bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complementary and alternative medicine for multiple sclerosis
Authors: Schwarz S , Knorr C , Geiger H , Flachenecker P 
Published: July 2008

We analyzed characteristics, motivation, and effectiveness of complementary and alternative medicine in a large sample of people with multiple sclerosis. A 53-item survey was mailed to the members of the German Multiple Sclerosis Society, chapter of Baden-Wuerttemberg. Surveys of 1573 patients (48.5 ± 11.7 years, 74% women, duration of illness 18.1 ± 10.5 years) were analyzed. In comparison with conventional medicine, more patients displayed a positive attitude toward complementary and alternative medicine (44% vs 38%, P < 0.05), with 70% reporting lifetime use of at least one method. Among a wide variety of complementary and alternative medicine, diet modification (41%), Omega-3 fatty acids (37%), removal of amalgam fillings (28%), vitamins E (28%), B (36%), and C (28%), homeopathy (26%), and selenium (24%) were cited most frequently. Most respondents (69%) were satisfied with the effects of complementary and alternative medicine. Use of complementary and alternative medicine was associated with religiosity, functional independence, female sex, white-collar job, and higher education ( P < 0.05). Compared with conventional therapies, complementary and alternative medicine rarely showed unwanted side effects (9% vs 59%, P < 0.00001). A total of 52% stated that the initial consultation with their physician lasted less than 15 min. To conclude, main reasons for the use of complementary and alternative medicine include the high rate of side effects and low levels of satisfaction with conventional treatments and brief patients/physicians contacts.
Survival and cause of death in multiple sclerosis: results from a 50-year follow-up in Western Norway
Authors: Grytten Torkildsen N , Lie SA , Aarseth JH , Nyland H , Myhr KM 
Published: July 2008

Background Survival time among patients with multiple sclerosis (MS) has varied considerably according to previous reports. Objectives Survival and cause of death were analyzed among all patients with MS (878) with onset of MS in Hordaland County, Western Norway during 1953–2003, of whom 198 were dead at follow-up on January 1, 2005. Methods Standardized mortality ratios (SMRs) and relative mortality ratios (RMRs) were calculated based on observed mortality in MS and expected mortality. Results Median survival from onset was 41 years versus 49 years in the corresponding population, and mortality (SMR) was 2.7-fold increased in MS. The median survival was 43 years among women and 36 years among men, but women had higher relative mortality, when compared with the corresponding population, than men (RMR = 1.40). The median survival time was 45 years among young-onset patients (21–30 years) and 23 years among older-onset patients (51–60 years), but young-onset patients had higher relative mortality than older-onset patients, as shown by a significant reduction by 10-year interval of age at onset (RMR = 0.65). Median survival from onset was longer (43 years) among relapsing–remitting MS than primary progressive MS ([PPMS]; 49 years), and the relative mortality was higher in the PPMS group, (RMR = 1.55). According to death certificates, 57% died from MS. Conclusion Female patients and patients with young onset had longer median time to death but higher relative risk of dying compared with the corresponding population. PPMS had both shorter median time to death from onset and a higher relative risk of dying.
A computational investigation of cation ordering phenomena in the binary
spinel system MgAl2O4-FeAl2O4
Authors: Palin E. J. , Harrison R. J. 
Published: July 2008

Abstract
The systematics of cation ordering in binary spinel solid solutions have been
investigated using an interatomic potential model combined with Monte Carlo
simulations. The formalism to describe a system containing three cation species
ordering over two non-equivalent sub-lattices is developed and the method applied
to the
MgAl2O4-FeAl2O4
binary solid solution. Our results compare favourably with experimental
measurements of site-occupancy data, although the experiments display a slightly
larger degree of non-ideality than the simulations. A possible kinetic origin of
the non-ideal behaviour was examined by performing simulations in which only
exchange of Mg and Fe2+ between tetrahedral and octahedral
sites was permitted below the Al-blocking temperature of 1160 K. This approach
improves the agreement with the experimental site occupancies, and suggests that
the blocking temperature for moving Mg and Fe2+ between
tetrahedral and octahedral sites is significantly lower than for moving
Al
Structural role of copper in the minerals of the pearceite-polybasite group:
the case of the new minerals cupropearceite and cupropolybasite
Authors: Bindi L. , Evain M. , Spry P. G. , Tait K. T. , Menchetti S. 
Published: July 2008

