bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extended-Range Forecasts of Atlantic Tropical Cyclone Events during 2012 Using the ECMWF 32-Day Ensemble Predictions*
Authors: Elsberry Russell L. , Tsai Hsiao-Chung , Jordan Mary S. 
Published: November 2013

Abstract
Previous studies have demonstrated the capability of the European Centre for Medium-Range Weather Forecasts (ECMWF) 51-member, 32-day ensemble to forecast tropical cyclone (TC) events (formation and tracks) in the western North Pacific on the extended range (5–30 days). In this study, the performance of the ECMWF ensemble in extended-range forecasting of Atlantic TCs during May–December 2012 is evaluated using similar approaches. The conclusion from this evaluation is that Atlantic TC events have lower forecastability using the ECMWF ensemble than in the western North Pacific. Hurricanes Kirk and Leslie and Tropical Storms (TSs) Joyce and Oscar were successfully forecast in weeks 1–4 and, thus, are labeled as highly forecastable. Somewhat forecastable storms that are only forecast in three of the four weeks include Hurricanes Ernesto, Isaac, Nadine, and Sandy plus TS Florence. The limited forecastable storms that were successful in only the first two weeks include Hurricanes Gordon and Rafael plus TS Debby. The surprising result was that two hurricanes (Chris and Michael) and three TSs (Helene, Patty, and Tony) were not even forecast in week 1 before the starting time in the National Hurricane Center working best track (WBT) for these storms. As was the case in the western North Pacific, a substantial number of false alarm storms (no matches with any WBT) are predicted, with about 35% occurring in the first week. Except for the African wave–type false alarms, three other false alarm types may be easily recognized. A larger sample will be required to statistically verify the reliability of the probabilistic forecasts for the African wave–type ensemble storms.
MUC1-C oncoprotein promotes FLT3 receptor activation in acute myeloid leukemia cells
Authors: Liu Suiyang , Yin Li , Stroopinsky Dina , Rajabi Hasan , Puissant Alexandre , Stegmaier Kimberly , Avigan David , Kharbanda Surender , Kufe Donald , Stone Richard 
Published: November 2013

Key Points
The MUC1-C oncoprotein is aberrantly expressed in AML cells and contributes to activation of the mutant FLT3 receptor. Targeting MUC1-C thus inhibits FLT3 signaling and represents a potential approach for AML cells resistant to FLT3 inhibitors.
BORIS/CTCFL is an RNA-binding protein that associates with polysomes
Authors: Ogunkolade Babatunji W , Jones Tania A , Aarum Johan , Szary Jaroslaw , Owen Nicholas , Ottaviani Diego , Mumin Muhammad A , Patel Shyam , Pieri Christopher A , Silver Andrew R , Sheer Denise 
Published: November 2013

Abstract

Background
BORIS (CTCFL), a paralogue of the multifunctional and ubiquitously expressed transcription factor CTCF, is best known for its role in transcriptional regulation. In the nucleus, BORIS is particularly enriched in the nucleolus, a crucial compartment for ribosomal RNA and RNA metabolism. However, little is known about cytoplasmic BORIS, which represents the major pool of BORIS protein.

Results
We show, firstly, that BORIS has a putative nuclear export signal in the C-terminal domain. Furthermore, BORIS associates with mRNA in both neural stem cells and young neurons. The majority of the BORIS-associated transcripts are different in the two cell types. Finally, by using polysome profiling we show that BORIS is associated with actively translating ribosomes.

Conclusion
We have demonstrated the RNA binding properties of cellular BORIS and its association with actively translating ribosomes. We suggest that BORIS is involved in gene expression at both the transcriptional and post-transcriptional levels.
Iterative feature removal yields highly discriminative pathways
Authors: O’Hara Stephen , Wang Kun , Slayden Richard A , Schenkel Alan R , Huber Greg , O’Hern Corey S , Shattuck Mark D , Kirby Michael 
Published: November 2013

Abstract

Background
We introduce Iterative Feature Removal (IFR) as an unbiased approach for selecting features with diagnostic capacity from large data sets. The algorithm is based on recently developed tools in machine learning that are driven by sparse feature selection goals. When applied to genomic data, our method is designed to identify genes that can provide deeper insight into complex interactions while remaining directly connected to diagnostic utility. We contrast this approach with the search for a minimal best set of discriminative genes, which can provide only an incomplete picture of the biological complexity.

