bluuebunny/crossref_metadata_2025_split huggingface dataset:
The light‐sensitive photoprotein berovin from the bioluminescent ctenophore Beroe abyssicola: a novel type of Ca2+‐regulated photoprotein
Authors: Markova Svetlana V. , Burakova Ludmila P. , Golz Stefan , Malikova Natalia P. , Frank Ludmila A. , Vysotski Eugene S. 
Published: January 2012

Light‐sensitive Ca2+‐regulated photoproteins are responsible for the bright bioluminescence of ctenophores. Using functional screening, four full‐size cDNA genes encoding the same 208‐amino‐acid polypeptide were isolated from two independent cDNA libraries prepared from two Beroe abyssicola specimens. Sequence analysis revealed three canonical EF‐hand calcium‐binding sites characteristic of Ca2+‐regulated photoproteins, but a very low degree of sequence identity (27–29%) with aequorin‐type photoproteins, despite functional similarities. Recombinant berovin was expressed in Escherichia coli cells, purified, converted to active photoprotein and characterized. Active berovin has absorption maxima at 280 and 437 nm. The Ca2+‐discharged protein loses visible absorption, but exhibits a new absorption maximum at 335 nm. The berovin bioluminescence is blue (λmax = 491 nm) and a change in pH over the range 6.0–9.5 has no significant effect on the light emission spectrum. By contrast, the fluorescence of Ca2+‐discharged protein (λex = 350 nm) is pH sensitive: at neutral pH the maximum is at 420 nm and at alkaline pH there are two maxima at 410 and 485 nm. Like native ctenophore photoproteins, recombinant berovin is also inactivated by light. The Ca2+ concentration–effect curve is a sigmoid with a slope on a log–log plot of ∼ 2.5. Although this curve for berovin is very similar to those obtained for obelin and aequorin, there are evident distinctions: berovin responds to calcium changes at lower concentrations than jellyfish photoproteins and its Ca2+‐independent luminescence is low. Recombinant berovin was successfully expressed in mammalian cells, thereby demonstrating potential for monitoring intracellular calcium.Database
The nucleotide sequences have been deposited in the GenBankTM/EBI Data Bank with accession numbers: apoberovin cDNA genes, JN673813 (BA1), JN673814 (BA2), JN673815 (BA3), JN673816 (BA4); fragment 18S rRNA, JN673817 (BA‐rRNA5).
Current protected sites do not allow the representation of endangered invertebrates: the Spanish case
Authors: HERNÁNDEZ‐MANRIQUE OLGA L. , NUMA CATHERINE , VERDÚ JOSE R. , GALANTE EDUARDO , LOBO JORGE M. 
Published: January 2012

Abstract.  1. Using a recently created database representing the joint effort of around 100 invertebrate taxonomists, this study uses the information on 52 arthropoda and 27 mollusca species that are endangered and critically endangered to examine to what extent invertebrate species are represented in existing Spanish protected areas.2. As distribution information is available at a 100 km2 resolution, we consider different area thresholds to judge cells as being protected.3. Approximately 19% of the area represented by the grid cells with observed occurrences rates as extant protected reserves, and 36% is included within the Natura 2000 network.4. If having 50% of the cell area as a Natura 2000 reserve is considered as sufficient to have effective protection, almost 68% of species and 32% of probable populations (contiguous cell groups) would be represented.5. However, 77% of species and 94% of probable populations are not represented in the current protected reserves if we establish that at least 95% of each cell area should belong to a reserve to provide effective protection.6. Thus, existing conservation strategies, which are based primarily on the protection of certain areas and vertebrate species, may be insufficient to ensure the conservation of invertebrate species.
Discovery of a Novel Circulating Biomarker in Patients with Abdominal Aortic Aneurysm: A Pilot Study Using a Proteomic Approach
Authors: Wallinder Jonas , Bergström Jörgen , Henriksson Anders E. 
Published: January 2012

