bluuebunny/crossref_metadata_2025_split huggingface dataset:
The association between blood pressure and cognitive function
Authors: Igase Michiya , Kohara Katsuhiko , Miki Tetsuro 
Published: February 2011

SummaryLonger lifespans have been accompanied by an increasing number of older people suffering from impaired cognitive function (dementia) including Alzheimer's disease (AD) and vascular dementia (VaD). Some studies have suggested that hypertension in old age correlates with the pathogenesis of dementia. Since hypertension is potentially reversible, a number of randomized trials have examined whether antihypertensive treatment may help to prevent dementia. We review five studies, all using subjects aged 60 years or older, which investigated different antihypertensive pharmacological treatments and found conflicting results regarding impact on dementia. At the same time, other studies have suggested that hypotension in older people, especially those with low diastolic blood pressure, are also at higher risk for developing dementia. Four studies are reviewed here, but none is able to determine unequivocally if hypotension is a cause or a consequence of dementia in old age.
Environmental control of dormancy in quinoa (Chenopodium quinoa) seeds: two potential genetic resources for pre-harvest sprouting tolerance
Authors: Ceccato Diana V. , Daniel Bertero H. , Batlla Diego 
Published: February 2011

AbstractPre-harvest sprouting (PHS) is a serious risk when adapting quinoa (Chenopodium quinoa) seed production to different temperate environments. Two quinoa accessions, ‘2-Want’ and ‘Chadmo’ were evaluated under field conditions in the Argentinean pampas over 2 years on five different sowing dates, to explore a range of climate conditions under which seed filling is manageable in this region. Both accessions exhibited dormancy during seed development and maturation under the conditions examined; however, dormancy expression was restricted to low temperatures in 2-Want, while seeds of Chadmo, originating from the humid island of Chiloe, southern Chile, expressed a high level of dormancy at all examined temperatures. Dormancy release was observed as a reduction in the lowest temperature permissible for seed germination, which broadened the optimal germination temperature window. Higher storage temperature increased the rate of dormancy release. The environment during seed development on the mother plant affected the levels and patterns of seed dormancy, with higher temperatures and longer photoperiods promoting dormancy. As dormancy was released before the next production period, the levels of dormancy observed in the accession would allow timely planting and uniform germination, while dormancy during seed maturation ensures the prevention of PHS. Chadmo showed deeper dormancy levels in all situations, compared with 2-Want, therefore greater PHS tolerance under various conditions in the pampas region can be expected for Chadmo, which makes this accession a better candidate to be included in adaptive breeding programmes for quinoa.
Ultrastructural changes of sheep cumulus–oocyte complexes following different methods of vitrification
Authors: Ebrahimi Bita , Valojerdi Mojtaba Rezazadeh , Eftekhari-Yazdi Poopak , Baharvand Hossein 
Published: February 2011

SummaryTo determine the ultrastructural changes of sheep cumulus–oocyte complexes (COCs) following different methods of vitrification, good quality isolated COCs (GV stage) were randomly divided into the non-vitrified control, conventional straw, cryotop and solid surface vitrification groups. In both conventional and cryotop methods, vitrified COCs were respectively loaded by conventional straws and cryotops, and then plunged directly into liquid nitrogen (LN2); whereas in the solid surface group, vitrified COCs were first loaded by cryotops and then cooled before plunging into LN2. Post-warming survivability and ultrastructural changes of healthy COCs in the cryotop group especially in comparison with the conventional group revealed better viability rate and good preservation of the ooplasm organization. However in all vitrification groups except the cryotop group, mitochondria were clumped. Solely in the conventional straw group, the mitochondria showed different densities and were extremely distended. Moreover in the latter group, plenty of large irregular connected vesicles in the ooplasm were observed and in some parts their membrane ruptured. Also, in the conventional and solid surface vitrification groups, cumulus cells projections became retracted from the zona pellucida in some parts. In conclusion, the cryotop vitrification method as compared with other methods seems to have a good post-warming survivability and shows less deleterious effects on the ultrastructure of healthy vitrified–warmed sheep COCs.
Stroop Effects in Persons with Traumatic Brain Injury: Selective Attention, Speed of Processing, or Color-Naming? A Meta-analysis
Authors: Ben-David Boaz M. , Nguyen Linh L.T. , van Lieshout Pascal H.H.M. 
Published: February 2011

