bluuebunny/crossref_metadata_2025 huggingface dataset:
TGFBR3 variation is not a common cause of Marfan-like syndrome and Loeys-Dietz-like syndrome
Authors: Singh Krishna K , Schmidtke Joerg , Keyser Britta , Arslan-Kirchner Mine
Published: March 2012

Marfan syndrome (MFS) is caused by mutations in the fibrillin-1 (FBN1) gene, and mutations in FBN1 are known to be responsible for over 90% of all MFS cases. Locus heterogeneity has also been reported and confirmed, with mutations in the receptor genes TGFBR1 and TGFBR2 identified in association with MFS-related phenotypes. It is now known that dysregulation of TGF-ß signaling is involved in MFS pathogenesis. To test the hypothesis that dysregulation of TGFBR3-associated TGF-ß signaling is implicated in MFS or related phenotype pathogenesis, we selected a cohort of 49 patients, fulfilling or nearly fulfilling the diagnostic criteria for MFS. The patients were known not to carry a mutation in the FBN1 gene (including three 5' upstream alternatively spliced exons), the TGFBR1 and TGFBR2 genes. Mutation screening for the TGFBR3 gene in these patients and in controls led to the identification of a total of ten exonic (one novel), four intronic (one novel) and one 3'UTR variant in the TGFBR3 gene. Our data suggest that variations in TGFBR3 gene appear not to be associated with MFS or related phenotype.
SiC surface orientation and Si loss rate effects on epitaxial graphene
Authors: Kim Moonkyung , Hwang Jeonghyun , Shields Virgil B , Tiwari Sandip , Spencer Michael G , Lee Jo-Won
Published: March 2012

We have explored the properties of SiC-based epitaxial graphene grown in a cold wall UHV chamber. The effects of the SiC surface orientation and silicon loss rate were investigated by comparing the characteristics of each formed graphene. Graphene was grown by thermal decomposition on both the silicon (0001) and carbon (000-1) faces of on-axis semi-insulating 6H-SiC with a "face-down" and "face-up" orientations. The thermal gradient, in relation to the silicon flux from the surface, was towards the surface and away from the surface, respectively, in the two configurations. Raman results indicate the disorder characteristics represented by ID/IG down to < 0.02 in Si-face samples and < 0.05 in C-faces over the 1 cm2 wafer surface grown at 1,450°C. AFM examination shows a better morphology in face-down surfaces. This study suggests that the optimum configuration slows the thermal decomposition and allows the graphene to form near the equilibrium. The Si-face-down orientation (in opposition to the temperature gradient) results in a better combination of low disorder ratio, ID/IG, and smooth surface morphology. Mobility of Si-face-down orientation has been measured as high as approximately 1,500 cm2/Vs at room temperature. Additionally, the field effect transistors have been fabricated on both Si-face-down and C-face-down showing an ambipolar behavior with more favorable electron conduction.
Conference highlights of the 5th international workshop on HIV persistence during therapy, 6-9 December 2011, St. Maartin, West Indies
Authors: Stevenson Mario , Chomont Nicolas , Lafeuillade Alain
Published: March 2012

The December 2011 5th International Workshop on HIV Persistence during Therapy addressed the issue of HIV persistence among 210 scientists from 10 countries involved in the study of HIV reservoirs and the search of an HIV cure. High quality abstracts were selected and discussed as oral or poster presentations. The aim of this review is to distribute the scientific highlights of this workshop outside the group as analyzed and represented by experts in retrovirology, immunology and clinical research.
Emergence of HIV‐1 drug resistance mutations among antiretroviral‐naïve HIV‐1‐infected patients after rapid scaling up of antiretroviral therapy in Thailand
Authors: Sungkanuparph Somnuek , Sukasem Chonlaphat , Kiertiburanakul Sasisopin , Pasomsub Ekawat , Chantratita Wasun
Published: March 2012

Background

After rapid scaling up of antiretroviral therapy in HIV‐1‐infected patients, the data of primary HIV‐1 drug resistance in Thailand is still limited. This study aims to determine the prevalence and associated factors of primary HIV‐1 drug resistance in Thailand.

Methods

A prospective observational study was conducted among antiretroviral‐naïve HIV‐1‐infected Thai patients from 2007 to 2010. HIV‐1 subtypes and mutations were assayed by sequencing a region of HIV‐1 pol gene. Surveillance drug resistance mutations recommended by the World Health Organization for surveillance of transmitted HIV‐1 drug resistance in 2009 were used in all analyses. Primary HIV‐1 drug resistance was defined as the presence of one or more surveillance drug resistance mutations.

Results

Of 466 patients with a mean age of 38.8 years, 58.6% were males. Risks of HIV‐1 infection included heterosexual (77.7%), homosexual (16.7%), and intravenous drug use (5.6%). Median (IQR) CD4 cell count and HIV‐1 RNA were 176 (42‐317) cells/mm3and 68,600 (19,515‐220,330) copies/mL, respectively. HIV‐1 subtypes were CRF01_AE (86.9%), B (8.6) and other recombinants (4.5%). The prevalence of primary HIV‐1 drug resistance was 4.9%; most of these (73.9%) had surveillance drug resistance mutations to only one class of antiretroviral drugs. The prevalence of patients with NRTI, NNRTI, and PI surveillance drug resistance mutations was 1.9%, 2.8% and 1.7%, respectively. From logistic regression analysis, there was no factor significantly associated with primary HIV‐1 drug resistance. There was a trend toward higher prevalence in females [odds ratio 2.18; 95% confidence interval 0.896‐5.304; p = 0.086].

