bluuebunny/crossref_metadata_2025 huggingface dataset:
MicroGen: a MIAME compliant web system for microarray experiment information and workflow management
Authors: Burgarella Sarah , Cattaneo Dario , Pinciroli Francesco , Masseroli Marco
Published: December 2005

Background

Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results.

Results

We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME) standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services.

Conclusion

MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production.
The impact of age on post-operative outcomes of colorectal cancer patients undergoing surgical treatment
Authors: Latkauskas Tadas , Rudinskaitė Giedrė , Kurtinaitis Juozas , Jančiauskienė Rasa , Tamelis Algimantas , Saladžinskas Žilvinas , Pavalkis Dainius
Published: December 2005

Background

the purpose of study was to evaluate the impact of age on outcomes in colorectal cancer surgery.

Methods

patients on hospital database treated for colorectal cancer during the period 1995 – 2002 were divided into two groups: Group 1 – patients of 75 years or older (n = 154), and Group 2 – those younger than 75 years (n = 532).

Results

In Group 1, for colon cancers, proximal tumors were significantly more common (23% vs. 13.5%, p < 0.05), complicated cases were more frequent (46 % vs. 33%, p = 0.002), bowel obstruction more common at presentation (40% vs. 26.5%, p = 0.001), and more frequent emergency surgery required (24% vs. 14%, p = 0.003). Postoperative overall morbidity was higher in the elderly group, but with no differences in surgical complications rate. Overall 5 year survival was 39% vs. 55% (p = 0.0006) and cancer related 5 year survival was 44% vs. 62% (p = 0.0006). Multivariate Cox analysis showed that age was not an independent risk factor for postoperative mortality.

Conclusion

Preoperative complications and co-morbidities, more advanced disease, and higher postoperative nonsurgical complication rates adversely affect postoperative outcomes after surgery for colorectal cancer in the elderly.
SLIM: an alternative Web interface for MEDLINE/PubMed searches – a preliminary study
Authors: Muin Michael , Fontelo Paul , Liu Fang , Ackerman Michael
Published: December 2005

Background

With the rapid growth of medical information and the pervasiveness of the Internet, online search and retrieval systems have become indispensable tools in medicine. The progress of Web technologies can provide expert searching capabilities to non-expert information seekers. The objective of the project is to create an alternative search interface for MEDLINE/PubMed searches using JavaScript slider bars. SLIM, or Slider Interface for MEDLINE/PubMed searches, was developed with PHP and JavaScript. Interactive slider bars in the search form controlled search parameters such as limits, filters and MeSH terminologies. Connections to PubMed were done using the Entrez Programming Utilities (E-Utilities). Custom scripts were created to mimic the automatic term mapping process of Entrez. Page generation times for both local and remote connections were recorded.

Results

Alpha testing by developers showed SLIM to be functionally stable. Page generation times to simulate loading times were recorded the first week of alpha and beta testing. Average page generation times for the index page, previews and searches were 2.94 milliseconds, 0.63 seconds and 3.84 seconds, respectively. Eighteen physicians from the US, Australia and the Philippines participated in the beta testing and provided feedback through an online survey. Most users found the search interface user-friendly and easy to use. Information on MeSH terms and the ability to instantly hide and display abstracts were identified as distinctive features.

Conclusion

SLIM can be an interactive time-saving tool for online medical literature research that improves user control and capability to instantly refine and refocus search strategies. With continued development and by integrating search limits, methodology filters, MeSH terms and levels of evidence, SLIM may be useful in the practice of evidence-based medicine.
Patterns of strain and activation in the thigh muscles of goats across gaits during level locomotion
Authors: Gillis Gary B. , Flynn John P. , McGuigan Polly , Biewener Andrew A.
Published: December 2005