AbstractThe color word Stroop test is the most common tool used to assess selective attention in persons with traumatic brain injury (TBI). A larger Stroop effect for TBI patients, as compared to controls, is generally interpreted as reflecting a decrease in selective attention. Alternatively, it has been suggested that this increase in Stroop effects is influenced by group differences in generalized speed of processing (SOP). The current study describes an overview and meta-analysis of 10 studies, where persons with TBI (N = 324) were compared to matched controls (N= 501) on the Stroop task. The findings confirmed that Stroop interference was significantly larger for TBI groups (p= .008). However, these differences may be strongly biased by TBI-related slowdown in generalized SOP (r2= .81 in a Brinley analysis). We also found that TBI-related changes in sensory processing may affect group differences. Mainly, a TBI-related increase in the latency difference between reading and naming the font color of a color-neutral word (r2= .96) was linked to Stroop effects. Our results suggest that, in using Stroop, it seems prudent to control for both sensory factors and SOP to differentiate potential changes in selective attention from other changes following TBI. (JINS, 2011,17, 354–363)
THE TRACE PROBLEM FOR TOTALLY POSITIVE ALGEBRAIC INTEGERS
Authors: LIANG YANHUA , WU QIANG 
Published: February 2011

AbstractLetαbe a totally positive algebraic integer of degreed≥2 andα1=α,α2,…,αdbe all its conjugates. We use explicit auxiliary functions to improve the known lower bounds ofSk/d, whereSk=∑di=1αki andk=1,2,3. These improvements have consequences for the search of Salem numbers with negative traces.
RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture
Authors: Rosenthal Adam Z , Matson Eric G , Eldar Avigdor , Leadbetter Jared R 
Published: February 2011

Abstract
The hindguts of wood-feeding termites typically contain hundreds of microbial species. Together with their insect host, these gut microbes degrade lignocellulose into usable catabolites. Although past research revealed many facets of the stepwise flow of metabolites in this scheme, not much is known about the breadth of interactions occurring between termite-gut microbes. Most of these microbes are thought to depend on, and to have co-speciated with, their host and each other for millions of years. In this study, we explored the interactions of two spirochetes previously isolated from the very same termite species. As hydrogen (H2) is the central free intermediate in termite-gut lignocellulose digestion, we focused on interactions between two closely related termite-gut spirochetes possessing complementary H2 physiologies: one produces H2, while the other consumes it. In vitro, these two Treponema species markedly enhanced each other's growth. RNA sequencing resolved the transcriptomes of these two closely related organisms, revealing that co-cultivation causes comprehensive changes in global gene expression. The expression of well over a 100 genes in each species was changed &gt;twofold, with over a dozen changed &gt;10-fold. Several changes implicating synergistic cross-feeding of known metabolites were validated in vitro. Additionally, certain activities beneficial to the host were preferentially expressed during consortial growth. However, the majority of changes in gene expression are not yet understandable, but indicate a broad, comprehensive and mutualistic interaction between these closely related, co-resident gut symbionts. The results suggest that staggeringly intricate networks of metabolic and gene interactions drive lignocellulose degradation and co-evolution of termite gut microbiota.
Lipid binding to cytoglobin leads to a change in haem co-ordination: a role for cytoglobin in lipid signalling of oxidative stress
Authors: Reeder Brandon J. , Svistunenko Dimitri A. , Wilson Michael T. 
Published: February 2011

