness. When Job realizes that his former complaints were a miscarriage of justice toward God, he repents. That is, he realizes that his claimed surplus of justice implied a deficiency of love. At this point, Job proves that he, at least, reveres God without expecting any reward (see 1:9). The satan is defeated and God comes out vindicated by his creature.
A Fine Balance between Hope and Despair: The Epilogue to 2 Kings (25:27-30)
Authors: Joo Samantha
Published: January 2013

Scholars have debated the theological significance of the epilogue to the books of Kings (2 Kgs 25:27-30) by examining the agenda of the Deuteronomistic historian. Rather than looking within the historian's ideology, it may prove beneficial to compare the epilogue to A Fine Balance in which the theme of hope is central to the storyline. Like A Fine Balance in which Rohinton Mistry uses a subdued but hopeful ending to balance the mostly hopeless historical novel, the Deuteronomistic historian adds a hopeful epilogue to the books of Kings to offset its deterministic ideology in which sins lead to punishment. This promising ending, reflecting the human need for hope, becomes an encouraging message for the exilic community.
An Examination of the Effects of Corruption on Financial Market Volatility
Authors: Zhang Aimao
Published: January 2013

Corruption has a profound impact on many aspects of a society, such as, productivity growth, foreign direct investment or income equality. We propose that corruption also has an impact on stability of financial markets. In this study, we demonstrate a strong correlation between corruption and financial market stability and compare corruption with other social and economic factors in terms of their correlations with financial market stability. The data used in this study include financial data of 29 countries’ index funds for the last five years (2002–07), the Corruption Perception Index 2007 and the Index of Economic Freedom 2007.

JEL Classification: D73, G15, G32
Influence of HRH2 promoter polymorphism on aberrant DNA methylation of DAPK and CDH1in the gastric epithelium
Authors: Nomura Tomoe , Tahara Tomomitsu , Shiroeda Hisakazu , Minato Takahiro , Matsue Yasuhiro , Hayashi Ranji , Matsunaga Kazuhiro , Otsuka Toshimi , Nakamura Masakatsu , Toshikuni Nobuyuki , Shibata Tomoyuki , Arisawa Tomiyasu
Published: January 2013

Background

Aberrant methylation patterns in CpG island are known to be influential in gene silencing. Histamine plays important physiological roles in the upper gastrointestinal tract and acts via the H2 receptor. We report an investigation into the effect of HRH2 promoter polymorphism (rs2607474 G > A) on the methylation of DAPK and CDH1.

Methods

Non cancerous gastric mucosa samples were obtained from 115 subjects with gastric cancer (GC) and 412 non-cancer subjects (non-GC). Methylation status of genes was determined by MSP. The genotyping of rs2607474 was performed by PCR-SSCP.

Results

Methylation of DAPK and CDH1 was observed in 296 and 246 subjects, respectively. The frequency of CDH1 methylation in the subjects with GC was significantly lower in cancer lesion than in non cancerous mucosa, whereas that of DAPK methylation was not different. The allelic distribution of rs2607474 was 401GG, 119GA and 7AA. The GG homozygote was associated with a significantly increased risk for methylation of both DAPK and CDH1 (p < 0.0001 and p = 0.0009, respectively). In the non-GC subjects or more than 60 years of age, GG homozygote was more closely associated with both DAPK and CDH1 methylation. However, this genotype did not show an increased risk for the development of methylation of both genes in patients with GC. In H. pylori negative subjects, GG homozygote showed an increased risk for the methylation of both DAPK and CDH1 (p = 0.0074 and p = 0.0016, respectively), whereas this genotype was associated with an increased risk for the development of DAPK methylation in H. pylori positive subjects (p = 0.0018). In addition, in subjects older than 60 years of age, atrophy and metaplasia scores were significantly higher in the GG homozygote (p = 0.011 and p = 0.039, respectively) and a significant correlation was observed between age and atrophy or metaplasia.