Unlike homologous muscles in many vertebrates, which appear to function similarly during a particular mode of locomotion (e.g. red muscle in swimming fish, pectoralis muscle in flying birds, limb extensors in jumping and swimming frogs), a major knee extensor in mammalian quadrupeds, the vastus lateralis, appears to operate differently in different species studied to date. In rats, the vastus undergoes more stretching early in stance than shortening in later stance. In dogs, the reverse is true; more substantial shortening follows small amounts of initial stretching. And in horses, while the vastus strain trajectory is complex, it is characterized mainly by shortening during stance. In this study, we use sonomicrometry and electromyography to study the vastus lateralis and biceps femoris of goats,with three goals in mind: (1) to see how these muscles work in comparison to homologous muscles studied previously in other taxa; (2) to address how speed and gait impact muscle actions and (3) to test whether fascicles in different parts of the same muscle undergo similar length changes. Results indicate that the biceps femoris undergoes substantial shortening through much of stance,with higher strains in walking and trotting [32–33% resting length(L0)] than galloping (22% L0). These length changes occur with increasing biceps EMG intensities as animals increase speed from walking to galloping. The vastus undergoes a stretch–shorten cycle during stance. Stretching strains are higher during galloping (15% L0) than walking and trotting (9%L0). Shortening strains follow a reverse pattern and are greatest in walking (24% L0), intermediate in trotting(20% L0) and lowest during galloping (17%L0). As a result, the ratio of stretching to shortening increases from below 0.5 in walking and trotting to near 1.0 during galloping. This increasing ratio suggests that the vastus does relatively more positive work than energy absorption at the slower speeds compared with galloping,although an understanding of the timing and magnitude of force production is required to confirm this. Length-change regimes in proximal, middle and distal sites of the vastus are generally comparable, suggesting strain homogeneity through the muscle. When strain rates are compared across taxa, vastus shortening velocities exhibit the scaling pattern predicted by theoretical and empirical work: fascicles shorten relatively faster in smaller animals than larger animals (strain rates near 2 L s–1 have been reported for trotting dogs and were found here for goats, versus0.6–0.8 L s–1 reported in horses). Interestingly, biceps shortening strain rates are very similar in both goats and rats during walking (1–1.5 L s–1) and trotting (1.5–2.5 L s–1, depending on speed of trot), suggesting that the ratio of in vivo shortening velocities(V) to maximum shortening velocities (Vmax) is smaller in small animals (because of their higher Vmax).
Stenosis of the internal auditory meatus masquerading as bilateral vestibular schwannomas: a cautionary tale
Authors: Sen Aloke , Khan M I J , Ramsden R T , Gillespie J E
Published: December 2005

Stenotic malformations of the internal auditory meatus (IAM) are rare. They are known to symptomatically mimic vestibular schwannomas leading to potential diagnostic error. We present a case (along with literature review) where a stenotic IAM was clinically and radiologically misdiagnosed as a vestibular schwannoma.
Leishmaniasis of the nasal cavity: a case report
Authors: Shareef M M , Trotter M I , Cullen R J
Published: December 2005

Establishing diagnosis of a granulomatous lesion of the nose is often difficult. Here we report a case of granulomatous lesion of the nose caused by Leishmania – an unlikely cause in the UK. The diagnosis and management of the case is discussed here.
Maturation sutures for the paediatric tracheostomy – an extra safety measure
Authors: Craig M F , Bajaj Y , Hartley B E J
Published: December 2005

Objective: Displacement of the tracheostomy tube in paediatric patients is a potentially fatal complication. We describe an extra safety measure which facilitates tube replacement.

Setting: Tertiary referral specialist paediatric centre.

Materials and methods: The method involves the placement of sutures between the anterior tracheal wall and skin to hasten the formation of a mature stoma (maturation sutures). We also undertook a retrospective case note review on patients from an academic tertiary referral centre. Thirty-five notes were reviewed. The most common indication for tracheostomy was airway obstruction (65 per cent). Fourteen patients had early and 10 had late complications with three tube displacements occurring. No added complications due to the use of sutures were found.

Conclusions: Our complication rates compare well with those in the literature, and we recommend considering the use of such a technique.
Thyroidectomy does not cause globus pattern symptoms
Authors: Maung K H , Hayworth D , Nix P A , Atkin S L , England R J A
Published: December 2005

Post-thyroidectomy patients often complain of globus pharyngeus type symptoms. One of the organic pathologies recognized as causing globus pattern symptoms is goitre. We conducted a prospective questionnaire-based study in the thyroid clinic at Hull Royal Infirmary to examine the relationship between goitre, thyroidectomy and globus pattern symptoms by using the Glasgow–Edinburgh Throat Scale. A questionnaire-based study in which 41 consecutive patients due to undergo thyroidectomy prospectively completed the questionnaire pre-operatively and 12 months post-operatively. A subset of 25 randomly selected patients also completed the questionnaire three months post-operatively. Globus symptoms were not worsened by thyroidectomy at three or 12 months. Indeed two of the questioned parameters were significantly improved at three months, and six at one year (p < 0.023). In conclusion, thyroidectomy does not exacerbate globus pharyngeus symptoms. Indeed, in the absence of other clinical causes, when a patient has a World Health Organization (WHO) 2 goitre or greater, thyroidectomy may improve them.
The use of uncemented extensively porous-coated femoral components in the management of Vancouver B2 and B3 periprosthetic femoral fractures
Authors: O’Shea K. , Quinlan J. F. , Kutty S. , Mulcahy D. , Brady O. H.
Published: December 2005

