bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sparse multivariate polynomial interpolation via the quotient-difference algorithm
Authors: Cuyt Annie , Lee Wen-shin 
Published: February 2009

To reconstruct a black box multivariate sparse polynomial from its floating point evaluations, the existing algorithms need to know upper bounds for both the number of terms in the polynomial and the partial degree in each of the variables [2]. On the other hand, Rutishauser's quotient-difference algorithm [7, 3], or the qd-algorithm, is an iterative method that can be use to determine the poles of a meromorphic function from its Taylor coefficients.
Combining the relation between the qd-algorithm, Prony's method and their connections to the Ben-Or/Tiwari algorithm [6], we present a new algorithm for reconstructing sparse multivariate polynomials in floating point arithmetic, in which neither the number of terms nor any partial degrees are required in the input [1].

For example, consider the bivariate black box polynomial function,
f
(
x
1
,
x
2
) = 1/3
x
6/1+4
x
4/2--2.1
x
4/1--4
x
2/2+
x
1
x
2
+4
x
2/1, termed the six-hump camel back function. Evaluate f (x1 , x2 ) at the non-equidistant s-th powers of (1/3, 1/5), in which 3 and 5 are relatively prime, and proceed with the qd-algorithm on the data
f
(1/3, 1/5),
f
(1/3
2
, 1/5
2
),
f
(1/3
3
, 1/5
3
), ....The magnitude of the values in the first five
e
-columns drops from 10
--2
to machine precision, while all values in the sixth
e
-column are of the order of machine precision. We conclude that the number of terms is 6 and obtain the multi-indices in the support directly from the
q
-values:

1/q
1
(S)
→ 9 = 3
2
.

1/q
2
(S)
→ 25 = 5
2
.

1/q
3
(S)
→ 625 = 5
4
.

1/q
2
(S)
→ 15 = 3
1
5
1
.

1/q
1
(S)
→ 81 = 3
4
.

1/q
1
(S)
→ 729 = 3
6
.

After all six multi-indices in
f
are known, the coefficients in
f
can be recovered by a linear system formed by (at least six) evaluations of
f
.

The convergence to zero of some e-columns in the qd-algorithm can be interpreted in an analogous way as the zero discrepancies in the early termination strategy [5, 4]. This is illustrated in Maple.
Our sparse interpolation can be extended to polynomials represented in certain non-standard bases [4]. We show an extension to sparse interpolation of polynomials in the Pochhammer basis and present our current research on sparse polynomial interpolation in the Chebyshev basis, both in floating point arithmetic.
The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH
Authors: Hellweg Christoph , Pühler Alfred , Weidner Stefan 
Published: February 2009

Abstract

Background
The symbiotic soil bacterium Sinorhizobium meliloti often has to face low pH in its natural habitats. To identify genes responding to pH stress a global transcriptional analysis of S. meliloti strain 1021 following a pH shift from pH 7.0 to pH 5.75 was carried out. In detail, oligo-based whole genome microarrays were used in a time course experiment. The monitoring period covered a time span of about one hour after the pH shift. The obtained microarray data was filtered and grouped by K-means clustering in order to obtain groups of genes behaving similarly concerning their expression levels throughout the time course.

Results
The results display a versatile response of S. meliloti 1021 represented by distinct expression profiles of subsets of genes with functional relation. The eight generated clusters could be subdivided into a group of four clusters containing genes that were up-regulated and another group of four clusters containing genes that were down-regulated in response to the acidic pH shift. The respective mean expression progression of the four up-regulated clusters could be described as (i) permanently and strong, (ii) permanently and intermediate, (iii) permanently and progressive, and (iv) transiently up-regulated. The expression profile of the four down-regulated clusters could be characterized as (i) permanently, (ii) permanently and progressive, (iii) transiently, and (iv) ultra short down-regulated. Genes coding for proteins with functional relation were mostly cumulated in the same cluster, pointing to a characteristic expression profile for distinct cellular functions. Among the strongest up-regulated genes lpiA, degP1, cah, exoV and exoH were found. The most striking functional groups responding to the shift to acidic pH were genes of the exopolysaccharide I biosynthesis as well as flagellar and chemotaxis genes. While the genes of the exopolysaccharide I biosynthesis (exoY, exoQ, exoW, exoV, exoT, exoH, exoK exoL, exoO, exoN, exoP) were up-regulated, the expression level of the flagellar and chemotaxis genes (visR, motA, flgF, flgB, flgC, fliE, flgG, flgE, flgL, flbT, mcpU) simultaneously decreased in response to acidic pH. Other responding functional groups of genes mainly belonged to nitrogen uptake and metabolism (amtB, nrtB, nirB, nirD), methionine metabolism (metA, metF, metH, metK, bmt and ahcY) as well as ion transport systems (sitABCD, phoCD). It is noteworthy, that several genes coding for hypothetical proteins of unknown function could be identified as up-regulated in response to the pH shift.

