bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of nif gene expression and the energetics of N2 fixation over the diel cycle in a hot spring microbial mat
Authors: Steunou Anne-Soisig , Jensen Sheila I , Brecht Eric , Becraft Eric D , Bateson Mary M , Kilian Oliver , Bhaya Devaki , Ward David M , Peters John W , Grossman Arthur R , Kühl Michael 
Published: March 2008

Abstract
Nitrogen fixation, a prokaryotic, O2-inhibited process that reduces N2 gas to biomass, is of paramount importance in biogeochemical cycling of nitrogen. We analyzed the levels of nif transcripts of Synechococcus ecotypes, NifH subunit and nitrogenase activity over the diel cycle in the microbial mat of an alkaline hot spring in Yellowstone National Park. The results showed a rise in nif transcripts in the evening, with a subsequent decline over the course of the night. In contrast, immunological data demonstrated that the level of the NifH polypeptide remained stable during the night, and only declined when the mat became oxic in the morning. Nitrogenase activity was low throughout the night; however, it exhibited two peaks, a small one in the evening and a large one in the early morning, when light began to stimulate cyanobacterial photosynthetic activity, but O2 consumption by respiration still exceeded the rate of O2 evolution. Once the irradiance increased to the point at which the mat became oxic, the nitrogenase activity was strongly inhibited. Transcripts for proteins associated with energy-producing metabolisms in the cell also followed diel patterns, with fermentation-related transcripts accumulating at night, photosynthesis- and respiration-related transcripts accumulating during the day and late afternoon, respectively. These results are discussed with respect to the energetics and regulation of N2 fixation in hot spring mats and factors that can markedly influence the extent of N2 fixation over the diel cycle.
Iterating the Cesàro operators
Authors: Galaz Fontes Fernando , Solís Francisco 
Published: March 2008

The discrete Cesàro operator

C
C

associates to a given complex sequence

s
=
{

s
n

}

s = \{s_n\}

the sequence

C
s
≡
{

b
n

}

Cs \equiv \{b_n \}

, where

b
n

=

s
0

+
⋯
+

s
n

n
+
1

,
n
=
0
,
1
,
…

b_n = \frac {s_0 + \dots + s_n}{n +1}, n = 0, 1, \ldots

. When

s
s

is a convergent sequence we show that

{

C
n

s
}

\{C^n s \}

converges under the sup-norm if, and only if,

s
0

=

lim

n
→
∞

s
n

s_0 = \lim _{n\rightarrow \infty } s_n

. For its adjoint operator

C
∗

C^*

, we establish that

{
(

C
∗

)
n

s
}

\{(C^*)^n s\}

converges for any

s
∈

ℓ
1

s \in \ell ^1

. The continuous Cesàro operator,

C

f
(
x
)

≡

1
x

∫

0

x

f
(
s
)
d
s

C\!f (x) \ \equiv \ \frac {1}{x} \int _{0}^ {x}\, f(s) ds

, has two versions: the finite range case is defined for

f
∈

L
∞

(
0
,
1
)

f \in L^\infty (0,1)

and the infinite range case for

f
∈

L
∞

(
0
,
∞
)

f \in L^\infty (0, \infty )

. In the first situation, when

f
:
[
0
,
1
]
→

C

f: [0, 1] \rightarrow \mathbb {C}

is continuous we prove that

{

C
n

f
}

\{C^n f \}

converges under the sup-norm to the constant function

f
(
0
)

f(0)

. In the second situation, when

f
:
[
0
,
∞
)
→

C

f: [0, \infty )\rightarrow \mathbb {C}

is a continuous function having a limit at infinity, we prove that

{

C
n

f
}

\{C^n f \}

converges under the sup-norm if, and only if,

f
(
0
)
=

lim

x
→
∞

f
(
x
)

f(0) = \lim _{x\rightarrow \infty }f(x)

.
On Mirković-Vilonen cycles and crystal combinatorics
Authors: Baumann Pierre , Gaussent Stéphane 
Published: March 2008

Let

G
G

be a complex connected reductive group and let

G

∨

G^{\vee }

be its Langlands dual. Let us choose a triangular decomposition

n

−
,

∨

⊕

h

∨

⊕

n

+
,

∨

{\mathfrak n}^{-,{\vee }} \oplus {\mathfrak h}^{\vee }\oplus {\mathfrak n}^{+,{\vee }}

of the Lie algebra of

G

∨

G^{\vee }

. Braverman, Finkelberg and Gaitsgory show that the set of all Mirković-Vilonen cycles in the affine Grassmannian