We assessed the outcome of patients with Vancouver type B2 and B3 periprosthetic fractures treated with femoral revision using an uncemented extensively porous-coated implant. A retrospective clinical and radiographic assessment of 22 patients with a mean follow-up of 33.7 months was performed. The mean time from the index procedure to fracture was 10.8 years. There were 17 patients with a satisfactory result. Complications in four patients included subsidence in two, deep sepsis in one, and delayed union in one. Concomitant acetabular revision was required in 19 patients. Uncemented extensively porous-coated femoral stems incorporate distally allowing stable fixation. We found good early survival rates and a low incidence of nonunion using this implant.
Validity of an oblique posterior condylar radiographic view for revision total knee arthroplasty
Authors: Miura H. , Matsuda S. , Okazaki K. , Kawano T. , Kawamura H. , Iwamoto Y.
Published: December 2005

We have previously developed a radiographic technique, the oblique posterior condylar view, for assessment of the posterior aspect of the femoral condyles after total knee arthroplasty. The purpose of this study was to confirm the validity of this radiographic view based upon intra-operative findings at revision total knee arthroplasty. Lateral and oblique posterior condylar views were performed for 11 knees prior to revision total knee arthroplasty, and radiolucent lines or osteolysis of the posterior aspect of the femoral condyles were identified. These findings were compared with the intra-operative appearance of the posterior aspects of the femoral condyles. Statistical analysis showed that sensitivity and efficacy were significantly better for the oblique posterior condylar than the lateral view. This method can, therefore, be considered as suitable for routine follow-up radiographs of the femoral component and in the pre-operative planning of revision surgery.
Molecular biology of channel catfish brain cytochrome P450 aromatase (CYP19A2): cloning, preovulatory induction of gene expression, hormonal gene regulation and analysis of promoter region
Authors: Kazeto Y , Trant J M
Published: December 2005

Cytochrome P450 aromatase (CYP19) converts androgens to estrogens. Unlike mammals, teleosts have two CYP19 genes, expressed differentially in ovary (CYP19A1) and neuronal tissues (CYP19A2). The primary purpose of this study was to demonstrate the potential involvement of CYP19A2 in the reproductive endocrinology of teleosts. Channel catfish CYP19A2 (ccCYP19A2) cDNAs were isolated from the brain using a PCR-based strategy. The ccCYP19A2 cDNA putatively encodes 500 amino acids which conferred aromatase activity in transfected COS-7 cells. Additionally, an alternatively spliced transcript was isolated which lacks the first 122 amino acids and is catalytically inactive. The brain and the pituitary were predominant sources of ccCYP19A2 transcript and the abundance in both tissues acutely increased prior to spawning. This preovulatory induction of ccCYP19A2 gene in the pituitary is remarkably similar to the pattern of gene expression for luteinizing hormone-β (LHβ). Estradiol-17β (E2) and testosterone enhanced the transcript abundance of ccCYP19A2 and LHβ in catfish pituitary cells cultured in vitro but the stimulatory effects of testosterone were abolished by an aromatase inhibitor, indicating an important role of E2, the product of CYP19A2 activity, in the regulation of CYP19A2 and LHβ. Structural and functional analysis of the 5′-flanking region of the gene suggested that the sequence from −1076 to − 435 bp is critical for the basal promoter activity in the pituitary. This report demonstrates that CYP19A2 functions as an important factor in the reproductive endocrinology of teleosts through the brain-pituitary-gonadal axis.
Scaffold attachment factor B1 directly interacts with nuclear receptors in living cells and represses transcriptional activity
Authors: Debril M-B , Dubuquoy L , Feige J-N , Wahli W , Desvergne B , Auwerx J , Gelman L
Published: December 2005