Conclusions

There is a significant emergence of primary HIV‐1 drug resistance in Thailand after rapid scaling up of antiretroviral therapy. Although HIV‐1 genotyping prior to antiretroviral therapy initiation is not routinely recommended in Thailand, our results raise concerns about the risk of early treatment failure in patients with primary HIV‐1 drug resistance. Interventions to prevent the transmission of HIV‐1 drug resistance and continuation of surveillance for primary HIV‐1 drug resistance in Thailand are indicated.
Inhibition of inflammation but not ankylosis by glucocorticoids in mice: further evidence for the entheseal stress hypothesis
Authors: Braem Kirsten , Deroose Christophe M , Luyten Frank P , Lories Rik J
Published: March 2012

Introduction

Studies in the spontaneous ankylosis model in aging male DBA/1 mice and in patients with ankylosing spondylitis provide evidence that inflammation and new tissue formation leading to joint or spine ankylosis are likely linked but largely uncoupled processes. We previously proposed the 'entheseal stress' hypothesis that defines microdamage or cell stress in the enthesis as a trigger for these disease processes. Here, we further investigated the relationship between inflammation and ankylosis by focusing on the early phase of the spontaneous arthritis model.

Methods

Aging male DBA/1 mice from different litters were caged together at the age of ten weeks and studied for signs of arthritis. A group of DBA/1 mice were treated daily with dexamethasone (0.5 μg/g body weight). Severity of disease was assessed by histomorphology and by positron emission tomography (PET) using 2-[18F]fluoro-2-deoxy-D-glucose (18F-FDG) as a tracer. Bone loss in dexamethasone-treated or control mice was determined by in vivo dual-energy X-ray absorptiometry. Chemokine gene expression was studied ex vivo in dissected paws and in vitro in mesenchymal cells (periosteal and bone marrow stromal cells) by quantitative real-time PCR in the presence or absence of bone morphogenetic protein 2 (BMP2) and dexamethasone.

Results

Dexamethasone treatment did not affect incidence or severity of ankylosis, but led to an expected reduction in inflammation in the paws at week 15 as measured by PET tracer uptake. Treatment with dexamethasone negatively affected bone mineral density. Chemokines attracting neutrophils and lymphocytes were expressed in affected paws. In vitro, BMP2 stimulation upregulated chemokines in different mesenchymal joint-associated cell types, an effect that was inhibited by dexamethasone.

Conclusions

BMP signaling may be a trigger for both inflammation and ankylosis in the spontaneous model of ankylosing enthesitis. The lack of inhibition by glucocorticoids on new bone formation while causing systemic bone loss highlights the paradoxical simultaneous loss and gain of bone in patients with ankylosing spondylitis.
Breastfeeding and the risk of breast cancer in BRCA1 and BRCA2 mutation carriers
Authors: Kotsopoulos Joanne , Lubinski Jan , Salmena Leonardo , Lynch Henry T , Kim-Sing Charmaine , Foulkes William D , Ghadirian Parviz , Neuhausen Susan L , Demsky Rochelle , Tung Nadine , Ainsworth Peter , Senter Leigha , Eisen Andrea , Eng Charis , Singer Christian , Ginsburg Ophira , Blum Joanne , Huzarski Tomasz , Poll Aletta , Sun Ping , Narod Steven A ,   the Hereditary Breast Cancer Clinical Study Group
Published: March 2012

Introduction

Breastfeeding has been inversely related to breast cancer risk in the general population. Clarifying the role of breastfeeding among women with a BRCA1 or BRCA2 mutation may be helpful for risk assessment and for recommendations regarding prevention. We present an updated analysis of breastfeeding and risk of breast cancer using a large matched sample of BRCA mutation carriers.

Methods

We conducted a case-control study of 1,665 pairs of women with a deleterious mutation in either BRCA1 (n = 1,243 pairs) or BRCA2 (n = 422 pairs). Breast cancer cases and unaffected controls were matched on year of birth, mutation status, country of residence and parity. Information about reproductive factors, including breastfeeding for each live birth, was collected from a routinely administered questionnaire. Conditional logistic regression was used to estimate the association between ever having breastfed, as well as total duration of breastfeeding, and the risk of breast cancer.

Results

Among BRCA1 mutation carriers, breastfeeding for at least one year was associated with a 32% reduction in risk (OR = 0.68; 95% CI 0.52 to 0.91; P = 0.008); breastfeeding for two or more years conferred a greater reduction in risk (OR = 0.51; 95% CI 0.35 to 0.74). Among BRCA2 mutation carriers, there was no significant association between breastfeeding for at least one year and breast cancer risk (OR = 0.83; 95% CI 0.53 to 1.31; P = 0.43).

