bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tornado Damage Estimation Using Polarimetric Radar
Authors: Bodine David J. , Kumjian Matthew R. , Palmer Robert D. , Heinselman Pamela L. , Ryzhkov Alexander V. 
Published: July 2012

Abstract
This study investigates the use of tornadic debris signature (TDS) parameters to estimate tornado damage severity using Norman, Oklahoma (KOUN), polarimetric radar data (polarimetric version of the Weather Surveillance Radar-1988 Doppler radar). Several TDS parameters are examined, including parameters based on the 10th or 90th percentiles of polarimetric variables (lowest tilt TDS parameters) and TDS parameters based on the TDS volumetric coverage (spatial TDS parameters). Two highly detailed National Weather Service (NWS) damage surveys are compared to TDS parameters. The TDS parameters tend to be correlated with the enhanced Fujita scale (EF) rating. The 90th percentile reflectivity, TDS height, and TDS volume increase during tornado intensification and decrease during tornado dissipation. For 14 tornado cases, the maximum or minimum TDS parameter values are compared to the tornado’s EF rating. For tornadoes with a higher EF rating, higher maximum values of the 90th percentile ZHH, TDS height, and volume, as well as lower minimum values of 10th percentile ρHV and ZDR, are observed. Maxima in spatial TDS parameters are observed after periods of severe, widespread tornado damage for violent tornadoes. This paper discusses how forecasters could use TDS parameters to obtain near-real-time information about tornado damage severity and spatial extent.
Weather Value at Risk: On the Measurement of Noncatastrophic Weather Risk
Authors: Toeglhofer Christoph , Mestel Roland , Prettenthaler Franz 
Published: July 2012

AbstractAn evaluation of weather risk entails two important objectives: indicating the economic impact of weather variability and climate change, and evaluating the use of weather derivatives in weather risk reduction and climate change adaptation strategy. This paper illustrates a straightforward approach for measuring weather risk, which captures both the exposure and the sensitivity of business and economic indicators to weather variability. Using the example of the accommodation industry in Kitzbuehel (Austria), it is demonstrated that the risk measure Weather-VaR can be used to serve both ends. It is found that compared to a normal climatological season, adverse snow conditions (at the level of a 1 in 20-yr event) result in a substantial financial loss of approximately 4 million euros. However, results show that quantification of weather risk is substantially affected by the choice of the weather variable or index, the time period under consideration, the model specification for estimating the sensitivity parameter, and whether time trends are considered when estimating the probability of unfavorable weather conditions.
Laughter and Hatred Are Neighbors
Authors: Clybor Shawn 
Published: July 2012

This article considers how Adolf Hoffmeister and E.F. Burian, influential members of the interwar avant-garde, struggled to define themselves as socialist realists in Czechoslovakia 1948-1956, even as they engaged in a parallel struggle to create works consistent with their artistic legacy. It argues that their ideas emerged both in cooperation with and in opposition to the increasingly repressive post-1948 communist regime, whose broader ideals they enthusiastically shared. Using these two intellectuals as case studies, the goal is thus to reframe our understanding of “complicity” under the 1950s Stalinist regime as a complex series of responses to the political, social, and intellectual questions of the era. Neither vacuous mouthpieces of the regime nor political dissidents, Hoffmeister and Burian stood at a critical historical juncture that linked the legacy of the interwar avant-garde to the cultural flowering of the 1960s Prague Spring. The article comprises three sections: The first offers a brief overview of the Stalinist era in Czechoslovakia, taking into account recent historical scholarship that recasts our understanding of the period. The second section examines the art and politics of Adolf Hoffmeister, who played a key role in the Stalinization of the Czechoslovak Fine Arts Union in 1952, revealing his attempts to both criticize and employ the violent rhetoric of the communist Terror. The third section considers E.F. Burian’s desperate attempt to save his interwar Theater D from nationalization, which ironically forced him into a relationship with the Ministry of Defense under the arch-Stalinist Alexej Čepička.
Breastfeeding at NICU Discharge
Authors: Davanzo Riccardo , Monasta Lorenzo , Ronfani Luca , Brovedani Pierpaolo , Demarini Sergio ,   for the Breastfeeding in Neonatal Intensive Care Unit Study Group
Published: July 2012

