bluuebunny/crossref_metadata_2025 huggingface dataset:
A panel of genes methylated with high frequency in colorectal cancer
Authors: Mitchell Susan M , Ross Jason P , Drew Horace R , Ho Thu , Brown Glenn S , Saunders Neil FW , Duesing Konsta R , Buckley Michael J , Dunne Rob , Beetson Iain , Rand Keith N , McEvoy Aidan , Thomas Melissa L , Baker Rohan T , Wattchow David A , Young Graeme P , Lockett Trevor J , Pedersen Susanne K , LaPointe Lawrence C , Molloy Peter L
Published: January 2014

Background

The development of colorectal cancer (CRC) is accompanied by extensive epigenetic changes, including frequent regional hypermethylation particularly of gene promoter regions. Specific genes, including SEPT9, VIM1 and TMEFF2 become methylated in a high fraction of cancers and diagnostic assays for detection of cancer-derived methylated DNA sequences in blood and/or fecal samples are being developed. There is considerable potential for the development of new DNA methylation biomarkers or panels to improve the sensitivity and specificity of current cancer detection tests.

Methods

Combined epigenomic methods – activation of gene expression in CRC cell lines following DNA demethylating treatment, and two novel methods of genome-wide methylation assessment – were used to identify candidate genes methylated in a high fraction of CRCs. Multiplexed amplicon sequencing of PCR products from bisulfite-treated DNA of matched CRC and non-neoplastic tissue as well as healthy donor peripheral blood was performed using Roche 454 sequencing. Levels of DNA methylation in colorectal tissues and blood were determined by quantitative methylation specific PCR (qMSP).

Results

Combined analyses identified 42 candidate genes for evaluation as DNA methylation biomarkers. DNA methylation profiles of 24 of these genes were characterised by multiplexed bisulfite-sequencing in ten matched tumor/normal tissue samples; differential methylation in CRC was confirmed for 23 of these genes. qMSP assays were developed for 32 genes, including 15 of the sequenced genes, and used to quantify methylation in tumor, adenoma and non-neoplastic colorectal tissue and from healthy donor peripheral blood. 24 of the 32 genes were methylated in >50% of neoplastic samples, including 11 genes that were methylated in 80% or more CRCs and a similar fraction of adenomas.

Conclusions

This study has characterised a panel of 23 genes that show elevated DNA methylation in >50% of CRC tissue relative to non-neoplastic tissue. Six of these genes (SOX21, SLC6A15, NPY, GRASP, ST8SIA1 and ZSCAN18) show very low methylation in non-neoplastic colorectal tissue and are candidate biomarkers for stool-based assays, while 11 genes (BCAT1, COL4A2, DLX5, FGF5, FOXF1, FOXI2, GRASP, IKZF1, IRF4, SDC2 and SOX21) have very low methylation in peripheral blood DNA and are suitable for further evaluation as blood-based diagnostic markers.
Patients’ preferences for osteoporosis drug treatment: a discrete-choice experiment
Authors: Hiligsmann Mickaël , Dellaert Benedict G , Dirksen Carmen D , van der Weijden Trudy , Goemaere Stefan , Reginster Jean-Yves , Watson Verity , Boonen Annelies
Published: January 2014

Introduction

The patient’s perspective is becoming increasingly important in clinical and policy decisions. In this study, we aimed to evaluate the preferences of patients with, or at risk of, osteoporosis for medication attributes, and to establish how patients trade between these attributes.

Methods

A discrete choice experiment survey was designed and patients were asked to choose between two hypothetical unlabelled drug treatments (and an opt-out option) that vary in five attributes: efficacy in reducing the risk of fracture, type of potential common side-effects, mode and frequency of administration and out-of-pocket costs. An efficient experimental design was used to construct the treatment option choice sets and a mixed logit panel data model was used to estimate patients’ preferences and trade-offs between attributes.

Results

A total of 257 patients with, or at risk of, osteoporosis completed the experiment. As expected, patients preferred treatment with higher effectiveness and lower cost. They also preferred either an oral monthly tablet or 6-month subcutaneous injection above weekly oral tablets, 3-month subcutaneous, 3-month intravenous or yearly intravenous injections. Patients disliked being at risk of gastro-intestinal disorders more than being at risk of skin reactions and flu-like symptoms. There was significant variation in preferences across the sample for all attributes except subcutaneous injection.

Conclusions

This study revealed that osteoporotic patients preferred 6-month subcutaneous injection and oral monthly tablet, and disliked gastro-intestinal disorders. Moreover, patients were willing to pay a personal contribution or to trade treatment efficacy for better levels of other attributes. Preferences for treatment attributes varied across patients and this highlights the importance of clinical decision-making taking individual preferences into account to improve osteoporosis care.
Interpreting with multiple wavelength curvature attributes
Authors: Giroldi Luis , Garossino Paul
Published: January 2014