Conclusions

Our results suggest that rs2607474 GG homozygote confers a significantly increased risk for age- and inflammation-related DAPK and CDH1 methylation.
Factors associated with the use of home-visit nursing services covered by the long-term care insurance in rural Japan: a cross-sectional study
Authors: Kashiwagi Masayo , Tamiya Nanako , Sato Mikiya , Yano Eiji
Published: January 2013

Background

In Japan, there is a large increase in the number of elderly persons who potentially need home-visit nursing services (VNS). However, the number of persons using the VNS has increased only little in comparison to the number of individuals who use home social services, which are also covered by the Long-Term Care Insurance (LTCI) system. This cross-sectional study investigated the predictors of the VNS used under the LTCI system in Japan.

Methods

We used 1,580 claim data from all the users of community-based services and 1,574 interview survey data collected in 2001 from the six municipal bodies in Japan. After we merged the two datasets, 1,276 users of community-based services under the LTCI were analyzed. Multiple logistic regression models stratified by care needs levels were used for analysis.

Results

Only 8.3% of the study subjects were VNS users. Even among study participants within the higher care-needs level, only 22.0% were VNS users. In the lower care level group, people with a higher care level (OR: 3.50, 95% CI: 1.50–8.93), those whose condition needed long term care due to respiratory or heart disease (OR: 4.31, 95% CI: 1.88–89.20), those whose period of needing care was two years or more (OR: 2.01, 95% CI: 1.14–3.48), those whose service plan was created by a medical care management agency (OR: 2.39, 95% CI: 1.31–4.33), those living with family (OR: 1.86, 95% CI: 1.00–3.42), and those who use home-help services (OR: 2.12, 95% CI: 1.17–3.83) were more likely to use the VNS. In the higher care level group, individuals with higher care level (OR: 3.63, 95% CI: 1.56–8.66), those with higher income (OR: 3.79, 95% CI: 1.01–14.25), and those who had regular hospital visits before entering the LTCI (OR: 2.36, 95% CI: 1.11–5.38) were more likely to use the VNS.

Conclusions

Our results suggested that VNS use is limited due to management by non-medical care management agencies, due to no caregivers being around or a low income household. The findings of this study provide valuable insight for LTCI policy makers: the present provision of VNS should be reconsidered.
A new tool for the paediatric HIV research: general data from the Cohort of the Spanish Paediatric HIV Network (CoRISpe)
Authors: de Jose Ma Isabel , Jiménez de Ory Santiago , Espiau Maria , Fortuny Claudia , Navarro Ma Luisa , Soler-Palacín Pere , Muñoz-Fernandez Ma Angeles ,   from the working groups of CoRISpe and HIV HGM BioBank
Published: January 2013

There are approximately from 1,100 to 1,200 HIV-infected children in a follow-up in Spain. In 2008 an open, multicentral, retrospective and prospective Cohort of the Spanish Paediatric HIV Network (CoRISpe) was founded. The CoRISpe is divided into the node 1 and node 2 representing geographically almost the whole territory of Spain. Since 2008 seventy-five hospitals have been participating in the CoRISpe. All the retrospective data of the HIV-infected children have been kept in the CoRISpe since 1995 and prospective data since 2008. In this article we are going to present the notion of CoRISpe, its role, the structure, how the CoRISpe works and the process how a child is transferred from Paediatric to Adults Units.

The main objective of the CoRISpe is to contribute to furthering scientific knowledge on paediatric HIV infection by providing demographic, sociopsychological, clinical and laboratory data from HIV-infected paediatric patients. Its aim is to enable high-quality research studies on HIV-infected children.
Aging is associated with increased activities of matrix metalloproteinase-2 and -9 in tenocytes
Authors: Yu Tung-Yang , Pang Jong-Hwei S , Wu Katie Pei-Hsuan , Chen Max J-L , Chen Chien-Hung , Tsai Wen-Chung
Published: January 2013

Background

Most tendon pathology is associated with degeneration, which is thought to involve cyclic loading and cumulative age-related changes in tissue architecture. However, the association between aging and degeneration of the extracellular matrix (ECM) in tendons has not been investigated extensively.