Background: Human milk is the optimal form of nutrition for infants, especially sick or compromised infants, yet international data suggest that breastfeeding (feeding at the breast) and the use of expressed human milk (mother’s and donor’s milk) are limited in patients cared for in the neonatal intensive care unit (NICU). Objective: The goal of this study was to examine feeding status at hospital discharge among high risk infants. Methods: We used the 1991 World Health Organization infant feeding definitions, applied to the 72 hour period preceding discharge from the NICU. The study sample consisted of all high risk infants discharged from July 1, 2005, to June 30, 2006 from 13 Italian NICUs. Data on infant feeding in the last 72 hours were collected at discharge from the medical records. Results: We recorded data from 2948 subjects with a median gestational age of 35 weeks (IQR, 32-38), a median birth weight of 2200 g (IQR, 1630-2920) and a median length of stay of 16 days (IQR, 8-33). At discharge, 28% of all infants were fed exclusively with human milk: 31%, 25%, 22% and 33% respectively in the <1500 g, 1500-2000 g, 2000-2499 g and ≥ 2500 g birth weight categories. The proportion of infants not fed with human milk varied from 6 to 82% across different centers. Conclusion: Our study found limited breastfeeding and use of human milk among the NICU infants at discharge. At discharge, infants with a birth weight 1500-2499 g were fed exclusively with human milk less than those in higher or lower birth weight categories.
Reliability and Validity of Swallows as a Measure of Breast Milk Intake in the First Days of Life
Authors: Côté-Arsenault Denise , McCoy Thomas P. 
Published: July 2012

Background: Breastfeeding assessment in the hospital to determine adequacy of feeds remains controversial. Swallow evaluation is integral to current assessment tools, but the literature is not clear about whether the number of swallows is an accurate indicator of breast milk intake in early postpartum. Objectives: To determine the reliability and validity of swallows as a measure of breast milk intake in the first days of a newborn’s life. Methods: Thirty mother-baby dyads were observed at one breastfeeding; pre- and postfeed weights were done, bedside audible swallows were counted, and feeds were videotaped for independent rating. Milk intake was determined from weight change, adjusted for insensible water loss. Results: Number of swallows was significantly and positively correlated with breast milk intake ( r = .71). Number of swallows alone, however, accounted for only 50.8% ( R2 = .508) of the variation in milk intake. Infant age was the best predictor of milk intake (βage = .56 vs βNo. swallows = .36), accounting for 68% of the variation in milk intake when combined with swallows. The majority of infants took in 10 g or less of breast milk (77%); length of feeds was variable. In-room (at bedside) lactation consultant (LC) and video rater LC swallow counts were significantly and positively correlated ( r = .93; P < .01). However, the 2 lactation consultant swallow numbers include clinically important discrepancies in a Bland-Altman analysis. Conclusions: Number of swallows was not supported as a reliable or valid indicator of milk intake and adequacy of a feed in the first few days of life.
A text-mining system for extracting metabolic reactions from full-text articles
Authors: Czarnecki Jan , Nobeli Irene , Smith Adrian M , Shepherd Adrian J 
Published: July 2012

Abstract

Background
Increasingly biological text mining research is focusing on the extraction of complex relationships relevant to the construction and curation of biological networks and pathways. However, one important category of pathway — metabolic pathways — has been largely neglected.
Here we present a relatively simple method for extracting metabolic reaction information from free text that scores different permutations of assigned entities (enzymes and metabolites) within a given sentence based on the presence and location of stemmed keywords. This method extends an approach that has proved effective in the context of the extraction of protein–protein interactions.

Results
When evaluated on a set of manually-curated metabolic pathways using standard performance criteria, our method performs surprisingly well. Precision and recall rates are comparable to those previously achieved for the well-known protein-protein interaction extraction task.