AbstractAbdominal aortic aneurysm (AAA) is a common condition with high mortality when ruptured. Most clinicians agree that small AAAs are best managed by ultrasonographic surveillance. However, it has been stated in recent reviews that a serum/plasma biomarker that predicts AAA rupture risk would be a powerful tool in stratifying patients with small AAA. Identification of such circulating biomarkers has been to date unsuccessful. In this study, we used a proteomic approach to find new, potential plasma AAA biomarker candidates. Prefractionated plasma samples were analyzed by two‐dimensional differential in‐gel electrophoresis to identify differentially expressed proteins between four patients with small AAA and four controls without aneurysm. Protein spots that differed significantly between patients and controls were selected and identified by mass spectrometry. Three protein spots had significantly different expression between patients and controls. The most interesting finding was that patients with small AAA had increased levels of the enzyme glycosylphosphatidylinositol‐specific phospholipase D (GPI‐PLD) compared with the controls without aneurysm. In conclusion, by using a proteomic approach, this pilot‐study provides evidence of GPI‐PLD as a novel potential plasma biomarker for AAA. Clin Trans Sci 2012; Volume 5: 56–59
Linkage Disequilibrium and Haplotype Analysis of COX‐2 and Risk of Colorectal Adenoma Development
Authors: Kwagyan John , Apprey Victor , Ashktorab Hassan 
Published: January 2012

AbstractSingle nucleotide polymorphisms (SNPs) in the promoter and untranslated region of cyclooxygenase (COX)‐2, an inducible enzyme responsible for the synthesis of prostaglandins, have been reported to modulate the risk for many human cancers. We performed comprehensive linkage disequilibrium (LD) and haplotype analyses of 13 single nucleotide polymorphisms of the COX‐2 gene and examined its susceptibility to adenoma development in 72 African American cases and 142 controls. Results revealed significant variation in LD patterns with consequence for adenoma development. Two distinct haplotype blocks were identified; one block covered the coding regions of exon 1, introns and a section of the 3′‐unstranslated region (3′‐UTR), whereas the second block resided solely in the 3′‐UTR region. A haplotype in block 1 increased the risk of adenoma development by threefold (odds ratio [OR]= 2.9, confidence interval [CI]= 1.8–3.7, P= 0.002). Regression analysis showed, increase in copies of minor alleles of 6,064(T>C) polymorphism associated with increased odds of adenoma development by 80% (OR = 1.80, CI = 1.09–3.21, P= 0.034), 10,848(G>A) by 84% (OR = 1.84, CI = 1.05–3.23, P= 0.034) and 10,935(A>G) by 32% (OR = 1.32, CI = 1.12–3.69, P= 0.036). These results support the hypothesis that COX‐2 gene might play a role in the etiology of colon cancer and warrant further investigation in other cancers. Besides, these variations should be taken into account for disease‐based association studies in which the COX‐2 polymorphism is considered as a candidate gene. Clin Trans Sci 2012; Volume 5: 60–64
Effect of pH on
In Vitro
Susceptibility of Candida glabrata and Candida albicans to 11 Antifungal Agents and Implications for Clinical Use
Authors: Danby Claire S. , Boikov Dina , Rautemaa-Richardson Rina , Sobel Jack D. 
Published: January 2012

ABSTRACT

The treatment of vulvovaginal candidiasis (VVC) due to
Candida glabrata
is challenging, with limited therapeutic options. Unexplained disappointing clinical efficacy has been reported with systemic and topical azole antifungal agents in spite of
in vitro
susceptibility. Given that the vaginal pH of patients with VVC is unchanged at 4 to 4.5, we studied the effect of pH on the
in vitro
activity of 11 antifungal agents against 40
C. glabrata
isolates and compared activity against 15 fluconazole-sensitive and 10 reduced-fluconazole-susceptibility
C. albicans
strains.
In vitro
susceptibility to flucytosine, fluconazole, voriconazole, posaconazole, itraconazole, ketoconazole, clotrimazole, miconazole, ciclopirox olamine, amphotericin B, and caspofungin was determined using the CLSI method for yeast susceptibility testing. Test media were buffered to pHs of 7, 6, 5, and 4. Under conditions of reduced pH,
C. glabrata
isolates remained susceptible to caspofungin and flucytosine; however, there was a dramatic increase in the MIC
90
for amphotericin B and every azole drug tested. Although susceptible to other azole drugs tested at pH 7,
C. albicans
strains with reduced fluconazole susceptibility also demonstrated reduced susceptibility to amphotericin B and all azoles at pH 4. In contrast, fluconazole-sensitive
C. albicans
isolates remained susceptible at low pH to azoles, in keeping with clinical observations. In selecting agents for treatment of recurrent
C. glabrata
vaginitis, clinicians should recognize the limitations of
in vitro
susceptibility testing utilizing pH 7.0.
Nonthermal Atmospheric Plasma Rapidly Disinfects Multidrug-Resistant Microbes by Inducing Cell Surface Damage
Authors: Kvam Erik , Davis Brian , Mondello Frank , Garner Allen L. 
Published: January 2012