Cytoglobin is a recently discovered hexa-co-ordinate haemoglobin that does not appear to function as a classical oxygen-binding protein. Its function is unknown and studies on the effects of changes in its expression have not decisively determined its role within the cell. In the present paper, we report that the protein is transformed from hexa-co-ordinate to penta-co-ordinate on binding a lipid molecule. This transformation occurs with the ferric oxidation state of the protein, but not the ferrous state, indicating that this process only occurs under an oxidative environment and may thus be related to redox-linked cell signalling mechanisms. Oleate binds to the protein in a 1:1 stoichiometry and with high affinity (Kd=0.7 μM); however, stopped-flow kinetic measurements yield a Kd value of 110 μM. The discrepancy between these Kd values may be rationalized by recognizing that cytoglobin is a disulfide-linked dimer and invoking co-operativity in oleate binding. The lipid-induced transformation of cytoglobin from hexa-co-ordinate to penta-co-ordinate does not occur with similar hexa-co-ordinate haemoglobins such as neuroglobin, and therefore appears to be a unique property of cytoglobin among the haemoglobin superfamily. The lipid-derived transformation may explain why cytoglobin has enhanced peroxidatic activity, converting lipids into various oxidized products, a property virtually absent from neuroglobin and much decreased in myoglobin. We propose that the binding of ferric cytoglobin to lipids and their subsequent transformation may be integral to the physiological function of cytoglobin, generating cell signalling lipid molecules under an oxidative environment.
A lipidomic screen of palmitate-treated MIN6 β-cells links sphingolipid metabolites with endoplasmic reticulum (ER) stress and impaired protein trafficking
Authors: Boslem Ebru , MacIntosh Gemma , Preston Amanda M. , Bartley Clarissa , Busch Anna K. , Fuller Maria , Laybutt D. Ross , Meikle Peter J. , Biden Trevor J. 
Published: February 2011

Saturated fatty acids promote lipotoxic ER (endoplasmic reticulum) stress in pancreatic β-cells in association with Type 2 diabetes. To address the underlying mechanisms we employed MS in a comprehensive lipidomic screen of MIN6 β-cells treated for 48 h with palmitate. Both the overall mass and the degree of saturation of major neutral lipids and phospholipids were only modestly increased by palmitate. The mass of GlcCer (glucosylceramide) was augmented by 70% under these conditions, without any significant alteration in the amounts of either ceramide or sphingomyelin. However, flux into ceramide (measured by [3H]serine incorporation) was augmented by chronic palmitate, and inhibition of ceramide synthesis decreased both ER stress and apoptosis. ER-to-Golgi protein trafficking was also reduced by palmitate pre-treatment, but was overcome by overexpression of GlcCer synthase. This was accompanied by increased conversion of ceramide into GlcCer, and reduced ER stress and apoptosis, but no change in phospholipid desaturation. Sphingolipid alterations due to palmitate were not secondary to ER stress since they were neither reproduced by pharmacological ER stressors nor overcome using the chemical chaperone phenylbutyric acid. In conclusion, alterations in sphingolipid, rather than phospholipid, metabolism are more likely to be implicated in the defective protein trafficking and enhanced ER stress and apoptosis of lipotoxic β-cells.
Structure and mechanism of the chalcogen-detoxifying protein TehB from Escherichia coli
Authors: Choudhury Hassanul G. , Cameron Alexander D. , Iwata So , Beis Konstantinos 
Published: February 2011

The oxyanion derivatives of the chalcogens tellurium and selenium are toxic to living organisms even at very low levels. Bacteria have developed mechanisms to overcome their toxicity by methylating them. The structure of TehB from Escherichia coli has been determined in the presence of the cofactor analogues SAH (S-adenosylhomocysteine) and sinefungin (a non-hydrolysable form of S-adenosyl-L-methionine) at 1.48 Å (1 Å=0.1 nm) and 1.9 Å respectively. Interestingly, our kinetic data show that TehB does not discriminate between selenium or tellurite oxyanions, making it a very powerful detoxifying protein. Analysis of the active site has identified three conserved residues that are capable of binding and orientating the metals for nucleophilic attack: His176, Arg177 and Arg184. Mutagenesis studies revealed that the H176A and R184A mutants retained most of their activity, whereas the R177A mutant had 65% of its activity abolished. Based on the structure and kinetic data we propose an SN2 nucleophilic attack reaction mechanism. These data provide the first molecular understanding of the detoxification of chalcogens by bacteria.
RECQL5 is an important determinant for camptothecin tolerance in human colorectal cancer cells
Authors: Wang Xiaoqi , Lu Xincheng , Zhou Guangjin , Lou Hua , Luo Guangbin 
Published: February 2011