Long-wavelength volumetric curvature attributes have become an integral part of the interpretation workflow and are extremely useful when working with structural and stratigraphic features. We present a modification of a previously introduced fractional derivative algorithm by adding a fractional integral, allowing us to calculate even longer wavelengths. This extends the available spectrum providing a variety of curvature scales. We illustrate their use by assessing an exploration area in Eastern Saudi Arabia.
Investigating fault continuity associated with geologic carbon storage planning in the Illinois Basin
Authors: McBride John H. , William Keach R. , Wolfe Eugene E. , Leetaru Hannes E. , Chandler Clayton K. , Greenhalgh Scott R.
Published: January 2014

Because the confinement of [Formula: see text] in a storage reservoir depends on a stratigraphically continuous set of seals to isolate the fluid in the reservoir, the detection of structural anomalies is critical for guiding any assessment of a potential subsurface carbon storage site. Employing a suite of 3D seismic attribute analyses (as opposed to relying upon a single attribute) maximizes the chances of identifying geologic anomalies or discontinuities (e.g., faults) that may affect the integrity of a seal that will confine the stored [Formula: see text] in the reservoir. The Illinois Basin, a major area for potential carbon storage, presents challenges for target assessment because geologic anomalies can be ambiguous and easily misinterpreted when using 2D seismic reflection data, or even 3D data, if only conventional display techniques are used. We procured a small 3D seismic reflection data set in the central part of the basin (Stewardson oil field) to experiment with different strategies for enhancing the appearance of discontinuities by integrating 3D seismic attribute analyses with conventional visualizations. Focusing on zones above and below the target interval of the Cambrian Mt. Simon Sandstone, we computed attribute traveltime slices (combined with vertical views) based on discontinuity computations, crossline-directed amplitude change, azimuth of the dip, shaded relief, and fault likelihood attributes. The results provided instructive examples of how discontinuities (e.g., subseismic scale faults) may be almost “invisible” on conventional displays but become detectable and mappable using an appropriate integration of 3D attributes. Strong discontinuities in underlying Precambrian basement rocks do not necessarily propagate upward into the target carbon storage interval. The origin of these discontinuities is uncertain, but we explored a possible strike-slip role that also explains the localization of a structural embayment developed in Lower Paleozoic strata above the basement discontinuities.
Deaths by suicide and their relationship with general and
psychiatric hospital discharge: 30-year record linkage study
Authors: Dougall Nadine , Lambert Paul , Maxwell Margaret , Dawson Alison , Sinnott Richard , McCafferty Susan , Morris Carole , Clark David , Springbett Anthea
Published: January 2014

Background

Studies have rarely explored suicides completed following discharge from
both general and psychiatric hospital settings. Such research might
identify additional opportunities for intervention.

Aims

To identify and summarise Scottish psychiatric and general hospital
records for individuals who have died by suicide.

Method

A linked data study of deaths by suicide, aged ⩾15 years from 1981 to
2010.

Results

This study reports on a UK data-set of individuals who died by suicide
(n = 16 411), of whom 66% (n = 10
907) had linkable previous hospital records. Those who died by suicide
were 3.1 times more frequently last discharged from general than from
psychiatric hospitals; 24% of deaths occurred within 3 months of hospital
discharge (58% of these from a general hospital). Only 14% of those
discharged from a general hospital had a recorded psychiatric diagnosis
at last visit; an additional 19% were found to have a previous lifetime
psychiatric diagnosis. Median time between last discharge and death was
fourfold greater in those without a psychiatric history. Diagnoses also
revealed that less than half of those last discharged from general
hospital had had a main diagnosis of ‘injury or poisoning’.

Conclusions

Suicide prevention activity, including a better psychiatric evaluation of
patients within general hospital settings deserves more attention.
Improved information flow between secondary and primary care could be
facilitated by exploiting electronic records of previous psychiatric
diagnoses.
The Applicability of near Infrared Spectroscopy for Monitoring Properties of Food Packaging Materials
Authors: Cattaneo Tiziana M.P. , Cremonesi Katia , Barzaghi Stefania
Published: January 2014

This paper reports the results of some preliminary experiments to assess the use of NIR spectroscopy in measuring the quality and the stability of a new, active food packaging material based on propolis and comparing it to paper and polythene–paper sheets.
Strategie polskich tłumaczy włoskich librett w XVIII wieku
Authors: Miszalska Jadwiga
Published: January 2014

Strategies in Translating Italian Librettos in 18th Century PolandPolish dramatic writers of the 18th century very often referred to the European repertoire. The majority of Polish dramas in fact were translations or adaptations of foreign texts. Among Italian sources opera and oratorio librettos were the mostimportant. The paper is an attempt to review Polish translations of Italian librettos in the 18th century, to reconstruct the translators’ motivation and to discover their translation strategies. In the first half of the 18th century a huge part of translated dramas were created by the Jesuits in order to be presented on school stage. Apart from this kind of texts at that time there were also Polish translations whose aim was to accompany performances in Italian language as texts „for reading”. Only in the late 18th century translation were used in performances with original music. Specific circumstances and finality of translations would have a decisive impact on translation strategies which could affect the story, the ideology but also the form of dramas and usually resulted in change of genre. These modifications prove that the translation of theater texts is especially submitted to a pressure of target system cultural context because the target text has to establish a direct contact with the public. Examining the history of translations and the evolution of translator’s approach helps to reconstruct an important share of the history of Polish dramaturgy and to indicate its sources.
Kilka uwag o recepcji współczesnego dramatu francuskiego w Polsce po 1989 roku
Authors: Paszkowska Alicja
Published: January 2014

