bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extendable pattern-oriented optimization directives
Authors: Cui Huimin , Xue Jingling , Wang Lei , Yang Yang , Feng Xiaobing , Fan Dongrui 
Published: October 2012

Algorithm-specific, that is, semantic-specific optimizations have been observed to bring significant performance gains, especially for a diverse set of multi/many-core architectures. However, current programming models and compiler technologies for the state-of-the-art architectures do not exploit well these performance opportunities. In this article, we propose a pattern-making methodology that enables algorithm-specific optimizations to be encapsulated into “optimization patterns”. Such optimization patterns are expressed in terms of preprocessor directives so that simple annotations can result in significant performance improvements. To validate this new methodology, a framework, named EPOD, is developed to map these directives into the underlying optimization schemes for a particular architecture.
It is difficult to create an exact performance model to determine an optimal or near-optimal optimization scheme (including which optimizations to apply and in which order) for a specific application, due to the complexity of applications and architectures. However, it is trackable to build individual optimization components and let compiler developers synthesize an optimization scheme from these components. Therefore, our EPOD framework provides an Optimization Programming Interface (OPI) for compiler developers to define new optimization schemes. Thus, new patterns can be integrated into EPOD in a flexible manner.
We have identified and implemented a number of optimization patterns for three representative computer platforms. Our experimental results show that a pattern-guided compiler can outperform the state-of-the-art compilers and even achieve performance as competitive as hand-tuned code. Therefore, such a pattern-making methodology represents an encouraging direction for domain experts' experience and knowledge to be integrated into general-purpose compilers.
Geminin Functions Downstream of p53 in K-ras–Induced Gene Amplification of Dihydrofolate Reductase
Authors: Shen Ling , Nishioka Takashi , Guo Jinjin , Chen Changyan 
Published: October 2012

Abstract
DNA strand breakage and perturbation of cell-cycle progression contribute to gene amplification events that can drive cancer. In cells lacking p53, DNA damage does not trigger an effective cell-cycle arrest and in this setting promotes gene amplification. This is also increased in cells harboring oncogenic Ras, in which cell-cycle arrest is perturbed and ROS levels that cause DNA single strand breaks are elevated. This study focused on the effects of v-K-ras and p53 on Methotrexate (MTX)-mediated DHFR amplification. Rat lung epithelial cells expressing v-K-ras or murine lung cancer LKR cells harboring active K-ras continued cell-cycle progression when treated with MTX. However, upon loss of p53, amplification of DHFR and formation of MTX-resistant colonies occurred. Expression levels of cyclin A, Geminin, and Cdt1 were increased in v-K-ras transfectants. Geminin was sufficient to prevent the occurrence of multiple replications via interaction with Cdt1 after MTX treatment, and DHFR amplification proceeded in v-K-ras transfectants that possess a functional p53 in the absence of geminin. Taken together, our findings indicate that p53 not only regulates cell-cycle progression, but also functions through geminin to prevent DHFR amplification and protect genomic integrity. Cancer Res; 72(23); 6153–62. ©2012 AACR.
S1P1 expression is controlled by the pro-oxidant activity of p66Shc and is impaired in B-CLL patients with unfavorable prognosis
Authors: Capitani Nagaja , Patrussi Laura , Trentin Livio , Lucherini Orso Maria , Cannizzaro Enrica , Migliaccio Enrica , Frezzato Federica , Gattazzo Cristina , Forconi Francesco , Pelicci Piergiuseppe , Semenzato Gianpietro , Baldari Cosima T. 
Published: October 2012