Conclusion
It was shown that the short term response to acidic pH stress does not result in a simple induction or repression of genes, but in a sequence of responses varying in their intensity over time. Obviously, the response to acidic pH is not based on a few specific genes, but involves whole sets of genes associated with various cellular functions.
Optimal use of tandem biotin and V5 tags in ChIP assays
Authors: Kolodziej Katarzyna E , Pourfarzad Farzin , de Boer Ernie , Krpic Sanja , Grosveld Frank , Strouboulis John 
Published: February 2009

Abstract

Background
Chromatin immunoprecipitation (ChIP) assays coupled to genome arrays (Chip-on-chip) or massive parallel sequencing (ChIP-seq) lead to the genome wide identification of binding sites of chromatin associated proteins. However, the highly variable quality of antibodies and the availability of epitopes in crosslinked chromatin can compromise genomic ChIP outcomes. Epitope tags have often been used as more reliable alternatives. In addition, we have employed protein in vivo biotinylation tagging as a very high affinity alternative to antibodies. In this paper we describe the optimization of biotinylation tagging for ChIP and its coupling to a known epitope tag in providing a reliable and efficient alternative to antibodies.

Results
Using the biotin tagged erythroid transcription factor GATA-1 as example, we describe several optimization steps for the application of the high affinity biotin streptavidin system in ChIP. We find that the omission of SDS during sonication, the use of fish skin gelatin as blocking agent and choice of streptavidin beads can lead to significantly improved ChIP enrichments and lower background compared to antibodies. We also show that the V5 epitope tag performs equally well under the conditions worked out for streptavidin ChIP and that it may suffer less from the effects of formaldehyde crosslinking.

Conclusion
The combined use of the very high affinity biotin tag with the less sensitive to crosslinking V5 tag provides for a flexible ChIP platform with potential implications in ChIP sequencing outcomes.
A-002 (Varespladib), a phospholipase A2inhibitor, reduces atherosclerosis in guinea pigs
Authors: Leite Jose O , Vaishnav Ushma , Puglisi Michael , Fraser Heather , Trias Joaquim , Fernandez Maria Luz 
Published: February 2009

AbstractBackgroundThe association of elevated serum levels of secretory phospholipase A2(sPLA2) in patients with cardiovascular disease and their presence in atherosclerotic lesions suggest the participation of sPLA2enzymes in this disease. The presence of more advanced atherosclerotic lesions in mice that overexpress sPLA2enzymes suggest their involvement in the atherosclerotic process. Therefore, the sPLA2family of enzymes could provide reasonable targets for the prevention and treatment of atherosclerosis. Thus, A-002 (varespladib), an inhibitor of sPLA2enzymes, is proposed to modulate the development of atherosclerosis.MethodsTwenty-four guinea pigs were fed a high saturated fat, high cholesterol diet (0.25%) for twelve weeks. Animals were treated daily with A-002 (n = 12) or vehicle (10% aqueous acacia; n = 12) by oral gavage. After twelve weeks, animals were sacrificed and plasma, heart and aorta were collected. Plasma lipids were measured by enzymatic methods, lipoprotein particles size by nuclear magnetic resonance, aortic cytokines by a colorimetric method, and aortic sinus by histological analyses.ResultsPlasma total cholesterol, HDL cholesterol and triglycerides were not different among groups. However, the levels of inflammatory cytokines interleukin (IL)-10, IL-12 and granulocyte-macrophage colony-stimulating factor (GM-CSF) were significantly reduced in the treatment group. This group also had a significant 27% reduction in cholesterol accumulation in aorta compared with placebo group. Morphological analysis of aortic sinus revealed that the group treated with A-002 reduced atherosclerotic lesions by 24%.ConclusionThe use of A-002 may have a beneficial effect in preventing diet-induced atherosclerosis in guinea pigs.
Isolation of osteogenic progenitors from human amniotic fluid using a single step culture protocol
Authors: Antonucci Ivana , Iezzi Irene , Morizio Elisena , Mastrangelo Filiberto , Pantalone Andrea , Mattioli-Belmonte Monica , Gigante Antonio , Salini Vincenzo , Calabrese Giuseppe , Tetè Stefano , Palka Giandomenico , Stuppia Liborio 
Published: February 2009