A few thoughts on the reception of Contemporary French Drama in Poland after 1989After 1989 Polish theatre went through a series of significant artistic and administrative changes. Those were reflected in a new theatrical repertoire. This article presents a few thoughts on interference and reception of contemporary French drama in Poland during last twenty years. The analysis is based on laws of interference between literary polysystems described by Itamar Even‑Zohar.
A Multiactivity Latent Attrition Model for Customer Base Analysis
Authors: Schweidel David A. , Park Young-Hoon , Jamal Zainab
Published: January 2014

Customer base analysis is a key element in customer valuation and can provide guidance for decisions such as resource allocation. Yet extant models often focus on a single activity, such as purchases from a retailer or donations to a nonprofit organization. These models do not consider other ways that an individual may engage with an organization, such as purchasing in multiple brands or contributing user-generated content. In this research, we propose a framework to generalize extant models for customer base analysis to multiple activities.

Using the data from a website that allows users to purchase digital content and/or post digital content at no charge, we develop a flexible “buy ‘til you die” model to empirically examine how the two activities are related. Compared with benchmarks, our model more accurately forecasts the future behavior for both types of activities. In addition to finding evidence of coincidence between the activities while customers are “alive,” we find that the latent attrition processes are related. This suggests that conducting one type of activity is informative of whether customers are still alive to conduct another type of activity and, consequently, affects inferences of customer value.
Volume Flexibility in Services: The Costs and Benefits of Flexible Labor Resources
Authors: Kesavan Saravanan , Staats Bradley R. , Gilland Wendell
Published: January 2014

Organizations can create volume flexibility—the ability to increase capacity up or down to meet demand for a single service—through the use of flexible labor resources (e.g., part-time and temporary workers, as compared to full-time workers). Although organizations are increasingly using these resources, the relationship between flexible labor resources and financial performance has not been examined empirically in the service setting. We use two years of archival data from 445 stores of a large retailer to study this relationship. We hypothesize and find that increasing the labor mix of temporary or part-time workers shows an inverted U-shaped relationship with sales and profit while temporary labor mix has a U-shaped relationship with expenses. Thus, although flexible labor resources can create volume flexibility for a firm along multiple dimensions, it is possible to have too much of a good thing.

This paper was accepted by Serguei Netessine, operations management.
Free vibration analysis of isotopic rectangular plate with one edge free of support (CSCF and SCFC plate)
Authors: Ebirim Stanley I , Ezeh J C , Ibearugbulem M Owus
Published: January 2014

The paper presents a theoretical formulation based on Ibearugbulems shape function and application of Ritz method. In this study, the free vibration of simply supported plate with one free edge was analyzed. The Ibearugbulems shape function derived was substituted into the potential energy functional, which was minimized to obtain the fundamental natural frequency. Aspect ratios from 0.1 to 2.0 with 0.1 increments were considered. The values of fundamental natural frequencies of the first mode were determined for different aspect ratio. For aspect ratio of 1.0, the value of non-dimensional parameter of fundamental natural frequency obtained was 23.86. Comparison was made for values of non-dimensional parameter of fundamental natural frequencies obtained in this study with those of previous research works. It was seen that there is no significant difference between values obtained in this study with those of previous studies. Keywords: fundamental natural frequency; Ibearugbulems shape function; CSCF plate; Ritz method; SCFC plate.
Einstellregeln für Füllstandsregelungen in der industriellen Praxis
Authors: Krämer Stefan , Völker Marten
Published: January 2014

Die Füllstandsregelung in chemischen Anlagen ist ein wichtiges praktisches Problem. Die Füllstände müssen entweder in bestimmten Grenzen gehalten oder auf einem festen Niveau geregelt werden. Diese Regelung ist eine besondere Herausforderung, da eine integrierende Strecke geregelt wird. Es werden im Allgemeinen PID-Regler des vorhandenen Leitsystems eingesetzt – oft ohne Nutzung des D-Anteils. In diesem Aufsatz werden die für Standregler in Chemieanlagen relevanten Fälle betrachtet. Der für die Fahrweise wichtige Fall der Störungsdämpfung durch Puffer wird besonders behandelt. Ziel des Beitrages ist es, auf Basis der analytischen Lösung des Problems und des H
∞-Ansatzes sehr einfache Formeln zu entwickeln, mit denen der Ingenieur vor Ort schnell und sicher Standregler einstellen kann.
A software environment for economic NMPC and dynamic real-time optimization of chemical processes
Authors: Elixmann David , Puschke Jennifer , Scheu Holger , Schneider René , Wolf Inga J. , Marquardt Wolfgang
Published: January 2014

This paper presents the OptoEcon-Toolbox, a modular software environment for the simulation of chemical and energy processes, and their control using optimizing sampled-data controllers.
Key features of this toolbox are modularity, which allows the realization of general multi-layer control architectures, and interfaces to powerful numerical software, which allows the usage of controller and plant surrogate models formulated in different modeling languages such as Modelica or gPROMS.
The capability of this toolbox is illustrated in a case study of an industrial copolymerization process.
Realisierung von Advanced Control in einem industriellen Polymerisationsprozess
Authors: Engell Sebastian , Finkler Tiago F. , Kawohl Michael , Piechottka Uwe
Published: January 2014