Abstract
Although intrinsic apoptosis defects are causal to the extended survival of chronic lymphocytic leukemia (CLL) B cells, several lines of evidence support a contribution of the peripheral lymphoid organs and BM microenvironment to the extended lifespan of leukemic B cells. Lymphocyte trafficking is controlled by homing signals provided by stromal cell–derived chemokines and egress signals provided by sphingosine-1-phosphate (S1P). In the present study, we show that expression of S1P1, the S1P receptor responsible for lymphocyte egress, is selectively reduced in CLL B cells with unmutated IGHV. Expression of S1P2, which controls B-cell homeostasis, is also impaired in CLL B cells but independently of the IGHV mutational status. We provide evidence herein that p66Shc, a Shc adaptor family member the deficiency of which is implicated in the apoptosis defects of CLL B cells, controls S1P1 expression through its pro-oxidant activity. p66Shc also controls the expression of the homing receptor CCR7, which opposes S1P1 by promoting lymphocyte retention in peripheral lymphoid organs. The results of the present study provide insights into the regulation of S1P1 expression in B cells and suggest that defective egress caused by impaired S1P1 expression contributes to the extended survival of CLL B cells by prolonging their residency in the prosurvival niche of peripheral lymphoid organs.
Transcriptome analyses of early cucumber fruit growth identifies distinct gene modules associated with phases of development
Authors: Ando Kaori , Carr Kevin M , Grumet Rebecca 
Published: October 2012

Abstract

Background
Early stages of fruit development from initial set through exponential growth are critical determinants of size and yield, however, there has been little detailed analysis of this phase of development. In this study we combined morphological analysis with 454 pyrosequencing to study transcript level changes occurring in young cucumber fruit at five ages from anthesis through the end of exponential growth.

Results
The fruit samples produced 1.13 million ESTs which were assembled into 27,859 contigs with a mean length of 834 base pairs and a mean of 67 reads per contig. All contigs were mapped to the cucumber genome. Principal component analysis separated the fruit ages into three groups corresponding with cell division/pre-exponential growth (0 and 4 days post pollination (dpp)), peak exponential expansion (8dpp), and late/post-exponential expansion stages of growth (12 and 16 dpp). Transcripts predominantly expressed at 0 and 4 dpp included homologs of histones, cyclins, and plastid and photosynthesis related genes. The group of genes with peak transcript levels at 8dpp included cytoskeleton, cell wall, lipid metabolism and phloem related proteins. This group was also dominated by genes with unknown function or without known homologs outside of cucurbits. A second shift in transcript profile was observed at 12-16dpp, which was characterized by abiotic and biotic stress related genes and significant enrichment for transcription factor gene homologs, including many associated with stress response and development.

Conclusions
The transcriptome data coupled with morphological analyses provide an informative picture of early fruit development. Progressive waves of transcript abundance were associated with cell division, development of photosynthetic capacity, cell expansion and fruit growth, phloem activity, protection of the fruit surface, and finally transition away from fruit growth toward a stage of enhanced stress responses. These results suggest that the interval between expansive growth and ripening includes further developmental differentiation with an emphasis on defense. The increased transcript levels of cucurbit-specific genes during the exponential growth stage may indicate unique factors contributing to rapid growth in cucurbits.
Comparison of transcriptome technologies in the pathogenic fungus Aspergillus fumigatus reveals novel insights into the genome and MpkA dependent gene expression
Authors: Müller Sebastian , Baldin Clara , Groth Marco , Guthke Reinhard , Kniemeyer Olaf , Brakhage Axel A , Valiante Vito 
Published: October 2012

Abstract

Background
The filamentous fungus Aspergillus fumigatus has become the most important airborne fungal pathogen causing life-threatening infections in immuno-compromised patients. Recently developed high-throughput transcriptome and proteome technologies, such as microarrays, RNA deep-sequencing, and LC-MS/MS of peptide mixtures, are of enormous value for systematically investigating pathogenic organisms. In the field of infection biology, one of the priorities is to collect and standardise data, in order to generate datasets that can be used to investigate and compare pathways and gene responses involved in pathogenicity. The “omics” era provides a multitude of inputs that need to be integrated and assessed. We therefore evaluated the potential of paired-end mRNA-Seq for investigating the regulatory role of the central mitogen activated protein kinase (MpkA). This kinase is involved in the cell wall integrity signalling pathway of A. fumigatus and essential for maintaining an intact cell wall in response to stress.