Methods

We examined tenocytes from Achilles tendons taken from rats of three different ages (2, 12, and 24 months). Tenocyte viability was assessed using the 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT) assay. Quantitative real-time polymerase chain reaction (PCR) was used to determine the levels of mRNAs that encode type-I collagen, matrix metalloproteinase (MMP)-2 and −9, tissue inhibitor of metalloproteinase (TIMP)-1 and −2 and transforming growth factor (TGF)-β1. Gelatin zymography was used to evaluate the enzymatic activities of MMP-2 and −9. Furthermore, the concentration of TGF-β1 in conditioned medium was evaluated using enzyme-linked immunosorbent assay (ELISA).

Results

The results of the MTT assay showed that the number of viable tenocytes decreased with age. No differences were observed in the levels of mRNAs that encode type-I collagen and TGF-β1 among the three age groups, and the TGF-β1 concentration did not change with age. However, mRNAs that encode MMP-2 and −9 were significantly more abundant in tenocytes from the aging group, and gelatin zymography revealed that the enzymatic activities of MMP-2 and −9 also increased significantly with age. Furthermore, as compared with young group, mRNAs that encode TIMP-1 and −2 were significantly decreased in tenocytes from the aging group.

Conclusions

Activities of MMP-2 and MMP-9 in tenocytes increase with age. This might provide a mechanistic explanation of how aging contributes to tendinopathy or tendon rupture with age.
The study of leachate treatment by using three advanced oxidation process based wet air oxidation
Authors: Karimi Behroz , Ehrampoush Mohammad Hassan , Ebrahimi Asghar , Mokhtari Mehdi
Published: January 2013

Wet air oxidation is regarded as appropriate options for wastewater treatment with average organic compounds. The general purpose of this research is to determine the efficiency of three wet air oxidation methods, wet oxidation with hydrogen peroxide and absorption with activated carbon in removing organic matter and nitrogenous compounds from Isfahan's urban leachate. A leachate sample with the volume of 1.5 liters entered into a steel reactor with the volume of three liters and was put under a 10-bar pressure, at temperatures of 100, 200, and 300° as well as three retention times of 30, 60, and 90 minutes. The sample was placed at 18 stages of leachate storage ponds in Isfahan Compost Plant with the volume of 20 liters, using three WPO, WAO methods and a combination of WAO/GAC for leachate pre-treatment. Thirty percent of pure oxygen and hydrogen peroxide were applied as oxidation agents. The COD removal efficiency in WAO method is 7.8-33.3%, in BOD is 14.7-50.6%, the maximum removal percentage (efficiency) for NH4-N is 53.3% and for NO3-N is 56.4-73.9%. The removal efficiency of COD and BOD5 is 4.6%-34 and 24%-50 respectively in WPO method. Adding GAC to the reactor, the removal efficiency of all parameters was improved. The maximum removal efficiency was increased 48% for COD, 31%-43.6 for BOD5 by a combinational method, and the ratio of BOD5/COD was also increased to 90%. In this paper, WAO and WPO process was used for Leachate pre-treatment and WAO/GAC combinational process was applied for improving the organic matter removal and leachate treatment; it was also determined that the recent process is much more efficient in removing resistant organic matter.
Plasminogen activator inhibitor-1 4G/5G polymorphism and retinopathy risk in type 2 diabetes: a meta-analysis
Authors: Zhang Tengyue , Pang Chong , Li Ningdong , Zhou Elaine , Zhao Kanxing
Published: January 2013

Background

Mounting evidence has suggested that plasminogen activator inhibitor-1 (PAI-1) is a candidate for increased risk of diabetic retinopathy. Studies have reported that insertion/deletion polymorphism in the PAI-1 gene may influence the risk of this disease. To comprehensively address this issue, we performed a meta-analysis to evaluate the association of PAI-1 4G/5G polymorphism with diabetic retinopathy in type 2 diabetes.

Methods

Data were retrieved in a systematic manner and analyzed using Review Manager and STATA Statistical Software. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of associations.