Der vorliegende Beitrag zeigt exemplarisch an einem industriellen Produktionsprozess das Potenzial modellbasierter Regelungsverfahren
auf. Ziel der Optimierung ist die Verbesserung der Produktqualität durch eine präzisere Temperaturregelung und die Reduzierung der
Batchzeiten. Hierfür wird ein nichtlinear modellbasierter prädiktiver Regler, welcher die Kühlleistung und die Monomerdosierung als
Stellgrößen nutzt, implementiert. In der Produktion kann die Regelgüte der Temperaturregelung wesentlich verbsssert und die Batchzeit
erheblich reduziert werden.
Adolescents’ view of health concept and its risk factors: a literature review
Authors: Parvizi Soroor , Hamzehgardeshi Zeinab
Published: January 2014

Background: Adolescence is the important period in human life. It is an essential prerequisite for playing social roles.

Objective: The current study conducted a review on the concept, dimensions, and influential factors on health and risk taking, instruments and measurements of high-risk behaviors, risk factors, and high-risk behavior protective factors through adolescent perspectives.

Methods: This literature review was conducted by electronic searching and library study on health and adolescents using Wiley Interscience, ScienceDirect, ProQuest, and Springer (1990–2012). The keywords for searching data collection sources included health, youth, young, adolescents, risk behaviors, risk taking, related factors, protective factors, risk factors, adolescent perspectives, quantitative study, qualitative study, measurement, and instrument.

Results: This literature review led to the arrangement of subjects in nine general categories titled definition of health concept and its dimensions, adolescents and health in adolescence, risk taking in adolescence and its measuring tools, gender differences in adolescence health and risk taking, adolescents’ health and relationships, socioeconomic conditions and health, adolescents and psychiatric health, religion, and health, educational facilities and health, non-governmental organizations and their role in adolescents’ health. What has been achieved from a review of these articles is that several personal, social, and family factors are associated with health and risk taking in adolescents.

Conclusion: Generally, adolescents cared more about the psychosocial aspects of health than the physical dimensions. They also considered factors such as independence, communication, socioeconomic conditions, mental health, religion, and educational facilities synonymous with the concept of health. Therefore, in formulation and implementation of health promotion programs for adolescents, the concept of health and its various dimensions must be considered from adolescent perspectives.
Quality of life measures and psychiatric symptoms in adolescents with systemic lupus erythematosus and familial Mediterranean fever
Authors: Düzçeker Yasemin , Kanbur Nuray Ö. , Demirkaya Erkan , Derman Orhan , Moorthy Lakshmi N. , Özen Seza
Published: January 2014

Purpose: To describe the relation between global Quality of Life (QL) and psychiatric symptoms in adolescents with systemic lupus erythematosus (SLE) and familial Mediterranean fever (FMF), and to analyze the perceptions of parents and adolescents.

Methods: This study included 51 adolescents diagnosed with SLE (n=25) and FMF (n=26), and 51 healthy adolescents. The Health Related QL (HRQL) of SLE patients was rated by parents and adolescents using the Simple Measurement of Impact of Lupus Erythematosus in Youngsters© (SMILEY©). The global QL of FMF patients and healthy adolescents was rated by the response given to the first question of the SMILEY© by each parent and adolescent. All participants completed the Brief Symptom Inventory (BSI), which measures psychiatric symptoms.

Results: In total, 92.3% with FMF, 56% with SLE and 76.5% of healthy adolescents reported their global QL as good and very good using the first question of the SMILEY©. The global QL perceptions of adolescents and their parents did not correlate (FMF, p=0.94; SLE, p=0.16). SLE patients had the highest rate of depression (54.2%), whereas hostility was detected among 54.9% of healthy adolescents. Significant relations were detected between BSI and SMILEY© scores.

Conclusion: The global QL perceptions of adolescents with FMF were better than those of healthy adolescents, which may be explained by their perceived relief of anguish they suffer during their short-lived attacks. The global QL perceptions of adolescents with SLE were the worst, most probably due to the chronic course resulting in an awareness of limitations and intense treatment. Adolescents with SLE had similar psychopathological symptom scores when compared with FMF patients and healthy adolescents. This could be explained by developing resilience. Differences in the perception of adolescents versus their parents regarding global QL emphasized the importance of adolescent-specific interviews for chronic illnesses and multidisciplinary follow-up with adolescent medicine.
Nonalcoholic fatty liver disease is a negative risk factor for prostate cancer recurrence
Authors: Choi Won-Mook , Lee Jeong-Hoon , Yoon Jung-Hwan , Kwak Cheol , Lee Young Ju , Cho Young Youn , Lee Yun Bin , Yu Su Jong , Kim Yoon Jun , Kim Hyeon Hoe , Kim Hyo-Cheol , Cho Sung Yong , Lee Seung Bae , Jeong Hyeon , Kim Chung Yong , Lee Hyo-Suk
Published: January 2014

