bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of a screening tool for detection of sleep-disordered breathing
Authors: Clark A L , Crabbe S , Aziz A , Reddy P , Greenstone M 
Published: February 2009

AbstractBackground:Sleep apnoea, whether obstructive or central, is usually diagnosed by polysomnography. A simpler tool for screening high risk populations may be of value.Methods:We compared a portable device using nasal pressure cannulae and a high-sensitivity pressure sensor (the ApneaLink®) with our standard polysomnography technique for diagnosing sleep apnoea (using the Embletta® device), in 67 patients being investigated for possible sleep apnoea. The patients' average age was 52.6, 79 per cent were male, the mean body mass index was 32.3, and the mean Epworth sleepiness score was 13.0.Results:Twenty-five patients (45 per cent) were identified as having an apnoea–hypopnoea index of >15, as measured by the Embletta. The mean (standard deviation) apnoea–hypopnoea index was 21.5 ± 23.0 as measured by the Embletta and 24.3 ± 26.2 as measured by the ApneaLink. The sensitivity of the ApneaLink for an apnoea–hypopnoea index cut-off point of 15 was 92 per cent and the specificity was 96.7 per cent. The negative predictive value of the ApneaLink for an apnoea–hypopnoea index of ≤15 was 94 per cent.Conclusions:The ApneaLink is a useful tool for screening patients thought to have possible sleep apnoea, and for selecting patients for definitive diagnostic testing.
The politics of anti-corruption reform in Africa
Authors: Lawson Letitia 
Published: February 2009

ABSTRACTPrevious research on anti-corruption reform in Africa falls into two camps. The first explores ‘best practices’ and policy approaches to controlling corruption, while the second focuses on the politics of anti-corruption ‘reform’, arguing that official anti-corruption campaigns aim to mollify donors while using corruption charges instrumentally to undermine rivals and shore up personal loyalty to the president, and thus have no chance of controlling corruption. This paper suggests that, while the neopatrimonial context is a very significant limiting factor in anti-corruption reform, limited progress is possible. Examining the motivations and effects, intended and unintended, of anti-corruption reforms in Kenya and Nigeria, it finds that while the Kenya Anti-Corruption Commission has indeed been politically marginalised and largely ineffectual, the more autonomous and activist, but politically instrumentalised, Economic and Financial Crimes Commission in Nigeria has had a measure of success. The analysis suggests that this is explained by the EFCC's independent prosecutorial powers and the institutionalisation strategies of its chairman.
Phase stabilization of the amplitude dividing four-beam combined laser system using stimulated Brillouin scattering phase conjugate mirrors
Authors: Kong H.J. , Shin J.S. , Yoon J.W. , Beak D.H. 
Published: February 2009

AbstractThe beam combination method using stimulated Brillouin scattering phase conjugate mirrors (SBS-PCMs) is a promising technique for a high energy and high power laser output operating with a high repetition rate. The two-beam combined system was previously demonstrated with an amplitude dividing method. A four-beam combined laser system with amplitude dividing method is demonstrated in this work, and the phase stabilization experiment of this system is performed using the self phase control and the long-term stabilization technique. The phase differences between the SBS waves are stabilized with λ/30 and the fluctuation of the four-beam combined output energy is 6.16% during 2000 shots (200 s).
Results from a 15-year study on hydrocarbon concentrations in water and sediment from Admiralty Bay, King George Island, Antarctica
Authors: Bícego Márcia C. , Zanardi-Lamardo Eliete , Taniguchi Satie , Martins César C. , da Silva Denis A.M. , Sasaki Sílvio T. , Albergaria-Barbosa Ana C.R. , Paolo Fernando S. , Weber Rolf R. , Montone Rosalinda C. 
Published: February 2009

AbstractAdmiralty Bay on the King George Island hosts the Brazilian, Polish and Peruvian research stations as well as the American and Ecuadorian field stations. Human activities in this region require the use of fossil fuels as an energy source, thereby placing the region at risk of hydrocarbon contamination. Hydrocarbon monitoring was conducted on water and sediment samples from the bay over 15 years. Fluorescence spectroscopy was used for the analysis of total polycyclic aromatic hydrocarbons (PAHs) in seawater samples and gas chromatography with flame ionization and/or mass spectrometric detection was used to analyse individual n-alkanes and PAHs in sediment samples. The results revealed that most sites contaminated by these compounds are around the Brazilian and Polish research stations due to the intense human activities, mainly during the summer. Moreover, the sediments revealed the presence of hydrocarbons from different sources, suggesting a mixture of the direct input of oil or derivatives and derived from hydrocarbon combustion. A decrease in PAH concentrations occurred following improvement of the sewage treatment facilities at the Brazilian research station, indicating that the contribution from human waste may be significant.
Expression of voltage-activated calcium channels in the early zebrafish embryo
Authors: Sanhueza Dayán , Montoya Andro , Sierralta Jimena , Kukuljan Manuel 
Published: February 2009

