bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in dietary intake from the first to the second trimester of pregnancy
Authors: Rifas‐Shiman Sheryl L. , Rich‐Edwards Janet W. , Willett Walter C. , Kleinman Ken P. , Oken Emily , Gillman Matthew W. 
Published: January 2006

SummaryMaternal diet may influence outcomes of pregnancy and childhood. Diet in the first trimester may be more important to development and differentiation of various organs, whereas diet later in pregnancy may be important for overall fetal growth as well as for brain development. To our knowledge, no studies have examined individual‐level changes in food and nutrient intake from the 1st to 2nd trimester of pregnancy. The objective of this study was to examine changes in dietary intake from the 1st to 2nd trimester of pregnancy. As part of the ongoing US prospective cohort study, Project Viva, we studied 1543 women who completed food‐frequency questionnaires that assessed dietary intakes during the 1st and 2nd trimester of pregnancy. For both foods and energy‐adjusted nutrients, we examined changes in dietary intake from 1st to 2nd trimester.Reported mean energy intake was similar for the 1st (2046 kcal) and 2nd (2137 kcal) trimesters. Foods and energy‐adjusted nutrients from foods whose overall mean intakes increased more than 5% from 1st to 2nd trimester were skim or 1% dairy foods (22%), whole‐fat dairy foods (15%), red and processed meat (11%), saturated fat (6%) and vitamin D (7%). Intake of caffeinated beverages (−30%) and alcoholic beverages (−88%) decreased more than 5%. Because mean multivitamin intake increased by 35% from the 1st to 2nd trimester, total micronutrient intake increased appreciably more than micronutrient intake from foods only. Correlations across trimesters ranged from 0.32 for vitamin B12 to 0.68 for fruit and vegetables.In conclusion, for many outcomes of pregnancy and childhood, the incremental information obtained from assessing complete diet in both early and late pregnancy may not outweigh the burden to participants and investigators. However, investigators should assess caffeine, alcohol, and vitamin and supplement use in both the 1st and 2nd trimester, and consider doing so for foods and nutrients for which trimester‐specific hypotheses are well substantiated.
Reproducibility of assays for steroid hormones, prolactin and insulin‐like growth factor‐1 in umbilical cord blood
Authors: Baik Inkyung , Liu Qin , Sturgeon Susan , Stanek Edward J. , Okulicz William , Hsieh Chung‐Cheng 
Published: January 2006

SummaryWe assessed the reproducibility of measurements of plasma hormone and binding protein levels in umbilical cord blood collected from 30 male and female babies. They were delivered as singleton births from full‐term pregnancies (gestational age ≥ 37 weeks) in a cord blood donation programme. We assayed three plasma replicates from each cord blood sample at two points in time. Plasma oestradiol, unconjugated oestriol, testosterone, progesterone, prolactin, sex‐hormone binding globulin (SHBG), insulin‐like growth factor‐1 (IGF‐1), and IGF binding protein‐3 (IGFBP‐3) levels were measured in duplicates in the same batch (batch 1). In addition, another set of assays was conducted for each cord blood 1 year apart in a different batch (batch 2). Means and standard deviations for each hormone and binding protein were similar in replicates assayed in batch 1 and 2. Pearson's correlation coefficients were 0.9 or higher in duplicates assayed in batch 1. The correlation coefficients were between 0.77 and 0.96 for between‐batch assays. Intra‐class correlation coefficients (ICC) were higher than 0.9 for assay of SHBG [95% CI 0.92, 1.0] and progesterone [95% CI 0.87, 0.97] and between 0.8 and 0.9 for assay of oestradiol, unconjugated oestriol, prolactin, IGF‐1, and IGFBP‐3. The lowest ICC value was found for testosterone (ICC = 0.74; [95% CI 0.56, 1.0]). These data indicate a high reproducibility of cord blood hormone measurements; minimal differences were observed between the calibrated and the original regression coefficients for the association of hormones/binding proteins with percent of CD34+ cells in mononuclear cells.
Methodological challenges in studying labour progression in contemporary practice
Authors: Vahratian Anjel , Troendle James F. , Siega‐Riz Anna Maria , Zhang Jun 
Published: January 2006