Nonalcoholic fatty liver disease (NAFLD) is closely related to the metabolic syndrome, which is associated with an increased risk of various malignancies. In this study, we investigated the association between NAFLD and prostate cancer biochemical recurrence (BCR) after radical prostatectomy. Consecutive prostate cancer patients who underwent radical prostatectomy were enrolled from two hospitals in Korea and randomly assigned to the training (n=147) or validation set (n=146). The presence of NAFLD, BMI, preoperative prostate-specific antigen, and histological findings including Gleason score (GSc) were analyzed in regard to their association with BCR. NAFLD was diagnosed based on ultrasonography or unenhanced computed tomography images. BCR-free survival rates were calculated using the Kaplan–Meier method. In the training set, 32 (21.8%) patients developed BCR during a median follow-up period of 51 (inter-quartile range, 35–65) months. In the multivariate analysis, the presence of NAFLD (hazard ratio (HR), 0.36; 95% CI, 0.14–0.97;P=0.04) was an independent negative predictive factor of BCR after adjustment for pathological GSc. Applied to the validation set, the presence of NAFLD maintained its prognostic value for longer time-to-BCR (HR, 0.17; 95% CI, 0.06–0.49;P=0.001). In the subgroup analysis of patients with NAFLD, NAFLD fibrosis score was a single independent negative predictor for BCR (HR, 0.54; 95% CI, 0.30–0.98;P=0.04). Our study demonstrated that NAFLD may play a protective role against BCR after radical prostatectomy for prostate cancer. Further study is warranted to elucidate the mechanism of protective effect in patients with NAFLD.
Ovarian steroids affect prostaglandin production in equine endometrial cells in vitro
Authors: Szóstek Anna Z , Galvão António M , Ferreira-Dias Graça M , Skarzynski Dariusz J
Published: January 2014

This study aimed to evaluate the influence of ovarian steroids on equine endometrial epithelial and stromal cells, specifically i) prostaglandin (PG) production in a time-dependent manner, ii) specific PG synthases mRNA transcription and protein expression, and iii) cell proliferation. After passage I, cells were exposed to vehicle, oxytocin (OT, positive control, 10−7M), progesterone (P4, 10−7M), 17β estradiol (E2, 10−9M), or P4+E2for 12, 24, 48, or 72 h. Following treatment, PG concentration was determined using the direct enzyme immunoassay (EIA) method. Alterations inPGsynthases mRNA transcriptions,PGsynthases protein expression, and cell proliferation in response to the treatments were determined after 24 h using real-time PCR, western blot, or 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide respectively. After 24 h, E2and P4+E2increased PGE2and PGF2αsecretion as well as specific prostaglandin-endoperoxide synthase-2 (PTGS2), PGE2synthases (PGES), and PGF2αsynthases (PGFS) expression in the epithelial cells (P<0.05). Additionally, E2and P4+E2increased PTGS2 expression in stromal cells after 24 h (P<0.05). In stromal cells, P4+E2increased PGE2production as well as PGES expression after 24 h (P<0.05). Both E2and P4+E2increased PGF2αproduction by stromal cells after 24 h (P<0.05). Ovarian steroids affected proliferation of stromal and epithelial cells during the 24-h incubation period (P<0.05). We provide evidence that ovarian steroids affect PG production in equine endometrial cells, upregulating PTGS2, PGES, and PGFS expression. Ovarian steroid-stimulated PG production could be an important mechanism occurring in the equine endometrium that is involved in the regulation of the estrous cycle and early pregnancy.
Relational Autonomy: Moving Beyond the Limits of Isolated Individualism
Authors: Walter Jennifer K. , Ross Lainie Friedman
Published: January 2014

Although clinicians may value respecting a patient’s or surrogate’s autonomy in decision-making, it is not always clear how to proceed in clinical practice. The confusion results, in part, from which conception of autonomy is used to guide ethical practice. Reliance on an individualistic conception such as the “in-control agent” model prioritizes self-sufficiency in decision-making and highlights a decision-maker’s capacity to have reason transcend one’s emotional experience. An alternative model of autonomy, relational autonomy, highlights the social context within which all individuals exist and acknowledges the emotional and embodied aspects of decision-makers. These 2 conceptions of autonomy lead to different interpretations of several aspects of ethical decision-making. The in-control agent model believes patients or surrogates should avoid both the influence of others and emotional persuasion in decision-making. As a result, providers have a limited role to play and are expected to provide medical expertise but not interfere with the individual’s decision-making process. In contrast, a relational autonomy approach acknowledges the central role of others in decision-making, including clinicians, who have a responsibility to engage patients’ and surrogates’ emotional experiences and offer clear guidance when patients are confronting serious illness. In the pediatric setting, in which decision-making is complicated by having a surrogate decision-maker in addition to a patient, these conceptions of autonomy also may influence expectations about the role that adolescents can play in decision-making.
Improving the culture of interdisciplinary collaboration in ecology by expanding measures of success
Authors: Goring Simon J , Weathers Kathleen C , Dodds Walter K , Soranno Patricia A , Sweet Lynn C , Cheruvelil Kendra S , Kominoski John S , Rüegg Janine , Thorn Alexandra M , Utz Ryan M
Published: January 2014