SummaryIncreases in cytosolic calcium concentrations regulate many cellular processes, including aspects of early development. Calcium release from intracellular stores and calcium entry through non-voltage-gated channels account for signalling in non-excitable cells, whereas voltage-gated calcium channels (CaV) are important in excitable cells. We report the expression of multiple transcripts of CaV, identified by its homology to other species, in the early embryo of the zebrafish,Danio rerio, at stages prior to the differentiation of excitable cells. CaV mRNAs and proteins were detected as early as the 2-cell stages, which indicate that they arise from both maternal and zygotic transcription. Exposure of embryos to pharmacological blockers of CaV does not perturb early development significantly, although late effects are appreciable. These results suggest that CaV may have a role in calcium homeostasis and control of cellular process during early embryonic development.
Connexin37 mRNA expression in in vivo and in vitro mouse oocyte
Authors: Yin Bao Ying , Zhang Yong , Sun Jian Hong , Li Ji Xia , Ma Ye Fei 
Published: February 2009

SummaryTo evaluate gene expression of Connexin37 (Cx37) in oocytes from in vitro follicles at different stages, mouse preantral follicles were isolated and cultured for 12 days in vitro. Compared with in vitro follicles, follicles grown in vivo were collected at day 14 (d14), d16, d18, d20, d22 and d24 with the same stages for gene expression of Cx37 in oocytes. Our results showed that Cx37 mRNA increased along with follicular development, reached the highest level at the onset of antrum cavity formation and decreased after antrum formation in both in vivo and in vitro mouse oocytes. However, Cx37 mRNA was significant higher (p < 0.01) in in vitro cultured oocytes than in vivo oocytes. Moreover, significantly higher levels of Cx37 mRNA were found in oocytes from in vitro disrupted follicles (p < 0.01) and non-grown follicles (p < 0.05) than those from normal follicles with a similar size. These data determine temporal gene expression of Cx37 in oocytes from follicules at different stages and indicate that the gene expression level of Cx37 in oocytes could be evaluated as a criterion to the regulatory mechanism of Cx37 in an in vitro model.
A non-termination criterion for binary constraint logic programs
Authors: PAYET ÉTIENNE , MESNARD FRED 
Published: February 2009

AbstractOn the one hand, termination analysis of logic programs is now a fairly established research topic within the logic programming community. On the other hand, non-termination analysis seems to remain a much less attractive subject. If we divide this line of research into two kinds of approaches, dynamic versus static analysis, this paper belongs to the latter. It proposes a criterion for detecting non-terminating atomic queries with respect to binary constraint logic programming (CLP) rules, which strictly generalizes our previous works on this subject. We give a generic operational definition and an implemented logical form of this criterion. Then we show that the logical form is correct and complete with respect to the operational definition.
Asymptotic depth of twisted higher direct image sheaves
Authors: Bär Renate , Brodmann Markus 
Published: February 2009

Let

π
:
X
→

X

0

\pi :X \rightarrow X_{0}

be a projective morphism of schemes, such that

X

0

X_{0}

is Noetherian and essentially of finite type over a field

K
K

. Let

i
∈

N

0

i \in \mathbb {N}_{0}

, let

F

{\mathcal {F}}

be a coherent sheaf of

O

X

{\mathcal {O}}_{X}

-modules and let

L

{\mathcal {L}}

be an ample invertible sheaf over

X
X

. Let

Z

0

⊆

X

0

Z_{0} \subseteq X_{0}

be a closed set. We show that the depth of the higher direct image sheaf

R

i

π

∗

(

L

n

⊗

O

X

F

)

{\mathcal {R}}^{i}\pi _{*}({\mathcal {L}}^{n} \otimes _{{\mathcal {O}}_{X}} {\mathcal {F}})

along

Z

0

Z_{0}

ultimately becomes constant as

n
n

tends to

−
∞

-\infty

, provided

X

0

X_{0}

has dimension

≤
2

\leq 2

. There are various examples which show that the mentioned asymptotic stability may fail if

dim
⁡
(

X

0

)
≥
3

\dim (X_{0}) \geq 3

. To prove our stability result, we show that for a finitely generated graded module

