bluuebunny/crossref_metadata_2025_split huggingface dataset:
Promoting ranking diversity for genomics search with relevance-novelty combined model
Authors: Yin Xiaoshi , Li Zhoujun , Huang Jimmy Xiangji , Hu Xiaohua 
Published: August 2011

Abstract

Background
In the biomedical domain, the desired information of a question (query) asked by biologists usually is a list of a certain type of entities covering different aspects that are related to the question, such as genes, proteins, diseases, mutations, etc. Hence it is important for a biomedical information retrieval system to be able to provide comprehensive and diverse answers to fulfill biologists’ information needs. However, traditional retrieval models assume that the relevance of a document is independent of the relevance of other documents. This assumption may result in high redundancy and low diversity in the retrieval ranked lists.

Results
In this paper, we propose a relevance-novelty combined model, named RelNov model, based on the framework of an undirected graphical model. It consists of two component models, namely the aspect-term relevance model and the aspect-term novelty model. They model the relevance of a document and the novelty of a document respectively. We show that our approach can achieve 16. 4% improvement over the highest aspect level MAP reported in the TREC 2007 Genomics track, and 9. 8% improvement over the highest passage level MAP reported in the TREC 2007 Genomics track.

Conclusions
The proposed combination model which models aspects, terms, topic relevance and document novelty as potential functions is demonstrated to be effective in promoting ranking diversity as well as in improving relevance of ranked lists for genomics search. We also show that the use of aspect plays an important role in the model. Moreover, the proposed model can integrate various different relevance and novelty measures easily.
Lipid-lowering drugs in ischaemic heart disease: A quasi-experimental uncontrolled before-and-after study of the effectiveness of clinical practice guidelines
Authors: Dalmau Rosa , Boira Miriam , Aguilar Carina , López Carlos , Rodríguez Dolors , Gentille Delicia , Bofill Domingo , Diogene Eduard , Pepió Josep M 
Published: August 2011

Abstract

Background
Cardiovascular diseases(CVD), specifically ischaemic heart disease(IHD), are the main causes of death in industrialized countries. Statins are not usually prescribed in the most appropriate way. To ensure the correct prescription of these drugs, it is necessary to develop, disseminate and implement clinical practice guidelines(CPGs), and subsequently evaluate them.
The main objective of this study is to evaluate the effectiveness of the implementation of consensual Lipid-lowering drugs (LLD) prescription guidelines in hospital and primary care settings, to improve the control of Low-Density Lipoprotein Cholesterol (LDL-C) levels in patients with IHD in the Terres de l'Ebre region covered by the Catalonian Health Institute. Secondary objectives are to assess the improvement of the prescription profile of these LLDs, to assess cardiovascular morbimortality and the professional profile and participant centre characteristics that govern the control of LDL-C.

Methods/Design
Design: Quasi-experimental uncontrolled before and after study. The intervention consists of the delivery of training strategies for guideline implementation (classroom clinical sessions and on-line courses) aimed at primary care and hospital physicians. The improvement in the control of LDL-C levels in the 3,402 patients with IHD in our territory is then assessed.
Scope: Primary care physicians from 11 basic health areas(BHAs) and two hospital services (internal medicine and cardiology).
Sample: 3,402 patients registered with IHD in the database of the Catalan Institute of Health(E-cap) before December 2008 and patients newly diagnosed during 2009-2010.
Variables: Percentage of patients achieving good control of LDL-C, measured in milligrams per decilitre. The aim of the intervention is to achieve levels of LDL-C < 100 mg/dl in patients with IHD. Secondary variables measure type and time of diagnosis of IHD, type and dose of prescribed cholesterol-lowering drugs, level of physician participation in training activities and their professional profile.

Discussion
The development of prescription guidelines previously agreed by various medical specialists involved in treating IHD patients have usually improved drug prescription. The guideline presented in this study aims to improve the control of LDL-C by training physicians through presential and on-line courses on the dissemination of this guideline, and by providing feedback on their personal results a year after this training intervention.
Kinetic Targeting of pegylated liposomal Doxorubicin: a new Approach to Reduce Toxicity during Chemotherapy (CARL-trial)
Authors: Eckes Jürgen , Schmah Oliver , Siebers Jan W , Groh Ursula , Zschiedrich Stefan , Rautenberg Beate , Hasenburg Annette , Jansen Martin , Hug Martin J , Winkler Karl , Pütz Gerhard 
Published: August 2011