CPTs (camptothecins) are an important class of effective anticancer agents that target type I topoisomerase in humans. Irinotecan and topotecan are currently used to treat various types of cancers and many CPT derivatives are being developed. However, these drugs are only effective in a small percentage of each type of cancer and the molecular underpinning for this individualized response to the drug has remained elusive. Thus, identification of the main determinants for cell survival in response to this unique class of drug should help to improve their clinical applications. In the present study, we examined whether RECQL5 constitutes an important determinant of CPT resistance in colon cancer cells. Specifically, RECQL5-deficient derivatives of both DDL1 and HCT116 cells, two colorectal cancer cell lines were generated by adenovirus-based somatic gene-targeting experiments and the CPT sensitivity between the RECQL5-proficient parental lines and their corresponding RECQL5-deficient derivatives were examined. We found that deletion of RECQL5 from DDL1 and HCT116 cells both resulted in a significant enhancement in CPT sensitivity under in vitro culture conditions. More importantly, xenograft tumours derived from RECQL5-deficient HCT116 cells, but not those from the parental line, could be cured by a CPT-based therapy in nude mice. Thus, the present study has identified RECQL5 as a major determinant for CPT resistance in colorectal cancer cells and a potential candidate as a biomarker for irinotecan-based treatment for colon cancer.
Multispectral labeling of antibodies with polyfluorophores on a DNA backbone and application in cellular imaging
Authors: Guo Jia , Wang Shenliang , Dai Nan , Teo Yin Nah , Kool Eric T. 
Published: February 2011

Most current approaches to multiantigen fluorescent imaging require overlaying of multiple images taken with separate filter sets as a result of differing dye excitation requirements. This requirement for false-color composite imaging prevents the user from visualizing multiple species in real time and disallows imaging of rapidly moving specimens. To address this limitation, here we investigate the use of oligodeoxyfluoroside (ODF) fluorophores as labels for antibodies. ODFs are short DNA-like oligomers with fluorophores replacing the DNA bases and can be assembled in many colors with excitation at a single wavelength. A DNA synthesizer was used to construct several short ODFs carrying a terminal alkyne group and having emission maxima of 410–670 nm. We developed a new approach to antibody conjugation, using Huisgen–Sharpless cycloaddition, which was used to react the alkynes on ODFs with azide groups added to secondary antibodies. Multiple ODF-tagged secondary antibodies were then used to mark primary antibodies. The set of antibodies was tested for spectral characteristics in labeling tubulin in HeLa cells and revealed a wide spectrum of colors, ranging from violet-blue to red with excitation through a single filter (340–380 nm). Selected sets of the differently labeled secondary antibodies were then used to simultaneously mark four antigens in fixed cells, using a single image and filter set. We also imaged different surface tumor markers on two live cell lines. Experiments showed that all colors could be visualized simultaneously by eye under the microscope, yielding multicolor images of multiple cellular antigens in real time.
Annotating genes and genomes with DNA sequences extracted from biomedical articles
Authors: Haeussler Maximilian , Gerner Martin , Bergman Casey M. 
Published: February 2011

Abstract
Motivation: Increasing rates of publication and DNA sequencing make the problem of finding relevant articles for a particular gene or genomic region more challenging than ever. Existing text-mining approaches focus on finding gene names or identifiers in English text. These are often not unique and do not identify the exact genomic location of a study.
Results: Here, we report the results of a novel text-mining approach that extracts DNA sequences from biomedical articles and automatically maps them to genomic databases. We find that ∼20% of open access articles in PubMed central (PMC) have extractable DNA sequences that can be accurately mapped to the correct gene (91%) and genome (96%). We illustrate the utility of data extracted by text2genome from more than 150 000 PMC articles for the interpretation of ChIP-seq data and the design of quantitative reverse transcriptase (RT)-PCR experiments.
Conclusion: Our approach links articles to genes and organisms without relying on gene names or identifiers. It also produces genome annotation tracks of the biomedical literature, thereby allowing researchers to use the power of modern genome browsers to access and analyze publications in the context of genomic data.
Availability and implementation: Source code is available under a BSD license from http://sourceforge.net/projects/text2genome/ and results can be browsed and downloaded at http://text2genome.org.
Contact: maximilianh@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Sediment accumulation and bioturbation rates in the deep Northeast Atlantic determined by radiometric techniques
Authors: Carvalho Fernando P. , Oliveira João M. , Soares António M. M. 
Published: February 2011