AbstractBackgroundStem cells isolated from amniotic fluid are known to be able to differentiate into different cells types, being thus considered as a potential tool for cellular therapy of different human diseases. In the present study, we report a novel single step protocol for the osteoblastic differentiation of human amniotic fluid cells.ResultsThe described protocol is able to provide osteoblastic cells producing nodules of calcium mineralization within 18 days from withdrawal of amniotic fluid samples. These cells display a complete expression of osteogenic markers (COL1, ONC, OPN, OCN, OPG, BSP, Runx2) within 30 days from withdrawal. In order to test the ability of these cells to proliferate on surfaces commonly used in oral osteointegrated implantology, we carried out cultures onto different test disks, namely smooth copper, machined titanium and Sandblasted and Acid Etching titanium (SLA titanium). Electron microscopy analysis evidenced the best cell growth on this latter surface.ConclusionThe described protocol provides an efficient and time-saving tool for the production of osteogenic cells from amniotic fluid that in the future could be used in oral osteointegrated implantology.
Comparison of molecular dynamics and superfamily spaces of protein domain deformation
Authors: Velázquez-Muriel Javier A , Rueda Manuel , Cuesta Isabel , Pascual-Montano Alberto , Orozco Modesto , Carazo José-María 
Published: February 2009

Abstract

Background
It is well known the strong relationship between protein structure and flexibility, on one hand, and biological protein function, on the other hand. Technically, protein flexibility exploration is an essential task in many applications, such as protein structure prediction and modeling. In this contribution we have compared two different approaches to explore the flexibility space of protein domains: i) molecular dynamics (MD-space), and ii) the study of the structural changes within superfamily (SF-space).

Results
Our analysis indicates that the MD-space and the SF-space display a significant overlap, but are still different enough to be considered as complementary. The SF-space space is wider but less complex than the MD-space, irrespective of the number of members in the superfamily. Also, the SF-space does not sample all possibilities offered by the MD-space, but often introduces very large changes along just a few deformation modes, whose number tend to a plateau as the number of related folds in the superfamily increases.

Conclusion
Theoretically, we obtained two conclusions. First, that function restricts the access to some flexibility patterns to evolution, as we observe that when a superfamily member changes to become another, the path does not completely overlap with the physical deformability. Second, that conformational changes from variation in a superfamily are larger and much simpler than those allowed by physical deformability. Methodologically, the conclusion is that both spaces studied are complementary, and have different size and complexity. We expect this fact to have application in fields as 3D-EM/X-ray hybrid models or ab initio protein folding.
BioSunMS: a plug-in-based software for the management of patients information and the analysis of peptide profiles from mass spectrometry
Authors: Cao Yuan , Wang Na , Ying Xiaomin , Li Ailing , Wang Hengsha , Zhang Xuemin , Li Wuju 
Published: February 2009

Abstract

Background
With wide applications of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), statistical comparison of serum peptide profiles and management of patients information play an important role in clinical studies, such as early diagnosis, personalized medicine and biomarker discovery. However, current available software tools mainly focused on data analysis rather than providing a flexible platform for both the management of patients information and mass spectrometry (MS) data analysis.

Results
Here we presented a plug-in-based software, BioSunMS, for both the management of patients information and serum peptide profiles-based statistical analysis. By integrating all functions into a user-friendly desktop application, BioSunMS provided a comprehensive solution for clinical researchers without any knowledge in programming, as well as a plug-in architecture platform with the possibility for developers to add or modify functions without need to recompile the entire application.

