bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparison study on algorithms of detecting long forms for short forms in biomedical text
Authors: Torii Manabu , Hu Zhang-zhi , Song Min , Wu Cathy H , Liu Hongfang 
Published: November 2007

Abstract

Motivation
With more and more research dedicated to literature mining in the biomedical domain, more and more systems are available for people to choose from when building literature mining applications. In this study, we focus on one specific kind of literature mining task, i.e., detecting definitions of acronyms, abbreviations, and symbols in biomedical text. We denote acronyms, abbreviations, and symbols as short forms (SFs) and their corresponding definitions as long forms (LFs). The study was designed to answer the following questions; i) how well a system performs in detecting LFs from novel text, ii) what the coverage is for various terminological knowledge bases in including SFs as synonyms of their LFs, and iii) how to combine results from various SF knowledge bases.

Method
We evaluated the following three publicly available detection systems in detecting LFs for SFs: i) a handcrafted pattern/rule based system by Ao and Takagi, ALICE, ii) a machine learning system by Chang et al., and iii) a simple alignment-based program by Schwartz and Hearst. In addition, we investigated the conceptual coverage of two terminological knowledge bases: i) the UMLS (the Unified Medical Language System), and ii) the BioThesaurus (a thesaurus of names for all UniProt protein records). We also implemented a web interface that provides a virtual integration of various SF knowledge bases.

Results
We found that detection systems agree with each other on most cases, and the existing terminological knowledge bases have a good coverage of synonymous relationship for frequently defined LFs. The web interface allows people to detect SF definitions from text and to search several SF knowledge bases.

Availability
The web site is http://gauss.dbb.georgetown.edu/liblab/SFThesaurus.
The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains
Authors: Brenchley Rachel , Tariq Humera , McElhinney Helen , Szöőr Balázs , Huxley-Jones Julie , Stevens Robert , Matthews Keith , Tabernero Lydia 
Published: November 2007

AbstractBackgroundThe genomes of the three parasitic protozoaTrypanosoma cruzi,Trypanosoma bruceiandLeishmania majorare the main subject of this study. These parasites are responsible for devastating human diseases known as Chagas disease, African sleeping sickness and cutaneous Leishmaniasis, respectively, that affect millions of people in the developing world. The prevalence of these neglected diseases results from a combination of poverty, inadequate prevention and difficult treatment. Protein phosphorylation is an important mechanism of controlling the development of these kinetoplastids. With the aim to further our knowledge of the biology of these organisms we present a characterisation of the phosphatase complement (phosphatome) of the three parasites.ResultsAn ontology-based scan of the three genomes was used to identify 86 phosphatase catalytic domains inT. cruzi, 78 inT. brucei, and 88 inL. major. We found interesting differences with other eukaryotic genomes, such as the low proportion of tyrosine phosphatases and the expansion of the serine/threonine phosphatase family. Additionally, a large number of atypical protein phosphatases were identified in these species, representing more than one third of the total phosphatase complement. Most of the atypical phosphatases belong to the dual-specificity phosphatase (DSP) family and show considerable divergence from classic DSPs in both the domain organisation and sequence features.ConclusionThe analysis of the phosphatome of the three kinetoplastids indicates that they possess orthologues to many of the phosphatases reported in other eukaryotes, including humans. However, novel domain architectures and unusual combinations of accessory domains, suggest distinct functional roles for several of the kinetoplastid phosphatases, which await further experimental exploration. These distinct traits may be exploited in the selection of suitable new targets for drug development to prevent transmission and spread of the diseases, taking advantage of the already extensive knowledge on protein phosphatase inhibitors.
Corticomuscular synchronization with small and large dynamic force output
Authors: Andrykiewicz Agnieszka , Patino Luis , Naranjo Jose Raul , Witte Matthias , Hepp-Reymond Marie-Claude , Kristeva Rumyana 
Published: November 2007

Abstract

Background
Over the last few years much research has been devoted to investigating the synchronization between cortical motor and muscular activity as measured by EEG/MEG-EMG coherence. The main focus so far has been on corticomuscular coherence (CMC) during static force condition, for which coherence in beta-range has been described. In contrast, we showed in a recent study [1] that dynamic force condition is accompanied by gamma-range CMC. The modulation of the CMC by various dynamic force amplitudes, however, remained uninvestigated. The present study addresses this question. We examined eight healthy human subjects. EEG and surface EMG were recorded simultaneously. The visuomotor task consisted in isometric compensation for 3 forces (static, small and large dynamic) generated by a manipulandum. The CMC, the cortical EEG spectral power (SP), the EMG SP and the errors in motor performance (as the difference between target and exerted force) were analyzed.