Conclusions

These data extend our previous findings that breastfeeding protects against BRCA1-, but not BRCA2-associated breast cancer. BRCA mutation carriers should be advised of the benefit of breastfeeding in terms of reducing breast cancer risk.
Tempted by the Big Apple: The fantasy of western spaces in Kabhi Alvida Naa Kehna
Authors: Kamble Jayashree
Published: March 2012

The 2006 romantic Hindi movie Kabhi Alvida Naa Kehna/Never Say Goodbye (Johar) is set in New York, with the city acting as the classic urban space in cinema that provides anonymity and permits characters to depart from expected norms. Since the movie's transgressive romance could have
been set in any sprawling Indian metropolis, however, this article explores the choice of this American city as the setting. The movie 'produces' a New York where the Indian characters start to question their marital choices but without referring to the Indian nationalist rhetoric that is
common in stories of the diaspora. New York provides not just the necessary urban space but a safe distance from which one can explore the institution of marriage as it currently exists in the home country – both arranged marriage as well as the 'love marriage' that has traditionally
been the teleology of romance movies in India.
BOOK REVIEWS
Authors: Chandra Paresh , Mubarki Meraj Ahmed
Published: March 2012

FRAMING THE NATION: LANGUAGES OF 'MODERNITY' IN INDIA, AJANTA SIRCAR (2011) Calcutta: Seagull University Press, 252 pp., ISBN 978-1906497309, HB, Rs. 595

ISLAMICATE CULTURES OF BOMBAY CINEMA, IRA BHASKAR AND RICHARD ALLEN (2009) New Delhi: Tulika Books, 346 pp., ISBN: 978-81-89487-53-9,
p/bk, Rs. 995
Improved Outcomes in a Quality Improvement Collaborative for Pediatric Inflammatory Bowel Disease
Authors: Crandall Wallace V. , Margolis Peter A. , Kappelman Michael D. , King Eileen C. , Pratt Jesse M. , Boyle Brendan M. , Duffy Lynn F. , Grunow John E. , Kim Sandra C. , Leibowitz Ian , Schoen Bess T. , Colletti Richard B. ,   for the ImproveCareNow Collaborative
Published: March 2012

OBJECTIVES:

Unintended variation in the care of patients with Crohn disease (CD) and ulcerative colitis (UC) may prevent achievement of optimal outcomes. We sought to improve chronic care delivery and outcomes for children with inflammatory bowel disease by using network-based quality improvement methods.

METHODS:

By using a modified Breakthrough Series collaborative structure, 6 ImproveCareNow Network care centers tested changes in chronic illness care and collected data monthly. We used an interrupted time series design to evaluate the impact of these changes.

RESULTS:

Data were available for 843 children with CD and 345 with UC. Changes in care delivery were associated with an increase in the proportion of visits with complete disease classification, measurement of thiopurine methyltransferase (TPMT) before initiation of thiopurines, and patients receiving an initial thiopurine dose appropriate to their TPMT status. These were significant in both populations for all process variables (P < .01) except for measurement of TPMT in CD patients (P = .12). There were significant increases in the proportion of CD (55%–68%) and UC (61%–72%) patients with inactive disease. There was also a significant increase in the proportion of CD patients not taking prednisone (86%–90%). Participating centers varied in the success of achieving these changes.

CONCLUSIONS:

Improvements in the outcomes of patients with CD and UC were associated with improvements in the process of chronic illness care. Variation in the success of implementing changes suggests the importance of overcoming organizational factors related to quality improvement success.
Tracking, recognition, and distance detection of hand gestures for a 3‐D interactive display
Authors: Huang Tzu‐Fan , Chao Paul C.‐P. , Kao Yung‐Yuan
Published: March 2012

Abstract— This study proposes an interactive system for displays, the technologies of which consists of three main parts: hand‐gesture tracking, recognition, and depth measurement. The proposed interactive system can be applied to a general 3‐D display. In this interactive system, for hand‐gesture tracking, Haar‐like features are employed to detect a specific hand gesture to start tracking, while the mean‐shift algorithm and Kalman filter are adopted for fast tracking. First, for recognizing hand gestures, a principal component analysis (PCA) algorithm is used to localize colored areas of skin, and then hand gestures are identified by comparison with a prepared database. Second, a simple optical system is set up with an infrared laser source and a grid mask in order to project a proposed horizontal stripe pattern. Third, the projected patterns are deciphered to extract the depth information using the Hough‐transform algorithm. The system containing hand‐gesture localization, recognition, and associated depth detection (the distance between the display and the hand), was included in a prototype of an interactive display. Demonstration of rotation recognition of a finger‐pointing hand gesture was successful by using the algorithm of radar‐like scanning.
Cognitive engineering, cognitive augmentation, and information display
Authors: Patterson Robert Earl
Published: March 2012

Abstract— From a perspective of cognitive engineering, this paper presents eight principles of good display design based on human cognition: (1) displays that divide attention will increase the cognitive load on working memory; (2) displays that continuously present the same information may compensate for the decay of short‐term memory; (3) displays that assist the viewer in mentally chunking information will decrease the cognitive load on working memory; (4) displays that present icons or images to direct attention to important visual stimuli will likely minimize inattentional blindness; (5) displays that help minimize attentional distractions and help focus attention on a given task will minimize the burden on working memory; (6) displays that present cues composed of strong singletons will capture and engage exogenous attention; (7) displays that help the viewer make a mental connection between an analogue and a target will assist in the induction of analogical reasoning; (8) displays that present over time multiple exposures consisting of statistical regularities may promote implicit learning and expertise development. Thus, information displays of the future can systematically engage high‐level human cognitive processes for purposes of improving human performance on a variety of tasks found in education, the military, and many other applications.
Non‐metamerism of boundary colors in multi‐primary displays
Authors: Centore Paul
Published: March 2012