ABSTRACT

Plasma, a unique state of matter with properties similar to those of ionized gas, is an effective biological disinfectant. However, the mechanism through which nonthermal or “cold” plasma inactivates microbes on surfaces is poorly understood, due in part to challenges associated with processing and analyzing live cells on surfaces rather than in aqueous solution. Here, we employ membrane adsorption techniques to visualize the cellular effects of plasma on representative clinical isolates of drug-resistant microbes. Through direct fluorescent imaging, we demonstrate that plasma rapidly inactivates planktonic cultures, with >5 log
10
kill in 30 s by damaging the cell surface in a time-dependent manner, resulting in a loss of membrane integrity, leakage of intracellular components (nucleic acid, protein, ATP), and ultimately focal dissolution of the cell surface with longer exposure time. This occurred with similar kinetic rates among methicillin-resistant
Staphylococcus aureus
(MRSA),
Pseudomonas aeruginosa
, and
Candida albicans
. We observed no correlative evidence that plasma induced widespread genomic damage or oxidative protein modification prior to the onset of membrane damage. Consistent with the notion that plasma is superficial, plasma-mediated sterilization was dramatically reduced when microbial cells were enveloped in aqueous buffer prior to treatment. These results support the use of nonthermal plasmas for disinfecting multidrug-resistant microbes in environmental settings and substantiate ongoing clinical applications for plasma devices.
In Vitro
Potential of Equine DEFA1 and eCATH1 as Alternative Antimicrobial Drugs in Rhodococcosis Treatment
Authors: Schlusselhuber Margot , Jung Sascha , Bruhn Oliver , Goux Didier , Leippe Matthias , Leclercq Roland , Laugier Claire , Grötzinger Joachim , Cauchard Julien 
Published: January 2012

ABSTRACT

Rhodococcus equi
, the causal agent of rhodococcosis, is a severe pathogen of foals but also of immunodeficient humans, causing bronchopneumonia. The pathogen is often found together with
Klebsiella pneumoniae
or
Streptococcus zooepidemicus
in foals. Of great concern is the fact that some
R. equi
strains are already resistant to commonly used antibiotics. In the present study, we evaluated the
in vitro
potential of two equine antimicrobial peptides (AMPs), eCATH1 and DEFA1, as new drugs against
R. equi
and its associated pathogens. The peptides led to growth inhibition and death of
R. equi
and
S. zooepidemicus
at low micromolar concentrations. Moreover, eCATH1 was able to inhibit growth of
K. pneumoniae
. Both peptides caused rapid disruption of the
R. equi
membrane, leading to cell lysis. Interestingly, eCATH1 had a synergic effect together with rifampin. Furthermore, eCATH1 was not cytotoxic against mammalian cells at bacteriolytic concentrations and maintained its high killing activity even at physiological salt concentrations. Our data suggest that equine AMPs, especially eCATH1, may be promising candidates for alternative drugs to control
R. equi
in mono- and coinfections.
Identification of salt-tolerant QTLs with strong genetic background effect using two sets of reciprocal introgression lines in rice
Authors: Cheng Lirui , Wang Yun , Meng Lijun , Hu Xia , Cui Yanru , Sun Yong , Zhu Linghua , Ali Jauhar , Xu Jianlong , Li Zhikang 
Published: January 2012

Effect of genetic background on detection of quantitative trait locus (QTL) governing salinity tolerance (ST) was studied using two sets of reciprocal introgression lines (ILs) derived from a cross between a moderately salinity tolerant japonica variety, Xiushui09 from China, and a drought tolerant but salinity susceptible indica breeding line, IR2061–520–6-9 from the Philippines. Salt toxicity symptoms (SST) on leaves, days to seedling survival (DSS), and sodium and potassium uptake by shoots were measured under salinity stress of 140 mmol/L of NaCl. A total of 47 QTLs, including 26 main-effect QTLs (M-QTLs) and 21 epistatic QTLs (E-QTLs), were identified from the two sets of reciprocal ILs. Among the 26 M-QTLs, only four (15.4%) were shared in the reciprocal backgrounds while no shared E-QTLs were detected, indicating that ST QTLs, especially E-QTLs, were very specific to the genetic background. Further, 78.6% of the M-QTLs for SST and DSS identified in the reciprocal ILs were also detected in the recombinant inbred lines (RILs) from the same cross, which clearly brings out the background effect on ST QTL detection and its utilization in ST breeding. The detection of ILs with various levels of pyramiding of nonallelic M-QTL alleles for ST from Xiushui09 into IR2061-520-6-9 allowed us to further improve the ST in rice.
Effect of inter-renal aortic coarctation-induced hypertension on function and expression of vascular α1A- and α1D-adrenoceptors
Authors: López-Islas Inés , López-Sánchez Pedro , Ibarra Maximiliano , Gallardo-Ortiz Itzell A. , Terrón José A. 
Published: January 2012

