bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hsp90 inhibitor 17-allylamino-17-demethoxygeldanamycin inhibits the proliferation of ARPE-19 cells
Authors: Yao Jia-Qi , Liu Qing-Huai , Chen Xi , Yang Qin , Xu Zhi-Yang , Hu Fan , Wang Lin , Li Jian-Min 
Published: April 2010

AbstractBackgroundThe antiproliferative effect of the Hsp90 inhibitor 17-AAG (17-allylamino-17-demethoxygeldanamycin) on human retinal pigment epithelial cells is investigated.MethodsMTT and flow cytometry were used to study the antiproliferative effects of the 17-AAG treatment of ARPE-19 cells. 2D gel electrophoresis (2-DE) and mass spectrometry were applied to detect the altered expression of proteins, which was verified by real-time PCR. Gene Ontology analysis and Ingenuity Pathway Analysis (IPA) were utilized to analyze the signaling pathways, cellular location, function, and network connections of the identified proteins. And SOD assay was employed to confirm the analysis.Results17-AAG suppressed the proliferation of ARPE-19 cells by inducing cell cycle arrest and apoptosis. Proteomic analysis revealed that the expression of 94 proteins was altered by a factor of more than 1.5 following exposure to 17-AAG. Of these 94, 87 proteins were identified. Real-time PCR results indicated that Hsp90 and Hsp70, which were not identified by proteomic analysis, were both upregulated upon 17-AAG treatment. IPA revealed that most of the proteins have functions that are related to oxidative stress, as verified by SOD assay, while canonical pathway analysis revealed glycolysis/gluconeogenesis.Conclusions17-AAG suppressed the proliferation of ARPE-19 cells by inducing cell cycle arrest and apoptosis, and possibly by oxidative stress.
BS Seeker: precise mapping for bisulfite sequencing
Authors: Chen Pao-Yang , Cokus Shawn J , Pellegrini Matteo 
Published: April 2010

Abstract

Background
Bisulfite sequencing using next generation sequencers yields genome-wide measurements of DNA methylation at single nucleotide resolution. Traditional aligners are not designed for mapping bisulfite-treated reads, where the unmethylated Cs are converted to Ts. We have developed BS Seeker, an approach that converts the genome to a three-letter alphabet and uses Bowtie to align bisulfite-treated reads to a reference genome. It uses sequence tags to reduce mapping ambiguity. Post-processing of the alignments removes non-unique and low-quality mappings.

Results
We tested our aligner on synthetic data, a bisulfite-converted Arabidopsis library, and human libraries generated from two different experimental protocols. We evaluated the performance of our approach and compared it to other bisulfite aligners. The results demonstrate that among the aligners tested, BS Seeker is more versatile and faster. When mapping to the human genome, BS Seeker generates alignments significantly faster than RMAP and BSMAP. Furthermore, BS Seeker is the only alignment tool that can explicitly account for tags which are generated by certain library construction protocols.

Conclusions
BS Seeker provides fast and accurate mapping of bisulfite-converted reads. It can work with BS reads generated from the two different experimental protocols, and is able to efficiently map reads to large mammalian genomes. The Python program is freely available at http://pellegrini.mcdb.ucla.edu/BS_Seeker/BS_Seeker.html.
Identification of Type 2 Diabetes-associated combination of SNPs using Support Vector Machine
Authors: Ban Hyo-Jeong , Heo Jee Yeon , Oh Kyung-Soo , Park Keun-Joon 
Published: April 2010

Abstract

Background
Type 2 diabetes mellitus (T2D), a metabolic disorder characterized by insulin resistance and relative insulin deficiency, is a complex disease of major public health importance. Its incidence is rapidly increasing in the developed countries. Complex diseases are caused by interactions between multiple genes and environmental factors. Most association studies aim to identify individual susceptibility single markers using a simple disease model. Recent studies are trying to estimate the effects of multiple genes and multi-locus in genome-wide association. However, estimating the effects of association is very difficult. We aim to assess the rules for classifying diseased and normal subjects by evaluating potential gene-gene interactions in the same or distinct biological pathways.