Results
For the static force condition we found the well-documented, significant beta-range CMC (15–30 Hz) over the contralateral sensorimotor cortex. Gamma-band CMC (30–45 Hz) occurred in both small and large dynamic force conditions without any significant difference between both conditions. Although in some subjects beta-range CMC was observed during both dynamic force conditions no significant difference between conditions could be detected. With respect to the motor performance, the lowest errors were obtained in the static force condition and the highest ones in the dynamic condition with large amplitude. However, when we normalized the magnitude of the errors to the amplitude of the applied force (relative errors) no significant difference between both dynamic conditions was observed.

Conclusion
These findings confirm that during dynamic force output the corticomuscular network oscillates at gamma frequencies. Moreover, we show that amplitude modulation of dynamic force has no effect on the gamma CMC in the low force range investigated. We suggest that gamma CMC is rather associated with the internal state of the sensorimotor system as supported by the unchanged relative error between both dynamic conditions.
Outcomes of patients hospitalized for acute decompensated heart failure: does nesiritide make a difference?
Authors: Carroll Richard J , Mulla Zuber D , Hauck Loran D , Westbrook Audrey 
Published: November 2007

Abstract

Background
Nesiritide is indicated in the treatment of acute decompensated heart failure. However, a recent meta-analysis reported that nesiritide may be associated with an increased risk of death. Our goal was to evaluate the impact of nesiritide treatment on four outcomes among adults hospitalized for congestive heart failure (CHF) during a three-year period.

Methods
CHF patients discharged between 1/1/2002 and 12/31/2004 from the Adventist Health System, a national, not-for-profit hospital system, were identified. 25,330 records were included in this retrospective study. Nesiritide odds ratios (OR) were adjusted for various factors including nine medications and/or an APR-DRG severity score.

Results
Initially, treatment with nesiritide was found to be associated with a 59% higher odds of hospital mortality (Unadjusted OR = 1.59, 95% confidence interval [CI]: 1.31–1.93). Adjusting for race, low economic status, APR-DRG severity of illness score, and the receipt of nine medications yielded a nonsignificant nesiritide OR of 1.07 for hospital death (95% CI: 0.85–1.35). Nesiritide was positively associated with the odds of prolonged length of stay (all adjusted ORs = 1.66) and elevated pharmacy cost (all adjusted ORs > 5).

Conclusion
In this observational study, nesiritide therapy was associated with increased length of stay and pharmacy cost, but not hospital mortality. Randomized trials are urgently needed to better define the efficacy, if any, of nesiritide in the treatment of decompensated heart failure.
Fabrication and in vitro deployment of a laser-activated shape memory polymer vascular stent
Authors: Baer Géraldine M , Small Ward , Wilson Thomas S , Benett William J , Matthews Dennis L , Hartman Jonathan , Maitland Duncan J 
Published: November 2007

Abstract

Background
Vascular stents are small tubular scaffolds used in the treatment of arterial stenosis (narrowing of the vessel). Most vascular stents are metallic and are deployed either by balloon expansion or by self-expansion. A shape memory polymer (SMP) stent may enhance flexibility, compliance, and drug elution compared to its current metallic counterparts. The purpose of this study was to describe the fabrication of a laser-activated SMP stent and demonstrate photothermal expansion of the stent in an in vitro artery model.

Methods
A novel SMP stent was fabricated from thermoplastic polyurethane. A solid SMP tube formed by dip coating a stainless steel pin was laser-etched to create the mesh pattern of the finished stent. The stent was crimped over a fiber-optic cylindrical light diffuser coupled to an infrared diode laser. Photothermal actuation of the stent was performed in a water-filled mock artery.