Results
The comparison of the transcriptome and proteome of an A. fumigatus wild-type strain with an mpkA null mutant strain revealed that 70.4% of the genome was found to be expressed and that MpkA plays a significant role in the regulation of many genes involved in cell wall remodelling, oxidative stress and iron starvation response, and secondary metabolite biosynthesis. Moreover, absence of the mpkA gene also strongly affects the expression of genes involved in primary metabolism. The data were further processed to evaluate the potential of the mRNA-Seq technique. We comprehensively matched up our data to published transcriptome studies and were able to show an improved data comparability of mRNA-Seq experiments independently of the technique used. Analysis of transcriptome and proteome data revealed only a weak correlation between mRNA and protein abundance.

Conclusions
High-throughput analysis of MpkA-dependent gene expression confirmed many previous findings that this kinase is important for regulating many genes involved in metabolic pathways. Our analysis showed more than 2000 differentially regulated genes. RNA deep-sequencing is less error-prone than established microarray-based technologies. It also provides additional information in A. fumigatus studies and as a result is more suitable for the creation of extensive datasets.
Correlation between Slug transcription factor and miR-221 in MDA-MB-231 breast cancer cells
Authors: Lambertini Elisabetta , Lolli Andrea , Vezzali Federica , Penolazzi Letizia , Gambari Roberto , Piva Roberta 
Published: October 2012

Abstract

Background
Breast cancer and its metastatic progression is mainly directed by epithelial to mesenchymal transition (EMT), a phenomenon supported by specific transcription factors and miRNAs.

Methods
In order to investigate a possible correlation between Slug transcription factor and miR-221, we performed Slug gene silencing in MDA-MB-231 breast cancer cells and evaluated the expression of genes involved in supporting the breast cancer phenotype, using qRT-PCR and Western blot analysis. Chromatin immunoprecipitation and wound healing assays were employed to determine a functional link between these two molecules.

Results
We showed that Slug silencing significantly decreased the level of miR-221 and vimentin, reactivated Estrogen Receptor α and increased E-cadherin and TRPS1 expression. We demonstrated that miR-221 is a Slug target gene, and identified a specific region of miR-221 promoter that is transcriptionally active and binds the transcription factor Slug “in vivo”. In addition, we showed that in Slug-silenced cells, wich retained residual miR-221 (about 38%), cell migration was strongly inhibited. Cell migration was inhibited, but to a less degree, following complete knockdown of miR-221 expression by transfection with antagomiR-221.

Conclusions
We report for the first time evidence of a correlation between Slug transcription factor and miR-221 in breast cancer cells. These studies suggest that miR-221 expression is, in part, dependent on Slug in breast cancer cells, and that Slug plays a more important role than miR-221 in cell migration and invasion.
Repeated in vivo inguinal measurements to estimate a single optimal mesh size for inguinal herniorrhaphy
Authors: Rabe Rannie , Yacapin Clarence Pio Rey , Buckley Brian S , Faylona Jose Macario 
Published: October 2012

Abstract

Background
Inguinal hernia is a common condition and its repair (herniorrhaphy) is one of the most commonly performed procedures in general surgery. The Lichtenstein herniorrhaphy technique is a widely used and effective surgery that uses mesh to reinforce the area of weakness. Although a wide range of mesh sizes are available for use in hernia repair, in low-resource health care settings the provision of multiple products may not be supportable and it may be necessary for the provision and use of a single mesh size. This study aimed to determine whether the recommended 7.0 cm x 15.0 cm size is an appropriate single mesh size.

Methods
In order to determine the optimal mesh size according to recommended surgical practices, in vivo measurements of key dimensions of the inguinal floor were taken in patients undergoing herniorrhaphy.

Results
Measurements were taken in 43 patients: 40 men and 3 women, mean age 43 years (SD 13.6); 39 with indirect hernias, 4 with direct. Allowing for recommended mesh overlaps, the optimal mesh size for provision to be appropriate for the majority of patients was determined to be 8.5 cm x 14.0 cm, 21% wider than the mesh size currently recommended for use in Lichtenstein herniorrhaphy.