Results
Microarray data sets typically contain far more features (genes) than samples. For this type of data, we demonstrate that there are many equivalently-predictive subsets of genes. We iteratively train a classifier using features identified via a sparse support vector machine. At each iteration, we remove all the features that were previously selected. We found that we could iterate many times before a sustained drop in accuracy occurs, with each iteration removing approximately 30 genes from consideration. The classification accuracy on test data remains essentially flat even as hundreds of top-genes are removed.
Our method identifies sets of genes that are highly predictive, even when comprised of genes that individually are not. Through automated and manual analysis of the selected genes, we demonstrate that the selected features expose relevant pathways that other approaches would have missed.

Conclusions
Our results challenge the paradigm of using feature selection techniques to design parsimonious classifiers from microarray and similar high-dimensional, small-sample-size data sets. The fact that there are many subsets of genes that work equally well to classify the data provides a strong counter-result to the notion that there is a small number of “top genes” that should be used to build classifiers. In our results, the best classifiers were formed using genes with limited univariate power, thus illustrating that deeper mining of features using multivariate techniques is important.
A transcriptomic approach to elucidate the physiological significance of human cytochrome P450 2S1 in bronchial epithelial cells
Authors: Madanayake Thushara W , Lindquist Ingrid E , Devitt Nicholas P , Mudge Joann , Rowland Aaron M 
Published: November 2013

Abstract

Background
Cytochrome P450 2S1 (CYP2S1) is an orphan P450 with an unknown biological function. Data from our laboratory and others suggest that CYP2S1 may have an important physiological role in modulating the synthesis and metabolism of bioactive lipids including prostaglandins and retinoids. CYP2S1 expression is elevated in multiple epithelial-derived cancers as well as in the chronic hyperproliferative disease psoriasis. Whether CYP2S1 expression in proliferative disease is protective, detrimental, or neutral to disease progression remains to be determined. Two human bronchial epithelial cells (BEAS-2B) were constructed to represent chronic depletion of CYP2S1 using short-hairpin RNA (shRNA) silencing directed toward the 3’UTR (759) and exon 3 (984) of the CYP2S1 gene and compared with a non-targeting shRNA control (SCRAM). Both CYP2S1 mRNA and protein were depleted by approximately 75% in stable cell lines derived from both targeted shRNA constructs (759 and 984). To elucidate the biological significance of CYP2S1, we analyzed transcriptome alterations in response to CYP2S1 depletion in human lung cells.

Results
RNA-sequencing (RNA-seq) analysis was performed to compare the transcriptome of the control (SCRAM) and the CYP2S1-depleted (759) BEAS-2B cell lines. Transcriptomes of the replicates from the two cell lines were found to be distinct populations as determined using Principal Component Analysis and hierarchical clustering. Approximately 1000 genes were differentially expressed in response to CYP2S1 depletion. Consistent with our previous phenotypes, DAVID analysis revealed altered regulation in key pathways implicated in cell proliferation and migration. Transcriptomic profiles were also consistent with the metabolism of proposed endogenous substrates. Pathway analysis also revealed significant expression changes within mTOR signaling, a critical pathway in cell growth. To determine whether these changes manifest as altered cell size, cell diameter and volume were calculated, revealing that CYP2S1 depletion promotes cell growth in BEAS-2B cells.

Conclusions
These data suggest that pathway analysis of sequence-based gene expression is a powerful method to identify pathways and phenotypic alterations in response to changes in orphan enzyme expression. Our results suggest a novel role for CYP2S1-mediated metabolism in modulating BEAS-2B cell size. These findings warrant further studies on CYP2S1 regulated pathways to elucidate potential substrates of CYP2S1.
Challenges in diagnostic accuracy studies in primary care: the fecal calprotectin example
Authors: Holtman Gea A , Yvonne Lisman-van Leeuwen , Kollen Boudewijn J , Escher Johanna C , Kindermann Angelika , Patrick F van Rheenen , Berger Marjolein Y 
Published: November 2013

Abstract

Background
Low disease prevalence and lack of uniform reference standards in primary care induce methodological challenges for investigating the diagnostic accuracy of a test. We present a study design that copes with these methodological challenges and discuss the methodological implications of our choices, using a quality assessment tool for diagnostic accuracy studies (QUADAS-2).