Results
At a physiological flow rate, the stent did not fully expand at the maximum laser power (8.6 W) due to convective cooling. However, under zero flow, simulating the technique of endovascular flow occlusion, complete laser actuation was achieved in the mock artery at a laser power of ~8 W.

Conclusion
We have shown the design and fabrication of an SMP stent and a means of light delivery for photothermal actuation. Though further studies are required to optimize the device and assess thermal tissue damage, photothermal actuation of the SMP stent was demonstrated.
An outbreak of cardiovascular syndromes requiring urgent medical treatment and its association with environmental factors: an ecological study
Authors: Turner Robin M , Muscatello David J , Zheng Wei , Willmore Alan , Arendts Glenn 
Published: November 2007

Abstract

Background
In April 2005, syndromic surveillance based on statistical control chart methods in Sydney, Australia, signalled increasing incidence of urgent emergency department visits for cardiovascular and chest pain syndromes compared to the preceding twelve months. This paper aimed to determine whether environmental factors could have been responsible for this 'outbreak'.

Methods
The outcome studied was daily counts of emergency department visits for cardiovascular or chest pain syndromes that were considered immediately or imminently life threatening on arrival at hospital. The outbreak had a mean daily count of 5.7 visits sustained for eight weeks, compared with 4.0 in the same months in previous years. Poisson regression was used to systematically assess the emergency department visits in relation to available daily weather and pollution variables by first finding the best model that explained short-term variation in the outcome over the period 25 January 2002 to 31 May 2005, and then assessing interactions of all available variables with the 'outbreak' period, April-May 2005. Rate ratios were estimated for an interquartile increase in each variable meaning that the ratio measures the relative increase (or decrease) in the emergency department visits for an interquartile increase in the weather or pollution variable. The rate ratios for the outbreak period measure the relative increase (or decrease) in the emergency department visits for an interquartile increase in the weather or pollution variable during the outbreak period only.

Results
The best fitting model over the whole study period included minimum temperature with a rate ratio (RR) of 0.86 (95% confidence interval (CI), 0.77–0.96), maximum relative humidity of 1.09 (95% CI 1.05–1.14) and minimum daily particulate matter less than 10 microns (PM10) of 1.05 (95% CI, 1.01–1.09). During the outbreak period, maximum temperature (RR 1.27, 95% CI 1.03–1.57), solar radiation (RR 1.44, 95% CI, 1.00–2.07) and ozone (RR 1.13, 95% CI 1.01–1.26) were associated with the outcome.

Conclusion
The increase may have been associated with photochemical pollution. Syndromic surveillance can identify outbreaks of non-communicable diseases associated with environmental factors.
Reactive oxygen species and p47phox activation are essential for the Mycobacterium tuberculosis-induced pro-inflammatory response in murine microglia
Authors: Yang Chul-Su , Lee Hye-Mi , Lee Ji-Yeon , Kim Jeong-Ah , Lee Sung Joong , Shin Dong-Min , Lee Young-Ho , Lee Dong-Seok , El-Benna Jamel , Jo Eun-Kyeong 
Published: November 2007