M
M

over a homogeneous Noetherian ring

R
=

⨁

n
≥
0

R

n

R=\bigoplus _{n \geq 0}R_{n}

for which

R

0

R_{0}

is essentially of finite type over a field and an ideal

a

0

⊆

R

0

\mathfrak {a}_{0} \subseteq R_{0}

, the

a

0

\mathfrak {a}_{0}

-depth of the

n
n

-th graded component

H

R

+

i

(
M

)

n

H^{i}_{R_{+}}(M)_{n}

of the

i
i

-th local cohomology module of

M
M

with respect to

R

+

:=

⨁

k
>
0

R

k

R_{+}:=\bigoplus _{k>0}R_{k}

ultimately becomes constant in codimension

≤
2

\leq 2

as

n
n

tends to

−
∞

-\infty

.
The ghost dimension of a ring
Authors: Hovey Mark , Lockridge Keir 
Published: February 2009

We introduce the concept of the ghost dimension gh.dim.

R
R

of a ring

R
R

. This is the longest nontrivial chain of maps in the derived category emanating from a perfect complex such that each map is zero on homology. We show that w.dim.

R
≤

R\leq

gh.dim.

R
R

with equality if

R
R

is coherent or w.dim.

R
=
1

R=1

.
Cyclic behavior of the Cesàro operator on 𝐿₂(0,∞)
Authors: González M. , León-Saavedra F. 
Published: February 2009

In this paper we study the cyclic properties of the infinite continuous Cesàro operator defined on

L
2

(
0
,
∞
)

L^2(0,\infty )

by

(

C
∞

f
)
(
x
)
=

1
x

∫
0
x

f
(
s
)
d
s

(C_\infty f)(x)=\frac {1}{x}\int _0^x f(s) ds

. Despite this operator being cyclic, we show that it is not supercyclic; even more, it is not weakly supercyclic. These results complement some recent ones on the cyclic behavior of Cesàro operators.
M are better than one: an ensemble-based motif finder and its application to regulatory element prediction
Authors: Yanover Chen , Singh Mona , Zaslavsky Elena 
Published: February 2009

Abstract
Motivation: Identifying regulatory elements in genomic sequences is a key component in understanding the control of gene expression. Computationally, this problem is often addressed by motif discovery, where the goal is to find a set of mutually similar subsequences within a collection of input sequences. Though motif discovery is widely studied and many approaches to it have been suggested, it remains a challenging and as yet unresolved problem.
Results: We introduce SAMF (Solution-Aggregating Motif Finder), a novel approach for motif discovery. SAMF is based on a Markov Random Field formulation, and its key idea is to uncover and aggregate multiple statistically significant solutions to the given motif finding problem. In contrast to many earlier methods, SAMF does not require prior estimates on the number of motif instances present in the data, is not limited by motif length, and allows motifs to overlap. Though SAMF is broadly applicable, these features make it particularly well suited for addressing the challenges of prokaryotic regulatory element detection. We test SAMF's ability to find transcription factor binding sites in an Escherichia coli dataset and show that it outperforms previous methods. Additionally, we uncover a number of previously unidentified binding sites in this data, and provide evidence that they correspond to actual regulatory elements.
Contact: cyanover@fhcrc.org, msingh@cs.princeton.edu,elenaz@cs.princeton.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A new ensemble-based algorithm for identifying breath gas marker candidates in liver disease using ion molecule reaction mass spectrometry
Authors: Netzer M. , Millonig G. , Osl M. , Pfeifer B. , Praun S. , Villinger J. , Vogel W. , Baumgartner C. 
Published: February 2009