Results

Nine studies with 1, 217 cases and 1, 459 controls were included. Allelic and genotypic comparisons between cases and controls were evaluated. Overall analysis suggests a marginal association of the 4G/5G polymorphism with diabetic retinopathy (for 4G versus 5G: OR 1.13, 95%CI 1.01 to 1.26; for 4G/4G versus 5G/5G: OR 1.30, 95%CI 1.04 to 1.64; for 4G/4G versus 5G/5G + 4G/5G: OR 1.26, 95%CI 1.05 to 1.52). In subgroup analysis by ethnicity, we found an association among the Caucasian population (for 4G versus 5G: OR 1.14, 95% CI 1.00 to 1.30; for 4G/4G versus 5G/5G: OR 1.33, 95%CI 1.02 to 1.74; for 4G/4G versus 5G/5G + 4G/5G: OR 1.41, 95%CI 1.13 to 1.77). When stratified by the average duration of diabetes, patients with diabetes histories longer than 10 years have an elevated susceptibility to diabetic retinopathy than those with shorter histories (for 4G/4G versus 5G/5G: OR 1.47, 95%CI 1.08 to 2.00). We also detected a higher risk in hospital-based studies (for 4G/4G versus 5G/5G+4G/5G: OR 1.27, 95%CI 1.02 to 1.57).

Conclusions

The present meta-analysis suggested that 4G/5G polymorphism in the PAI-1 gene potentially increased the risk of diabetic retinopathy in type 2 diabetes and showed a discrepancy in different ethnicities. A higher susceptibility in patients with longer duration of diabetes (more than 10 years) indicated a gene-environment interaction in determining the risk of diabetic retinopathy.
Examination of soluble integrin resistant mutants of foot-and-mouth disease virus
Authors: Lawrence Paul , LaRocco Michael , Baxt Barry , Rieder Elizabeth
Published: January 2013

Background

Foot-and-mouth disease virus (FMDV) initiates infection via recognition of one of at least four cell-surface integrin molecules αvβ1, αvβ3, αvβ6, or αvβ8 by a highly conserved Arg-Gly-Asp (RGD) amino acid sequence motif located in the G-H loop of VP1. Within the animal host, the αvβ6 interaction is believed to be the most relevant. Sub-neutralizing levels of soluble secreted αvβ6 (ssαvβ6) was used as a selective pressure during passages in vitro to explore the plasticity of that interaction.

Results

Genetically stable soluble integrin resistant (SIR) FMDV mutants derived from A24 Cruzeiro were selected after just 3 passages in cell culture in the presence of sub-neutralizing levels of ssαvβ6. SIR mutants were characterized by: replication on selective cell lines, plaque morphology, relative sensitivity to ssαvβ6 neutralization, relative ability to utilize αvβ6 for infection, as well as sequence and structural changes. All SIR mutants maintained an affinity for αvβ6. Some developed the ability to attach to cells expressing heparan sulfate (HS) proteoglycan, while others appear to have developed affinity for a still unknown third receptor. Two classes of SIR mutants were selected that were highly or moderately resistant to neutralization by ssαvβ6. Highly resistant mutants displayed a G145D substitution (RGD to RDD), while moderately resistant viruses exhibited a L150P/R substitution at the conserved RGD + 4 position. VP1 G-H loop homology models for the A-type SIR mutants illustrated potential structural changes within the integrin-binding motif by these 2 groups of mutations. Treatment of O1 Campos with ssαvβ6 resulted in 3 SIR mutants with a positively charged VP3 mutation allowing for HS binding.

Conclusions

These findings illustrate how FMDV particles rapidly gain resistance to soluble receptor prophylactic measures in vitro. Two different serotypes developed distinct capsid mutations to circumvent the presence of sub-neutralizing levels of the soluble cognate receptor, all of which resulted in a modified receptor tropism that expanded the cell types susceptible to FMDV. The identification of some of these adaptive mutations in known FMDV isolates suggests these findings have implications beyond the cell culture system explored in these studies.
Tool for evaluating research implementation challenges: A sense-making protocol for addressing implementation challenges in complex research settings
Authors: Simpson Kelly M , Porter Kristie , McConnell Eleanor S , Colón-Emeric Cathleen , Daily Kathryn A , Stalzer Alyson , Anderson Ruth A
Published: January 2013

Background

Many challenges arise in complex organizational interventions that threaten research integrity. This article describes aTool forEvaluating Research ImplementationChallenges (TECH), developed using a complexity science framework to assist research teams in assessing and managing these challenges.