Results
We analyzed the importance of gene-gene interactions in T2D susceptibility by investigating 408 single nucleotide polymorphisms (SNPs) in 87 genes involved in major T2D-related pathways in 462 T2D patients and 456 healthy controls from the Korean cohort studies. We evaluated the support vector machine (SVM) method to differentiate between cases and controls using SNP information in a 10-fold cross-validation test. We achieved a 65.3% prediction rate with a combination of 14 SNPs in 12 genes by using the radial basis function (RBF)-kernel SVM. Similarly, we investigated subpopulation data sets of men and women and identified different SNP combinations with the prediction rates of 70.9% and 70.6%, respectively. As the high-throughput technology for genome-wide SNPs improves, it is likely that a much higher prediction rate with biologically more interesting combination of SNPs can be acquired by using this method.

Conclusions
Support Vector Machine based feature selection method in this research found novel association between combinations of SNPs and T2D in a Korean population.
Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes
Authors: Wang Jianping , Roe Bruce , Macmil Simone , Yu Qingyi , Murray Jan E , Tang Haibao , Chen Cuixia , Najar Fares , Wiley Graham , Bowers John , Van Sluys Marie-Anne , Rokhsar Daniel S , Hudson Matthew E , Moose Stephen P , Paterson Andrew H , Ming Ray 
Published: April 2010

AbstractBackgroundSugarcane (Saccharumspp.) has become an increasingly important crop for its leading role in biofuel production. The high sugar content speciesS. officinarumis an octoploid without known diploid or tetraploid progenitors. Commercial sugarcane cultivars are hybrids betweenS. officinarumand wild speciesS. spontaneumwith ploidy at ~12×. The complex autopolyploid sugarcane genome has not been characterized at the DNA sequence level.ResultsThe microsynteny between sugarcane and sorghum was assessed by comparing 454 pyrosequences of 20 sugarcane bacterial artificial chromosomes (BACs) with sorghum sequences. These 20 BACs were selected by hybridization of 1961 single copy sorghum overgo probes to the sugarcane BAC library with one sugarcane BAC corresponding to each of the 20 sorghum chromosome arms. The genic regions of the sugarcane BACs shared an average of 95.2% sequence identity with sorghum, and the sorghum genome was used as a template to order sequence contigs covering 78.2% of the 20 BAC sequences. About 53.1% of the sugarcane BAC sequences are aligned with sorghum sequence. The unaligned regions contain non-coding and repetitive sequences. Within the aligned sequences, 209 genes were annotated in sugarcane and 202 in sorghum. Seventeen genes appeared to be sugarcane-specific and all validated by sugarcane ESTs, while 12 appeared sorghum-specific but only one validated by sorghum ESTs. Twelve of the 17 sugarcane-specific genes have no match in the non-redundant protein database in GenBank, perhaps encoding proteins for sugarcane-specific processes. The sorghum orthologous regions appeared to have expanded relative to sugarcane, mostly by the increase of retrotransposons.ConclusionsThe sugarcane and sorghum genomes are mostly collinear in the genic regions, and the sorghum genome can be used as a template for assembling much of the genic DNA of the autopolyploid sugarcane genome. The comparable gene density between sugarcane BACs and corresponding sorghum sequences defied the notion that polyploidy species might have faster pace of gene loss due to the redundancy of multiple alleles at each locus.
Serum tartrate-resistant acid phosphatase 5b activity as a prognostic marker of survival in breast cancer with bone metastasis
Authors: Wu Yi-Ying , Janckila Anthony J , Ku Chih-Hung , Yu Cheng-Ping , Yu Jyh-Cherng , Lee Su-Hui , Liu Hsin-Yi , Yam Lung T , Chao Tsu-Yi 
Published: April 2010