SummaryIn the 1950s, Emanuel Friedman described the first comprehensive method of evaluating labour in clinical practice. In this landmark work, Friedman described the relationship between the duration of labour and cervical dilation as a sigmoid curve and outlined a tool for following labour progression and for identifying abnormal labour. His definitions of labour protraction and arrest continue to be applied in contemporary obstetric practice, although there have been considerable changes since in the clinical management of labour and delivery. This paper provides an overview of Friedman's work, addresses various methodological challenges in studying labour progression, and describes the utility of more advanced statistical methods for studying labour progression, such as survival analysis, compared with other approaches. Additional research that utilises and refines such methods will provide greater insight into labour progression and may assist in updating the diagnostic criteria for labour protraction and arrest disorders in contemporary obstetric practice. Moreover, such detailed information could have important clinical implications towards reducing the rate of primary caesarean delivery in the United States.
Plastid marker‐gene excision by transiently expressed CRE recombinase
Authors: Lutz Kerry A. , Bosacchi Massimo H. , Maliga Pal 
Published: January 2006

SummaryWe report plastid marker‐gene excision with a transiently expressed CRE, site‐specific recombinase. This is a novel protocol that enables rapid removal of marker genes from the approximately 10 000 plastid genome copies without transformation of the plant nucleus. Plastid marker excision was tested in tobacco plants transformed with a prototype polycistronic plastid vector, pPRV110L, designed to express multiple genes organized in an operon. The pMHB10 and pMHB11 constructs described here are dicistronic and encode genes for herbicide (bar) and spectinomycin (aadA) resistance. In vector pMHB11, expression of herbicide resistance is dependent on conversion of an ACG codon to an AUG translation initiation codon by mRNA editing, a safety feature that prevents translation of the mRNA in prokaryotes and in the plant nucleus. In the vectors, the marker gene (aadA) is flanked by 34‐bp loxP sites for excision by CRE. Marker excision by a transiently expressed CRE involves introduction of CRE in transplastomic leaves by agro‐infiltration, followed by plant regeneration. In tobacco transformed with vectors pMHB10 and pMHB11, Southern analysis and PCR identified approximately 10% of the regenerated plants as marker‐free.
Light‐dependent hypersensitive response and resistance signaling against Turnip Crinkle Virus in Arabidopsis
Authors: Chandra‐Shekara A. C. , Gupte Manisha , Navarre Duroy , Raina Surabhi , Raina Ramesh , Klessig Daniel , Kachroo Pradeep 
Published: January 2006

SummaryResistance to Turnip Crinkle Virus (TCV) in Arabidopsis ecotype Dijon (Di)‐17 is conferred by the resistance gene HRT and a recessive locus rrt. In Di‐17, TCV elicits a hypersensitive response (HR), which is accompanied by increased expression of pathogenesis‐related (PR) genes and high levels of salicylic acid (SA). We have previously shown that HRT‐mediated resistance to TCV is dependent on SA‐mediated signal transduction and that increased levels of SA confer enhanced resistance to TCV via upregulation of the HRT gene. Here we show that HRT‐mediated HR and resistance are dependent on light. A dark treatment immediately following TCV inoculation suppressed HR, resistance and activation of the majority of the TCV‐induced genes. However, the absence of light did not affect either TCV‐induced elevated levels of free SA or the expression of HRT. Interestingly, in the dark, transgenic plants overexpressing HRT showed susceptibility, but overexpression of HRT coupled with high levels of endogenous SA resulted in pronounced resistance. Consistent with these results is the finding that exogenous application of SA prior to TCV inoculation partially overcame the requirement for light. Light was also required for N gene‐mediated HR and resistance to Tobacco Mosaic Virus, suggesting that it is an important factor which may be generally required during defense signaling.
Islands of co‐expressed neighbouring genes in Arabidopsis thaliana suggest higher‐order chromosome domains
Authors: Zhan Shuhua , Horrocks Julie , Lukens Lewis N. 
Published: January 2006