Conclusions
An appropriate size for routine provision in low-resource settings, or other settings where the provision of several mesh sizes is not supportable, may be 8.5 cm x 14.0 cm.
Exposure to second-hand smoke and direct healthcare costs in children – results from two German birth cohorts, GINIplus and LISAplus
Authors: Batscheider Ariane , Zakrzewska Sylwia , Heinrich Joachim , Teuner Christina M , Menn Petra , Bauer Carl Peter , Hoffmann Ute , Koletzko Sibylle , Lehmann Irina , Herbarth Olf , von Berg Andrea , Berdel Dietrich , Krämer Ursula , Schaaf Beate , Wichmann H-Erich , Leidl Reiner ,   the GINIplus and LISAplus study groups
Published: October 2012

AbstractBackgroundAlthough the negative health consequences of the exposure to second hand tobacco smoke during childhood are already known, evidence on the economic consequences is still rare. The aim of this study was to estimate excess healthcare costs of exposure to tobacco smoke in German children.MethodsThe study is based on data from two birth cohort studies of 3,518 children aged 9-11 years with information on healthcare utilisation and tobacco smoke exposure: the GINIplus study (German Infant Study On The Influence Of Nutrition Intervention Plus Environmental And Genetic Influences On Allergy Development) and the LISAplus study (Influence of Life-Style Factors On The Development Of The Immune System And Allergies In East And West Germany Plus The Influence Of Traffic Emissions And Genetics). Direct medical costs were estimated using a bottom-up approach (base year 2007). We investigated the impact of tobacco smoke exposure in different environments on the main components of direct healthcare costs using descriptive analysis and a multivariate two-step regression analysis.ResultsDescriptive analysis showed that average annual medical costs (physician visits, physical therapy and hospital treatment) were considerably higher for children exposed to second-hand tobacco smoke at home (indoors or on patio/balcony) compared with those who were not exposed. Regression analysis confirmed these descriptive trends: the odds of positive costs and the amount of total costs are significantly elevated for children exposed to tobacco smoke at home after adjusting for confounding variables. Combining the two steps of the regression model shows smoking attributable total costs per child exposed at home of €87 [10–165] (patio/balcony) and €144 [6–305] (indoors) compared to those with no exposure. Children not exposed at home but in other places showed only a small, but not significant, difference in total costs compared to those with no exposure.ConclusionsThis study shows adverse economic consequences of second-hand smoke in children depending on proximity of exposure. Tobacco smoke exposure seems to affect healthcare utilisation in children who are not only exposed to smoke indoors but also if parents reported exclusively smoking on patio or balcony. Preventing children from exposure to second-hand tobacco smoke might thus be desirable not only from a health but also from an economic perspective.
Tumor biobanks in translational medicine
Authors: Botti Gerardo , Franco Renato , Cantile Monica , Ciliberto Gennaro , Ascierto Paolo Antonio 
Published: October 2012

Abstract
The concept of tissue banking as a “bio-repository” aimed to collection, storing and distribution of human biological material and clinical information, is emerging as a successful strategy to support clinical and translational research. In particular, Tumor Biobanks represent a key resource for diagnosis, research and experimental therapies, especially for those correlated to clinical application of a new type of medicine known as “intelligent drugs”.
Biobanks are not “spontaneous” collections, but they needs an institutional organization, basically a research unit, whose effectiveness and quality can be guaranteed only if it is carefully organized according to precise and shared rules.
Wildlife uses and hunting patterns in rural communities of the Yucatan Peninsula, Mexico
Authors: Santos-Fita Dídac , Naranjo Eduardo J , Rangel-Salazar José Luis 
Published: October 2012