AbstractBackgroundActivated microglia elicits a robust amount of pro-inflammatory cytokines, which are implicated in the pathogenesis of tuberculosis in the central nervous system (CNS). However, little is known about the intracellular signaling mechanisms governing these inflammatory responses in microglia in response toMycobacterium tuberculosis(Mtb).MethodsMurine microglial BV-2 cells and primary mixed glial cells were stimulated with sonicated Mtb (s-Mtb). Intracellular ROS levels were measured by staining with oxidative fluorescent dyes [2',7'-Dichlorodihydrofluorescein diacetate (H2DCFDA) and dihydroethidium (DHE)]. NADPH oxidase activities were measured by lucigenin chemiluminescence assay. S-Mtb-induced MAPK activation and pro-inflammatory cytokine release in microglial cells were measured using by Western blot analysis and enzyme-linked immunosorbent assay, respectively.ResultsWe demonstrate that s-Mtb promotes the up-regulation of reactive oxygen species (ROS) and the rapid activation of mitogen-activated protein kinases (MAPKs), including p38 and extracellular signal-regulated kinase (ERK) 1/2, as well as the secretion of tumor necrosis factor (TNF)-α, interleukin (IL)-6, and IL-12p40 in murine microglial BV-2 cells and primary mixed glial cells. Both NADPH oxidase and mitochondrial electron transfer chain subunit I play an indispensable role in s-Mtb-induced MAPK activation and pro-inflammatory cytokine production in BV-2 cells and mixed glial cells. Furthermore, the activation of cytosolic NADPH oxidase p47phox and MAPKs (p38 and ERK1/2) is mutually dependent on s-Mtb-induced inflammatory signaling in murine microglia. Neither TLR2 nor dectin-1 was involved in s-Mtb-induced inflammatory responses in murine microglia.ConclusionThese data collectively demonstrate that s-Mtb actively induces the pro-inflammatory response in microglia through NADPH oxidase-dependent ROS generation, although the specific pattern-recognition receptors involved in these responses remain to be identified.
Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?
Authors: Lovelock Paul K , Spurdle Amanda B , Mok Myth TS , Farrugia Daniel J , Lakhani Sunil R , Healey Sue , Arnold Stephen , Buchanan Daniel , Investigators kConFab , Couch Fergus J , Henderson Beric R , Goldgar David E , Tavtigian Sean V , Chenevix-Trench Georgia , Brown Melissa A 
Published: November 2007

Abstract
Introduction
Many of the DNA sequence variants identified in the breast cancer susceptibility gene BRCA1 remain unclassified in terms of their potential pathogenicity. Both multifactorial likelihood analysis and functional approaches have been proposed as a means to elucidate likely clinical significance of such variants, but analysis of the comparative value of these methods for classifying all sequence variants has been limited.

Methods
We have compared the results from multifactorial likelihood analysis with those from several functional analyses for the four BRCA1 sequence variants A1708E, G1738R, R1699Q, and A1708V.

Results
Our results show that multifactorial likelihood analysis, which incorporates sequence conservation, co-inheritance, segregation, and tumour immunohistochemical analysis, may improve classification of variants. For A1708E, previously shown to be functionally compromised, analysis of oestrogen receptor, cytokeratin 5/6, and cytokeratin 14 tumour expression data significantly strengthened the prediction of pathogenicity, giving a posterior probability of pathogenicity of 99%. For G1738R, shown to be functionally defective in this study, immunohistochemistry analysis confirmed previous findings of inconsistent 'BRCA1-like' phenotypes for the two tumours studied, and the posterior probability for this variant was 96%. The posterior probabilities of R1699Q and A1708V were 54% and 69%, respectively, only moderately suggestive of increased risk. Interestingly, results from functional analyses suggest that both of these variants have only partial functional activity. R1699Q was defective in foci formation in response to DNA damage and displayed intermediate transcriptional transactivation activity but showed no evidence for centrosome amplification. In contrast, A1708V displayed an intermediate transcriptional transactivation activity and a normal foci formation response in response to DNA damage but induced centrosome amplification.

Conclusion
These data highlight the need for a range of functional studies to be performed in order to identify variants with partially compromised function. The results also raise the possibility that A1708V and R1699Q may be associated with a low or moderate risk of cancer. While data pooling strategies may provide more information for multifactorial analysis to improve the interpretation of the clinical significance of these variants, it is likely that the development of current multifactorial likelihood approaches and the consideration of alternative statistical approaches will be needed to determine whether these individually rare variants do confer a low or moderate risk of breast cancer.
Inhibition of the RAGE products increases survival in experimental models of severe sepsis and systemic infection
Authors: Lutterloh Emily C , Opal Steven M , Pittman Debra D , Keith James C , Tan Xiang-Yang , Clancy Brian M , Palmer Helen , Milarski Kim , Sun Ying , Palardy John E , Parejo Nicholas A , Kessimian Noubar 
Published: November 2007

Abstract
Introduction
The receptor for advanced glycation end products (RAGE), a multi-ligand member of the immunoglobulin superfamily, contributes to acute and chronic disease processes, including sepsis.

Methods
We studied the possible therapeutic role of RAGE inhibition in the cecal ligation and puncture (CLP) model of polymicrobial sepsis and a model of systemic listeriosis using mice genetically deficient in RAGE expression or mice injected with a rat anti-murine RAGE monoclonal antibody.