Abstract— A control sequence gives the intensities of the primaries for a pixel of a display device. The display gamut, i.e., the set of all the colors that a display can produce, is a zonohedral subset of CIE XYZ space and contains both boundary and interior colors. Displays with four primaries or more exhibit metamerism, in which different control sequences produce colors that appear identical to an observer. This paper shows mathematically that, provided no three primaries are linearly dependent, metamerism can only occur for interior colors. When there are four or more primaries, metamers can always be found for interior colors. A color on the gamut boundary, by contrast, is only produced by a unique control sequence. The proof used for displays can be extended to object‐color solids, to show that optimal colors, which are on the boundary of an object‐color solid, have unique reflectance functions.
Resolution enhancement of integral‐imaging three‐dimensional display using directional elemental image projection
Authors: Alam Md. Ashraful , Baasantseren Ganbat , Erdenebat Munkh‐Uchral , Kim Nam , Park Jae‐Hyeung
Published: March 2012

Abstract— A new approach to resolution enhancement of an integral‐imaging (II) three‐dimensional display using multi‐directional elemental images is proposed. The proposed method uses a special lens made up of nine pieces of a single Fresnel lens which are collected from different parts of the same lens. This composite lens is placed in front of the lens array such that it generates nine sets of directional elemental images to the lens array. These elemental images are overlapped on the lens array and produce nine point light sources per each elemental lens at different positions in the focal plane of the lens array. Nine sets of elemental images are projected by a high‐speed digital micromirror device and are tilted by a two‐dimensional scanning mirror system, maintaining the time‐multiplexing sequence for nine pieces of the composite lens. In this method, the concentration of the point light sources in the focal plane of the lens array is nine‐times higher, i.e., the distance between two adjacent point light sources is three times smaller than that for a conventional II display; hence, the resolution of three‐dimensional image is enhanced.
Editorial
Authors: Ashley Kevin
Published: March 2012

Kevin Ashley, Chief Editor, introduces Volume 7, Issue 1 (2012) of the International Journal of Digital Curation.
Managing Risks in the Preservation of Research Data with Preservation Networks
Authors: Conway Esther , Matthews Brian , Giaretta David , Lambert Simon , Wilson Michael , Draper Nick
Published: March 2012

Network modelling provides a framework for the systematic analysis of needs and options for preservation. A number of general strategies can be identified, characterised and applied to many situations; these strategies may be combined to produce robust preservation solutions tailored to the needs of the community and responsive to their environment. This paper provides an overview of this approach. We describe the components of a Preservation Network Model and go on to show how it may be used to plan preservation actions according to the requirements of the particular situation using illustrative examples from scientific archives.
Towards the Development of a Test Corpus of Digital Objects for the Evaluation of File Format Identification Tools and Signatures
Authors: Fetherston Andrew , Gollins Tim
Published: March 2012

The digital preservation community currently utilises a number of tools and automated processes to identify and validate digital objects. The identification of digital objects is a vital first step in their long-term preservation, but the results returned by tools used for this purpose are lacking in transparency, and are not easily tested or verified. This paper suggests that a test corpus of digital objects is one way of providing this verification and validation, ultimately improving trust in the tools, and providing further stimulus to their development. Issues to be considered are outlined, and attention is drawn to particular examples of existing digital corpora which could conceivably provide a useable framework or starting point for our own communities needs. This paper does not seek to answer all questions in this area, but merely attempts to set out areas for consideration in any next step that is taken.
Requirements for Provenance on the Web
Authors: Groth Paul , Gil Yolanda , Cheney James , Miles Simon
Published: March 2012

From where did this tweet originate? Was this quote from the New York Times modified? Daily, we rely on data from the Web, but often it is difficult or impossible to determine where it came from or how it was produced. This lack of provenance is particularly evident when people and systems deal with Web information or with any environment where information comes from sources of varying quality. Provenance is not captured pervasively in information systems. There are major technical, social, and economic impediments that stand in the way of using provenance effectively. This paper synthesizes requirements for provenance on the Web for a number of dimensions, focusing on three key aspects of provenance: the content of provenance, the management of provenance records, and the uses of provenance information. To illustrate these requirements, we use three synthesized scenarios that encompass provenance problems faced by Web users today.
A Short Story about XML Schemas, Digital Preservation and Format Libraries
Authors: Knight Steve
Published: March 2012

