bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nitrogen fixation in an anticyclonic eddy in the oligotrophic North Pacific Ocean
Authors: Fong Allison A , Karl David M , Lukas Roger , Letelier Ricardo M , Zehr Jonathan P , Church Matthew J 
Published: February 2008

Abstract
Mesoscale physical processes (for example eddies, frontal meanders and planetary waves) can play important roles in controlling ocean biogeochemistry. We examined spatial variations in upper ocean (0–100 m) nutrient inventories, N2 fixing microorganism diversity and abundance, and rates of N2 fixation in an anticyclonic eddy near Station ALOHA (22° 45′ N, 158° 00′ W) in the North Pacific Subtropical Gyre (NPSG). In July 2005, satellite-based sea surface altimetry and ocean color observation revealed an anticyclonic eddy with enhanced chlorophyll in the upper ocean in the vicinity of Station ALOHA. Within the eddy, near-surface ocean chlorophyll concentrations were ∼5-fold greater than in the surrounding waters. Inventories of nitrate and phosphate in the eddy were similar to the concentrations historically observed at Station ALOHA, while silicic acid inventories were significantly depleted (one-way analysis of variance, P&lt;0.01). Quantitative PCR determinations of nifH gene copies revealed relatively high abundances of several N2 fixing cyanobacteria, including Trichodesmium spp., Crocosphaera watsonii and Richelia intracellularis. Reverse transcriptase PCR (RT-PCR) amplified nitrogenase (nifH) gene transcripts were cloned and sequenced to examine the diversity of active N2 fixing microorganisms; these clone libraries were dominated by sequence-types 97%–99% identical to the filamentous cyanobacteria Trichodesmium spp. Near-surface ocean rates of N2 fixation were 2–18 times greater (averaging 8.6±5.6 nmol N per l per day) than previously reported measurements at Station ALOHA. These results suggest that mesoscale physical variability can play an important role in modifying the abundances of N2 fixing microorganisms and associated rates of N2 fixation in open ocean ecosystems.
Maintenance of Weight Loss in Overweight Middle‐aged Women Through the Internet
Authors: Cussler Ellen C. , Teixeira Pedro J. , Going Scott B. , Houtkooper Linda B. , Metcalfe Lauve L. , Blew Robert M. , Ricketts Jennifer R. , Lohman J'Fleur , Stanford Vanessa A. , Lohman Timothy G. 
Published: February 2008

Objective: The purpose of this study was to compare weight regain in a group of perimenopausal women (48.0 ± 4.4 years old), randomized to a 12‐month weight maintenance Internet intervention or to self‐directed weight maintenance after a 4‐month weight loss treatment.Methods and Procedures: After a 4‐month behavioral weight loss program, 135 women were randomized to either Internet or self‐directed groups. The Internet group (n = 66) used a website to gain information and complete logs concerning their weight, diet, and exercise progress over a 12‐month follow‐up. The 69 self‐directed women had no contact with study staff. All women were measured for weight and body composition, and diet intake, and were interviewed using the 7‐day physical activity questionnaires at baseline, 4 months, and 16 months.Results: At the end of the 12‐month follow‐up, the Internet and self‐directed groups had regained on average 0.4 ± 5.0 kg and 0.6 ± 4.0 kg, respectively (P = 0.5). In within‐group analyses, Internet diet‐log entries were correlated with follow‐up weight change (r = −0.29; P < 0.05) and moderately with change in exercise energy expenditure (EEE; r = 0.44; P < 0.01). Follow‐up weight change was not correlated with change in dietary intake.Discussion: While significant weight loss was maintained over follow‐up by both groups of women, Internet use did not surpass self‐direction in helping to sustain weight loss. Among Internet users, Internet use was related to weight change and EEE.
Decidual expression and maternal serum levels of heme oxygenase 1 are increased in pre‐eclampsia
Authors: EIDE IRINA P. , ISAKSEN CHRISTINA V. , SALVESEN KJELL Å. , LANGAAS METTE , SCHØNBERG SVANHILD A. , AUSTGULEN RIGMOR 
Published: February 2008