Interdisciplinary collaboration is essential to understand ecological systems at scales critical to human decision making. Current reward structures are problematic for scientists engaged in interdisciplinary research, particularly early career researchers, because academic culture tends to value only some research outputs, such as primary‐authored publications. Here, we present a framework for the costs and benefits of collaboration, with a focus on early career stages, and show how the implementation of novel measures of success can help defray the costs of collaboration. Success measures at team and individual levels include research outputs other than publications, including educational outcomes, dataset creation, outreach products (eg blogs or social media), and the application of scientific results to policy or management activities. Promotion and adoption of new measures of success will require concerted effort by both collaborators and their institutions. Expanded measures should better reflect and reward the important work of both disciplinary and interdisciplinary teams at all career stages, and help sustain and stimulate a collaborative culture within ecology.
Completing the data life cycle: using information management in macrosystems ecology research
Authors: Rüegg Janine , Gries Corinna , Bond-Lamberty Ben , Bowen Gabriel J , Felzer Benjamin S , McIntyre Nancy E , Soranno Patricia A , Vanderbilt Kristin L , Weathers Kathleen C
Published: January 2014

An important goal of macrosystems ecology (MSE) research is to advance understanding of ecological systems at both fine and broad temporal and spatial scales. Our premise in this paper is that MSE projects require integrated information management at their inception. Such efforts will lead to improved communication and sharing of knowledge among diverse project participants, better science outcomes, and more transparent and accessible (ie “open”) science. We encourage researchers to “complete the data life cycle” by publishing well‐documented datasets, thereby facilitating re‐use of the data to answer new and different questions from the ones conceived by those involved in the original projects. The practice of documenting and submitting datasets to data repositories that are publicly accessible ensures that research results and data are available to and use‐able by other researchers, thus fostering open science. However, ecologists are often unfamiliar with the requirements and information management tools for effectively preserving data and receive little institutional or professional incentive to do so. Here, we provide recommendations for achieving these ends and give examples from current MSE projects to demonstrate why information management is critical for ensuring that scientific results can be reproduced and that data can be shared for future use.
Macrosystems ecology: understanding ecological patterns and processes at continental scales
Authors: Heffernan James B , Soranno Patricia A , Angilletta Michael J , Buckley Lauren B , Gruner Daniel S , Keitt Tim H , Kellner James R , Kominoski John S , Rocha Adrian V , Xiao Jingfeng , Harms Tamara K , Goring Simon J , Koenig Lauren E , McDowell William H , Powell Heather , Richardson Andrew D , Stow Craig A , Vargas Rodrigo , Weathers Kathleen C
Published: January 2014

Macrosystems ecology is the study of diverse ecological phenomena at the scale of regions to continents and their interactions with phenomena at other scales. This emerging subdiscipline addresses ecological questions and environmental problems at these broad scales. Here, we describe this new field, show how it relates to modern ecological study, and highlight opportunities that stem from taking a macrosystems perspective. We present a hierarchical framework for investigating macrosystems at any level of ecological organization and in relation to broader and finer scales. Building on well‐established theory and concepts from other subdisciplines of ecology, we identify feedbacks, linkages among distant regions, and interactions that cross scales of space and time as the most likely sources of unexpected and novel behaviors in macrosystems. We present three examples that highlight the importance of this multiscaled systems perspective for understanding the ecology of regions to continents.
Approaches to advance scientific understanding of macrosystems ecology
Authors: Levy Ofir , Ball Becky A , Bond-Lamberty Ben , Cheruvelil Kendra S , Finley Andrew O , Lottig Noah R , Punyasena Surangi W , Xiao Jingfeng , Zhou Jizhong , Buckley Lauren B , Filstrup Christopher T , Keitt Tim H , Kellner James R , Knapp Alan K , Richardson Andrew D , Tcheng David , Toomey Michael , Vargas Rodrigo , Voordeckers James W , Wagner Tyler , Williams John W
Published: January 2014

The emergence of macrosystems ecology (MSE), which focuses on regional‐ to continental‐scale ecological patterns and processes, builds upon a history of long‐term and broad‐scale studies in ecology. Scientists face the difficulty of integrating the many elements that make up macrosystems, which consist of hierarchical processes at interacting spatial and temporal scales. Researchers must also identify the most relevant scales and variables to be considered, the required data resources, and the appropriate study design to provide the proper inferences. The large volumes of multi‐thematic data often associated with macrosystem studies typically require validation, standardization, and assimilation. Finally, analytical approaches need to describe how cross‐scale and hierarchical dynamics and interactions relate to macroscale phenomena. Here, we elaborate on some key methodological challenges of MSE research and discuss existing and novel approaches to meet them.
Iodine Uptake and Prostate Cancer in the TRAMP Mouse Model
Authors: Olvera-Caltzontzin Paloma , Delgado Guadalupe , Aceves Carmen , Anguiano Brenda
Published: January 2014