Design
The study investigates the diagnostic value of fecal calprotectin for detecting inflammatory bowel disease in children presenting with chronic gastrointestinal symptoms in primary care. It is a prospective cohort study including two cohorts of children: one cohort will be recruited in primary care and the other in secondary/tertiary care. Test results of fecal calprotectin will be compared to one of the two reference standards for inflammatory bowel disease: endoscopy with histopathological examination of mucosal biopsies or assessment of clinical symptoms at 1-year follow-up.

Discussion
According to QUADAS-2 the use of two reference standards and the recruitment of patients in two populations may cause differential verification bias and spectrum bias, respectively. The clinical relevance of this potential bias and methods to adjust for this are presented. This study illustrates the importance of awareness of the different kinds of bias that result from choices in the design phase of a diagnostic study in a low prevalence setting. This approach is exemplary for other diagnostic research in primary care.
National trends in advanced outpatient diagnostic imaging utilization: an analysis of the medical expenditure panel survey, 2000-2009
Authors: Lang Kathleen , Huang Huan , Lee David W , Federico Victoria , Menzin Joseph 
Published: November 2013

Abstract

Background
Concerns have been raised regarding growth in advanced diagnostic imaging use. This study evaluated trends in national outpatient MRI/CT utilization rates during 2000-2009 and factors associated with utilization.

Methods
This retrospective database analysis used data on all respondents in the nationally representative U.S. Medical Expenditure Panel Survey (MEPS) during 2000-2009. Visits involving advanced diagnostic imaging were identified based on self-reported use of MRI or CT tests at emergency departments, office-based medical providers, and outpatient departments. The imaging utilization rate was defined as the number of outpatient visits with MRI/CT per 1,000 person-years. Results were weighted to create nationally representative estimates at the person-year level for each year and the pooled 10-year period. A multivariate logistic regression was estimated to identify predictors of imaging use.

Results
A total of 319,246 person-years were included in the analysis. MRI/CT utilization rates increased from 64.3 to 109.1 per 1,000 person years from 2000 to 2009, with older persons, females and Medicare enrollees having higher rates of use. Growth in imaging slowed in recent years; the average annual decline in the imaging growth rate was larger than that for all outpatient services (4.7% vs. 0.9%). The percentage of respondents with MRI/CT use (6.7% during 2000-2009) also increased at a slower rate in later years and declined during 2007-2009. The average number of MRI/CT visits among imaging users was steady at about 1.5 visits during 2000-2009. Age, female gender, White race, HMO participation, and all payer types (vs. uninsured) were significant predictors of imaging use. Compared to 2005, years 2000-2003 were associated with a significantly lower likelihood of imaging use, while years 2004-2009 were not significantly associated, suggesting a slow-down in later years.

Conclusions
Growth in advanced imaging utilization appears to have slowed in recent years, a finding of potential interest to policy-makers and payers.
Aqueous extracts of Liriope platyphylla induced significant laxative effects on loperamide-induced constipation of SD rats
Authors: Kim Ji Eun , Lee Young Ju , Kwak Moon Hwa , Ko Jun , Hong Jin Tae , Hwang Dae Youn 
Published: November 2013

Abstract

Background

Liriope platyphylla has long been reported as a therapeutic drug for treatment of various human chronic diseases including inflammation, diabetes, neurodegenerative disorders, obesity, and atopic dermatitis. To investigate the laxative effects of L. platyphylla, alterations in excretion parameters, histological structure, mucin secretion, and related protein levels were investigated in rats with loperamide (Lop)-induced constipation after treatment with aqueous extract of L. platyphylla (AEtLP).

Methods
Alterations on constipation phenotypes were measured in rats with Lop-induced constipation after treatment with AEtLP using excretion parameter analysis, histological analysis, RT-PCR, western blot and transmission electron microscope (TEM) analysis.