SummaryBiochemical and cytogenetic experiments have led to the hypothesis that eukaryotic chromatin is organized into a series of distinct domains that are functionally independent. Two expectations of this hypothesis are: (i) adjacent genes are more frequently co‐expressed than is expected by chance; and (ii) co‐expressed neighbouring genes are often functionally related. Here we report that over 10% of Arabidopsis thaliana genes are within large, co‐expressed chromosomal regions. Two per cent (497/22 520) of genes are highly co‐expressed (r > 0.7), about five times the number expected by chance. These genes fall into 226 groups distributed across the genome, and each group typically contains two to three genes. Among the highly co‐expressed groups, 40% (91/226) have genes with high amino acid sequence similarity. Nonetheless, duplicate genes alone do not explain the observed levels of co‐expression. Co‐expressed, non‐homologous genes are transcribed in parallel, share functions, and lie close together more frequently than expected. Our results show that the A. thaliana genome contains domains of gene expression. Small domains have highly co‐expressed genes that often share functional and sequence similarity and are probably co‐regulated by nearby regulatory sequences. Genes within large, significantly correlated groups are typically co‐regulated at a low level, suggesting the presence of large chromosomal domains.
Rice plants take up iron as an Fe3+‐phytosiderophore and as Fe2+
Authors: Ishimaru Yasuhiro , Suzuki Motofumi , Tsukamoto Takashi , Suzuki Kazumasa , Nakazono Mikio , Kobayashi Takanori , Wada Yasuaki , Watanabe Satoshi , Matsuhashi Shinpei , Takahashi Michiko , Nakanishi Hiromi , Mori Satoshi , Nishizawa Naoko K. 
Published: January 2006

SummaryOnly graminaceous monocots possess the Strategy II iron (Fe)‐uptake system in which Fe is absorbed by roots as an Fe3+‐phytosiderophore. In spite of being a Strategy II plant, however, rice (Oryza sativa) contains the previously identified Fe2+ transporter OsIRT1. In this study, we isolated the OsIRT2 gene from rice, which is highly homologous to OsIRT1. Real‐time PCR analysis revealed that OsIRT1 and OsIRT2 are expressed predominantly in roots, and these transporters are induced by low‐Fe conditions. When expressed in yeast (Saccharomyces cerevisiae) cells, OsIRT2 cDNA reversed the growth defects of a yeast Fe‐uptake mutant. This was similar to the effect of OsIRT1 cDNA. OsIRT1– and OsIRT2–green fluorescent protein fusion proteins localized to the plasma membrane when transiently expressed in onion (Allium cepa L.) epidermal cells. OsIRT1 promoter–GUS analysis revealed that OsIRT1 is expressed in the epidermis and exodermis of the elongating zone and in the inner layer of the cortex of the mature zone of Fe‐deficient roots. OsIRT1 expression was also detected in the ccompanion cells. Analysis using the positron‐emitting tracer imaging system showed that rice plants are able to take up both an Fe3+‐phytosiderophore and Fe2+. This result indicates that, in addition to absorbing an Fe3+‐phytosiderophore, rice possesses a novel Fe‐uptake system that directly absorbs the Fe2+, a strategy that is advantageous for growth in submerged conditions.
RABBIT EARS is a second‐whorl repressor of AGAMOUS that maintains spatial boundaries in Arabidopsis flowers
Authors: Krizek Beth A. , Lewis Michael W. , Fletcher Jennifer C. 
Published: January 2006

SummaryThe RABBIT EARS (RBE) gene has been identified as a regulator of petal development in Arabidopsis thaliana. We find that second‐whorl petals in rbe mutants can be replaced with staminoid organs, stamens or filaments and that some rbe flowers have increased numbers of sepals and exhibit fusion of sepals. We show that these rbe defects are due to AGAMOUS (AG) misexpression in the second whorl. Consistent with its role in maintaining the spatial boundary of AG expression, rbe enhanced the second‐whorl defects present in ap2‐1, lug‐1 and clf‐2 mutants. In the development of second‐whorl organs, RBE acts in the same pathway and downstream of UNUSUAL FLORAL ORGANS (UFO). Enhanced first‐whorl organ fusion in ap2‐2 rbe‐3, ant‐4 rbe‐3 and cuc2‐1 rbe‐3 double mutants supports an additional role for RBE in organ separation. RBE thus acts to maintain two different types of spatial boundaries in young flowers: boundaries between organ primordia within a whorl and boundaries of homeotic gene expression between whorls.
A universal algorithm for genome‐wide in silicio identification of biologically significant gene promoter putative cis‐regulatory‐elements; identification of new elements for reactive oxygen species and sucrose signaling in Arabidopsis
Authors: Geisler Matt , Kleczkowski Leszek A. , Karpinski Stanislaw 
Published: January 2006