One morning we came in to work to find that one of our servers had made 1.5 million attempts to contact an external server in the preceding hour. It turned out that the calls were being generated by the Library’s digital preservation system (Rosetta) while attempting to validate XML Schema Definition (XSD) declarations included in the XML files of the Library’s online newspaper application Papers Past, which we were in the process of loading into Rosetta. This paper describes our response to this situation and outlines some of the issues that needed to be canvassed before we were able to arrive at a suitable solution, including the digital preservation status of these XSDs; their impact on validation tools, such as JHOVE; and where these objects should reside if they are considered material to the digital preservation process.
Understanding the ‘Intensive’ in ‘Data Intensive Research’: Data Flows in Next Generation Sequencing and Environmental Networked Sensors
Authors: McNally Ruth , Mackenzie Adrian , Hui Allison , Tomomitsu Jennifer
Published: March 2012

Genomic and environmental sciences represent two poles of scientific data. In the first, highly parallel sequencing facilities generate large quantities of sequence data. In the latter, loosely networked remote and field sensors produce intermittent streams of different data types. Yet both genomic and environmental sciences are said to be moving to data intensive research. This paper explores and contrasts data flow in these two domains in order to better understand how data intensive research is being done. Our case studies are next generation sequencing for genomics and environmental networked sensors.Our objective was to enrich understanding of the ‘intensive’ processes and properties of data intensive research through a ‘sociology’ of data using methods that capture the relational properties of data flows. Our key methodological innovation was the staging of events for practitioners with different kinds of expertise in data intensive research to participate in the collective annotation of visual forms. Through such events we built a substantial digital data archive of our own that we then analysed in terms of three traits of data flow: durability, replicability and metrology.Our findings are that analysing data flow with respect to these three traits provides better insight into how doing data intensive research involves people, infrastructures, practices, things, knowledge and institutions. Collectively, these elements shape the topography of data and condition how it flows. We argue that although much attention is given to phenomena such as the scale, volume and speed of data in data intensive research, these are measures of what we call ‘extensive’ properties rather than intensive ones. Our thesis is that extensive changes, that is to say those that result in non-linear changes in metrics, can be seen to result from intensive changes that bring multiple, disparate flows into confluence.If extensive shifts in the modalities of data flow do indeed come from the alignment of disparate things, as we suggest, then we advocate the staging of workshops and other events with the purpose of developing the ‘missing’ metrics of data flow.
The Informatics Transform: Re-Engineering Libraries for the Data Decade
Authors: Lyon Liz
Published: March 2012

In this paper, Liz Lyon explores how libraries can re-shape to better reflect the requirements and challenges of today’s data-centric research landscape. The Informatics Transform presents five assertions as potential pathways to change, which will help libraries to re-position, re-profile, and re-structure to better address research data management challenges. The paper deconstructs the institutional research lifecycle and describes a portfolio of ten data support services which libraries can deliver to support the research lifecycle phases. Institutional roles and responsibilities for research data management are also unpacked, building on the framework from the earlier Dealing with Data Report. Finally, the paper examines critical capacity and capability challenges and proposes some innovative steps to addressing the significant skills gaps.
Golden Trail: Retrieving the Data History that Matters from a Comprehensive Provenance Repository
Authors: Missier Paolo , Ludäscher Bertram , Dey Saumen , Wang Michael , McPhillips Tim , Bowers Shawn , Agun Michael , Altintas Ilkay
Published: March 2012

Experimental science can be thought of as the exploration of a large research space, in search of a few valuable results. While it is this “Golden Data” that gets published, the history of the exploration is often as valuable to the scientists as some of its outcomes. We envision an e-research infrastructure that is capable of systematically and automatically recording such history – an assumption that holds today for a number of workflow management systems routinely used in e-science. In keeping with our gold rush metaphor, the provenance of a valuable result is a “Golden Trail”. Logically, this represents a detailed account of how the Golden Data was arrived at, and technically it is a sub-graph in the much larger graph of provenance traces that collectively tell the story of the entire research (or of some of it).In this paper we describe a model and architecture for a repository dedicated to storing provenance traces and selectively retrieving Golden Trails from it. As traces from multiple experiments over long periods of time are accommodated, the trails may be sub-graphs of one trace, or they may be the logical representation of a virtual experiment obtained by joining together traces that share common data.The project has been carried out within the Provenance Working Group of the Data Observation Network for Earth (DataONE) NSF project. Ultimately, our longer-term plan is to integrate the provenance repository into the data preservation architecture currently being developed by DataONE.
Building an Open Data Repository for a Specialized Research Community: Process, Challenges and Lessons
Authors: Peer Limor , Green Ann
Published: March 2012

In 2009, the Institution for Social and Policy Studies (ISPS) at Yale University began building an open access digital collection of social science experimental data, metadata, and associated files produced by ISPS researchers. The digital repository was created to support the replication of research findings and to enable further data analysis and instruction. Content is submitted to a rigorous process of quality assessment and normalization, including transformation of statistical code into R, an open source statistical software. Other requirements included: (a) that the repository be integrated with the current database of publications and projects publicly available on the ISPS website; (b) that it offered open access to datasets, documentation, and statistical software program files; (c) that it utilized persistent linking services and redundant storage provided within the Yale Digital Commons infrastructure; and (d) that it operated in accordance with the prevailing standards of the digital preservation community. In partnership with Yale’s Office of Digital Assets and Infrastructure (ODAI), the ISPS Data Archive was launched in the fall of 2010. We describe the process of creating the repository, discuss prospects for similar projects in the future, and explain how this specialized repository fits into the larger digital landscape at Yale.
Opening Up Climate Research: A Linked Data Approach to Publishing Data Provenance
Authors: Shaon Arif , Callaghan Sarah , Lawrence Bryan , Matthews Brian , Osborn Timothy , Harpham Colin , Woolf Andrew
Published: March 2012