Abstract
Carvalho, F. P., Oliveira, J. M., and Soares, A. M. M. 2011. Sediment accumulation and bioturbation rates in the deep Northeast Atlantic determined by radiometric techniques. – ICES Journal of Marine Science, 68: . The upper layers of boxcore bottom-sediment samples from the Porcupine Abyssal Plain (five cores) and from the Iberian Abyssal Plain (eight cores) in the Northeast Atlantic were analysed for porosity, grain size, organic carbon, calcium carbonate, and radionuclides. Radiometric ages of sediment layers were determined using 230Th excess (the 230Thexc/232Th ratio method) and 14C radionuclides. Sediment accumulation rates were 0.14 and 3.2 cm kyear−1 at the Porcupine and Iberian Abyssal Plains, respectively. Sediment mixing, determined through 210Pb excess, was in the upper 5–11 cm sediment layer, likely as a result of infauna activity. Biodiffusion coefficients averaged 0.40 ± 0.37 and 1.05 ± 1.02 cm2 year–1 and were not significantly different in the sediments of either abyssal plain. The low rates of sediment accumulation and bioturbation in the abyssal depths of the Northeast Atlantic suggested that immobilization of sediment-reactive man-made radionuclides released near the seafloor will take place very slowly and with limited sediment burial.
New Insights Into the Pathogenesis of Inflammatory Bowel Disease: Transcription Factors Analysis in Bioptic Tissues From Pediatric Patients
Authors: Pierdomenico Maria , Stronati Laura , Costanzo Manuela , Vitali Roberta , Di Nardo Giovanni , Nuti Federica , Oliva Salvatore , Cucchiara Salvatore , Negroni Anna 
Published: February 2011

ABSTRACTObjectives:Our work is aimed at identifying ex vivo new transcription factors, potentially involved in the pathogenesis of pediatric inflammatory bowel disease (IBD), by using a microarray approach.Patients and Methods:Microarray, including 84 transcription factors, was performed in inflamed and uninflamed mucosal tissues of pediatric patients with Crohn disease (CD) and in healthy controls. Real‐time polymerase chain reaction was used to confirm microarray results on a larger size of CD and patients with ulcerative colitis (UC). Protein expression was evaluated by Western blot assay.Results:Microarray assay showed 40 genes differentially regulated in the inflamed mucosa and 17 in the uninflamed mucosa of patients with CD as compared with controls. Real‐time polymerase chain reaction analysis revealed 10 transcripts in CD and 4 in UC, selected among those with higher differences as compared with healthy controls, significantly overexpressed in the inflamed tissues of patients. Moreover, 4 transcripts in CD and 2 in UC were found significantly upregulated in the uninvolved tissue. A further investigation evidenced an increased protein expression of activating transcription factor 3 and hypoxia‐inducible transcription factor‐1α in patients with CD as well as in Caco2 cell line stimulated by cytokines and hypoxia.Conclusions:The present study shows an evident upregulation of several transcription factors in the inflamed and uninflamed mucosa of children with IBD, suggesting that the inflammatory process is somehow activated at molecular levels even in the macroscopically normal mucosa of patients. A differential pattern of gene expression between CD and UC indicates distinct molecular mechanisms underlying the pathogenesis of 2 diseases. Finally, activating transcription factor 3 and hypoxia‐inducible transcription factor‐1α are proposed as new transcription factors potentially involved in the onset and maintenance of IBD.