SummaryShort motifs of many cis‐regulatory elements (CREs) can be found in the promoters of most Arabidopsis genes, and this raises the question of how their presence can confer specific regulation. We developed a universal algorithm to test the biological significance of CREs by first identifying every Arabidopsis gene with a CRE and then statistically correlating the presence or absence of the element with the gene expression profile on multiple DNA microarrays. This algorithm was successfully verified for previously characterized abscisic acid, ethylene, sucrose and drought responsive CREs in Arabidopsis, showing that the presence of these elements indeed correlates with treatment‐specific gene induction. Later, we used standard motif sampling methods to identify 128 putative motifs induced by excess light, reactive oxygen species and sucrose. Our algorithm was able to filter 20 out of 128 novel CREs which significantly correlated with gene induction by either heat, reactive oxygen species and/or sucrose. The position, orientation and sequence specificity of CREs was tested in silicio by analyzing the expression of genes with naturally occurring sequence variations. In three novel CREs the forward orientation correlated with sucrose induction and the reverse orientation with sucrose suppression. The functionality of the predicted novel CREs was experimentally confirmed using Arabidopsis cell‐suspension cultures transformed with short promoter fragments or artificial promoters fused with the GUS reporter gene. Our genome‐wide analysis opens up new possibilities for in silicio verification of the biological significance of newly discovered CREs, and allows for subsequent selection of such CREs for experimental studies.
Self‐expanding metallic stents in the treatment of benign colorectal disease: indications and outcomes
Authors: Forshaw M. J. , Sankararajah D. , Stewart M. , Parker M. C. 
Published: January 2006

AbstractObjective  The use of stents for benign colorectal obstruction is considered controversial because of a lack of data and perceived high failure and complication rates. The aim of this study was to evaluate the indications and outcomes following stent placement for benign colorectal disease in a UK district general hospital and to review the published literature.Patients and methods  Between 1997 and 2004, 11 of 90 attempted stent insertions were performed for benign colorectal disease (diverticular disease, 4; anastomotic strictures, 4; idiopathic rectal stricture, 1; rectal endometriosis, 1; caecal volvulus, 1). Complications and outcomes were analysed from a prospective database.Results  Stent insertion was successful in nine patients. Early complications occurred in two patients (both with diverticular disease): one patient failed to decompress and needed a colostomy and laparotomy was performed in a second patient who developed peritonitis after five days although no stent perforation of the bowel was identified. Two patients were successfully decompressed and underwent subsequent elective surgery with full bowel preparation. Stent placement resulted in symptomatic improvement in three out of four patients with anastomotic strictures (allowing closure of defunctioning stomas) and in the one patient with an idiopathic rectal stricture. Stent migration occurred in two of these patients without recurrence of symptoms. Stent fracture occurred in one patient, who remained symptomatic.Conclusions  Self‐expanding metallic stents are an effective treatment for benign colorectal obstructions, especially anastomotic strictures with long‐term patency. Stents should be avoided in acute diverticular disease because of a higher incidence of complications.
Mortality after acute surgery for complications of diverticular disease of the sigmoid colon is almost exclusively due to patient related factors
Authors: Oomen J. L. T. , Engel A. F. , Cuesta M. A. 
Published: January 2006

AbstractObjective  Auditing the outcome of surgery for complicated diverticulitis of the sigmoid colon is difficult. A comparison of studies is hardly possible because risk factors both in terms of the severity of diverticulitis and patient‐related risk factors are neither well described nor standardized. The purpose of this study was to define morbidity and mortality of primary surgery for acute complications of diverticular disease of the sigmoid colon and to identify the relation between risk factors and morbidity and mortality.Methods  In a prospective computerized morbidity and mortality registration from 1990 to 2002, 114 patients, who underwent surgery on an acute or urgent base for acute complications of diverticular disease of the sigmoid colon, were identified. In all patients the POSSUM score was calculated. To audit mortality rates a POSSUM based scoring system was introduced.Results  Mortality was 16.7%, and morbidity 71.1%. Higher morbidity rates were significantly related to a higher POSSUM physiological score (P = 0.012) and to older age (P < 0.001). Higher mortality rates also were significantly related to a higher POSSUM physiological score (P < 0.001) and older age (P = 0.003). Patients who died had significantly more sepsis (P < 0.001), multiple organ failure (P = 0.027), cardiac (P < 0.001) and pulmonary (P = 0.013) complications. Gender, operation indication and type of neither surgery nor surgeon had a significant relation with morbidity or mortality.Conclusion  Surgery for acute complications of diverticular disease of the sigmoid colon carries a high morbidity rate and a substantial mortality rate. The majority of deceased patients had severe comorbidity. Post‐operative mortality and morbidity are to a large extent driven by patient related factors. Elevated physiological severity scores and a lack of peri‐operative management failures express this in the majority of deceased patients.
Reducing surgical outpatient waiting is not the solution to meeting the 2005 colorectal cancer target
Authors: Rao G. N. , Basnyat P. , Taffinder N. , Hudson C. , Insall R. 
Published: January 2006