Abstract
The pearceite-polybasite group of minerals, general formula
[M6T2S7][Ag9CuS4]
with M = Ag, Cu; and T = As, Sb, show a crystal structure which can be described
as the succession, along the c axis, of two pseudo-layer modules: a
[M6T2S7]2–A
module layer and a
[Ag9CuS4]2+B
module layer. Copper is present in one structural position of the
B module layer and replaces Ag in the only fully
occupied M position of the A module layer. When the Cu
content is >4.00 a.p.f.u., the structural position of the
A module layer becomes Cu-dominant and,
consequently, the mineral deserves its own name. In this paper we report the
crystal-chemical characterization of two Cu-rich members exhibiting the 111
unitcell type (corresponding to the Tac polytype). One sample (space group
(P)m1,
a 7.3218(8), c
11.8877(13) Å, V 551.90(10) Å3, Z
= 1) having As >Sb and with the structural position of the
A module layer dominated by Cu, has been named
cupropearceite and the other sample (space group (P3̄)m1, a 7.3277(3), c
11.7752(6) Å, V 547.56(8) Å3, Z =
1) having Sb >As has been named cupropolybasite.
Both the new minerals and mineral names have been approved by the
IMA-CNMNC.
Crystal chemistry of leucite from the Roman Comagmatic Province (central
Italy): a multi-methodological study
Authors: Gatta G. D. , Rotiroti N. , Bellatreccia F. , Della Ventura G. 
Published: July 2008

Abstract
A multi-methodological study, based on electron microprobe analysis (in
wavelength dispersive mode), single-crystal X-ray diffraction (XRD), transmission
electron microscopy and single-crystal Fourier transform infrared spectroscopy was
performed in order to describe the crystal chemistry of four leucite samples from
different localities of the Roman Comagmatic Province (central Italy). All the
crystals examined were found to be tetragonal (space group
I41/a with a = 13.076–13.103 Å
and c = 13.744–13.784 Å) and characterized by a complex twinning (merohedric
twins: on the tetragonal planes (110) and (1̄10) with the two individuals having
parallel crystallographic axes with a and b interchanged; pseudo-merohedric twins:
on the tetragonal planes (101), (011), (1̄01), (01̄ 1), with the two individuals
having parallel a (or b) axes and the remaining two axes not parallel). The
chemical analyses show that all the samples contain minor Na and Fe. Infrared
spectroscopy shows that all samples contain structurally bound water molecules, up
to unexpectedly large amounts (~0.4 wt.%) for a nominally anhydrous mineral,
suggesting that ‘analcime-like’ substitution (K to Na + H2O)
occurs in the leucite samples investigated here. The detection limits of the
‘analcime-like’ substitution by singlecrystal XRD are also discussed.
Function2Gene: A gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge
Authors: Armstrong Don L , Jacob Chaim O , Zidovetzki Raphael 
Published: July 2008

Abstract

Background
Many common disorders have multiple genetic components which convey increased susceptibility. SNPs have been used to identify genetic components which are associated with a disease. Unfortunately, many studies using these methods suffer from low reproducibility due to lack of power.

Results
We present a set of programs which implement a novel method for searching for disease-associated genes using prior information to select and order genes from publicly available databases by their prior likelihood of association with the disease. These programs were used in a published study of childhood-onset SLE which yielded novel associations with modest sample size.

Conclusion
Using prior information to decrease the size of the problem space to an amount commensurate with available samples and resources while maintaining appropriate power enables researchers to increase their likelihood of discovering reproducible associations.
Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection
Authors: Ojosnegros Samuel , Agudo Rubén , Sierra Macarena , Briones Carlos , Sierra Saleta , González- López Claudia , Domingo Esteban , Cristina Juan 
Published: July 2008

Abstract

Background
The molecular events and evolutionary forces underlying lethal mutagenesis of virus (or virus extinction through an excess of mutations) are not well understood. Here we apply for the first time phylogenetic methods and Partition Analysis of Quasispecies (PAQ) to monitor genetic distances and intra-population structures of mutant spectra of foot-and-mouth disease virus (FMDV) quasispecies subjected to mutagenesis by base and nucleoside analogues.