G

(

C

(
(
t
)
)

)

/

G

(

C

[
[
t
]
]

)

G\bigl (\mathbb C((t))\bigr )/G\bigl (\mathbb C[[t]]\bigr )

is a crystal isomorphic to the crystal of the canonical basis of

U
(

n

+
,

∨

)

U({\mathfrak n}^{+,{\vee }})

. Starting from the string parameter of an element of the canonical basis, we give an explicit description of a dense subset of the associated MV cycle. As a corollary, we show that the varieties involved in Lusztig’s algebraic-geometric parametrization of the canonical basis are closely related to MV cycles. In addition, we prove that the bijection between LS paths and MV cycles constructed by Gaussent and Littelmann is an isomorphism of crystals.
Inference of biochemical network models in S-system using multiobjective optimization approach
Authors: Liu Pang-Kai , Wang Feng-Sheng 
Published: March 2008

Abstract
Motivation: The inference of biochemical networks, such as gene regulatory networks, protein–protein interaction networks, and metabolic pathway networks, from time-course data is one of the main challenges in systems biology. The ultimate goal of inferred modeling is to obtain expressions that quantitatively understand every detail and principle of biological systems. To infer a realizable S-system structure, most articles have applied sums of magnitude of kinetic orders as a penalty term in the fitness evaluation. How to tune a penalty weight to yield a realizable model structure is the main issue for the inverse problem. No guideline has been published for tuning a suitable penalty weight to infer a suitable model structure of biochemical networks.
Results: We introduce an interactive inference algorithm to infer a realizable S-system structure for biochemical networks. The inference problem is formulated as a multiobjective optimization problem to minimize simultaneously the concentration error, slope error and interaction measure in order to find a suitable S-system model structure and its corresponding model parameters. The multiobjective optimization problem is solved by the ε-constraint method to minimize the interaction measure subject to the expectation constraints for the concentration and slope error criteria. The theorems serve to guarantee the minimum solution for the ε-constrained problem to achieve the minimum interaction network for the inference problem. The approach could avoid assigning a penalty weight for sums of magnitude of kinetic orders.
Contact: chmfsw@ccu.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
e-LiSe—an online tool for finding needles in the ‘(Medline) haystack’
Authors: Gladki Arek , Siedlecki Pawel , Kaczanowski Szymon , Zielenkiewicz Piotr 
Published: March 2008

Abstract
Summary: Using literature databases one can find not only known and true relations between processes but also less studied, non-obvious associations. The main problem with discovering such type of relevant biological information is ‘selection’. The ability to distinguish between a true correlation (e.g. between different types of biological processes) and random chance that this correlation is statistically significant is crucial for any bio-medical research, literature mining being no exception. This problem is especially visible when searching for information which has not been studied and described in many publications. Therefore, a novel bio-linguistic statistical method is required, capable of ‘selecting’ true correlations, even when they are low-frequency associations. In this article, we present such statistical approach based on Z-score and implemented in a web-based application ‘e-LiSe’.
Availability: The software is available at http://miron.ibb.waw.pl/elise/
Contact: piotr@ibb.waw.pl
Supplementary information: Supplementary materials are available at http://miron.ibb.waw.pl/elise/supplementary/
Global zoogeography of fragile macrozooplankton in the upper 100–1000 m inferred from the underwater video profiler
Authors: Stemmann Lars , Youngbluth Marsh , Robert Kevin , Hosia Aino , Picheral Marc , Paterson Harriet , Ibanez Frederic , Guidi Lionel , Lombard Fabien , Gorsky Gabriel 
Published: March 2008