Conclusions
We conclude that automated metabolic pathway construction is more tractable than has often been assumed, and that (as in the case of protein–protein interaction extraction) relatively simple text-mining approaches can prove surprisingly effective. It is hoped that these results will provide an impetus to further research and act as a useful benchmark for judging the performance of more sophisticated methods that are yet to be developed.
Differential gene expression profiling of porcine epithelial cells infected with three enterotoxigenic Escherichia coli strains
Authors: Zhou Chuanli , Liu Zhengzhu , Jiang Jicai , Yu Ying , Zhang Qin 
Published: July 2012

Abstract

Background
Enterotoxigenic Escherichia coli (ETEC) is one of the most important pathogenic bacteria causing severe diarrhoea in human and pigs. In ETEC strains, the fimbrial types F4 and F18 are commonly found differently colonized within the small intestine and cause huge economic losses in the swine industry annually worldwide. To address the underlying mechanism, we performed a transcriptome study of porcine intestinal epithelial cells (IPEC-J2) with and without infection of three representative ETEC strains.

Results
A total 2443, 3493 and 867 differentially expressed genes were found in IPEC-J2 cells infected with F4ab ETEC (CF4ab), with F4ac ETEC (CF4ac) and with F18ac ETEC (CF18ac) compared to the cells without infection (control), respectively. The number of differentially expressed genes between CF4ab and CF4ac, CF4ab and CF18ac, and CF4ac and CF18ac were 77, 1446 and 1629, respectively. The gene ontology and pathway analysis showed that the differentially expressed genes in CF4ab
vs control are significantly involved in cell-cycle progress and amino acid metabolism, while the clustered terms of the differentially expressed genes in CF4ac
vs control comprise immune, inflammation and wounding response and apoptosis as well as cell cycle progress and proteolysis. Differentially expressed genes between CF18ac
vs control are mainly involved in cell-cycle progression and immune response. Furthermore, fundamental differences were observed in expression levels of immune-related genes among the three ETEC treatments, especially for the important pro-inflammatory molecules, including IL-6, IL-8, TNF-α, CCL20, CXCL2 etc.

Conclusions
The discovery in this study provides insights into the interaction of porcine intestinal epithelial cells with F4 ETECs and F18 ETEC, respectively. The genes induced by ETECs with F4 versus F18 fimbriae suggest why ETEC with F4 may be more virulent compared to F18 which seems to elicit milder effects.
A microRNA activity map of human mesenchymal tumors: connections to oncogenic pathways; an integrative transcriptomic study
Authors: Fountzilas Elena , Kelly Andrew D , Perez-Atayde Antonio R , Goldsmith Jeffrey , Konstantinopoulos Panagiotis A , Francoeur Nancy , Correll Mick , Rubio Renee , Hu Lan , Gebhardt Mark C , Quackenbush John , Spentzos Dimitrios 
Published: July 2012

Abstract

Background
MicroRNAs (miRNAs) are nucleic acid regulators of many human mRNAs, and are associated with many tumorigenic processes. miRNA expression levels have been used in profiling studies, but some evidence suggests that expression levels do not fully capture miRNA regulatory activity. In this study we integrate multiple gene expression datasets to determine miRNA activity patterns associated with cancer phenotypes and oncogenic pathways in mesenchymal tumors – a very heterogeneous class of malignancies.

Results
Using a computational method, we identified differentially activated miRNAs between 77 normal tissue specimens and 135 sarcomas and we validated many of these findings with microarray interrogation of an independent, paraffin-based cohort of 18 tumors. We also showed that miRNA activity is imperfectly correlated with miRNA expression levels. Using next-generation miRNA sequencing we identified potential base sequence alterations which may explain differential activity. We then analyzed miRNA activity changes related to the RAS-pathway and found 21 miRNAs that switch from silenced to activated status in parallel with RAS activation. Importantly, nearly half of these 21 miRNAs were predicted to regulate integral parts of the miRNA processing machinery, and our gene expression analysis revealed significant reductions of these transcripts in RAS-active tumors. These results suggest an association between RAS signaling and miRNA processing in which miRNAs may attenuate their own biogenesis.