Results
Phylogenetic and PAQ analyses have revealed a highly dynamic variation of intrapopulation diversity of FMDV quasispecies. The population diversity first suffers striking expansions in the presence of mutagens and then compressions either when the presence of the mutagenic analogue was discontinued or when a mutation that decreased sensitivity to a mutagen was selected. The pattern of mutations found in the populations was in agreement with the behavior of the corresponding nucleotide analogues with FMDV in vitro. Mutations accumulated at preferred genomic sites, and dn/ds ratios indicate the operation of negative (or purifying) selection in populations subjected to mutagenesis. No evidence of unusually elevated genetic distances has been obtained for FMDV populations approaching extinction.

Conclusion
Phylogenetic and PAQ analysis provide adequate procedures to describe the evolution of viral sequences subjected to lethal mutagenesis. These methods define the changes of intra-population structure more precisely than mutation frequencies and Shannon entropies. PAQ is very sensitive to variations of intrapopulation genetic distances. Strong negative (or purifying) selection operates in FMDV populations subjected to enhanced mutagenesis. The quantifications provide evidence that extinction does not imply unusual increases of intrapopulation complexity, in support of the lethal defection model of virus extinction.
RAS gene polymorphisms, classical risk factors and the advent of coronary artery disease in the Portuguese population
Authors: Freitas Ana I , Mendonça Isabel , Brión Maria , Sequeira Miguel M , Reis Roberto P , Carracedo Angel , Brehm António 
Published: July 2008

Abstract

Background
Several polymorphisms within the renin-angiotensin system cluster of genes have been associated with the advent of coronary artery disease (CAD) or related pathologies. We investigated the distribution of 5 of these polymorphisms in order to find any association with CAD development and distinguish if any of the biochemical and behavioural factors interact with genetic polymorphisms in the advent of the disease.

Methods

ACE I/D (rs4340), ACE A11860G (rs4343), AT1R A1166C (rs5186), AGT T174M (rs4762) and AGT M235T (rs699) gene polymorphisms were PCR-RFLP analysed in 298 CAD patients and 510 controls from Portugal. Several biochemical and behavioural markers were obtained.

Results

ACE I/D DD and ACE11860 GG genotypes are risk factors for CAD in this population. The simultaneous presence of ACE I/D I and ACE11860 A alleles corresponds to a significant trend towards a decrease in CAD incidence. We found several synergistic effects between the studied polymorphisms and classical risk factors such as hypertension, obesity, diabetes and dyslipidaemia: the presence of the DD genotype of ACE I/D (and also ACE11860 GG) increases the odds of developing CAD when associated to each one of these classical risk factors, particularly when considering the male and early onset CAD subgroup analysis; AGT235 TT also increases the CAD risk in the presence of hypertension and dyslipidaemia, and AT1R1166 interacts positively with hypertension, smoking and obesity.

Conclusion

ACE polymorphisms were shown to play a major role in individual susceptibility to develop CAD. There is also a clear interaction between RAS predisposing genes and some biochemical/environmental risk factors in CAD onset, demonstrating a significant enhancement of classical markers particularly by ACE I/D and ACE11860.
Dinucleotide repeat polymorphism in Fms-like tyrosine kinase-1 (Flt-1) gene is not associated with preeclampsia
Authors: Kim Shin-Young , Lim Ji-Hyae , Yang Jae-Hyug , Kim Moon-Young , Han Jung-Yeol , Ahn Hyun-Kyong , Choi Jun-Seek , Park So-Yeon , Kim Mi-Jin , Ryu Hyun-Mee 
Published: July 2008

Abstract

Background
Preeclampsia is a major cause of maternal and perinatal mortality and morbidity. The etiology of preeclampsia remains unclear. Recently, it was shown that misregulation of fms-like tyrosine kinase-1 (Flt-1) in the peripheral blood mononuclear cells of pregnant women results in over-expression of the soluble splice variant of Flt-1, sFlt-1, producing an additional (extra-placental) source of sFlt-1 that can contribute to the etiology of preeclampsia. The aim of this study was to investigate the relationship between preeclampsia and a dinucleotide (threonine-glycine; TG)n repeat polymorphism in the 3' non-coding region of the Flt-1 gene.