AbstractBackground. Pre‐eclampsia (PE) is associated with increased oxidative stress and excessive maternal inflammatory response. Heme oxygenase 1 (HMOX1) is an important stress response enzyme and a mediator of cytoprotection against a wide variety of tissue injuries. Methods. In the present study, microarray technology was used to compare the expression of HMOX1 and other genes involved in stress and inflammatory responses in decidua basalis from 16 pregnancies complicated by PE and 17 healthy controls. In addition, the presence of HMOX1 protein in decidua basalis was examined by means of immunohistochemistry, and ELISA was used to measure the maternal serum concentration of HMOX1. Results. Fifteen transcripts involved in stress response including HMOX1 were up‐regulated in cases, using a cut‐off value at p = 0.01. HMOX1 protein expression in decidua basalis was significantly increased in cases compared to controls reflected by more pronounced intensity of HMOX1 positive decidual cells (1.8±0.3 versus 1.5±0.4, p = 0.02) and an increased proportion of HMOX1 positive decidual leukocytes (31±29 versus 9±6%, p = 0.001). Finally, serum HMOX1 levels were significantly higher among cases compared to controls (3.1±1.3 versus 1.9±0.5 ng/ml, p = 0.008). Conclusions. Increased decidual and serum HMOX1 levels, together with altered decidual expression of some stress‐related genes in cases, support the role of oxidative stress and excessive maternal inflammatory response in the pathogenesis of PE.
Smoking during pregnancy from 1999 to 2004: a study from the Medical Birth Registry of Norway
Authors: KVALVIK LIV GRIMSTVEDT , SKJÆRVEN ROLV , HAUG KJELL 
Published: February 2008

AbstractBackground. The aims of the study were to describe changes in smoking habits and evaluate secular trends among all Norwegian pregnant women during the period 1999–2004. We wanted to investigate whether there was a general decline in smoking habits among pregnant women. We also wanted to identify population subgroups with diverging trends. Methods. The Medical Birth Registry of Norway (MBR) has national coverage of all births of 16 or more gestational weeks. Since 1999, women have been asked about tobacco smoking at the beginning and at the end of pregnancy. We included records from 304,905 women giving birth in the period January 1999 through April 2004. Women born outside Norway were handled separately. The selection left a dataset containing 259,573 Norwegian‐born women. Results. We obtained information on smoking habits from 86% at the end of pregnancy. Among those, the daily smoking prevalence was reduced from 17.3% in 1999–2001 to 13.2% in 2002–2004. Higher smoking prevalence was found among multiparous (3+), teenage mothers, single women, and women with low educational level. Conclusions. From 1999 to 2004, a substantial decline in smoking prevalence among Norwegian pregnant women was identified in all subgroups. However, an increasing social polarisation with regard to education and smoking habits was observed in the study period. In order to reduce the smoking‐related risks for unsuccessful pregnancy outcome, special attention should be paid to smoking habits among multiparous, teenage women, single women and women with low education.
Validation study of the capacity of the reference curves of ultrasonographic measurements of the umbilical cord to identify deviations in estimated fetal weight
Authors: BARBIERI CRISTIANE , GUILHERME CECATTI JOSE , KRUPA FABIANA , FRANCISCO MARUSSI EMILIO , VILTON COSTA JOSE 
Published: February 2008

AbstractBackground. The objective of this study was to evaluate the capacity of the cross‐sectional area and diameter of the umbilical cord, and the area of Wharton's jelly (WJ), to predict abnormalities in estimated fetal weight (EFW) in 20–40 week, low‐risk pregnancies. Methods. A validation study was performed in 1,828 pregnant women. Fetal weight was estimated by ultrasonography and classified as: small for gestational age (SGA), appropriate for gestational age (AGA) or large for gestational age (LGA) according to the 10th and 90th percentiles of the reference curve. Measurements of the parameters of the cord were used to classify it as thin, normal or thick using the 10th and 90th percentiles of the reference curves as limits. The capacity of the diameter and total area of the cord and the area of WJ to predict abnormal EFW was calculated for different gestational ages. Results. The capacity of the diameter of thin cords to predict SGA fetuses (S =8.3%, PPV =16.5%) or thick cords to predict LGA fetuses (S =5.5%, PPV =30.1) was weak, similar to the capacity of the area of the umbilical cord to predict SGA (S =8.3%; PPV =16.3%) or LGA fetuses (S =5.5%; PPV =27.8%). The capacity of the area of WJ to predict SGA fetuses (S =5.7%, PPV =11.7%) was similar to its capacity to predict LGA fetuses (S =4%, PPV =27.1%). Conclusion. Despite the correlation between the diameter and cross‐sectional area of the cord and EFW, these measurements were not found to be useful in predicting alterations in EFW and should not be used for this purpose.
Tracing evolutionary pressure
Authors: Ye Kai , Vriend Gert , IJzerman Adriaan P. 
Published: February 2008