Conclusions
Our study represents the first gene expression-based investigation of miRNA regulatory activity in human sarcomas, and our findings indicate that miRNA activity patterns derived from integrated transcriptomic data are reproducible and biologically informative in cancer. We identified an association between RAS signaling and miRNA processing, and demonstrated sequence alterations as plausible causes for differential miRNA activity. Finally, our study highlights the value of systems level integrative miRNA/mRNA assessment with high-throughput genomic data, and the applicability of paraffin-tissue-derived RNA for validation of novel findings.
A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development
Authors: Yamamoto Masahiro , Yamaguchi Rui , Munakata Kaori , Takashima Kiyoe , Nishiyama Mitsue , Hioki Kyoji , Ohnishi Yasuyuki , Nagasaki Masao , Imoto Seiya , Miyano Satoru , Ishige Atsushi , Watanabe Kenji 
Published: July 2012

AbstractBackgroundEpidemiological studies have suggested that the encounter with commensal microorganisms during the neonatal period is essential for normal development of the host immune system. Basic research involving gnotobiotic mice has demonstrated that colonization at the age of 5 weeks is too late to reconstitute normal immune function. In this study, we examined the transcriptome profiles of the large intestine (LI), small intestine (SI), liver (LIV), and spleen (SPL) of 3 bacterial colonization models—specific pathogen-free mice (SPF), ex-germ-free mice with bacterial reconstitution at the time of delivery (0WexGF),and ex-germ-free mice with bacterial reconstitution at 5 weeks of age (5WexGF)—and compared them with those of germ-free (GF) mice.ResultsHundreds of genes were affected in all tissues in each of the colonized models; however, a gene set enrichment analysis method, MetaGene Profiler (MGP),demonstrated that the specific changes of Gene Ontology (GO) categories occurred predominantly in 0WexGF LI, SPF SI,and 5WexGF SPL, respectively. MGP analysis on signal pathways revealed prominent changes in toll-like receptor (TLR)- and type 1 interferon (IFN)-signaling in LI of 0WexGF and SPF mice, but not 5WexGF mice, while 5WexGF mice showed specific changes in chemokine signaling. RT-PCR analysis of TLR-related genes showed that the expression of interferon regulatory factor 3 (Irf3), a crucial rate-limiting transcription factor in the induction of type 1 IFN, prominently decreased in 0WexGF and SPF mice but not in 5WexGF and GF mice.ConclusionThe present study provides important new information regarding the molecular mechanisms of the so-called "hygiene hypothesis".
New highly sensitive rodent and human tests for soluble amyloid precursor protein alpha quantification: preclinical and clinical applications in Alzheimer’s disease
Authors: Rose Christiane , Peoc’h Katell , Chasseigneaux Stéphanie , Paquet Claire , Dumurgier Julien , Bourasset Fanchon , Calon Frédéric , Laplanche Jean-Louis , Hugon Jacques , Allinquant Bernadette 
Published: July 2012

Abstract

Background
Amyloid precursor protein (APP), a key molecule in Alzheimer’s disease (AD), is metabolized in two alternative cleavages, generating either the amyloidogenic peptides involved in AD pathology or the soluble form of APP (sAPPα). The level of amyloidogenic peptides in human cerebrospinal fluid (CSF) is considered to be a biomarker of AD, whereas the level of sAPPα in CSF as a biomarker has not been clearly established. sAPPα has neurotrophic and neuroprotective properties. Stimulating its formation and secretion is a promising therapeutic target in AD research. To this end, very sensitive tests for preclinical and clinical research are required.

Methods
The tests are based on homogenous time-resolved fluorescence and require no washing steps.

Results
We describe two new rapid and sensitive tests for quantifying mouse and human sAPPα. These 20 μl-volume tests quantify the levels of: i) endogenous mouse sAPPα in the conditioned medium of mouse neuron primary cultures, as well as in the CSF of wild-type mice, ii) human sAPPα in the CSF of AD mouse models, and iii) human sAPPα in the CSF of AD and non-AD patients. These tests require only 5 μl of conditioned medium from 5 × 104 mouse primary neurons, 1 μl of CSF from wild-type and transgenic mice, and 0.5 μl of human CSF.