Results
The amounts of stool and urine excretion were significantly higher in the Lop + AEtLP-treated group than in the Lop + vehicle-treated group, whereas food intake and water consumption were maintained at constant levels. AEtLP treatment also induced an increase in villus length, crypt layer, and muscle thickness in the constipation model. Total mucin secretion was higher in the Lop + AEtLP-treated group than in the Lop + vehicle-treated group, although mucin secretion per crypt was very similar among all groups. Furthermore, RT-PCR and western blot revealed a dramatic reduction of key factors level on the muscarinic acetylcholine receptors (mAChRs) signaling pathway in the Lop + AEtLP-treated group relative to the Lop + vehicle-treated group. Especially, the accumulation of lipid droplets in enterocytes of crypts following Lop treatment was improved to the level of the No-treated group in response to AEtLP treatment.

Conclusion
These results suggest that AEtLP improves constipation induced by Lop treatment through an increase in crypt layer and stimulation of lipid droplet secretions. These data are the first to show that the laxative effects of AEtLP are closely related to the down-regulation of mAchRs and their downstream signals.
Cardiotonic pill attenuates white matter and hippocampal damage via inhibiting microglial activation and downregulating ERK and p38 MAPK signaling in chronic cerebral hypoperfused rat
Authors: Lee Ki Mo , Bang Ji Hye , Han Jung-Soo , Kim Bu Yeo , Lee In Sun , Kang Hyung Won , Jeon Won Kyung 
Published: November 2013

AbstractBackgroundThe cardiotonic pill (CP) is a herbal medicine composed ofSalvia miltiorrhiza(SM),Panax notoginseng(PN), andDryobalanops aromatica Gaertner(DAG) that is widely used to treat cardiovascular diseases. The present experiment was conducted to examine the effects of CP on white matter and hippocampal damage induced by chronic cerebral hypoperfusion.MethodsChronic cerebral hypoperfusion was induced in male Wistar rats by permanent bilateral common carotid artery occlusion (BCCAo). Daily oral administration of CP (200 mg/kg) began 21 days after BCCAo and continued for 42 days. The levels of microglial activation and myelin basic protein (MBP) were measured in the white matter and hippocampus of rats with chronic BCCAo, and the expression levels of mitogen-activated protein kinases (MAPKs) and inflammatory markers such as cyclooxygenase-2, interleukin-1β, and interleukin-6 were examined.ResultsMBP expression was reduced in the white matter and hippocampal regions of rats that received BCCAo. In contrast, reduced levels of MBP were not observed in BCCAo rats given CP treatments. The administration of CP alleviated microglial activation, the alteration of ERK and p38 MAPK signaling, and inflammatory mediator expression in rats with chronic BCCAo.ConclusionThese results suggest that CP may have protective effects against chronic BCCAo-induced white matter and hippocampal damage by inhibiting inflammatory processes including microglial activation and proinflammatory mediator expression, and downreguating the hyperphosphorylation of ERK and p38 MAPK signaling.
Should level V be included in lateral neck dissection in treating papillary thyroid carcinoma?
Authors: Zhang Xiao-Jun , Liu Dan , Xu De-Bin , Mu Ya-Qi , Chen Wen-Kuan 
Published: November 2013

Abstract

Background
The study was designed to explore the regular patterns of level V lymph node metastasis (LNM) in papillary thyroid carcinoma (PTC), and to indicate whether level V should be included in the management of lateral neck dissection when treating PTC.

Methods
This retrospective study consisted of 330 patients diagnosed with PTC from January 1994 to July 2009 who underwent an operation that included therapeutic lateral neck dissection (levels II to V). The patterns of lateral neck LNM were analyzed and the relevant risk factors of level V LNM were analyzed with univariate and multivariate analysis, respectively.

Results
All the patients underwent lateral neck dissection at levels II to V. The predominant site of metastasis was level III (247/330 (74.8%)), followed by level IV (233/330 (70.6%)), and level II (215/330 (65.3%)). Simultaneous multilevel involvement (level II, III, and IV) of lymphatic metastases presented in 46.1% (152/330) of the cases. Level V showed 28.8% (95/330) of nodal metastasis. Multivariate analysis showed that level V LNM was significantly associated with location (whole thyroid), gross extrathyroidal extension and simultaneous multilevel involvement (level II, III and IV). (P <0.05).