AbstractStemmann, L., Youngbluth, M., Robert, K., Hosia, A., Picheral, M., Paterson, H., Ibanez, F., Guidi, L., Lombard, F., and Gorsky, G. 2008. Global zoogeography of fragile macrozooplankton in the upper 100–1000 m inferred from the underwater video profiler. – ICES Journal of Marine Science, 65: 433–442. Mesopelagic gelatinous zooplankton fauna are insufficiently known because of inappropriate and infrequent sampling, but may have important trophic roles. In situ imaging systems and undersea vehicles have been used to investigate their diversity, distribution, and abundance. The use of different platforms, however, restricts the comparison of data from different regions. Starting in 2001, the underwater video profiler (UVP) was deployed during 12 cruises in six oceanic regimes (Mediterranean Sea, North Atlantic shelves, Mid-Atlantic Ridge, tropical Pacific Ocean, eastern Indian Ocean, and Subantarctic Ocean) to determine the vertical distribution of organisms in the upper 1000 m. Nine oceanic regions were identified based on the hydrological properties of the water column. They correspond to nine of the biogeochemical provinces defined by Longhurst. In all, 21 morphotypes were recognized: sarcodines (eight groups), ctenophores (two groups), siphonophores, medusae (five groups), crustaceans (one group), chaetognaths, appendicularians, salps, and fish. The similarity in the community assemblages of zooplankton in the 100–1000 m layer was significantly greater within regions than between regions, in most cases. The regions with comparable composition were located in the North Atlantic with adjacent water masses, suggesting that the assemblages were either mixed by advective transport or that environmental conditions were similar in mesopelagic layers. The data suggest that the spatial structuring of mesopelagic macrozooplankton occurs on large scales (e.g. basin scales) but not necessarily on smaller scales (e.g. oceanic front).
Arabidopsis Ribosomal Proteins RPL23aA and RPL23aB Are Differentially Targeted to the Nucleolus and Are Disparately Required for Normal Development
Authors: Degenhardt Rory F. , Bonham-Smith Peta C. 
Published: March 2008

AbstractProtein synthesis is catalyzed by the ribosome, a two-subunit enzyme comprised of four ribosomal RNAs and, in Arabidopsis (Arabidopsis thaliana), 81 ribosomal proteins (r-proteins). Plant r-protein genes exist as families of multiple expressed members, yet only one r-protein from each family is incorporated into any given ribosome, suggesting that many r-protein genes may be functionally redundant or development/tissue/stress specific. Here, we characterized the localization and gene-silencing phenotypes of a large subunit r-protein family, RPL23a, containing two expressed genes (RPL23aA and RPL23aB). Live cell imaging of RPL23aA and RPL23aB in tobacco with a C-terminal fluorescent-protein tag demonstrated that both isoforms accumulated in the nucleolus; however, only RPL23aA was targeted to the nucleolus with an N-terminal fluorescent protein tag, suggesting divergence in targeting efficiency of localization signals. Independent knockdowns of endogenous RPL23aA and RPL23aB transcript levels using RNA interference determined that an RPL23aB knockdown did not alter plant growth or development. Conversely, a knockdown of RPL23aA produced a pleiotropic phenotype characterized by growth retardation, irregular leaf and root morphology, abnormal phyllotaxy and vasculature, and loss of apical dominance. Comparison to other mutants suggests that the phenotype results from reduced ribosome biogenesis, and we postulate a link between biogenesis, microRNA-target degradation, and maintenance of auxin homeostasis. An additional RNA interference construct that coordinately silenced both RPL23aA and RPL23aB demonstrated that this family is essential for viability.
Loss of phospholipid membrane asymmetry and sialylated glycoconjugates from erythrocyte surface in haemoglobin E β‐thalassaemia
Authors: Basu Sumanta , Banerjee Debasis , Chandra Sarmila , Chakrabarti Abhijit 
Published: March 2008

SummaryThis study aimed to investigate any correlation between the extent of phosphatidylserine (PS) asymmetry and sialylated glycoconjugate levels with the faster clearance of circulating erythrocytes in haemoglobin E (HbE) β‐thalassaemia. Erythrocytes from peripheral blood samples of different HbEβ‐thalassaemia patients showed loss of PS asymmetry measured by annexin V binding using flow cytometry. Maximum PS exposure was found when HbE was 50–60% and HbF was <20% indicating a possible correlation with severity of the disease. Separation of erythrocytes into aged and younger cells showed higher loss of PS asymmetry in the younger erythrocytes of HbEβ‐thalassaemia patients when compared with normal blood, where PS asymmetry was lost only in the older cells. Sialylated glycoconjugate measurement using the lectins wheatgerm agglutinin and pokeweed mitogen showed loss of sialic acid and N‐acetyl‐d‐glucosamine‐bearing glycoproteins in the order normal<homozygous E<HbEβ‐thalassaemic upon ageing. A possible correlation was found between the loss of PS asymmetry with HbE level and the reduction of glycophorins from the cell surface, mediated by membrane vesiculation. A more facilitated vesiculation process in HbEβ‐thalassaemic erythrocytes could lead to faster shedding of glycophorin‐containing microvesicles, leaving highly PS‐exposed erythrocytes accessible to phagocytes.
Expression of the human germinal‐centre‐associated lymphoma protein in diffuse large B‐cell lymphomas in patients with rheumatoid arthritis
Authors: Baecklund Eva , Natkunam Yasodha , Backlin Carin , Iliadou Anastasia , Askling Johan , Ekbom Anders , Feltelius Nils , Klareskog Lars , Enblad Gunilla , Lossos Izidore S. , Levy Ronald , Sundström Christer , Rosenquist Richard 
Published: March 2008