Conclusions
The high sensitivity of the mouse sAPPα test will allow high-throughput investigations of molecules capable of increasing the secretion of endogenous sAPPα in primary neurons, as well as the in vivo validation of molecules of interest through the quantification of sAPPα in the CSF of treated wild-type mice. Active molecules could then be tested in the AD mouse models by quantifying human sAPPα in the CSF through the progression of the disease. Finally, the human sAPPα test could strengthen the biological diagnosis of AD in large clinical investigations. Taken together, these new tests have a wide field of applications in preclinical and clinical studies.
Myeloid malignancies: mutations, models and management
Authors: Murati Anne , Brecqueville Mandy , Devillier Raynier , Mozziconacci Marie-Joelle , Gelsi-Boyer Véronique , Birnbaum Daniel 
Published: July 2012

Abstract
Myeloid malignant diseases comprise chronic (including myelodysplastic syndromes, myeloproliferative neoplasms and chronic myelomonocytic leukemia) and acute (acute myeloid leukemia) stages. They are clonal diseases arising in hematopoietic stem or progenitor cells. Mutations responsible for these diseases occur in several genes whose encoded proteins belong principally to five classes: signaling pathways proteins (e.g. CBL, FLT3, JAK2, RAS), transcription factors (e.g. CEBPA, ETV6, RUNX1), epigenetic regulators (e.g. ASXL1, DNMT3A, EZH2, IDH1, IDH2, SUZ12, TET2, UTX), tumor suppressors (e.g. TP53), and components of the spliceosome (e.g. SF3B1, SRSF2). Large-scale sequencing efforts will soon lead to the establishment of a comprehensive repertoire of these mutations, allowing for a better definition and classification of myeloid malignancies, the identification of new prognostic markers and therapeutic targets, and the development of novel therapies. Given the importance of epigenetic deregulation in myeloid diseases, the use of drugs targeting epigenetic regulators appears as a most promising therapeutic approach.
Antitumor activity of zoledronic acid in primary breast cancer cells determined by the ATP tumor chemosensitivity assay
Authors: Fehm Tanja , Zwirner Manfred , Wallwiener Diethelm , Seeger Harald , Neubauer Hans 
Published: July 2012

Abstract

Background
The NeoAzure study has demonstrated that the use of the bisphosphonate zoledronic acid (Zol) in the neoadjuvant setting increases the rate of complete response in primary breast cancer and therefore indicates direct antitumor activity. The purpose of this study was to compare the antitumor effect of Zol with standard chemotherapy in primary breast cancer cells using ATP-tumor chemosensitivity assay (ATP-TCA).

Methods
Breast cancer specimens were obtained from patients with breast cancer who underwent primary breast cancer surgery at the Department of Obstetrics and Gynecology, Tübingen, Germany, between 2006 through 2009. Antitumor effects of Zol, TAC (Docetaxel, Adriamycin, Cyclophosphamide) and FEC (5-Fluorouracil, Epirubicin, Cyclophosphamide) were tested in 116 fresh human primary breast cancer specimens using ATP-TCA. ATP-TCA results were analyzed with different cut-off levels for the half maximal inhibitory concentration (IC50), for IC90 and for the sensitivity index (IndexSUM). Each single agent or combination was tested at six doubling dilutions from 6.25, 12.5, 25, 50, 100, and 200% of test drug concentrations (TDC) derived from the plasma peak concentrations determined by pharmacokinetic data. The assay was carried out in duplicate wells with positive and negative controls.

Results
The median IndexSUM value was lower for Zol than for the combined regimen FEC (36.8%) and TAC (12.9%), respectively, indicating increased antitumor activity of Zol in primary breast cancer cells. The difference regarding Zol and FEC was significant (p < 0.05). The median IC50 value for Zol (8.03% TDC) was significantly lower than the IC50 values for FEC (33.5% TDC) and TAC (19.3% TDC) treatment (p < 0.05). However, the median IC90 value for Zol (152.5% TDC) was significantly higher than the IC90 value obtained with TAC (49.5% TDC; p < 0.05), but similar to the IC90 value for FEC (180.9% TDC). In addition a significant positive correlation was observed for the IndexSum of Zol and the ER status (p < 0.01).

Conclusion
Zoledronic acid has a strong antitumor effect on primary breast cancer cells in vitro which is equal or superior to commonly used chemotherapeutic regimens for treating breast cancer.