Abstract

Background
The therapeutic success of chemotherapeutic agents is often limited by severe adverse effects. To reduce toxicity of these drugs, nanoscale particle-based drug delivery systems (DDS) are used. DDS accumulate to some extent in tumor tissues, but only a very small portion of a given dose reaches this target. Accumulation of DDS in tumor tissues is supposed to be much faster than in certain other tissues in which side effects occur ("Kinetic Targeting"). Once saturation in tumor tissue is achieved, most of the administered DDS still circulate in the plasma. The extracorporeal elimination of these circulating nanoparticles would probably reduce toxicity.

Methods
For the CARL-trial (Controlled Application and Removal of Liposomal chemotherapeutics), pegylated liposomal doxorubicin (PLD) was used as chemotherapeutic agent and double filtration plasmapheresis (DFPP) was performed for extracorporeal elimination of liposomes. PLD was given as 40 mg/m2 every 3 weeks in combination with vinorelbine 2 × 25 mg/m2 (neoadjuvant treatment of breast cancer, 12 patients), or as 40 mg/m2 every 4 weeks (recurrent ovarian cancer, 3 patients). Primary endpoints were the efficiency and safety profile of DFPP, and secondary endpoints were side effects and tumor response.

Results
DFPP eliminated ~62% of circulating PLD, corresponding to ~45% of the total dose (n = 57 cycles). AUC of doxorubicin was reduced by 50%. No leakage of doxorubicin was detected during elimination, and no relevant DFPP-related side effects occurred. Reduction in tumor size > 30% occurred in 10/12 (neoadjuvant) and in 1/3 patients (recurrent). Only five grade 2 events and one grade 3 event (mucositis, neutropenia or leucopenia) and a single palmar-plantar erythrodysesthesia grade 2 were reported.

Conclusion
Extracorporeal elimination of PLD by DFPP is safe and efficient. CARL can diminish the main dose-limiting side effects of PLD, and probably many different DDS alike.

Trial registration
DRKS00000163
A novel inhibitor of hypoxia-inducible factor-1α P3155 also modulates PI3K pathway and inhibits growth of prostate cancer cells
Authors: Manohar Sonal M , Padgaonkar Amol A , Jalota-Badhwar Archana , Sonawane Vinay , Rathos Maggie J , Kumar Sanjay , Joshi Kalpana S 
Published: August 2011

AbstractBackgroundHypoxia-inducible factor-1 (HIF-1) is a master regulator of the transcriptional response to hypoxia. It is essential for angiogenesis and is associated with tumor progression and overexpression of HIF-1α has been demonstrated in many common human cancers. Therefore, HIF-1α is one of the most compelling anticancer targets.MethodsTo identify HIF-1α inhibitors, luciferase reporter gene assay under hypoxia and normoxia was used. Detailed studies such as western blotting, RT-PCR, immunofluorescence were carried out to elucidate its mechanism of action. Antiangiogenic activity of P3155 was demonstrated by migration assay and tube formation assay. Efficacy study of P3155 was performed on PC-3 xenograft model.ResultsP3155 showed specific HIF-1α inhibition with IC50of 1.4 μM under hypoxia. It suppressed HIF-1α expression as well as PI3K/Akt pathway and abrogated expression of HIF-1-inducible gene viz. vascular endothelial growth factor (VEGF). P3155 in combination with HIF-1α siRNA showed significant synergistic effect. In addition, it demonstrated significantin vivoefficacy and antiangiogenic potential in prostate cancer cell lines.ConclusionWe have identified a novel HIF-1α inhibitor P3155 that also modulates PI3K/Akt pathway, which may contribute to its significantin vitroandin vivoantitumor activity.
Influence of in vitro supplementation with lipids from conventional and Alpine milk on fatty acid distribution and cell growth of HT-29 cells
Authors: Degen Christian , Lochner Alfred , Keller Sylvia , Kuhnt Katrin , Dänicke Sven , Jahreis Gerhard 
Published: August 2011