Abstract
Motivation: Recent advances in sequencing techniques have yielded enormous amounts of protein sequence data from various species. This large dataset allows sequence comparison between paralogous and orthologous proteins to identify motifs or functional positions that account for the differences of functional subgroups (‘specificity’ positions). Algorithms such as SDPpred and the two-entropies analysis (TEA) have been developed to detect such specificity positions from a multiple sequence alignment (MSA) grouped into classes according to certain biological functions. Other algorithms such as TreeDet compute a classification and then predict specificity positions associated with it. However, there are still many unresolved questions: Was the optimal subdivision of a protein family achieved? Do the definitions at different levels of the phylogenetic tree affect the prediction of specificity positions? Can the whole phylogenetic tree be used instead of only one level in it to predict specificity positions?
Results: Here we present a novel method, TEA-O (Two-entropies analysis—Objective), to trace the evolutionary pressure from the root to the branches of the phylogenetic tree. At each level of the tree, a TEA plot is produced to capture the signal of the evolutionary pressure. A consensus TEA-O plot is composed from the whole series of plots to provide a condensed representation. Positions related to functions that evolved early (conserved) or later (specificity) are close to the lower-left or upper-left corner of the TEA-O plot, respectively. This novel approach allows an unbiased, user-independent, analysis of residue relevance in a protein family.
We compared our TEA-O method with various algorithms using both synthetic and real protein sequences. The results show that our method is robust, sensitive to subtle differences in evolutionary pressure during evolution and comprehensive because all positions in the MSA are presented in the consensus plot.
Availability: All computer programs and datasets used in this work are available at http://nava.liacs.nl/kye/TEA-O/ for academic use
Contact: k.ye@lacdr.leidenuniv.nl
FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors
Authors: Park Jongsun , Park Jaejin , Jang Suwang , Kim Seryun , Kong Sunghyung , Choi Jaeyoung , Ahn Kyohun , Kim Juhyeon , Lee Seungmin , Kim Sunggon , Park Bongsoo , Jung Kyongyong , Kim Soonok , Kang Seogchan , Lee Yong-Hwan 
Published: February 2008

Abstract
Summary: Genomes of more than 60 fungal species have been sequenced to date, yet there has been no systematic approach to analyze fungal transcription factors (TFs) kingdom widely. We developed a standardized pipeline for annotating TFs in fungal genomes. Resulting data have been archived in a new database termed the Fungal Transcription Factor Database (FTFD). In FTFD, 31 832 putative fungal TFs, identified from 62 fungal and 3 Oomycete species, were classified into 61 families and phylogenetically analyzed. The FTFD will serve as a community resource supporting comparative analyses of the distribution and domain structure of TFs within and across species.
Availability: All data described in this study can be browsed through the FTFD web site at http://ftfd.snu.ac.kr/.
Contact: yonglee@snu.ac.kr
DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra
Authors: Mayampurath Anoop M. , Jaitly Navdeep , Purvine Samuel O. , Monroe Matthew E. , Auberry Kenneth J. , Adkins Joshua N. , Smith Richard D. 
Published: February 2008

Abstract
Summary: DeconMSn accurately determines the monoisotopic mass and charge state of parent ions from high-resolution tandem mass spectrometry data, offering significant improvement for LTQ_FT and LTQ_Orbitrap instruments over the commercially delivered Thermo Fisher Scientific's extract_msn tool. Optimal parent ion mass tolerance values can be determined using accurate mass information, thus improving peptide identifications for high-mass measurement accuracy experiments. For low-resolution data from LCQ and LTQ instruments, DeconMSn incorporates a support-vector-machine-based charge detection algorithm that identifies the most likely charge of a parent species through peak characteristics of its fragmentation pattern.
Availability: http://ncrr.pnl.gov/software/ or http://www.proteomicsresource.org/
Contact: rds@pnl.gov
Supplementary information: PowerPoint presentation/Poster on http://ncrr.pnl.gov/software/.
Metabolic and Developmental Adaptations of Growing Potato Tubers in Response to Specific Manipulations of the Adenylate Energy Status
Authors: Riewe David , Grosman Lukasz , Zauber Henrik , Wucke Cornelia , Fernie Alisdair R. , Geigenberger Peter 
Published: February 2008