Methods
The number of the d(TG)n repeats was analyzed in 170 patients with preeclampsia and in 202 normotensive pregnancies. The region containing the dinucleotide repeat polymorphism of the Flt-1 gene was amplified by polymerase chain reaction (PCR) from the DNA samples and was analyzed by direct PCR sequencing.

Results
We found 10 alleles of the dinucleotide repeat polymorphism and designated these as allele*12 (A1) through allele*23 (A12) according to the number of the TG repeats, from 12 to 23. The frequency of the 14-repeat allele (A3) was most abundant (63.82% in preeclampsia and 69.06% in controls), followed by the 21-repeat allele (A10; 28.53% in preeclampsia and 23.76% in controls). There was no significant difference in the allele frequency between patients with preeclampsia and normal controls. The most common genotype in preeclamptic and normotensive pregnancies was heterozygous (TG)14/(TG)21 (41.76%) and homozygous (TG)14/(TG)14 (45.05%), respectively. However, the genotype frequencies were not significantly different between preeclamptic patients and controls.

Conclusion
This is the first study to characterize the dinucleotide repeat polymorphism of the Flt-1 gene in patients with preeclampsia. We found no differences in the allele or genotype frequencies between patients with preeclampsia and normal pregnancies. Although limited by a relatively small sample size, our study suggests that the d(TG)n repeat polymorphism of the Flt-1 gene is not associated with the development of preeclampsia in Korean pregnant women.
Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure
Authors: Chakravarty Suvobrata , Godbole Sucheta , Zhang Bing , Berger Seth , Sanchez Roberto 
Published: July 2008

Abstract

Background
Although multiple templates are frequently used in comparative modeling, the effect of inclusion of additional template(s) on model accuracy (when compared to that of corresponding single-template based models) is not clear. To address this, we systematically analyze two-template models, the simplest case of multiple-template modeling. For an existing target-template pair (single-template modeling), a two-template based model of the target sequence is constructed by including an additional template without changing the original alignment to measure the effect of the second template on model accuracy.

Results
Even though in a large number of cases a two-template model showed higher accuracy than the corresponding one-template model, over the entire dataset only a marginal improvement was observed on average, as there were many cases where no change or the reverse change was observed. The increase in accuracy due to the structural complementarity of the templates increases at higher alignment accuracies. The combination of templates showing the highest potential for improvement is that where both templates share similar and low (less than 30%) sequence identity with the target, as well as low sequence identity with each other. The structural similarity between the templates also helps in identifying template combinations having a higher chance of resulting in an improved model.

Conclusion
Inclusion of additional template(s) does not necessarily improve model quality, but there are distinct combinations of the two templates, which can be selected a priori, that tend to show improvement in model quality over the single template model. The benefit derived from the structural complementarity is dependent on the accuracy of the modeling alignment. The study helps to explain the observation that a careful selection of templates together with an accurate target:template alignment are necessary to the benefit from using multiple templates in comparative modeling and provides guidelines to maximize the benefit from using multiple templates. This enables formulation of simple template selection rules to rank targets of a protein family in the context of structural genomics.
Fractal parameters and vascular networks: facts & artifacts
Authors: Mancardi Daniele , Varetto Gianfranco , Bucci Enrico , Maniero Fabrizio , Guiot Caterina 
Published: July 2008

Abstract

Background
Several fractal and non-fractal parameters have been considered for the quantitative assessment of the vascular architecture, using a variety of test specimens and of computational tools. The fractal parameters have the advantage of being scale invariant, i.e. to be independent of the magnification and resolution of the images to be investigated, making easier the comparison among different setups and experiments.

Results
The success of several commercial and/or free codes in computing the fractal parameters has been tested on well known exact models. Based on such a preliminary study, we selected the code Frac-lac in order to analyze images obtained by visualizing the angiogenetic process occurring in chick Chorio Allontoic Membranes (CAM), assumed to be paradigmatic of a realistic 2D vascular network. Among the parameters investigated, the fractal dimension Df proved to be the most robust estimator for CAM vascular networks. Moreover, only Df was able to discriminate between effective and elusive increases in vascularization after drug-induced angiogenic stimulations on CAMs.