Traditionally, the formal scientific output in most fields of natural science has been limited to peer-reviewed academic journal publications, with less attention paid to the chain of intermediate data results and their associated metadata, including provenance. In effect, this has constrained the representation and verification of the data provenance to the confines of the related publications. Detailed knowledge of a dataset’s provenance is essential to establish the pedigree of the data for its effective re-use, and to avoid redundant re-enactment of the experiment or computation involved. It is increasingly important for open-access data to determine their authenticity and quality, especially considering the growing volumes of datasets appearing in the public domain. To address these issues, we present an approach that combines the Digital Object Identifier (DOI) – a widely adopted citation technique – with existing, widely adopted climate science data standards to formally publish detailed provenance of a climate research dataset as an associated scientific workflow. This is integrated with linked-data compliant data re-use standards (e.g. OAI-ORE) to enable a seamless link between a publication and the complete trail of lineage of the corresponding dataset, including the dataset itself.
The comparison of techniques and methods for L-ascorbic acid determination in the fruits
Authors: Cvetkovic Biljana , Malbasa Radomir , Loncar Eva , Njezic Zvonko , Simurina Olivera , Filipcev Bojana , Tepic Aleksandra
Published: March 2012

Vitamin C is an essential vitamin for human nutrition; with the L-ascorbic
acid (AA) being the active form of vitamin C. Hence, determination of the
L-ascorbic acid in the natural and processed foods is very important. In the
past, plenty of methods based on the reversible redox reaction of AA
oxidation/DHA reduction were developed. Because of L-ascorbic acid
instability in aqueous solutions, it is useful to analyze various types of
extraction. The aim of this study is to compare three different methods and
three different extractants for the L-ascorbic acid determination. Fruits
(kiwi, lemon, orange, and grapefruit) were purchased from a local market. The
L-ascorbic acid in these four samples was determined by the three different
methods: the AOAC, the HPLC method with three different types of extractions,
and the colorimetric method using ascorbate-oxidase. For the HPLC
measurements, one part of the fruits was extracted with distilled water, the
second with potassium hydrogen phosphate, and the third with 3%
meta-phosphoric acid (MPA) in 8% acetic acid. The HPLC measurements of each
sample were repeated three times, the AOAC titration was repeated five times,
and in the calorimetric method three measurements were performed. The results
were statistically evaluated related to sample basis. Statistical analysis
shows that there is a significant difference between the results for all
three methods of extraction for all samples, except for the grapefruit sample
where no significant difference was observed between the results obtained
after the buffer extraction (E2) and the metaphosphoric acid in acetic acid
extraction (E3). Discriminative analysis for the HPLC determinations proves
that there is a clear difference and defined border between the samples in
relation to the methods of extraction during the HPLC determination.
Topological algebras with maximal regular ideals closed
Authors: Abel Mati
Published: March 2012

It is shown that all maximal regular ideals in a Hausdorff topological algebra A are closed if the von Neumann bornology of A has a pseudo-basis which consists of idempotent and completant absolutely pseudoconvex sets. Moreover, all ideals in a unital commutative sequentially Mackey complete Hausdorff topological algebra A with jointly continuous multiplication and bounded elements are closed if the von Neumann bornology of A is idempotently pseudoconvex.
Submitting a paper to an academic peer-reviewed journal, where to start?
Authors: Van Teijlingen E , Simkhada PP , Rizyal A
Published: March 2012

DOI: http://dx.doi.org/10.3126/hren.v10i1.5997 HREN 2012; 10(1): 1-4
Racial differences of colorectal cancer in a single institution in Northeast Louisiana primarily serving the underserved population
Authors: Devkota B , Arnbrecht ES
Published: March 2012

Background: Colorectal cancer (CRC) screening has helped decrease the incidence of CRC in the last two decades. Still African Americans share a higher burden of CRC disease in the United States in comparison to Caucasians. Objective: To study racial differences of colorectal cancer in low income patients. Methods: Retrospective chart review of all admitted patients with a diagnosis of CRC was done by the lead author over a period of eight months. Results: This study, drawn from a poor, diverse population of Louisiana residents suggests socioeconomic factors may explain observed differences in CRC rates between African Americans and Caucasians. Conclusion: Large scale surveillance studies that address social determinants of CRC are needed to further explore this association. DOI: http://dx.doi.org/10.3126/hren.v10i1.5998 HREN 2012; 10(1): 5-7
A prospective study on clinical outcome of complicated external hernias
Authors: Shakya VC , Agrawal CS , Adhikary S
Published: March 2012