Iodine supplementation exerts antitumor effects in several types of cancer. Iodide (I−) and Iodine (I2) reduce cell proliferation and induce apoptosis in human prostate cancer cells (LNCaP and DU-145). Both chemical species decrease tumor growth in athymic mice xenografted with DU-145 cells. The aim of this study was to analyze the uptake and effects of iodine in a preclinical model of prostate cancer (transgenic adenocarcinoma of the mouse prostate [TRAMP] mice/SV40-TAG antigens), which develops cancer by 12 wks of age. 125I− and 125I2 uptake was analyzed in prostates from wild-type and TRAMP mice of 12 and 24 wks in the presence of perchlorate (inhibitor of the Na+/I− symporter [NIS]). NIS expression was quantified by quantitative polymerase chain reaction (qPCR). Mice (6 wks old) were supplemented with 0.125 mg I− plus 0.062 mg I2/mouse/day for 12 or 24 wks. The weight of the genitourinary tract (GUT), the number of acini with lesions, cell proliferation (levels of proliferating cell nuclear antigen [PCNA] by immunohistochemistry), p53 and p21 expression (by qPCR) and apoptosis (relative amount of nucleosomes by enzyme-linked immunosorbent assay) were evaluated. In both age-groups, normal and tumoral prostates take up both forms of iodine, but only I− uptake was blocked by perchlorate. Iodine supplementation prevented the overexpression of NIS in the TRAMP mice, but had no effect on the GUT weight, cell phenotype, proliferation or apoptosis. In TRAMP mice, iodine increased p53 expression but had no effect on p21 (a p53-dependent gene). Our data corroborate NIS involvement in I− uptake and support the notion that another transporter mediates I2 uptake. Iodine did not prevent cancer progression. This result could be explained by a strong inactivation of the p53 pathway by TAG antigens.
Uniqueness of the Suction Stress Characteristic Curve under Different Confining Stress Conditions
Authors: Oh Seboong , Lu Ning
Published: January 2014

The soil water retention curve (SWRC) describes a soil's constitutive relation between matric suction and volumetric water content. The suction stress characteristic curve (SSCC) describes a soil's constitutive relation between suction stress and volumetric water content. Both the SWRC and SSCC are often established assuming a soil is nondeformable. Under a shallow field environment, however, the total stress can change several hundreds of kilopascals due to self‐weight variation with depth, surface structural loading, or soil excavation, leading to changes in volumetric strain and consequently the SWRC and SSCC. This work experimentally examined the effect of a confining stress on the SWRC and SSCC under both drying and wetting conditions through a silty sand. The SWRCs were measured under different confining stresses up to 200 kPa, allowing assessment of the uniqueness of the SWRC or SSCC. We found that under wetting conditions, even though the SWRCs and SSCCs were different under different confining stresses, a unique SWRC or SSCC could be defined if the effective degree of saturation was used. Under drying conditions, the uniqueness of the SWRC or SSCC held approximately; the differences mainly reflecting in the air‐entry pressure. Furthermore, the failure envelope by the effective stress representation based on the SWRC was unique for either wetting or drying and was well represented by the saturated failure envelope. The SSCC inferred from the shear strength tests was similar to that from the SWRC measurement under the respective wetting or drying states. Therefore, the SWRC and SSCC are practically independent of the confining stress up to 200 kPa for a silty sand.
Effective Stress in Clays of Various Mineralogy
Authors: Baille Wiebke , Tripathy Snehasis , Schanz Tom
Published: January 2014

The effective stress in clays possessing a significant proportion of one of the clay minerals kaolinite, illite, or montmorillonite was determined based on the suction stress characteristic curves (SSCCs) of the clays. The SSCCs were determined based on the drying soil‐water characteristic curves of the clays for a suction range of 0.03 to about 219.0 MPa. One‐dimensional compressibility behavior of initially saturated clays was also studied by loading clay specimens up to a maximum vertical stress of 21.0 MPa. The effective stress–void ratio responses of the clays during the drying process were compared with their saturated counterparts. The shapes of SSCCs and the magnitudes of minimum and maximum suction stress were strongly dependent on the mineralogy and the properties of the clays. For the clays with kaolinite and illite as the dominant clay minerals, the suction stress decreased, remained nearly constant, and then increased with an increase in the applied suction, whereas it decreased monotonically with increasing suction for the montmorillonite clay. A decrease in the suction stress caused an increase in the effective stress, which in turn reduced the volume of the clays. For applied suctions smaller than the air‐entry value of any clay, equal magnitudes of suction stress and effective stress produced a similar volume change of the clay. The study clearly showed that suction changes beyond the air‐entry value are less effective in producing volume changes in unsaturated soils, primarily because of a decrease in the effective stress due to an increase in the suction stress.
Numerical Model for Colloidal Silica Injected Column Tests
Authors: Hamderi M. , Gallagher P. M. , Lin Y.
Published: January 2014