Abstract
Motivation: Alcoholic fatty liver disease (AFLD) and non-AFLD (NAFLD) can progress to severe liver diseases such as steatohepatitis, cirrhosis and cancer. Thus, the detection of early liver disease is essential; however, minimal invasive diagnostic methods in clinical hepatology still lack specificity.
Results: Ion molecule reaction mass spectrometry (IMR-MS) was applied to a total of 126 human breath gas samples comprising 91 cases (AFLD, NAFLD and cirrhosis) and 35 healthy controls. A new feature selection modality termed Stacked Feature Ranking (SFR) was developed to identify potential liver disease marker candidates in breath gas samples, relying on the combination of different entropy- and correlation-based feature ranking methods including statistical hypothesis testing using a two-level architecture with a suggestion and a decision layer. We benchmarked SFR against four single feature selection methods, a wrapper and a recently described ensemble method, indicating a significantly higher discriminatory ability of up to 10–15% for the SFR selected gas compounds expressed by the area under the ROC curve (AUC) of 0.85–0.95. Using this approach, we were able to identify unexpected breath gas marker candidates in liver disease of high predictive value. A literature study further supports top-ranked markers to be associated with liver disease. We propose SFR as a powerful tool for biomarker search in breath gas and other biological samples using mass spectrometry.
Availability: The algorithm SFR and IMR-MS datasets are available under http://biomed.umit.at/page.cfm?pageid=526
Contact: michalel.netzer@umit.at; christian.baumgartner@umit.at
Benthic impacts of recreational divers in a Mediterranean Marine Protected Area
Authors: Luna Beatriz , Pérez Carlos Valle , Sánchez-Lizaso Jose Luis 
Published: February 2009

Abstract
Luna, B., Valle Pérez, C., and Sánchez-Lizaso, J. L. 2009. Benthic impacts of recreational divers in a Mediterranean Marine Protected Area. – ICES Journal of Marine Science, 66: 517–523. The features of many Marine Protected Areas (MPAs) have increased scuba diving tourism in these areas. Impacts caused by recreational scuba activity vary widely among different divers with differing underwater behaviour. We studied diver underwater behaviour, the effects on the natural environment, and the characteristics that may influence diver behaviour. In all, 181 recreational divers were followed, and contacts and the effects produced were recorded. Information on diver profile and dive features was recorded. Field sampling revealed that 175 of the divers observed (96.7%) made at least one contact with the seabed, with a mean contact of 41.20 ± 3.55 (mean ± s.e.) per diver per 10 min. Flapping was the most frequent type of contact, and the main damage by this action was to raise sediment. Contact with the seabed was greater for males than for females, inexperienced divers than for experienced divers, camera or lantern (dive light) users than for non-users, and divers unaccompanied by a dive leader or who had not been briefed about avoiding seabed contact before undertaking a dive than for accompanied or briefed divers. A greater understanding of the causes of harmful behaviour may be useful for stricter management, reducing diving damage and assuring the sustainability of this activity in MPAs.
TheArabidopsisProteasome RPT5 Subunits Are Essential for Gametophyte Development and Show Accession-Dependent Redundancy
Authors: Gallois Jean-Luc , Guyon-Debast Anouchka , Lécureuil Alain , Vezon Daniel , Carpentier Virginie , Bonhomme Sandrine , Guerche Philippe 
Published: February 2009

AbstractWe investigated the role of the ubiquitin proteasome system (UPS), which allows proteins to be selectively degraded, during gametophyte development in Arabidopsis thaliana. Three mutant alleles altering the UPS were isolated in the Wassilewskija (Ws) accession: they affect the Regulatory Particle 5a (RPT5a) gene, which (along with RPT5b) encodes one of the six AAA-ATPases of the proteasome regulatory particle. In the heterozygous state, all three mutant alleles displayed 50% pollen lethality, suggesting that RPT5a is essential for male gametophyte development. However, a fourth mutant in the Columbia (Col) accession did not display such a phenotype because the RPT5b Col allele complements the rpt5a defect in the male gametophyte, whereas the RPT5b Ws allele does not. Double rpt5a rpt5b mutants showed a complete male and female gametophyte lethal phenotype in a Col background, indicating that RPT5 subunits are essential for both gametophytic phases. Mitotic divisions were affected in double mutant gametophytes correlating with an absence of the proteasome-dependent cyclinA3 degradation. Finally, we show that RPT5b expression is highly increased when proteasome functioning is defective, allowing complementation of the rpt5a mutation. In conclusion, RPT5 subunits are not only essential for both male and female gametophyte development but also display accession-dependent redundancy and are crucial in cell cycle progression.
Arabidopsis Photorespiratory Serine Hydroxymethyltransferase Activity Requires the Mitochondrial Accumulation of Ferredoxin-Dependent Glutamate Synthase
Authors: Jamai Aziz , Salomé Patrice A. , Schilling Stephen H. , Weber Andreas P.M. , McClung C. Robertson 
Published: February 2009