AbstractBackgroundTo date, the influence of milk and dairy products on carcinogenesis remains controversial. However, lipids of ruminant origin such as conjugated linoleic acids (CLA) are known to exhibit beneficial effectsin vitroandin vivo. The aim of the present study was to determine the influence of milk lipids of different origin and varying quality presenting as free fatty acid (FFA) solutions on cellular fatty acid distribution, cellular viability, and growth of human colon adenocarcinoma cells (HT-29).MethodsFAME of conventional and Alpine milk lipids (MLcon, MLalp) and cells treated with FFA derivatives of milk lipids were analyzed by means of GC-FID and Ag+-HPLC. Cellular viability and growth of the cells were determined by means of CellTiter-Blue®-assay and DAPI-assay (4',6-diamidino-2-phenylindole dihydrochloride), respectively.ResultsSupplementation with milk lipids significantly decreased viability and growth of HT-29 cells in a dose- and time-dependent manner. MLalpshowed a lower SFA/MUFA ratio, a 8 fold increased CLA content, and different CLA profile compared to MLconbut did not demonstrate additional growth-inhibitory effects. In addition, total concentration and fatty acid distribution of cellular lipids were altered. In particular, treatment of the cells yielded highest amounts of two types of milk specific major fatty acids (μg FA/mg cellular protein) after 8 h of incubation compared to 24 h; 200 μM of MLcon(C16:0, 206 ± 43), 200 μM of MLalp(C18:1c9, (223 ± 19). Vaccenic acid (C18:1t11) contained in milk lipids was converted toc9,t11-CLA in HT-29 cells. Notably, the ratio oft11,c13-CLA/t7,c9-CLA, a criterion for pasture feeding of the cows, was significantly changed after incubation for 8 h with lipids from MLalp(3.6 - 4.8), compared to lipids from MLcon(0.3 - 0.6).ConclusionsNatural lipids from conventional and Alpine milk showed similar growth inhibitory effects. However, different changes in cellular lipid composition suggested a milk lipid-depending influence on cell sensitivity. It is expected that similar changes may also be evident in other cell lines. To our knowledge, this is the first study showing a varied impact of complex milk lipids on fatty acid distribution in a colon cancer cell line.
Phosphoproteins regulated by heat stress in rice leaves
Authors: Chen Xinhai , Zhang Wenfeng , Zhang Baoqian , Zhou Jiechao , Wang Yongfei , Yang Qiaobin , Ke Yuqin , He Huaqin 
Published: August 2011

Abstract

Background
High temperature is a critical abiotic stress that reduces crop yield and quality. Rice (Oryza sativa L.) plants remodel their proteomes in response to high temperature stress. Moreover, phosphorylation is the most common form of protein post-translational modification (PTM). However, the differential expression of phosphoproteins induced by heat in rice remains unexplored.

Methods
Phosphoprotein in the leaves of rice under heat stress were displayed using two-dimensional electrophoresis (2-DE) and Pro-Q Diamond dye. Differentially expressed phosphoproteins were identified by MALDI-TOF-TOF-MS/MS and confirmed by Western blotting.

Results
Ten heat-phosphoproteins were identified from twelve protein spots, including ribulose bisphos-phate carboxylase large chain, 2-Cys peroxiredoxin BAS1, putative mRNA binding protein, Os01g0791600 protein, OSJNBa0076N16.12 protein, putative H(+)-transporting ATP synthase, ATP synthase subunit beta and three putative uncharacterized proteins. The identification of ATP synthase subunit beta was further validated by Western-blotting. Four phosphorylation site predictors were also used to predict the phosphorylation sites and the specific kinases for these 10 phosphoproteins.

Conclusion
Heat stress induced the dephosphorylation of RuBisCo and the phosphorylation of ATP-β, which decreased the activities of RuBisCo and ATP synthase. The observed dephosphorylation of the mRNA binding protein and 2-Cys peroxiredoxin may be involved in the transduction of heat-stress signaling, but the functional importance of other phosphoproteins, such as H+-ATPase, remains unknown.
Reliability and validity of the Spanish version of the 10-item Connor-Davidson Resilience Scale (10-item CD-RISC) in young adults
Authors: Notario-Pacheco Blanca , Solera-Martínez Montserrat , Serrano-Parra María D , Bartolomé-Gutiérrez Raquel , García-Campayo Javier , Martínez-Vizcaíno Vicente 
Published: August 2011

Abstract

Background
The 10-item Connor-Davidson Resilience Scale (10-item CD-RISC) is an instrument for measuring resilience that has shown good psychometric properties in its original version in English. The aim of this study was to evaluate the validity and reliability of the Spanish version of the 10-item CD-RISC in young adults and to verify whether it is structured in a single dimension as in the original English version.