AbstractBackgroundSerum tartrate-resistant acid phosphatase 5b (TRACP 5b) activity is a marker of osteoclast number and is elevated in breast cancer (BC) patients with extensive bone metastasis, which might in turn reflect the tumour burden. We tested the hypothesis that baseline serum TRACP 5b activity and its interval change are potential prognostic markers of survival in BC patients with bone metastasis.MethodsWe analyzed the data from previous prospective studies. A total of 100 patients with newly diagnosed bone metastasis were included. Cox proportional regression model was used to evaluate the correlation between the overall survival time (OS) and baseline serum TRACP 5b activity and its interval changes. The least significant change (LSC) of TRACP 5b was calculated from data obtained from 15 patients with early BC.ResultsEstrogen receptor status (Hazard Ratio (HR) = 0.397;p= 0.003) and visceral metastasis (HR = 0.492;p= 0.0045) were significantly correlated with OS. The OS was significantly shorter in those patients with higher baseline TRACP 5b activity based on a cut-off value to delineate the highest tertile (HR = 3.524;p< 0.0001). Further analysis demonstrated that among patients in the highest tertile, OS was significantly longer in those patients who had achieved a decrease of serum TRACP 5b activity greater than the LSC (38.59%) (p= 0.0015).ConclusionsWe found that TRACP 5b activity and its interval change after treatment bore a prognostic role in BC patients with bone metastasis and a high baseline serum TRACP 5b activity. Further prospective phase II study is necessary to confirm these results.
PRevalence of Abuse and Intimate Partner Violence Surgical Evaluation (P.R.A.I.S.E.): rationale and design of a multi-center cross-sectional study.
Authors:   PRAISE Investigators
Published: April 2010

Abstract

Background
Intimate partner violence (IPV) is described by the American Medical Association as "a pattern of coercive behaviors that may include repeated battering and injury, psychological abuse, sexual assault, progressive social isolation, deprivation, and intimidation." The long-term consequences of IPV include health risks, posttraumatic stress disorder, depression, and staggering economic costs for health care of victims. Intimate partner violence is often underreported among women who seek medical attention. The current study seeks to address the issue of possible underreporting of IPV in orthopaedic fracture clinics by establishing prevalence rates of IPV among women seeking treatment for musculoskeletal injuries.

Methods/Design
We propose a cross-sectional multicenter study wherein 3,600 women will complete a self-reported written questionnaire across clinical sites in North America, Europe, and Australia. Recruitment of participants will take place at orthopaedic fracture clinics at each clinical site. The questionnaire will contain a validated set of questions used to screen for IPV, as well as questions that pertain to the participant's demographic, injury characteristics, and experiences with health care utilization. Female patients presenting to the orthopaedic fracture clinics will complete two validated self-reported written questionnaires (Woman Abuse Screening Tool (WAST) and the Partner Violence Screen (PVS)) to determine the prevalence of IPV in the past 12 months and in their lifetime. The two questionnaires were designed for rapid assessment of IPV status in emergency departments, family practice, and women's health clinics that we believe are similar to our intended setting of an orthopaedic clinic.

Discussion
If the prevalence of IPV among women attending orthopaedic clinics is greater than the current perceptions of orthopaedic surgeons, this study will serve to advocate for the continued education of medical professionals to better recognize probable IPV cases and offer existing services to enhance the care of these patients.
Doxorubicin and etoposide sensitize small cell lung carcinoma cells expressing caspase-8 to TRAIL
Authors: Vaculova Alena , Kaminskyy Vitaliy , Jalalvand Elham , Surova Olga , Zhivotovsky Boris 
Published: April 2010

Abstract

Background
TRAIL is considered as a promising anti-cancer agent, because of its ability to induce apoptosis in cancer but not in most normal cells. However, growing evidence exist that many cancer cells are resistant to its apoptotic effects. SCLC is a typical example of tumor entity where TRAIL monotherapy is not efficient.

Results
We demonstrated that doxorubicin and etoposide markedly sensitized SCLC cells expressing caspase-8 to apoptotic effects of TRAIL. The drug-mediated sensitization of these cells was associated with increase of surface and total DR5 protein level, specific cleavage of cFLIPL, decrease of cFLIPS level, and a strong activation of caspase-8. The involvement of mitochondria-mediated pathway was demonstrated by enhanced Bid cleavage, Bax activation, and cytochrome c release. Activation of caspase-8 induced by combined treatment was shown to occur upstream of mitochondria and effector caspases.