Abstract
The dual affinity of ribulose-1,5-bisphosphate carboxylase/oxygenase for O2 and CO2 results in the net loss of fixed carbon and energy in a process termed photorespiration. The photorespiratory cycle is complex and occurs in three organelles, chloroplasts, peroxisomes, and mitochondria, which necessitates multiple steps to transport metabolic intermediates. Genetic analysis has identified a number of mutants exhibiting photorespiratory chlorosis at ambient CO2, including several with defects in mitochondrial serine hydroxymethyltransferase (SHMT) activity. One class of mutants deficient in SHMT1 activity affects SHM1, which encodes the mitochondrial SHMT required for photorespiration. In this work, we describe a second class of SHMT1-deficient mutants defective in a distinct gene, GLU1, which encodes Ferredoxin-dependent Glutamate Synthase (Fd-GOGAT). Fd-GOGAT is a chloroplastic enzyme responsible for the reassimilation of photorespiratory ammonia as well as for primary nitrogen assimilation. We show that Fd-GOGAT is dual targeted to the mitochondria and the chloroplasts. In the mitochondria, Fd-GOGAT interacts physically with SHMT1, and this interaction is necessary for photorespiratory SHMT activity. The requirement of protein–protein interactions and complex formation for photorespiratory SHMT activity demonstrates more complicated regulation of this crucial high flux pathway than anticipated.
Crystal structure of trypanosoma cruzi tyrosine aminotransferase: Substrate specificity is influenced by cofactor binding mode
Authors: Blankenfeldt Wulf , Montemartini‐Kalisz Marisa , Kalisz Henryk M. , Hecht Hans‐Jürgen , Nowicki Cristina 
Published: February 2009

AbstractThe crystal structure of tyrosine aminotransferase (TAT) from the parasitic protozoan Trypanosoma cruzi, which belongs to the aminotransferase subfamily Iγ, has been determined at 2.5 Å resolution with the R‐value R = 15.1%. T. cruzi TAT shares less than 15% sequence identity with aminotransferases of subfamily Iα but shows only two larger topological differences to the aspartate aminotransferases (AspATs). First, TAT contains a loop protruding from the enzyme surface in the larger cofactor‐binding domain, where the AspATs have a kinked α‐helix. Second, in the smaller substrate‐binding domain, TAT has a four‐stranded antiparallel β‐sheet instead of the two‐stranded β‐sheet in the AspATs. The position of the aromatic ring of the pyridoxal‐5′‐phosphate cofactor is very similar to the AspATs but the phosphate group, in contrast, is closer to the substrate‐binding site with one of its oxygen atoms pointing toward the substrate. Differences in substrate specificities of T. cruzi TAT and subfamily Iα aminotransferases can be attributed by modeling of substrate complexes mainly to this different position of the cofactor‐phosphate group. Absence of the arginine, which in the AspATs fixes the substrate side‐chain carboxylate group by a salt bridge, contributes to the inability of T. cruzi TAT to transaminate acidic amino acids. The preference of TAT for tyrosine is probably related to the ability of Asn17 in TAT to form a hydrogen bond to the tyrosine side‐chain hydroxyl group.
Carbocations in the synthesis of prostaglandins by the cyclooxygenase of pgh synthase? a radical departure!
Authors: Dean Antony M. , Dean Francis M. 
Published: February 2009

AbstractEvidence already available is used to demonstrate that although prostaglandin G/H synthase hydroxylates arachidonic acid through radical intermediates, it effects cyclizations through a carbocation center at C‐10. This is produced following migration of H to the initial radical at C‐13 and a 1 oxidation. Under orbital symmetry control, the cyclizations can give only the ring size andtransstereochemistry actually observed. After cyclization, the H‐shift reverses to take the sequence back into current radical theory for hydroxylation at C‐15. Thus 10, 10‐difluoroarachidonic acid cannot be cyclized, although it can be hydroxylated. Acetylation of Ser516 in the isoform synthase‐2 is considered to oppose carbocation formation and/or H‐migration and so prevent cyclizations while permitting hydroxylations; the associated inversion of chirality at C‐15 can then readily be accommodated without the change in conformation required by other schemes. Suicide inhibition occurs when carbocations form stable bonds upon (thermal) contact with adjacent heteroatoms, etc. Because the cyclooxygenase and peroxidase functions operate simultaneously through the same heme, phenol acts as reducing cosubstrate for the cyclooxygenase, thus enabling it to promote PGG2production and protect the enzyme from oxidative destruction.