Methods

During the implementation of a multi-site, randomized controlled trial (RCT) of organizational interventions to reduce resident falls in eight nursing homes, we inductively developed, and later codified the TECH. The TECH was developed through processes that emerged from interactions among research team members and nursing home staff participants, including a purposive use of complexity science principles.

Results

The TECH provided a structure to assess challenges systematically, consider their potential impact on intervention feasibility and fidelity, and determine actions to take. We codified the process into an algorithm that can be adopted or adapted for other research projects. We present selected examples of the use of the TECH that are relevant to many complex interventions.

Conclusions

Complexity theory provides a useful lens through which research procedures can be developed to address implementation challenges that emerge from complex organizations and research designs. Sense-making is a group process in which diverse members interpret challenges when available information is ambiguous; the groups’ interpretations provide cues for taking action. Sense-making facilitates the creation of safe environments for generating innovative solutions that balance research integrity and practical issues. The challenges encountered during implementation of complex interventions are often unpredictable; however, adoption of a systematic process will allow investigators to address them in a consistent yet flexible manner, protecting fidelity. Research integrity is also protected by allowing for appropriate adaptations to intervention protocols that preserve the feasibility of ‘real world’ interventions.
Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0
Authors: Weber Michael , Henkel Sebastian G , Vlaic Sebastian , Guthke Reinhard , van Zoelen Everardus J , Driesch Dominik
Published: January 2013

Background

Inference of gene-regulatory networks (GRNs) is important for understanding behaviour and potential treatment of biological systems. Knowledge about GRNs gained from transcriptome analysis can be increased by multiple experiments and/or multiple stimuli. Since GRNs are complex and dynamical, appropriate methods and algorithms are needed for constructing models describing these dynamics. Algorithms based on heuristic approaches reduce the effort in parameter identification and computation time.

Results

The NetGenerator V2.0 algorithm, a heuristic for network inference, is proposed and described. It automatically generates a system of differential equations modelling structure and dynamics of the network based on time-resolved gene expression data. In contrast to a previous version, the inference considers multi-stimuli multi-experiment data and contains different methods for integrating prior knowledge. The resulting significant changes in the algorithmic procedures are explained in detail. NetGenerator is applied to relevant benchmark examples evaluating the inference for data from experiments with different stimuli. Also, the underlying GRN of chondrogenic differentiation, a real-world multi-stimulus problem, is inferred and analysed.

Conclusions

NetGenerator is able to determine the structure and parameters of GRNs and their dynamics. The new features of the algorithm extend the range of possible experimental set-ups, results and biological interpretations. Based upon benchmarks, the algorithm provides good results in terms of specificity, sensitivity, efficiency and model fit.
Interactions of commonly used dietary supplements with cardiovascular drugs: a systematic review
Authors: Kanji Salmaan , Seely Dugald , Yazdi Fatemeh , Tetzlaff Jennifer , Singh Kavita , Tsertsvadze Alexander , Tricco Andrea C , Sears Margaret E , Ooi Teik C , Turek Michele A , Skidmore Becky , Ansari Mohammed T
Published: January 2013

Background

The objective of this systematic review was to examine the benefits, harms and pharmacokinetic interactions arising from the co-administration of commonly used dietary supplements with cardiovascular drugs. Many patients on cardiovascular drugs take dietary supplements for presumed benefits and may be at risk for adverse supplement-drug interactions.

Methods

The Allied and Complementary Medicine Database, the Cochrane Library, EMBASE, International Bibliographic Information on Dietary Supplements and MEDLINE were searched from the inception of the review to October 2011. Grey literature was also reviewed.