Conclusion
The fractal dimension Df is likely to be the most promising tool for monitoring the effectiveness of anti-angiogenic therapies in various clinical contexts.
CD45 immunoaffinity depletion of vesicles from Jurkat T cells demonstrates that exosomes contain CD45: no evidence for a distinct exosome/HIV-1 budding pathway
Authors: Coren Lori V , Shatzer Teresa , Ott David E 
Published: July 2008

AbstractThe presence of relatively high levels of cellular protein contamination in density-purified virion preparations is a confounding factor in biochemical analyses of HIV and SIV produced from hematopoietic cells. A major source of this contamination is from vesicles, either microvesicles or exosomes, that have similar physical properties as virions. Thus, these particles can not be removed by size or density fractionation. Although virions and vesicles have similar cellular protein compositions, CD45 is excluded from HIV-1 yet is present in vesicles produced from hematopoietic cells. By exploiting this finding, we have developed a CD45 immunoaffinity depletion procedure that removes vesicles from HIV-1 preparations. While this approach has been successfully applied to virion preparations from several different cell types, some groups have concluded that "exosomes" from certain T cell lines, specifically Jurkat, do not contain CD45. If this interpretation is correct, then these vesicles could not be removed by CD45 immunoaffinity depletion. Here we show that dense vesicles produced by Jurkat and SupT1/CCR5 cells contain CD45 and are efficiently removed from preparations by CD45-immunoaffinity depletion. Also, contaminating cellular proteins were removed from virion preparations produced by these lines. Previously, the absence of CD45 from both "exosomes" and virions has been used to support the so called Trojan exosome hypothesis, namely that HIV-1 is simply an exosome containing viral material. The presence of CD45 on vesicles, including exosomes, and its absence on virions argues against a specialized budding pathway that is shared by both exosomes and HIV-1.
Genes responsive to both oxidant stress and loss of estrogen receptor function identify a poor prognosis group of estrogen receptor positive primary breast cancers
Authors: Yau Christina , Benz Christopher C 
Published: July 2008

Abstract
Introduction
Oxidative stress can modify estrogen receptor (ER) structure and function, including induction of progesterone receptor (PR), altering the biology and clinical behavior of endocrine responsive (ER-positive) breast cancer.

Methods
To investigate the impact of oxidative stress on estrogen/ER-regulated gene expression, RNA was extracted from ER-positive/PR-positive MCF7 breast cancer cells after 72 hours of estrogen deprivation, small-interfering RNA knockdown of ER-α, short-term (8 hours) exposure to various oxidant stresses (diamide, hydrogen peroxide, and menadione), or simultaneous ER-α knockdown and oxidant stress. RNA samples were analyzed by high-throughput expression microarray (Affymetrix), and significance analysis of microarrays was used to define gene signatures responsive to estrogen/ER regulation and oxidative stress. To explore the association of these signatures with breast cancer biology, microarray data were analyzed from 394 ER-positive primary human breast cancers pooled from three independent studies. In particular, an oxidant-sensitive estrogen/ER-responsive gene signature (Ox-E/ER) was correlated with breast cancer clinical parameters and disease-specific patient survival (DSS).

Results
From 891 estrogen/ER-regulated probes, a core set of 75 probes (62 unique genes) responsive to all three oxidants were selected (Ox-E/ER signature). Ingenuity pathway analysis of this signature highlighted networks involved in development, cancer, and cell motility, with intersecting nodes at growth factors (platelet-derived growth factor-BB, transforming growth factor-β), a proinflammatory cytokine (tumor necrosis factor), and matrix metalloproteinase-2. Evaluation of the 394 ER-positive primary breast cancers demonstrated that Ox-E/ER index values correlated negatively with PR mRNA levels (rp = -0.2; P = 0.00011) and positively with tumor grade (rp = 0.2; P = 9.741 × e-5), and were significantly higher in ER-positive/PR-negative versus ER-positive/PR-positive breast cancers (t-test, P = 0.0008). Regardless of PR status, the Ox-E/ER index associated with reduced DSS (n = 201; univariate Cox, P = 0.078) and, using the optimized cut-point, separated ER-positive cases into two significantly different DSS groups (log rank, P = 0.0009).

Conclusion
An oxidant-sensitive subset of estrogen/ER-responsive breast cancer genes linked to cell growth and invasion pathways was identified and associated with loss of PR and earlier disease-specific mortality, suggesting that oxidative stress contributes to the development of an aggressive subset of primary ER-positive breast cancers.