We investigated the effect of inter-renal aortic coarctation on the function and expression of vascular α1A- and α1D-adrenoceptors and plasma angiotensin II (ATII) in rats. Male Wistar rats, either sham operated (SO), or with aortic coarctation for 7 (AC7) and 14 days (AC14) were used for agonist-induced pressor responses in vehicle (physiological saline)- and antagonist-treated anesthetized animals, immunoblot analysis (α1A- and α1D-adrenoceptor in aorta and caudal arteries), and immunoassay (plasma ATII). The α1D-adrenoceptor antagonist, BMY-7378 (BMY) blocked noradrenaline-induced responses in the order SO > AC7 ≫ AC14; in contrast, the α1A-adrenoceptor antagonist RS-100329 (RS), produced a marginal shift to the right of the dose–response curve to noradrenaline, along with a strong decrease of the maximum pressor effect in the order SO > AC7 = AC14. The potency of the α1A-adrenoceptor agonist A-61603 increased in rats with AC14, and responses were inhibited by RS in the order AC14 > AC7 > SO. In aorta, α1D-adrenoceptor protein increased in AC7 and decreased in AC14; α1A-adrenoreceptor protein increased in the caudal artery of AC7 and returned to control values in AC14. Plasma ATII increased in AC7 and AC14, compared with SO rats. These results suggest an early and direct relationship between ATII and α1D-adrenoreceptors in the development of hypertension in this experimental model.
Effective focused retrieval by exploiting query context and document structure
Authors: Kaptein Rianne 
Published: January 2012

The classic IR model of the search process consists of three elements: query, documents and search results. A user looking to fulfil an information need formulates a query usually consisting of a small set of keywords summarising the information need. The goal of an IR system is to retrieve documents containing information which might be useful or relevant to the user. Throughout the search process there is a loss of focus, because keyword queries entered by users often do not suitably summarise their complex information needs, and IR systems do not sufficiently interpret the contents of documents, leading to result lists containing irrelevant and redundant information. The main research objective of this thesis is to exploit query context and document structure to provide for more focused retrieval.
The short keyword query used as input to the retrieval system can be supplemented with topic categories from structured Web resources such as DMOZ and Wikipedia. Topic categories can be used as query context to retrieve documents that are not only relevant to the query but also belong to a relevant topic category. Category information is especially useful for the task of entity ranking where the user is searching for a certain type of entity such as companies or persons. Category information can help to improve the search results by promoting in the ranking pages belonging to relevant topic categories, or categories similar to the relevant categories. By following external links and searching for the retrieved Wikipedia entities in a general Web collection, we can also exploit the structure of Wikipedia to rank entities on the general Web. Wikipedia, in contrast to the general Web, does not contain much redundant information. This absence of redundant information can be exploited by using Wikipedia as a pivot to search the general Web.
A typical query returns thousands or millions of documents, but searchers hardly ever look beyond the first result page. Since space on the result page is limited, we can show only a few documents in the result list. Word clouds can be used to summarise groups of documents into a set of keywords which allows users to quickly get a grasp on the underlying data. Instead of using user-assigned tags we generate word clouds from the textual contents of documents themselves as well as the anchor text ofWeb documents. Improvements over word clouds that are created using simple term frequency counting include using a parsimonious term weighting scheme, including bigrams and biasing the word cloud towards the query. We find that word clouds can to a certain degree quickly convey the topic and relevance of a set of search results. Available online at: http://dare.uva.nl/record/39569.
Hedgehog and Notch Signaling Regulate Self-Renewal of Undifferentiated Pleomorphic Sarcomas
Authors: Wang Chang Ye Yale , Wei Qingxia , Han Ilkyu , Sato Shingo , Azarnier Ronak Ghanbari- , Whetstone Heather , Poon Raymond , Hu Jiayi , Zheng Feifei , Zhang Phil , Wang Weishi , Wunder Jay S. , Alman Benjamin A. 
Published: January 2012