Background: External hernias are relatively simple diseases in themselves to treat; however, complications developing in them, such as irreducibility, obstruction and strangulation, may present as a life-threatening one. Objective: To study the characteristics of these patients and identification of risk factors that may predict development of these complications would help place the patient in a high-risk group and subsequent intervention. Methods: It is a prospective descriptive study in patients presenting to Surgery Department of BPKIHS, Dharan, Nepal with a diagnosis of complicated external hernias from December 2009 to July 2011. Results: There were a total of 63 patients including 53 males (84.1%) and 10 females (15.8%). The average age of the patients was 49.23+21.4 years (range 10 days-85 years). The average duration of hernia was 6.36+6.57 years (range 5 hours -30 years). The median duration of complications was 2 days (range 5 hours-15 years). There were 7 mortalities (11.11%). The morbidity rate was 33.33% (21 cases). Risk factors identified for mortality were age >65 years (p=0.004), inguinal hernias (p<0.001), presence of co-morbid diseases (p<0.001), presence of strangulation (p=0.007) and bowel resection (p<0.001); and for morbidities were type of hernia (p<0.001), presence of co-morbid diseases (p=0.013), and bowel resection (p=0.002). Conclusion: Elderly males with co-morbid diseases with inguinal hernia and with strangulation and needing bowel resection are most likely to die from more complications. Such patients when seen in the outpatient department should be given priority admission and taken up for early elective surgery. DOI: http://dx.doi.org/10.3126/hren.v10i1.6002 HREN 2012; 10(1): 20-26
Colonoscopy in patients without sedation: an experience from Nepal
Authors: Pradhan B , Pandey N
Published: March 2012

Background: Colonoscopy is considered a painful procedure requiring routine intravenous sedation, however there are number of potential advantages to performing colonoscopy without sedation. Objective: To determine the effect of unsedated colonoscopy on the success rate of caecal intubation. Methods: All charts of patients who had unsedated colonoscopy from September 2010 to August 2011 were reviewed. Patient characteristics including age, gender, and mode of presentation were collected. The reasons for incomplete colonoscopy and sites reached were recorded. Results: During the study period, 127 examinations were performed without sedation. The mean age of the patients was 41.9 years with 79% males. The most common indication for performing colonoscopy was irritable bowel syndrome and the predominant endoscopic finding was colitis other than inflammatory bowel disease. The completion rate was 80.3%. Conclusion: In this study, sedation probably affects the overall success rate of cecal intubation. But unsedated colonoscopy can be used in resource poor settings to minimize direct and indirect costs of colonoscopy. DOI: http://dx.doi.org/10.3126/hren.v10i1.6003 HREN 2012; 10(1): 27-29
An evaluation of merocel and neosporin impregnated ribbon gauze packs in patients following nasal surgery: a prospective randomised trial
Authors: Joshi RR , Nepal A , Chhetri S Thapa , Bhandary S , Panta TB , Regmi D
Published: March 2012

Background: Packs are placed following nasal surgeries to arrest haemorrhage, to prevent septal haematoma and synechie formation. Despite Merocel, a tampon constructed from a foam polymer of hydroxylated polyvinyl acetate, which is less abrasive and hence associated with the less pain, we still use Neosporine Impregnated Ribbon Gauze (NIRG). Objective: To compare Merocel and the Neosporine Impregnated Ribbon gauze (NIRG) packs in regards to the post-operative pain levels caused by them and their ability to prevent haemorrhage, crusting and synechie. Methods: The nose was packed after surgery either with the Merocel pack or Neosporin Impregnated Ribbon Gauze (NIRG) according to the randomisation. The pain score was noted on the Visual analog score while packs were in situ and again immediately after the pack removal. The haemorrhage, crusting and synechie were noted if present. Results: Among 106 patients, 61 were male and 45 were female. In Merocel group there were 51 patients and in NIRG group 55. The mean pain score for merocel was 4.15 while in situ and 3.66 immediately after removal where as mean pain score for NIRG was 6 while in situ and 3.78 immediately after removals. Post-operative crusting and synechie were seen relatively more in NIRG pack group. Conclusion: Merocel is superior in terms of both patient comfort and pain. DOI: http://dx.doi.org/10.3126/hren.v10i1.6004 HREN 2012; 10(1): 30-34
Depression in seizure disorder
Authors: Shakya DR
Published: March 2012

Depression, a psychiatric disorder is common and can present with various forms in seizures. Here is a seizure case with depression, as manifestation and as co-morbidity, presented to highlight the prevalence and management issues. A 35-year married female presented to a health-camp with unresponsive spells and depressive symptoms. For 5 years, she had altered consciousness spells associated with deviation of mouth and turning head to left and stiffening of right limbs, followed by GTCS every 15-90 days. The frequency increased in last 6 months. Her supportive mother-in-law died 12 months back and, she started worrying about her illness and family. Her sleep and appetite decreased. She frequently cried alone, more in 2-3 days after seizure spells, in last 7 months. She repeatedly expressed guilt and death wish, and once attempted hanging. Referral was made from the camp for hospital admission. After EEG report of ‘left temporal seizure’, mood stabilizing anti-epileptic and seizure friendly antidepressant were started with diagnosis of ‘Seizure and severe depression’. DOI: http://dx.doi.org/10.3126/hren.v10i1.6010 HREN 2012; 10(1): 59-61
Injection Molding of Water Containing Thermoplastic Polyolefin
Authors: Mulyana R. , Cabrera E. , Castro J. M. , Lee L. J. , Min Y.
Published: March 2012