Conclusions
Our results highlight significant applicability of doxorubicin and etoposide in sensitization of SCLC cells expressing caspase-8 to treatment with TRAIL.
Indoor insect allergens are potent inducers of experimental eosinophilic esophagitis in mice
Authors: Rayapudi Madhavi , Mavi Parm , Zhu Xiang , Pandey Akhilesh K , Abonia J Pablo , Rothenberg Marc E , Mishra Anil 
Published: April 2010

Abstract
Indoor insect allergens can induce EE providing a potential link to clinical observations where EE patients are often sensitized to indoor insect allergens.
EE is an emerging disease reported in children and adults of urbanized countries, where indoor insect allergens are major health risk factors. Review of our hospital patient database uncovered that a number of EE patients have hypersensitivity to indoor cat, dog, cockroach, and dust mite allergens. We tested the hypothesis whether inhaled indoor insect allergens are effective inducers of experimental EE. We delivered cat, dog, cockroach, and dust mite allergen extracts intranasally to wild-type and eotaxin-1/2-, CCR3-, and IL-5-deficient mice. Interestingly, wild-type mice exposed to cockroach or dust mite allergens develop a significant increase in the levels of esophageal eosinophils and mast cells compared with saline-challenged mice. The eosinophil numbers in the esophagus of cockroach- and dust mite-exposed mice were 18.3 ± 6.8/mm2 and 33.4 ± 11.1/mm2 compared with 2.3 ± 1.8/mm2 and 2.1 ± 1.2/mm2 in saline-challenged mice. Additionally, we observed an additive effect of these two allergens in inducing esophageal eosinophilia and mastocytosis. Histopathological analysis detected intraepithelial esophageal eosinophilia in mice exposed to both allergens. Furthermore, mice exposed to cockroach and/or dust mite had increased levels of total IgE and antigen-specific IgG1 in the blood and increased esophageal expression of eosinophil-active cytokines (IL-13) and chemokines (eotaxin-1). Notably, mice deficient in eotaxin-1/2, CCR3, and IL-5 showed ablated esophageal eosinophilia following cockroach or dust mite allergen exposure. These data indicate that indoor insect allergens are potent inducers of IL-5 and eotaxin-mediated esophageal eosinophilia. These experimental studies are in accordance with clinical data but may have some limitations inherent to animal models of human disease.
The real quadrangle of type E
6
Authors: Kurth Torsten , Gramlich Ralf , Kramer Linus 
Published: April 2010

Abstract
Based on the first author's diploma thesis [Kurth, On a real form of E
6 and its related generalized quadrangle, 2000] we use the theories of Lie groups and of Tits buildings in order to describe a Veronese embedding of the real quadrangle of type E
6, i.e., the C
2 sub-building of the complex E
6 building corresponding to the real form E
6(–14) of the semisimple complex Lie group of type E
6.
The case of equality for an inverse Santaló functional inequality
Authors: Fradelizi M. , Gordon Y. , Meyer M. , Reisner S. 
Published: April 2010

Abstract
Let be a log-concave function such that ƒ(x
1, . . . , x

n
) = ƒ(|x
1|, . . . , |x

n
|) for every and . It was proved in [Fradelizi, Meyer, Positivity 12: 407–420, 2008] and [Fradelizi, Meyer, Adv. Math. 218: 1430–1452, 2008] that if for , , then

We characterize here the case of equality: one has P(ƒ) = 4
n
if and only if ƒ can be written as
ƒ (x
1, x
2) = e
−‖x
1‖K
1

1

K
2
(x
2),
where and , n
1 + n
2 = n, are unconditional convex bodies such that , i = 1, 2, where denotes the polar of Ki
. These last bodies were characterized in [Meyer, Israel J. Math. 55: 317–326, 1986] and [Reisner, J. London Math. Soc. 36: 126–136, 1987].
Effect of Self‐Efficacy and Social Support on Adherence to Antihypertensive Drugs
Authors: Criswell Thomas J. , Weber Cynthia A. , Xu Yinghui , Carter Barry L. 
Published: April 2010