Abstract
Like many solid tumors, sarcomas are heterogeneous and include a small fraction of the so-called side population (SP) cells with stem-like tumor-initiating potential. Here, we report that SP cells from a soft tissue tumor of enigmatic origin termed undifferentiated pleomorphic sarcoma (also known as malignant fibrous histiocytoma or MFH sarcoma) display activation of both the Hedgehog and Notch pathways. Blockade to these pathways in murine xenograft models, this human cancer decreased the proportion of SP cells present and suppressed tumor self-renewal, as illustrated by the striking inability of xenograft tumors subjected to pathway blockade to be serially transplanted to new hosts. In contrast, conventional chemotherapies increased the proportion of SP cells present in tumor xenografts and did not affect their ability to be serially transplanted. SP cells from these tumors displayed an unexpectedly high proliferation rate which was selectively inhibited by Hedgehog and Notch blockade compared with conventional chemotherapies. Together, our findings deepen the concept that Hedgehog and Notch signaling are fundamental drivers of tumor self-renewal, acting in a small population of tumor-initiating cells present in tumors. Furthermore, our results suggest not only novel treatment strategies for deadly recurrent unresectable forms of this soft tumor subtype, but also potential insights into its etiology which has been historically controversial. Cancer Res; 72(4); 1013–22. ©2012 AACR.
Australian youth still have limited awareness of headspace: Results from a national survey
Authors: Yap Marie B , Reavley Nicola J , Jorm Anthony F 
Published: January 2012

Objectives: The aim of this paper is to assess Australian young people’s awareness of mental health services available for their age group. Of particular interest was awareness of headspace, which was created in 2006 to provide youth-oriented mental health services, and has expanded to 30 centres nationally in 5 years. Method: In 2011, a telephone interview was conducted with a national sample of 3021 Australians aged between 15 and 25 years. Participants were asked questions about awareness of mental health organizations, where they would seek help for themselves and how they would assist a peer with a mental health problem. Results: There were very low frequencies of spontaneous mentions of headspace as a mental health organization, or as a service where respondents would seek help for themselves or refer a peer to. However, when prompted, about half of respondents recognized headspace as a mental health organization. Living within a headspace service area predicted better recognition of headspace. However, past-year psychological distress was unrelated to recognition of headspace as a mental health organization. Conclusions: In order to reach them more effectively, young people need to be aware of youth-oriented services that are available to them and their peers. Awareness campaigns need to be targeted to the subgroups of young people who have the greatest need for headspace services, namely those with recent mental health problems.
Stereotaxic localisation of the dorsolateral prefrontal cortex for transcranial magnetic stimulation is superior to the standard reference position
Authors: Bradfield Nicholas I , Reutens David C , Chen Jian , Wood Amanda G 
Published: January 2012

Objective: To determine whether the standard method of localisation of the dorsolateral prefrontal cortex for repetitive transcranial magnetic stimulation is accurate and reliable, and to develop an empirically based method for operational localisation of the dorsolateral prefrontal cortex with reference to the motor hand area. Method: We compared stereotaxic localisation of the dorsolateral prefrontal cortex with the commonly used operational definition of 6 cm anterior to the site of the abductor pollicis brevis muscle in healthy participants ( n = 18). We also report the average translational distance from the site of the abductor pollicis brevis to the stereotaxically defined dorsolateral prefrontal cortex. Results: The stereotaxic method was less variable than the operational method of localisation and more frequently targeted the middle frontal gyrus. The average translational distance from the site of the abductor pollicis brevis to the stereotaxically targeted dorsolateral prefrontal cortex was x = −5 mm, y = 53 mm and z = −31 mm. Conclusions: Operational localisation of the dorsolateral prefrontal cortex for repetitive transcranial magnetic stimulation with reference to the motor hand area is more variable than stereotaxic localisation. If future studies choose to use an operational definition of the left dorsolateral prefrontal cortex, we suggest it should be 5 mm lateral, 53 mm anterior and 31 mm inferior to the site of the abductor pollicis brevis.