AbstractObjectives  The majority of colorectal cancers (CRC) are not diagnosed through the Rapid access route (RAR) and follow‐ups (FU) may prolong outpatient‐waiting time for new referrals. The aim of this study was to assess the relative contributions of an efficient colorectal clinic and a stringent colonoscopy booking system on the total journey time for CRC.Patients and methods  We reduced the number of follow‐up appointments with the introduction of ‘Paper clinics’. The composition of the new clinic was determined by the known cancer yield through RAR and non‐RAR route. A prospective analysis of clinics and CRC journey times was undertaken from November 2003 for 13 months, with the new outpatient clinic template introduced in December 2003. This coincided with a stringent policy on referral pattern for colonoscopy.Results  In our hospital, only 4% of RAR yield CRC. Seventy‐five percent of our CRC are referred through the non‐RAR route. Eighty‐one percent of follow‐ups in a ‘paper clinic’ were discharged. A flexible template for the outpatient clinics, introduced a corresponding reduction in follow‐up and increased urgent and routine slots. There was a progressive drop in the follow‐up to new ratio and the waiting times for routine and urgent category decreased from a median of 15.9 and 3.4 weeks to 6.7 and 0.7 weeks, respectively (P < 0.001). Average waiting times for all categories fell from 13.35 weeks in November 2003 to 3.5 weeks in December 2004, while the number of patients waiting less than 4 weeks rose from 46% to 71%. This was associated with reduction in total journey times from 93 days to 62 days (P < 0.05). DNA rates remained unaffected.Conclusion  Modifying outpatient clinic composition with ‘paper clinics’ reduces the waiting time for all referrals to a surgical clinic with a modest effect on CRC clinic waiting time. Reduction in the total waiting time to first treatment (for CRC) is due to reducing the demand on colonoscopy in favour of barium enema. Redirecting the flow of patients towards barium enema is perhaps one way of improving the existing CRC journey time to first treatment, within existing resources. Achieving the 62 day target for cancer journey time will be difficult unless traditional surgical clinic habits are challenged.
A comparison of segmental vs subtotal/total colectomy for colonic Crohn's disease: a meta‐analysis
Authors: Tekkis P. P. , Purkayastha S. , Lanitis S. , Athanasiou T. , Heriot A. G. , Orchard T. R. , Nicholls R. J. , Darzi A. W. 
Published: January 2006

AbstractObjective  Using meta‐analytical techniques the present study evaluated differences in short‐term and long‐term outcomes of adult patients with colonic Crohn's disease who underwent either colectomy with ileorectal anastomosis (IRA) or segmental colectomy (SC).Methods  Comparative studies published between 1988 and 2002, of subtotal/total colectomy and ileorectal anastomosis vs segmental colectomy, were used. The study end points included were surgical and overall recurrence, time to recurrence, postoperative morbidity and incidence of permanent stoma. Random and fixed‐effect meta‐analytical models were used to evaluate the study outcomes. Sensitivity analysis, funnel plot and meta‐regressive techniques were carried out to explain the heterogeneity and selection bias between the studies.Results  Six studies, consisting of a total of 488 patients (223 IRA and 265 SC) were included. Analysis of the data suggested that there was no significant difference between IRA and SC in recurrence of Crohn's disease. Time to recurrence was longer in the IRA group by 4.4 years (95% CI: 3.1–5.8), P < 0.001. There was no difference between the incidence of postoperative complications (OR = 1.4., 95% CI 0.16–12.74) or the need for a permanent stoma between the two groups (OR = 2.75, 95% CI 0.78–9.71). Patients with two or more colonic segments involved were associated with lower re‐operation rate in the IRA group, a difference which did not reach statistical significance (P = 0.177).Conclusions  Both procedures were equally effective as treatment options for colonic Crohn's disease however, patients in the SC group exhibited recurrence earlier than those in the IRA group. The choice of operation is dependent on the extent of colonic disease, with a trend towards better outcomes with IRA for two or more colonic segments involved. Since no prospective randomised study has been undertaken, a clear view about which approach is more suitable for localised colonic Crohn's disease cannot be obtained.