Conclusion
BioSunMS provides a plug-in-based solution for managing, analyzing, and sharing high volumes of MALDI-TOF or SELDI-TOF MS data. The software is freely distributed under GNU General Public License (GPL) and can be downloaded from http://sourceforge.net/projects/biosunms/.
Switching from premixed insulin to glargine-based insulin regimen improves glycaemic control in patients with type 1 or type 2 diabetes: a retrospective primary care-based analysis
Authors: Sharplin Peter , Gordon Jason , Peters John R , Tetlow Anthony P , Longman Andrea J , McEwan Philip 
Published: February 2009

Abstract

Background
Insulin glargine (glargine) and premixed insulins (premix) are alternative insulin treatments. This analysis evaluated glycaemic control in 528 patients with type 1 (n = 183) or type 2 (n = 345) diabetes, after switching from premix to a glargine-based regimen, using unselected general practice (GP) data.

Methods
Data for this retrospective observational analysis were extracted from a UK GP database (The Health Improvement Network). Patients were required to have at least 12 months of available data, before and after, switching from premix to a glargine-based regimen. The principal analysis was the change in HbA1c after 12 months of treatment with glargine; secondary analyses included change in weight, bolus usage and total daily insulin dose. Inconsistent reporting of hypoglycemic episodes precludes reliable assessment of this outcome. Multivariate analyses were used to adjust for baseline characteristics and confounding variables.

Results
Both cohorts showed significant reduction in mean HbA1c 12 months after the switch: by -0.67% (p < 0.001) in the type 1 cohort and by -0.53% (p < 0.001) in the type 2 cohort (adjusted data). The size of HbA1c improvement was positively correlated with baseline HbA1c; patients with a baseline HbA1c ≥ 10% had the greatest mean reduction in HbA1c, by -1.7% (p < 0.001) and -1.2% (p < 0.001), respectively. The proportion of patients receiving co-bolus prescriptions increased in the type 1 (mean 24.6% to 95.1%, p < 0.001) and type 2 (mean 16.2% to 73.9%, p < 0.001) cohorts. There was no significant change in weight in either cohort. Total mean insulin use increased in type 2 diabetes patients (from 0.67 ± 1.35 U/Kg to 0.88 ± 1.33 U/Kg, p < 0.001) with a slight decrease in type 1 diabetes patients (from 1.04 ± 2.51 U/Kg to 0.98 ± 2.58 U/Kg, p < 0.001).

Conclusion
In everyday practice, patients with type 1 or type 2 diabetes inadequately controlled by premix insulins experienced significant improvement in glycaemic control over 12 months after switching to a glargine-based insulin regimen. These findings support the use of a basal-bolus glargine-based regimen in patients poorly controlled on premix.
Surface displaced alfa-enolase of Lactobacillus plantarum is a fibronectin binding protein
Authors: Castaldo Cristiana , Vastano Valeria , Siciliano Rosa Anna , Candela Marco , Vici Manuela , Muscariello Lidia , Marasco Rosangela , Sacco Margherita 
Published: February 2009

Abstract

Background
Lactic acid bacteria of the genus Lactobacillus and Bifidobacterium are one of the most important health promoting groups of the human intestinal microbiota. Their protective role within the gut consists in out competing invading pathogens for ecological niches and metabolic substrates. Among the features necessary to provide health benefits, commensal microorganisms must have the ability to adhere to human intestinal cells and consequently to colonize the gut. Studies on mechanisms mediating adhesion of lactobacilli to human intestinal cells showed that factors involved in the interaction vary mostly among different species and strains, mainly regarding interaction between bacterial adhesins and extracellular matrix or mucus proteins. We have investigated the adhesive properties of Lactobacillus plantarum, a member of the human microbiota of healthy individuals.

Results
We show the identification of a Lactobacillus plantarum LM3 cell surface protein (48 kDa), which specifically binds to human fibronectin (Fn), an extracellular matrix protein. By means of mass spectrometric analysis this protein was identified as the product of the L. plantarum enoA1 gene, coding the EnoA1 alfa-enolase. Surface localization of EnoA1 was proved by immune electron microscopy. In the mutant strain LM3-CC1, carrying the enoA1 null mutation, the 48 kDa adhesin was not anymore detectable neither by anti-enolase Western blot nor by Fn-overlay immunoblotting assay. Moreover, by an adhesion assay we show that LM3-CC1 cells bind to fibronectin-coated surfaces less efficiently than wild type cells, thus demonstrating the significance of the surface displaced EnoA1 protein for the L. plantarum LM3 adhesion to fibronectin.