SummaryDiffuse large B‐cell lymphomas (DLBCL) can be subdivided into germinal centre (GC)‐like and non‐GC‐like subtypes by CD10, BCL6 and MUM1/IRF4 status. We previously reported that patients with severe rheumatoid arthritis (RA) are at increased risk of non‐GC DLBCL. This study examined a new GC‐marker, human germinal‐centre‐associated lymphoma (HGAL) protein, in RA‐DLBCL. Of 111, 38 (34%) DLBCL were HGAL‐positive and showed less disseminated disease and a tendency toward improved overall survival compared to HGAL‐negative cases. This supports that a majority of RA‐DLBCL are of non‐GC origin, indicating a specific role for activated peripheral B cells in the pathogenesis of RA‐DLBCL.
Alternate day pomalidomide retains anti‐myeloma effect with reduced adverse events and evidence of in vivo immunomodulation
Authors: Streetly Matthew J. , Gyertson Kylie , Daniel Yvonne , Zeldis Jerome B. , Kazmi Majid , Schey Stephen A. 
Published: March 2008

SummaryWe previously reported that daily dose pomalidomide (CC‐4047), a thalidomide analogue, has excellent anti‐myeloma activity but is associated with myelosuppression and deep vein thrombosis. We report here a phase 1 study to determine the maximum tolerated dose (MTD) of pomalidomide at 1 mg, 2 mg, 5 mg and 10 mg on alternate days (ad). Twenty patients with relapsed myeloma were treated. Grade 4 neutropenia occurred in all patients receiving 10 mg and the MTD was defined as 5 mg ad. No thrombotic events were observed. Pomalidomide was continued following the 4‐week MTD study in 17/20 patients for a median of 14 months. 10% of patients had a complete response and >50% reduction in paraprotein was achieved in 50% of subjects. Progression‐free survival was 10·5 months and median overall survival was 33 months. A significant rise was observed in the proportion of CD8+ cells. Alternate day pomalidomide was associated with a marked reduction in the incidence of thrombosis whilst maintaining excellent anti‐myeloma activity. This trial provides further in vivo evidence that pomalidomide modulates the immune system in myeloma patients. Phase 2 studies to further assess the optimal schedule of administration and anti‐myeloma activity of this agent are planned.
Adverse outcomes of blood transfusion in children: analysis of UK reports to the serious hazards of transfusion scheme 1996–2005
Authors: Stainsby D. , Jones H. , Wells A. W. , Gibson B. , Cohen H. ,   on behalf of the SHOT Steering Group
Published: March 2008

SummaryBetween 1996 and 2005 the Serious Hazards of Transfusion (SHOT) scheme analysed 3239 reports of adverse reactions and events associated with transfusion of labile blood components in the UK. 321 reports (10%) related to transfusion of children under 18 years and 147/3239 (4·5%) to infants less than 12 months of age. There were 264 cases in children of ‘incorrect blood component transfused’, resulting from errors at all stages in the transfusion chain; 26/264 suffered actual or potential morbidity. Thirty acute transfusion reactions, three delayed transfusion reactions, 20 cases (three fatal) of transfusion‐related acute lung injury, two cases (both fatal) of transfusion‐associated graft‐versus‐host disease and two transfusion transmitted infections were reported. A population‐based epidemiological study of transfused patients in 2004 showed that 4·2% of red cells are transfused to patients less than 18 years and 1·7% to infants less than 12 months. Interpretation of SHOT data against this context enabled the estimation of the incidence of an adverse outcome to be 18:100 000 red cells issued for children less than 18 years and 37:100 000 for infants less than 12 months, compared to 13:100 000 for adults. Adherence to relevant guidelines, knowledge of specialist transfusion needs of children and good communication are essential if this risk is to be reduced.
Calibration model of microbial biomass carbon and nitrogen concentrations in soils using ultraviolet absorbance and soil organic matter
Authors: Xu X. , Zhang T. , Liu Z. 
Published: March 2008