AbstractBackgroundSubsistence hunting is a traditional practice providing food and many other goods for households in the Yucatan Peninsula, southeast Mexico. Economic, demographic, and cultural change in this region drive wildlife habitat loss and local extinctions. Improving our understanding about current practices of wildlife use may support better management strategies for conserving game species and their habitat. We aimed to evaluate if wildlife use remained relevant for the subsistence of rural residents of the Yucatan Peninsula, as well as if local hunting practices were related to environmental, geographical, and cultural factors.MethodsFieldwork was done between March 2010 and March 2011. Information was obtained through conversations, interviews, and participant observation. Record forms allowed recording animals hunted, biomass extracted, distance intervals to hunting sites, habitat types and seasonality of wildlife harvests. Data were analyzed using one-way Analysis of Variance, and Generalized Linear Models.ResultsForty-six terrestrial vertebrate species were used for obtaining food, medicine, tools, adornments, pets, ritual objects, and for sale and mitigating damage. We recorded 968 animals taken in 664 successful hunting events. The Great Curassow, Ocellated Turkey, paca, white-tailed deer, and collared peccary were the top harvested species, providing 80.7% of biomass (10,190 kg). The numbers of animals hunted and biomass extracted declined as hunting distances increased from villages. Average per capita consumption was 4.65 ± 2.7 kg/person/year. Hunting frequencies were similar in forested and agricultural areas.DiscussionWildlife use, hunting patterns, and technologies observed in our study sites were similar to those recorded in previous studies for rural Mayan and mestizo communities in the Yucatan Peninsula and other Neotropical sites. The most heavily hunted species were those providing more products and by-products for residents. Large birds such as the Great Curassow and the Ocellated Turkey were extremely important for local hunters, representing around 40% of total prey taken.Final considerationsOur results suggest that hunting is frequent in our study areas. Low human densities allow low hunting pressure on most game species and favor conservation of the tropical forest. We suggest that co-management may help regulating hunting, prioritizing cultural practices of sustainable use and conservation for benefiting local users and animal populations.
Chronic hepatitis E virus infection in a patient with leukemia and elevated transaminases: a case report
Authors: Gauss Annika , Wenzel Juergen J , Flechtenmacher Christa , Navid Mojdeh Heidary , Eisenbach Christoph , Jilg Wolfgang , Stremmel Wolfgang , Schnitzler Paul 
Published: October 2012

Abstract

Introduction
Acute hepatitis E virus infection may cause mild, self-limiting hepatitis, either as epidemic outbreaks or sporadic cases, the latter of which have been reported in industrialized countries. Chronic infections are uncommon and have been reported in immunosuppressed patients, patients with human immunodeficiency virus infection, and patients with hematological malignancies.

Case presentation
A 46-year-old Caucasian man was admitted to the gastroenterology clinic with a history of increasing transaminases, persistent exhaustion, and occasional right-side abdominal pain over the course of a 6-month period. B-cell chronic lymphocytic leukemia had been diagnosed several years earlier, and the patient was treated with rituximab, pentostatin, and cyclophosphamide. A diagnostic workup ruled out autoimmune and metabolic liver disease, hepatitis A-C, and herpes virus infection. A physical examination revealed enlarged axillary lymph nodes. The results of an abdominal ultrasound examination were otherwise unremarkable. Hepatitis E virus infection was diagnosed by detection of hepatitis E virus-specific antibodies. Blood samples were positive for hepatitis E virus ribonucleic acid with high viral loads for at least 8 months, demonstrating a rare chronic hepatitis E virus infection. Sequencing and phylogenetic analysis revealed hepatitis E virus genotype 3c with homologies to other European isolates from humans and swine, indicating an autochthonous infection.

Conclusions
Usually, hepatitis E virus infection appears as an acute infection; rare chronic infections have been reported for transplant patients, patients with human immunodeficiency virus, and patients with hematological malignancies. The chronic nature of hepatitis E infection in our patient was most likely induced by the immunosuppressive B-cell chronic lymphocytic leukemia treatment. The differential diagnosis in patients with unexplained hepatitis should include hepatitis E virus infection, and appropriate laboratory analyses should be considered.