In this paper, we present a novel injection molding approach using water containing thermoplastic polyolefin (TPO) to reduce the cycle time and to improve the dimensional stability of parts without any equipment or mold modifications. A small amount of water was pressurized into TPO pellets pre-mixed with water carrier particles such as highly porous activated carbon or tubular-shaped nanoclay. Our results showed that the cycle time could be drastically reduced with substantially reduced surface sink mark and part warpage without any adverse effects on mechanical properties. Water evaporation during molding resulted in internal cooling, which led to a large reduction in cycle time. This phenomenon, however, could not be explained by the average water content in TPO alone. It is believed that the accumulation of water in the thickest section of the mold cavity, i.e., the base of the conical shaped sprue in the molds used in the study, during injection molding played a major role. The lower sink mark and part warpage were due to water induced internal cooling and foaming. Complete filling of thin parts could also be achieved at a lower packing pressure in the presence of water, perhaps due to steam (from water evaporation) induced mold cavity heating during filling. This was supported by the measured temperature rise at the mold surface in the early stage of the molding cycle.
Measurement Modification of Barrier Properties against UV Irradiation of PP Composite Fibres
Authors: Ujhelyiová A. , Dulíková M. , Borsig E. , Alexy P. , Brejka O. , Marcinčin A.
Published: March 2012

Besides comfort and hygiene of textile materials sufficient barrier properties, such as protection against ultraviolet (UV) irradiation, are also often required. For the evaluation of barrier properties of textile materials against UV irradiation, a quantitative expression, “ultraviolet protection factor (UPF)”, is used. This factor correlates with the time period of human skin protection against UV irradiation in the open air. One of the experimental methods for quantitative UPF evaluation involves a spectrophotometric method of fabric testing. This paper describes a novel modification approach to transfer this method to non-woven and non-knitted fabrics. The aim of the transformation was to modify the used method to determine barrier properties of polymer composite fibres so that the measurement could be simplified while keeping the reliability of the obtained results. As a testing material samples of polypropylene fibres with dispersed nanoTiO2filler reeled on the sheet-metal frame were used. The results show that this modified method gives reliable results and is suitable for development of new kinds of fibres with higher barrier protection against UV irradiation.
Stages of Carcinoma Breast at Presentation in Rural Bangladeshi Women
Authors: Arif AS , Rahman MM
Published: March 2012

Carcinoma breast is the leading cause death from cancer in women between 20-59 years.. The slow natural history makes it a potentially curable disease if presented early. Unfortunately the rural women in Bangladesh frequently present with late carcinoma breast. The objective of this study is to find out the stages of the disease when presented for the first time to a qualified doctor. The study shows that about 43% of our womenfolk present with late stage when the prognosis in terms of survival rate is not so optimistic. Even when they present with early breast cancer, most of them are at stage II. There is scope to improve the scenario by educating them on screening of breast carcinoma by self examination, mammogeusly, avoidance of risk factors and advantages of FNAC & biopsy from any breat lump. DOI: http://dx.doi.org/10.3329/akmmcj.v3i1.10106 AKMMCJ 2012; 3(1): 10-12
Evaluation of Uterine Scar on Repeat Second Cesarean Section in Patients with Previous Cesarean Section
Authors: Nargis N , Al-Mahmood AK , Akhter D
Published: March 2012

To evaluate the safety and integrity of uterine scar at repeat cesarean section in patients with previous one cesarean section (C/S). A prospective study was Carried out in a tertiary care, obstetric unit over a period of one year, 2010. All pregnant mothers who underwent cesarean section either emergency or elective with history of previous one cesarean sections were included in this study. The variables noted were age, parity, socioeconomic status, residential area, location of previous cesarean section, previous wound infection and associated complaints. Data was analyzed on SPSS 11 Operative findings during cesarean sections were recorded in terms of thinning of scar, dehiscence or rupture. One hundred and twenty cesarean section patients were included in the study. Out of all patients, extreme thinning of scar was noted in 28 (23.33%) patients. Four patients (3.33%) had scar dehiscence,only 3( 2.5%) patients with scar dehiscence had associated complaint of scar tenderness, while 17 (14.16%) of 120 cases of scar thinning were having scar tenderness. All 4 cases of scar dehiscence had their previous c/s at peripheral hospitals. No patient underwent hysterectomy and all patients with scar dehiscence had successful repair. Our findings shows relatively inadequate scar thickness rate but at the same time relatively acceptable scar dehiscence rate. Thus it seems to be a safe approach to make trial of labour after meticulous scrutinization and individualization. DOI: http://dx.doi.org/10.3329/akmmcj.v3i1.10108 AKMMCJ 2012; 3(1): 16-19
Granular Cell Tumour of The Vulva: A Case Report
Authors: Khodeza SM , Begum Nahar , Begum Nishat
Published: March 2012

Vulvar granular cell tumours are uncommon neoplasms of neural origin. The clinical presentations, surgical findings and histology of Granular Cell Tumour (GCT) of the vulva in a 50 year old lady is presented. Although rare, this benign lesion must be considered in the differential diagnosis of the labia majora masses, such as Bartholin,s duct cyst, Lipoma, Papilloma, Hydradenoma and Fibroma. DOI: http://dx.doi.org/10.3329/akmmcj.v3i1.10111 AKMMCJ 2012; 3(1): 28-30