SummaryThere is a need for a rapid, simple and reliable method of determining soil microbial biomass (SMB) for all soils because traditional methods are laborious. Earlier studies have reported that SMB‐C and ‐N concentrations in grassland and arable soils can be estimated by measurement of UV absorbance in soil extracts. However, these previous studies focused on soils with small soil organic matter (SOM) contents, and there was no consideration of SOM content as a covariate to improve the estimation. In this study, using tropical and temperate forest soils with a wide range of total C (5–204 mg C g−1 soil) and N (1–12 mg N g−1 soil) contents and pH values (4.1–5.9), it was found that increase in UV absorbance of soil extracts at 280 nm (UV280) after fumigation could account for 92–96% of the variance in estimates of the SMB‐C and ‐N concentrations measured by chloroform fumigation and extraction (P < 0.001). The data were combined with those of earlier workers to calibrate UV‐based regression models for all the soils, by taking into account their varying SOM content. The validation analysis of the calibration models indicated that the SMB‐C and ‐N concentrations in the 0–5 cm forest soils simulated by using the increase in UV280 and SOM could account for 86–93% of the variance in concentrations determined by chloroform fumigation and extraction (P < 0.001). The slope values of linear regression equations between measured and simulated values were 0.94 ± 0.03 and 0.94 ± 0.04, respectively, for the SMB‐C and ‐N. However, simulation using the regression equations obtained by using only the data for forest profile soils gave less good agreement with measured values. Hence, the calibration models obtained by using the increase in UV280 and SOM can give a rapid, simple and reliable method of determining SMB for all soils.
Predictors of gross N mineralization and immobilization during decomposition of stabilized organic matter in agricultural soil
Authors: Herrmann A. M. , Witter E. 
Published: March 2008

SummaryLong‐term additions of different types of organic amendments affect the amount of soil organic matter. Less is known about how this in turn affects carbon (C) and nitrogen (N) mineralization from the pool of stabilized soil organic matter, or the extent to which gross N immobilization influences the net amount of N mineralized. Soils, differing in the quantity and quality of organic matter inputs they had received since 1956, were sampled approximately 6 or 18 months after the most recent applications of organic amendments. Two laboratory experiments were carried out to: (i) evaluate if, and how, the organic amendments had affected C mineralization, gross and net N mineralization; (ii) examine the relation between gross N immobilized and free‐light fraction of organic matter; and (iii) assess predictors for gross N mineralization and immobilization rates in soils. The amount of soil organic C and N were major determinants of C and gross N mineralization, but not of net N mineralization. Carbon mineralization was related to gross N mineralization, but the ratio between the two was not constant. Gross N immobilization was related to the amount of free‐light fraction material in the soil with 90% variation explained. For most common organic amendments applied in autumn, our results support the use of total soil organic N and C mineralization as predictors of gross N mineralization from stabilized soil organic matter. In addition, we propose that the amount of free‐light fraction material present in the soil in spring is adequate as a predictor of the immobilization potential of the soil, without a need to consider the C‐to‐N ratio of this material.
Midazolam conscious sedation in a large Danish municipal dental service for children and adolescents
Authors: ULDUM BIRGITTE , HALLONSTEN ANNA‐LENA , POULSEN SVEN 
Published: March 2008

Objective.  The aim of this study was to describe the introduction and the first six years use of midazolam for conscious sedation in a municipal dental service in Denmark.Methods.  In 1998, all dentists were introduced to midazolam conscious sedation. A sedation chart was filled in for each session, and parents’ assessment was obtained. In 2004, all clinical materials were collected.Results.  Six hundred and eighty sessions were performed; 63.7% of the children were between 2 and 6 years of age; 88.5% belonged to American Society of Anesthesiologists grade 1; 74.8% of the sedations performed used the oral route of administration. Restorations were performed during 60.3% of the sessions, and extractions during 38.4%. Complications during the sessions were rare, the most frequent being double vision (6.1%), hiccups (2.7%), and paradoxical reaction (2.0%). Using Wilton's sedation scale, 42.9% were calm and 27.7% were agitated during treatment, whereas after treatment 61.7% were calm; 80.4% of the parents were very positive towards this sedation method.Conclusion.  Sedation with midazolam for dental treatment of children with dental fear and anxiety is a feasible and an efficient method with a low rate of complications. It can probably reduce the need for dental treatment under general anaesthesia.