The UTCHEM flood simulator was used to develop a numerical model to simulate colloidal silica transport through sand columns. Most existing numerical models for colloidal silica modeling include the gelation process, in which the viscosity gradually becomes orders of magnitude greater than the initial grout viscosity. However, in field grouting applications of shallow, loose, cohesionless deposits, injection at high viscosities may be limited due to allowable pressure limitations. In these cases, the injection is planned to be completed just before the gelling reaction begins. Thus, modeling the gelation process may not be necessary. The UTCHEM simulator accounts for fluids with varying densities and viscosities, making it a useful tool for simulating colloidal silica injection in cases where gelation does not need to be modeled explicitly. The model was validated using laboratory data from five column tests in which loose sand was treated with colloidal silica grout and one column test in which sand was treated with sodium silicate. The numerical model accurately represented the physical experiments. The numerical model provides a validated tool that can be used to design and optimize stabilizer delivery for laboratory and field applications in which gelation does not need to be modeled explicitly.
Surface Complexation of Oxytetracycline by Magnetite: Effect of Solution Properties
Authors: Rakshit Sudipta , Sarkar Dibyendu , Elzinga Evert J. , Punamiya Pravin , Datta Rupali
Published: January 2014

Few studies have reported on the sorptive interactions of oxytetracycline (OTC), a veterinary antibiotic frequently detected in wastewater, surface water, and soils, with common Fe oxide minerals. The primary objective of this study was to investigate the sorption behavior of OTC on magnetite (Fe3O4) as a function of different solution properties such as pH, ionic strength, and initial OTC concentration. Results indicated that sorption of OTC by magnetite was rapid and complete within 24 h. The effect of ionic strength on sorption was negligible at low OTC surface coverage. The sorption envelope indicated that with increasing pH, OTC sorption on Fe3O4 decreased. Surface complexation modeling of magnetite–OTC interactions suggested the interactions of divalent anionic species of OTC with the magnetite surface. Four possible surface complexation reactions were postulated to explain the pH dependence of OTC sorption, indicating a rather complex potential sorption mechanism. Our results suggest that magnetite has the capability of immobilizing OTC in the environment, which may be of use to scientists in predicting the fate of OTC in Fe‐oxide‐rich soil.
Adverse Effects of the Oral Anticancer Drug S-1: Lacrimal Passage Impairment and Specific Features of Corneal Epitheliopathy
Authors: Sato Ken-ichi , Nishimura Shin-ichi
Published: January 2014

We report the incidence of lacrimal passage impairment and specific features of corneal epitheliopathy as
adverse effects of the oral anticancer drug S-1, and examine the relationship between the two pathologies. We conducted a
retrospective chart review of 84 patients prescribed the anticancer drug S-1. The incidence of lacrimal passage impairment
and corneal epitheliopathy was 8% and 6%, respectively. Three patients experienced both pathologies, demonstrating a
moderate probability of both occurring in the same patient (kappa coefficient = 0.46). The findings show that lacrimal
passage impairment and specific features of corneal epitheliopathy are likely to occur in the same individual as adverse
effects of S-1.
Ralstonia solanacearum: A new threat to potato production in Serbia
Authors: Milijasevic-Marcic Svetlana , Todorovic Biljana , Potocnik Ivana , Rekanovic Emil , Stepanovic Milos , Mitrovic Jelena , Duduk Bojan
Published: January 2014

A survey of ware potatoes (a total of 1127 samples) from localities in Serbia
during two consecutive years resulted in detection and identification of R.
solanacearum in 17 tuber samples. The monitoring detected the causal agent of
bacterial wilt and brown rot of potato in three districts of Vojvodina
province. In 2011, the infection by R. solanacearum was confirmed in 7
samples of ware potato tubers (varieties - Saturna, Pirol, Hermes, Panda) in
West Backa and South Backa Districts. In 2012, the infection by R.
solanacearum was confirmed in 10 potato tuber samples (Lady Claire, Desiree,
Panda, Red Fantasy and Vineta varieties) from two districts: South Backa and
Central Banat. Bacterial strains obtained from positive samples were
identified as R. solanacearum biovar 2 using PCR/RFLP analysis, pathogenicity
test on tomato transplants, and nutritional, enzymatic and biovar
determination tests. To our best knowledge, these are the only findings of R.
solanacearum infection in ware potatoes in Serbia. R. solanacearum was not
detected in tomato or any other host plant tested in this study. Furthermore,
the bacterium was not found in any of the water samples tested, including
those originating from areas in which the bacterium was found in ware potato
samples.
Natural evolution of experimental vitreous hemorrhage and effects of corticosteroids on its course
Authors: Vukovic Dragan
Published: January 2014

Introduction. The course and prognosis of vitreous hemorrhage (VH) are
difficult to predict in spite of so far published experimental and clinical
studies. Objective. The goal of this study was to follow the course and
evaluate prognosis of vitreous hemorrhage. Methods. The experiment was
performed on 19 Chinchilla rabbits (Oryctolagus cuniculus), both males and
females (38 eyes), weighing 2500-3000 g, which were treated with autologous
blood (B) from marginal ear vein - the first group, and the second group was
treated with both blood and corticosteroids (B+CS). The course of vitreous
hemorrhage was examined. Results. Our results have shown that the cellular
reaction to vitreous hemorrhage is different, compared to hemorrhage in
other types of tissue, which is due to absence of an early polymorphonuclear
cellular reaction. Number of cells within vitreous body is very low.
Conclusion. Vitreous hemorrhage has unusual course followed by a small
number of cells (mostly poly-morphonuclear cells). This is most important
fact why VH is cleared very slowly (about 6 to 9 weeks). CS has moderate
influence on the acceleration of VH absorption.