Conclusion
Adhesion to host tissues represents a crucial early step in the colonization process of either pathogens or commensal bacteria. We demonstrated the involvement of the L. plantarum Eno A1 alfa-enolase in Fn-binding, by studying LM3 and LM3-CC1 surface proteins. Isolation of LM3-CC1 strain was possible for the presence of expressed enoA2 gene in the L. plantarum genome, giving the possibility, for the first time to our knowledge, to quantitatively compare adhesion of wild type and mutant strain, and to assess doubtless the role of L. plantarum Eno A1 as a fibronectin binding protein.
Brachytherapy versus radical hysterectomy after external beam chemoradiation: a non-randomized matched comparison in IB2-IIB cervical cancer patients
Authors: Cetina Lucely , Garcia-Arias Alicia , Candelaria Myrna , Cantú David , Rivera Lesbia , Coronel Jaime , Bazan-Perkins Blanca , Flores Vladimir , Gonzalez Aaron , Dueñas-González Alfonso 
Published: February 2009

Abstract

Background
A current paradigm in the treatment of cervical cancer with radiation therapy is that intracavitary brachytherapy is an essential component of radical treatment. This is a matched retrospective comparison of the results of treatment in patients treated with external beam chemoradiation (EBRT-CT) and radical hysterectomy versus those treated with identical chemoradiation followed by brachytherapy.

Methods
In this non-randomized comparison EBRT-CT protocol was the same in both groups of 40 patients. In the standard treated patients, EBRT-CT was followed by one or two intracavitary Cesium (low-dose rate) applications within 2 weeks of finishing external radiation to reach a point A dose of at least 85 Gy. In the surgically treated patients, radical hysterectomy with bilateral pelvic lymph node dissection and para-aortic lymph node sampling were performed within 7 weeks after EBRT-CT. Response, toxicity and survival were evaluated.

Results
A total of 80 patients were analyzed. The patients receiving EBRT-CT and surgery were matched with the standard treated cases. There were no differences in the clinicopathological characteristics between groups or in the delivery of EBRT-CT. The pattern of acute and late toxicity differed. Standard treated patients had more chronic proctitis while the surgically treated had acute complications of surgery and hydronephrosis. At a maximum follow-up of 60 months, median follow-up 26 (2–31) and 22 (3–27) months for the surgery and standard therapy respectively, eight patients per group have recurred and died. The progression free and overall survival are the same in both groups.

Conclusion
The results of this study suggest that radical hysterectomy can be used after EBRT-CT without compromising survival in FIGO stage IB2-IIB cervical cancer patients in settings were brachytherapy is not available. A randomized study is needed to uncover the value of surgery after EBRT-CT.
Indexing TNF-αgene expression using a gene-targeted reporter cell line
Authors: Yan Ziying , Lei-Butters Diana , Engelhardt John F , Leno Gregory H 
Published: February 2009

AbstractBackgroundCurrent cell-based drug screening technologies utilize randomly integrated reporter genes to index transcriptional activity of an endogenous gene of interest. In this context, reporter expression is controlled by known genetic elements that may only partially capture gene regulation and by unknown features of chromatin specific to the integration site. As an alternative technology, we applied highly efficient gene-targeting with recombinant adeno-associated virus to precisely integrate a luciferase reporter gene into exon 1 of the HeLa cell tumor necrosis factor-alpha (TNF-α) gene. Drugs known to induceTNF-αexpression were then used to compare the authenticity of gene-targeted and randomly integrated transcriptional reporters.ResultsTNF-α-targeted reporter activity reflected endogenousTNF-αmRNA expression, whereas randomly integratedTNF-αreporter lines gave variable expression in response to transcriptional and epigenetic regulators. 5,6-Dimethylxanthenone-4-acetic acid (DMXAA), currently used in cancer clinical trials to induceTNF-αgene transcription, was only effective at inducing reporter expression fromTNF-αgene-targeted cells.ConclusionWe conclude that gene-targeted reporter cell lines provide predictive indexing of gene transcription for drug discovery.