Results
The 7-day survival rates after CLP were 80% for RAGE-/- mice (n = 15) (P < 0.01 versus wild-type), 69% for RAGE+/- mice (n = 23), and 37% for wild-type mice (n = 27). Survival benefits were evident in BALB/c mice given anti-RAGE antibody (n = 15 per group) over serum-treated control animals (P < 0.05). Moreover, delayed treatment with anti-RAGE antibody up to 24 hours after CLP resulted in a significant survival benefit compared with control mice. There was no significant increase in tissue colony counts from enteric Gram-negative or Gram-positive bacteria in animals treated with anti-RAGE antibody. RAGE-/-, RAGE+/-, and anti-RAGE antibody-treated animals were resistant to lethality from Listeria monocytogenes by almost two orders of magnitude compared with wild-type mice.

Conclusion
Further studies are warranted to determine the clinical utility of anti-RAGE antibody as a novel treatment for sepsis.
PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
Authors: Gnad Florian , Ren Shubin , Cox Juergen , Olsen Jesper V , Macek Boris , Oroshi Mario , Mann Matthias 
Published: November 2007

AbstractPHOSIDA http://www.phosida.com, a phosphorylation site database, integrates thousands of high-confidence in vivo phosphosites identified by mass spectrometry-based proteomics in various species. For each phosphosite, PHOSIDA lists matching kinase motifs, predicted secondary structures, conservation patterns, and its dynamic regulation upon stimulus. Using support vector machines, PHOSIDA also predicts phosphosites.
Special Programmes in Scotland: the first year of YOP
Authors: Raffe David 
Published: November 2007

In 1977 the Manpower Services Commission published the Holland Report on Young People at Work which proposed a new programme to give unemployed young people the chance to gain work experience or to attend courses that would help prepare them for work. The Youth Opportunities Programme (YOP) was accordingly set into operation from 1 April 1978, and it provided schemes of work experience or work preparation for some 162,200 young persons in 1978/9 and for 216,400 in 1979/80. The programme has continued to expand and in its fourth year of operation (1981/2) it is planned to cater for 440,000 entrants. YOP did not start from scratch; one of the main proposals of the Holland Report was to rationalise and coordinate the wide variety of special programmes that already catered for young people. However the Report proposed that these schemes should be extended, and it suggested additional objectives for the new programmes.
One set of objectives concerned the kinds of young people for whom the schemes should be provided.
Description and Validation of a Novel Real-Time RT-PCR Enterovirus Assay
Authors: Hymas Weston C , Aldous Wade K , Taggart Edward W , Stevenson Jeffery B , Hillyard David R 
Published: November 2007

AbstractBackground: Enteroviruses are a leading cause of aseptic meningitis in adult and pediatric populations. We describe the development of a real-time RT-PCR assay that amplifies a small target in the 5′ nontranslated region upstream of the classical Rotbart enterovirus amplicon. The assay includes an RNA internal control and incorporates modified nucleotide chemistry.Methods: We evaluated the performance characteristics of this design and performed blinded parallel testing on clinical samples, comparing the results with a commercially available RT-PCR assay (Pan-Enterovirus OligoDetect kit) that uses an enzyme immunoassay–like plate end detection.Results: We tested 778 samples and found 14 discrepant samples between the 2 assays. Of these, the real-time assay detected 6 samples that were negative by the OligoDetect kit, 5 of which were confirmed as positive by sequence analysis using an alternative primer set. Eight discrepant samples were positive by the OligoDetect kit and real-time negative, with 6 confirmed by sequencing. Overall, detection rates of 97% and 96% were obtained for the OligoDetect kit and real-time assays, respectively. Sequence analysis revealed the presence of a number of single nucleotide polymorphisms in the targeted region. The comparative sensitivities of the 2 assays were equivalent, with the limit of detection for the real-time assay determined to be approximately 430 copies per milliliter in cerebrospinal fluid.Conclusions: This novel real-time enterovirus assay is a sensitive and suitable assay for routine clinical testing. The presence of single nucleotide polymorphisms can affect real-time PCR assays.