Two reviewers independently screened records to identify studies comparing a supplement plus cardiovascular drug(s) with the drug(s) alone. Reviewers extracted data using standardized forms, assessed the study risk of bias, graded the strength of evidence and reported applicability.

Results

Evidence was obtained from 65 randomized clinical trials, 2 controlled clinical trials and 1 observational study. With only a few small studies available per supplement, evidence was insufficient for all predefined gradable clinical efficacy and harms outcomes, such as mortality and serious adverse events. One long-term pragmatic trial showed no benefit from co-administering vitamin E with aspirin on a composite cardiovascular outcome. Evidence for most intermediate outcomes was insufficient or of low strength, suggesting no effect. Incremental benefits were noted for triglyceridemia with omega-3 fatty acid added to statins; and there was an improvement in levels of high-density lipoprotein cholesterol with garlic supplementation when people also consumed nitrates

Conclusions

Evidence of low-strength indicates benefits of omega-3 fatty acids (plus statin, or calcium channel blockers and antiplatelets) and garlic (plus nitrates or warfarin) on triglycerides and HDL-C, respectively. Safety concerns, however, persist.
Microwave-assisted polystyrene sulfonate-catalyzed synthesis of novel pyrroles
Authors: Cárdenas Rosario Astrid Vargas , Leal Blanca Olinda Quintanilla , Reddy Ashwini , Bandyopadhyay Debasish , Banik Bimal K
Published: January 2013

Background

Pyrroles are widely distributed in nature and important biologically active molecules. The reaction of amines with 2,5-dimethoxytetrahydrofuran is a promising pathway for the synthesis of pharmacologically active pyrroles under microwave irradiation.

Results

Microwave-induced polystyrenesulfonate-catalyzed synthesis of pyrroles from amines and 2,5-diemthoxytetrahydrofuran has been accomplished with excellent yield. This method produces pyrroles with polyaromatic amines.

Conclusion

The present procedure for the synthesis of N-aromatic substituted pyrroles will find useful application in the area of pharmacologically active molecules.
Integrating stakeholder perspectives into the translation of cell-free fetal DNA testing for aneuploidy
Authors: Sayres Lauren C , Allyse Megan , Cho Mildred K
Published: January 2013

Background

The translation of novel genomic technologies from bench to bedside enjoins the comprehensive consideration of the perspectives of all stakeholders who stand to influence, or be influenced by, the translational course. Non-invasive prenatal aneuploidy testing that utilizes cell-free fetal DNA (cffDNA) circulating in maternal blood is one example of an innovative technology that promises significant benefits for its intended end users; however, it is currently uncertain whether it will achieve widespread clinical implementation. We conducted qualitative interviews with 18 diverse stakeholders in this domain, including prospective users of the technology and healthcare personnel, researchers and developers, and experts in social, legal, and regulatory aspects of genetic technology, and a pilot survey of 62 obstetric healthcare providers. Analysis of interview and survey data was combined with a review of the proceedings of a full-day, multidisciplinary conference on the topic and published scientific and ethics literature surrounding this and other relevant technologies.

Discussion

We constructed potential pathways for technological implementation, identified broad stakeholder classes party to these translational processes, and performed a preliminary assessment of the viewpoints and interrelations among these diverse stakeholders. Some of the stakeholders whose priorities are critical to understand and integrate into translation include pregnant women and their families; healthcare providers; scientists, their institutions or companies, and the funding agencies that support them; regulatory and judicial bodies; third-party payers; professional societies; educational systems; disability rights communities; and other representatives from civil society. Stakeholder interviews, survey findings, and conference proceedings add complexity to these envisioned pathways and also demonstrate a paramount need to incorporate an iterative stakeholder analysis early and throughout the translational endeavor. We believe that the translational framework that we have developed will help guide crucial future stakeholder mapping and engagement activities for cffDNA aneuploidy testing and inform novel methods of technology assessment for other developments in the growing field of genomic medicine.

Mapping potential pathways for implementation and exploring the attitudes and interrelations of diverse stakeholders may lead to more effective translation of a novel method of prenatal aneuploidy testing.