Findings
Cross-sectional observational study including 681 university students ranging in age from 18 to 30 years. The number of latent factors in the 10 items of the scale was analyzed by exploratory factor analysis. Confirmatory factor analysis was used to verify whether a single factor underlies the 10 items of the scale as in the original version in English. The convergent validity was analyzed by testing whether the mean of the scores of the mental component of SF-12 (MCS) and the quality of sleep as measured with the Pittsburgh Sleep Index (PSQI) were higher in subjects with better levels of resilience. The internal consistency of the 10-item CD-RISC was estimated using the Cronbach α test and test-retest reliability was estimated with the intraclass correlation coefficient.
The Cronbach α coefficient was 0.85 and the test-retest intraclass correlation coefficient was 0.71. The mean MCS score and the level of quality of sleep in both men and women were significantly worse in subjects with lower resilience scores.

Conclusions
The Spanish version of the 10-item CD-RISC showed good psychometric properties in young adults and thus can be used as a reliable and valid instrument for measuring resilience. Our study confirmed that a single factor underlies the resilience construct, as was the case of the original scale in English.
Evaluation of a TDMA-based energy efficient MAC protocol for multiple capsule networks
Authors: Lin Lin , Wong Kai-Juan , Kumar Arun , Lu Zongqing , Tan Su-Lim , Phee Soo Jay 
Published: August 2011

Abstract
Wireless capsule endoscopy is a new kind of medical device, which monitors the gastrointestinal tract of the human body. It can be envisaged that in the future more than one capsule could be ingested by the patient and they operate collaboratively in the gastrointestinal (GI) tract to perform certain diagnostic and therapeutic tasks. These mobile capsules and the coordinator node, which is attached to the abdomen of the patient, form a wireless network. The capsule devices are typically powered by batteries, therefore, energy efficient medium access control (MAC) protocols for multiple capsule networks are necessary. This article proposes a novel energy efficient MAC protocol for multiple capsule networks based on time division multiple access (TDMA). An asymmetric up/down link network architecture is introduced. A novel TDMA slot assignment scheme is proposed and simulation results using Qualnet show that the proposed MAC protocol achieves lower energy consumption than B-MAC and star topology TDMA.
Common fixed point and invariant approximation in hyperbolic ordered metric spaces
Authors: Abbas Mujahid , Khamsi Mohamed Amine , Khan Abdul Rahim 
Published: August 2011

AbstractWe prove a common fixed point theorem for four mappings defined on an ordered metric space and apply it to find new common fixed point results. The existence of common fixed points is established for two or three noncommuting mappings where T is either ordered S-contraction or ordered asymptotically S-nonexpansive on a nonempty ordered starshaped subset of a hyperbolic ordered metric space. As applications, related invariant approximation results are derived. Our results unify, generalize, and complement various known comparable results from the current literature.2010 Mathematics Subject Classification:47H09, 47H10, 47H19, 54H25.
Opportunistic illnesses in Brazilian children with AIDS: results from two national cohort studies, 1983-2007
Authors: Ramos Alberto N , Matida Luiza H , Hearst Norman , Heukelbach Jorg 
Published: August 2011

AbstractBackgroundHAART has significantly reduced AIDS-related morbidity in children. However, limited evidence is available from developing countries regarding patterns of opportunistic illnesses. We describe these events and their associated factors in children with AIDS in Brazil.MethodsThis study is based on two representative retrospective multi-center cohorts including a total 1,859 children with AIDS, infected via mother-to-child transmission (MTCT), between 1983-2002. Opportunistic illnesses were described and analyzed over time. The association of demographic, clinical and operational data with the occurrence of opportunistic diseases was assessed.ResultsIn total, 1,218 (65.5%) had at least one event of an opportunistic disease. Variables significantly associated with occurrence of these events included: region of residence (OR 2.68-11.33, as compared to the Northern region), age < 1 year at diagnosis (OR 2.56, 95% CI 1.81-3.61, p < 0.001), and non-performance of MTCT prevention measures (OR 1.58, 95% CI 1.21-2.07, p < 0.001). Protective factors included year of HIV diagnosis in the HAART era (OR 0.34, 95% CI 0.15-0.76, p = 0.009) and ART use (OR 0.58, 95% CI 0.44-0.77, p < 0.001). In both periods bacterial infections represented the most common opportunistic events (58.6 vs. 34.7%; p < 0.001), followed byPneumocystis jiroveciipneumonia (21.9 vs. 13.2%; p < 0.001), and bacterial meningitis/sepsis (16.8 vs. 7.4%; p < 0.001).ConclusionsDespite the significant reduction in recent years, opportunistic illnesses are still common in Brazilian children with AIDS in the HAART era, especially bacterial diseases. The data reinforce the need for scaling up prevention of MTCT, early diagnosis of infection, and improvement of comprehensive pediatric care.
Sequence analysis reveals mosaic genome of Aichi virus
Authors: Han Xiaohong , Zhang Wen , Xue Yanjun , Shao Shihe 
Published: August 2011