AbstractHeterotrophic carbon metabolism has been demonstrated to be limited by oxygen availability in a variety of plant tissues, which in turn inevitably affects the adenylate status. To study the effect of altering adenylate energy metabolism, without changing the oxygen supply, we expressed a plastidially targeted ATP/ADP hydrolyzing phosphatase (apyrase) in tubers of growing potato (Solanum tuberosum) plants under the control of either inducible or constitutive promoters. Inducible apyrase expression in potato tubers, for a period of 24 h, resulted in a decrease in the ATP-content and the ATP-ADP ratio in the tubers. As revealed by metabolic profiling, this was accompanied by a decrease in the intermediates of sucrose to starch conversion and several plastidially synthesized amino acids, indicating a general depression of tuber metabolism. Constitutive tuber-specific apyrase expression did not lead to a reduction of ATP, but rather a decrease in ADP and an increase in AMP levels. Starch accumulation was strongly inhibited and shifted to the production of amylopectin instead of amylose in these tubers. Furthermore, the levels of almost all amino acids were decreased, although soluble sugars and hexose-Ps were highly abundant. Respiration was elevated in the constitutively expressing lines indicating a compensation for the dramatic increase in ATP hydrolysis. The increase in respiration did not affect the internal oxygen tensions in the tubers. However, the tubers developed a ginger-like phenotype having an elevated surface-volume ratio and a reduced mass per tuber. Decreased posttranslational redox activation of ADP-glucose pyrophosphorylase and a shift in the ratio of soluble starch synthase activity to granule-bound starch synthase activity were found to be partially responsible for the alterations in starch structure and abundance. The activity of alcohol dehydrogenase was decreased and pyruvate decarboxylase was induced, but this was neither reflected by an increase in fermentation products nor in the cellular redox state, indicating that fermentation was not yet induced in the transgenic lines. When taken together the combined results of these studies allow the identification of both short- and long-term adaptation of plant metabolism and development to direct changes in the adenylate status.
Engineering membrane protein overproduction in Escherichia coli
Authors: Molina Daniel Martinez , Cornvik Tobias , Eshaghi Said , Haeggström Jesper Z. , Nordlund Pär , Sabet Marina Ignatushchenko 
Published: February 2008

AbstractMembrane proteins play a fundamental role in human disease and therapy, but suffer from a lack of structural and functional information compared to their soluble counterparts. The paucity of membrane protein structures is primarily due to the unparalleled difficulties in obtaining detergent‐solubilized membrane proteins at sufficient levels and quality. We have developed an in vitro evolution strategy for optimizing the levels of detergent‐solubilized membrane protein that can be overexpressed and purified from recombinant Escherichia coli. Libraries of random mutants for nine membrane proteins were screened for expression using a novel implementation of the colony filtration blot. In only one cycle of directed evolution were significant improvements of membrane protein yield obtained for five out of nine proteins. In one case, the yield of detergent‐solubilized membrane protein was increased 40‐fold.
Clinical features and mismatch repair genes analyses of Chinese suspected hereditary non‐polypsis colorectal cancer: A cost‐effective screening strategy proposal
Authors: Yan Hong‐Li , Hao Li‐Qiang , Jin Hei‐Ying , Xing Qing‐He , Xue Geng , Mei Qian , He Jin , He Lin , Sun Shu‐Han 
Published: February 2008