Study Objective. To determine the relationship between poor adherence and self‐efficacy or social support after a pharmacist intervention.Design. Post‐hoc analysis of data from two randomized controlled trials of physician‐pharmacist collaborative interventions (6 and 9 mo, respectively) to improve blood pressure control.Setting. Eleven university‐affiliated primary care clinics.Patients. Five hundred eighty‐four patients (aged 21–85 yrs) with uncontrolled primary hypertension; 296 were in the intervention group and 288 were in the control group.Intervention. Pharmacists provided intensified hypertension management and drug adherence counseling to patients in the intervention group.Measurements and Main Results. Social support and self‐efficacy questionnaires were administered at baseline and end‐of‐study visits. Patient adherence was monitored by using the Morisky self‐reported adherence questionnaire. Self‐reported adherence scores improved significantly in the control group (p=0.0053) but not in the intervention group; however, adherence at baseline in both groups was high. There were small, but significant, improvements in self‐efficacy (p<0.04) and social support (p<0.05) scores in the intervention group but not the control group at the end of the study. Social support and, to a lesser extent, self‐efficacy improved as a function of duration of study participation (9–mo vs 6–mo intervention), regardless of whether the patient received the intervention. Blood pressure control in both groups improved significantly at the end of the study; however, mean blood pressure was significantly lower in the intervention group (129.7/76.6 mm Hg) compared with the control group (140.8/78.9 mm Hg; p<0.0001 for systolic, p=0.032 for diastolic).Conclusion. Social support and self‐efficacy improved significantly in the intervention group at the end of the pharmacist intervention. Drug adherence was correlated with self‐efficacy even though drug adherence did not improve significantly in the intervention group. The fact that social support and self‐efficacy improved as a function of duration of study participation suggests that participation in a research study may have had a positive influence on these measures. Even though the changes in social support, self‐efficacy and drug adherence were modest, there was significantly better blood pressure control in the intervention group compared with the control group. These findings indicate that changes in drug adherence, self‐efficacy or social support probably played a minor role in the blood pressure outcomes in these studies.
Anticipatory‐Conjectural Policy Problems: A Case Study of the Avian Influenza
Authors: DeLeo Rob A. 
Published: April 2010

AbstractRarely, if ever, is the American policymaking process described as being a proactive one wherein policymakers strive to stave off or prepare for problems that have yet to have any substantive impact on a given population. Such problems, or “anticipatory‐conjectural policy problems,” are marked by acute uncertainty and thus demand a reconsideration of many of our fundamental assumptions about the nature of public policymaking. Using the H5N1 strain of avian influenza as a case study, the following work seeks to expand Thomas Birkland's concept of focusing events to encompass anticipatory‐conjectural policy problems. In addition, I will explore the unique agenda setting dynamics of these problems, paying particularly close attention to their definitional characteristics.
Securitization of Disease in the United States: Globalization, Public Policy, and Pandemics
Authors: Cook Alethia H 
Published: April 2010

AbstractRecent spread of the diseases SARS, Bird Flu, and H1N1 have raised questions about how the US government will address the implications of a major pandemic. One of the key issues is whether a disease can become part of the national security agenda. This paper examines recent government activities in response to diseases to determine whether any disease has actually become a national security issue and the conditions under which this might happen in the future.
A Portrait of Complexity: New Actors and Contemporary Challenges in the Global Energy System and the Role of Energy Infrastructure Security
Authors: Giroux Jennifer 
Published: April 2010

AbstractThis article analyses the emergence of new actors and contemporary challenges that have increased the complexity of the global energy system and brought to light the significant role of energy infrastructure security. Working in two parts, the article first provides a general overview of ONG supply‐demand trends and the role of energy infrastructure (EI) in production and transport activities. The second part examines new security‐risks to EI by exploring similarities and distinctions of natural and human‐caused threats to EI. The argues concludes that energy infrastructure security will become a centerpiece in future energy security debate due to the growing dependence on ONG imports from conflict‐prone supplier and transit regions as well as the vulnerability of EI to natural disasters brought on by climate change.