Conclusions
Due to relatively high rate of level V involvement and its correlation with location (whole thyroid), gross extrathyroidal extension and multilevel involvement, we consider that it may be more rational to include level V in the therapeutic lateral neck dissection when treating PTC, especially for those who have any one of these three independent risk factors.
IL-27 inhibits epithelial-mesenchymal transition and angiogenic factor production in a STAT1-dominant pathway in human non-small cell lung cancer
Authors: Kachroo Puja , Lee Mi-Heon , Zhang Ling , Baratelli Felicita , Lee Gina , Srivastava Minu K , Wang Gerald , Walser Tonya C , Krysan Kostyantyn , Sharma Sherven , Dubinett Steven M , Lee Jay M 
Published: November 2013

Abstract

Background
Interleukin-27 signaling is mediated by the JAK-STAT pathway via activation of STAT1 and STAT3, which have tumor suppressive and oncogenic activities, respectively. Epithelial–mesenchymal transition (EMT) and angiogenesis are key processes in carcinogenesis. Although IL-27 has been shown to have potent anti-tumor activity in various cancer models, the role of IL-27 in EMT and angiogenesis is poorly understood. In this study, we investigated the role of IL-27 in regulating EMT and angiogenesis through modulation of the STAT pathways in human non-small cell lung carcinoma (NSCLC) cells.

Methods
STAT activation following IL-27 exposure was measured in human NSCLC cell lines. Expression of epithelial (E-cadherin, γ-catenin) and mesenchymal (N-cadherin, vimentin) markers were assessed by Western blot analysis. Production of pro-angiogenic factors (VEGF, IL-8/CXCL8, CXCL5) were examined by ELISA. Cell motility was examined by an in vitro scratch and transwell migration assays. Selective inhibitors of STAT1 (STAT1 siRNAs) and STAT3 (Stattic) were used to determine whether both STAT1 and STAT3 are required for IL-27 mediated inhibition of EMT and secretion of angiogenic factors.

Results
Our results demonstrate that IL-27 stimulation in NSCLC resulted in 1) STAT1 and STAT3 activation in a JAK-dependent manner, 2) development of epithelial phenotypes, including a decrease in the expression of a transcriptional repressor for E-cadherin (SNAIL), and mesenchymal marker (vimentin) with a reciprocal increase in the expression of epithelial markers, 3) inhibition of cell migration, and 4) reduced production of pro-angiogenic factors. STAT1 inhibition in IL-27–treated cells reversed the IL-27 effect with resultant increased expression of Snail, vimentin and the pro-angiogenic factors. The inhibition of STAT3 activation had no effect on the development of the epithelial phenotype.

Conclusion
IL-27 induces mesenchymal to epithelial transition and inhibits the production of pro-angiogenic factors in a STAT1–dominant pathway. These findings highlight the importance of STAT1 in repressing lung carcinogenesis and describe a new anti-tumor mechanism of IL-27.
Local change of butterfly species in response to global warming and reforestation in Korea
Authors: Kwon Tae-Sung , Kim Sung-Soo , Lee Cheol Min 
Published: November 2013

Abstract

Background
It is expected that the successful nationwide reforestation and global warming will greatly change the butterfly fauna in South Korea. We compared current data (2002 to 2007) regarding the abundance and presence of butterfly species at two sites in the central portion of the Korean Peninsula with similar data from the late 1950s and early 1970s for the same sites. The expected changes were documented by an abundance change of butterflies at the two study sites in a previous study. Using the same data, the most greatly changed species and the change of species presence were analyzed.

Results
Population changes of 99 butterfly species which occurred at both sites were significantly correlated between the two sites. The greatly increased species included three southern (S) species and one northern (N) species. However, the species showing great decline included five N species and no S species.

Conclusions
This change is consistent with the expectation of northward movement of butterfly species due to global warming. The current status of the greatly changed species is discussed along with other studies. The binary data (presence/absence) in the present study support the expected changes of butterfly species based on global warming and reforestation. The interactive effect of two environmental changes was also recognized, as well as the change of abundance in the previous study.