China has the largest numbers of hereditary non‐polyposis colorectal cancer (HNPCC) patients based on its population of 1.4 billion. However, the clinical data and mismatch repair (MMR) gene analyses have been limited. Here we performed microsatellite instability (MSI) and immunohistochemistry (IHC) analyses on a series of patients with a high‐risk for HNPCC: 61 patients with family histories fulfilling Amsterdam criteria II (ACII‐HNPCC) or suspected HNPCC criteria (S‐HNPCC), and 106 early onset colorectal cancer (CRC) patients. Sixty late‐onset CRC patients were used as control. Methylation of the hMLH1 promoter was analyzed on tumors lacking hMLH1 expression. MMR germ‐line mutations were screened on patients with tumors classified as MSI‐H/L or negative for IHC. We identified 27 germ‐line MMR variants in the 167 patients with a high‐risk for HNPCC while only one germ‐line mutation in hMSH6 was found in the late‐onset CRC group. Of those, 23 were pathogenic mutations. The high incidence of gastric and hepatobiliary cancers coupled with the increasing number of small families in China reduces the sensitivity (43.5%, 30.4%) and positive predictive value (PPV) (45.5%, 17.9%) of the ACII‐ or S‐HNPCC criteria. MSI or IHC testing are highly sensitive in detecting pathogenic mutations (sensitivities = 91.3% and 95.6%, respectively), but the PPVs are quite low (25.6% and 27.8%, respectively). Considering that all 12 tumors with pathogenic mutations in hMLH1 also showed promoter unmethylation, the sensitivity of IHC in conjunction with hMLH1 promoter methylation analysis is not reduced, but the PPV was increased from 27.8% to 61.1%, and the total cost was greatly reduced. (Cancer Sci 2008; 99: 770–780)
MAGE‐C1/CT‐7 expression in plasma cell myeloma: Sub‐cellular localization impacts on clinical outcome
Authors: Tinguely M. , Jenni B. , Knights A. , Lopes B. , Korol D. , Rousson V. , Curioni Fontecedro A. , Cogliatti S. B. , Bittermann A. G. , Schmid U. , Dommann‐Scherrer C. , Maurer R. , Renner C. , Probst‐Hensch N. M. , Moch H. , Knuth A. , Zippelius A. 
Published: February 2008

Plasma cell myelomas (PMs) have a poor prognosis. Cancer‐testis (CT) antigens are immunogenic proteins, representing potential targets for tumor vaccination strategies. The expression of the CT antigens GAGE, MAGE‐A4, MAGE‐C1/CT‐7, and NY‐ESO‐1 was investigated on paraffin‐embedded bone marrow biopsies from 219 PM and 8 monoclonal gammopathy of undetermined significance (MGUS) patients. The frequency and prognostic impact of these CT antigens were compared with known morphological prognostic markers (i.e. Mib1 labeling index) and the presence of the translocations t(4;14)(p16.3; q32) and t(11;14)(q13;q32). We show that MAGE‐C1/CT‐7 is the most prevalent CT antigen, expressed in 57% of PMs in a high percentage of tumor cells. While MAGE‐C1/CT‐7 was absent in non‐malignant plasma cells, plasma cells of patients with MGUS did express MAGE‐C1/CT‐7, but no other CT antigens. MAGE‐C1/CT‐7 was more frequently expressed in PMs with an elevated proliferation rate (Mib1 >10%) compared to PMs with a low proliferation rate (Mib1 ≤10%, 71%versus 29%, P < 0.001) and correlated with overall survival, depending on its subcellular distribution. PMs with pure cytoplasmic MAGE‐C1/CT‐7 expression showed a better prognosis (48 months versus 33 months, P < 0.05) than PMs with combined nuclear‐cytoplasmic or nuclear expression only. Thus, expression of MAGE‐C1/CT‐7 in patients with monoclonal gammopathies represents a predictor of outcome and overt malignant transformation. (Cancer Sci 2008; 99: 720–725)
High prevalence of apical periodontitis amongst smokers in a sample of Spanish adults
Authors: Segura‐Egea J. J. , Jiménez‐Pinzón A. , Ríos‐Santos J. V. , Velasco‐Ortega E. , Cisneros‐Cabello R. , Poyato‐Ferrera M. M. 
Published: February 2008

AbstractAim  To study the prevalence of apical periodontitis in smoker and nonsmoker patients.Methodology  In a cross‐sectional study, the records of 180 subjects, 109 smokers and 71 nonsmokers, were examined. All participants underwent a full‐mouth radiographic survey incorporating 14 periapical radiographs. The periapical region of all teeth, excluding third molars, was examined. Periapical status was assessed using the Periapical Index score. Statistical analyses were conducted using the Cohen’s Kappa test, analysis of variance and logistic regression.Results  Apical periodontitis in at least one tooth was found in 74% of smokers and in 41% of nonsmokers (P < 0.01; odds ratio = 4.2; 95% C. I. = 2.2–7.9). Amongst smoker patients 5% of the teeth had apical periodontitis, whereas in nonsmoker subjects 3% of teeth were affected (P = 0.008; odds ratio = 1.5; 95% C. I. = 1.1–2.1). The percentage of root filled teeth in smoker and nonsmoker patients was 2.5% and 1.5%, respectively (P < 0.05; odds ratio = 1.7; C. I. 95% = 1.0–2.6).Conclusions  In this study population, smoking was significantly associated with a greater frequency of root canal treatment and with an increased prevalence of apical periodontitis.