Abstract
Aichi virus is a positive-sense and single-stranded RNA virus, which demonstrated to be related to diarrhea of Children. In the present study, phylogenetic and recombination analysis based on the Aichi virus complete genomes available in GenBank reveal a mosaic genome sequence [GenBank: FJ890523], of which the nt 261-852 region (the nt position was based on the aligned sequence file) shows close relationship with AB010145/Japan with 97.9% sequence identity, while the other genomic regions show close relationship with AY747174/German with 90.1% sequence identity. Our results will provide valuable hints for future research on Aichi virus diversity.
Aichi virus is a member of the Kobuvirus genus of the Picornaviridae family [1, 2] and belongs to a positive-sense and single-stranded RNA virus. Its presence in fecal specimens of children suffering from diarrhea has been demonstrated in several Asian countries [3–6], in Brazil and German [7], in France [8] and in Tunisia [9]. Some reports showed the high level of seroprevalence in adults [7, 10], suggesting the widespread exposure to Aichi virus during childhood.
The genome of Aichi virus contains 8,280 nucleotides and a poly(A) tail. The single large open reading frame (nt 713-8014 according to the strain AB010145) encodes a polyprotein of 2,432 amino acids that is cleaved into the typical picornavirus structural proteins VP0, VP3, VP1, and nonstructural proteins 2A, 2B, 2C, 3A, 3B, 3C and 3D [2, 11]. Based on the phylogenetic analysis of 519-bp sequences at the 3C-3D (3CD) junction, Aichi viruses can be divided into two genotypes A and B with approximately 90% sequence homology [12]. Although only six complete genomes of Aichi virus were deposited in GenBank at present, mosaic genomes can be found in strains from different countries.
Prestimulus vigilance predicts response speed in an easy visual discrimination task
Authors: Minkwitz Juliane , Trenner Maja U , Sander Christian , Olbrich Sebastian , Sheldrick Abigail J , Schönknecht Peter , Hegerl Ulrich , Himmerich Hubertus 
Published: August 2011

Abstract

Background
Healthy adults show considerable within-subject variation of reaction time (RT) when performing cognitive tests. So far, the neurophysiological correlates of these inconsistencies have not yet been investigated sufficiently. In particular, studies rarely have focused on alterations of prestimulus EEG-vigilance as a factor which possibly influences the outcome of cognitive tests. We hypothesised that a low EEG-vigilance state immediately before a reaction task would entail a longer RT. Shorter RTs were expected for a high EEG-vigilance state.

Methods
24 female students performed an easy visual discrimination task while an electroencephalogram (EEG) was recorded. The vigilance stages of 1-sec-EEG-segments before stimulus presentation were classified automatically using the computer-based Vigilance Algorithm Leipzig (VIGALL). The mean RTs of each EEG-vigilance stage were calculated for each subject. A paired t-test for the EEG-vigilance main stage analysis (A vs. B) and a variance analysis for repeated measures for the EEG-vigilance sub-stage analysis (A1, A2, A3, B1, B2/3) were calculated.

Results
Individual mean RT was significantly shorter for events following the high EEG-vigilance stage A compared to the lower EEG-vigilance stage B. The main effect of the sub-stage analysis was marginal significant. A trend of gradually increasing RT was observable within the EEG-vigilance stage A.

Conclusion
We conclude that an automatically classified low EEG-vigilance level is associated with an increased RT. Thus, intra-individual variances in cognitive test might be explainable in parts by the individual state of EEG-vigilance. Therefore, the accuracy of neuro-cognitive investigations might be improvable by simultaneously controlling for vigilance shifts using the EEG and VIGALL.