Transcriptional activity relies on coregulators that modify the chromatin structure and serve as bridging factors between transcription factors and the basal transcription machinery. Using the DE domain of human peroxisome proliferator-activated receptor gamma (PPARγ) as bait in a yeast two-hybrid screen of a human adipose tissue library, we isolated the scaffold attachment factor B1 (SAFB1/HET/HAP), which was previously shown to be a corepressor of estrogen receptor α. We show here that SAFB1 has a very broad tissue expression profile in human and is also expressed all along mouse embryogenesis. SAFB1 interacts in pull-down assays not only with PPARγ but also with all nuclear receptors tested so far, albeit with different affinities. The association of SAFB1 and PPARγ in vivo is further demonstrated by fluorescence resonance energy transfer (FRET) experiments in living cells. We finally show that SAFB1 is a rather general corepressor for nuclear receptors. Its change in expression during the early phases of adipocyte and enterocyte differentiation suggests that SAFB1 potentially influences cell proliferation and differentiation decisions.
Characteristics of the renal C-type natriuretic peptide receptor in hypertrophied and developing rat kidney
Authors: Woodard G E , Li Xiaohong , Rosado J A
Published: December 2005

This study investigates the effect of hypertrophy, using one kidney and one kidney/one clip rats, and development, comparing 3- and 12-week-old rats, on the expression of the 28-amino acid atrial natriuretic peptide (ANP1–28) binding sites in rat kidney. Here we report an increased Bmax value of glomerular binding sites for ANP1–28 and C-type natriuretic peptide 1–22 (CNP1–22) in hypertrophied and developing kidney, without modifying their affinity, an effect that was prevented in the presence of the synthetic des[Gln18, Ser19, Gly20, Leu21, Gly22]ANP4–23-amide (C-ANF), suggesting that natriuretic peptide receptor (NPR)-C binding sites might be enhanced. The enhanced Bmax was only detected in the high affinity binding site for CNP1–22, which has been identified as the 67 kDa NPR-C-like protein. A similar effect was observed in renal glomeruli from 3-week-old rats compared with 12-week-old rats. Our results indicate that ANP1–28, CNP1–22 and C-ANF inhibited cAMP synthesis stimulated by the physiological agonists histamine and 5-hydroxytryptamine or directly by forskolin. The inhibitory effect was found to be significantly greater in 1-kidney and 1-kidney/1-clip rats than in controls, and in 3-week-old rats compared with 12-week-old rats. Our observations suggest that this effect must be attributed to the 67 kDa NPR-C-like protein due to the enhanced Bmax values and the reported inhibitory role for this receptor on adenylyl cyclase activity. The enhanced inhibitory role of natriuretic peptides on cAMP synthesis in hypertrophied and developing kidney may influence glomerular function in the rat kidney and suggests a role for the 67 kDa NPR-C-like protein in growth.
Single Nucleotide Polymorphisms and Insertion–Deletions for Genetic Markers and Anchoring the Maize Fingerprint Contig Physical Map
Authors: Vroh Bi I. , McMullen M. D. , Sanchez‐Villeda H. , Schroeder S. , Gardiner J. , Polacco M. , Soderlund C. , Wing R. , Fang Z. , Coe E. H.
Published: December 2005

Single nucleotide polymorphisms (SNPs) and insertion–deletions (InDels) are becoming important genetic markers for major crop species. In this study we demonstrate their utility for locating fingerprint contigs (FPCs) to the genetic map. To derive SNP and InDel markers, we amplified genomic regions corresponding to 3000 unigenes across 12 maize (Zea mays L.) lines, of which 194 unigenes (6.4%) showed size polymorphism InDels between B73 and Mo17 on agarose gels. The analysis of these InDels in 83 diverse inbred lines showed that InDels are often multiallelic markers in maize. Single nucleotide polymorphism discovery conducted on 592 unigenes revealed that 44% of the unigenes contained B73/Mo17 SNPs, while 8% showed no sequence variation among the 12 inbred lines. On average, SNPs and InDels occurred every 73 and 309 bp, respectively. Multiple SNPs within unigenes led to a SNP haplotype genetic diversity of 0.61 among inbreds. The unigenes were previously assigned to maize FPCs by overgo hybridization. From this set of unigenes, 311 (133 SNP and 178 InDel) loci were mapped on the intermated B73 × Mo17 (IBM) high‐resolution mapping population. These markers provided unambiguous anchoring of 129 FPCs and orientation for 30 contigs. The FPC anchored map of maize will be useful for map‐based cloning, for genome sequencing efforts in maize, and for comparative genomics in grasses. The amplification primers for all mapped InDel and SNP loci, the diversity information for SNPs and InDels, and the corresponding overgoes to anchor bacterial artificial chromosome (BAC) contigs are provided as genetic resources.
Influence of Large Amounts of Nitrogen on Nonirrigated and Irrigated Soybean
Authors: Ray Jeffery D. , Heatherly Larry G. , Fritschi Felix B.
Published: December 2005

Nitrogen supplied by N2 fixation to soybean [Glycine max (L.) Merr.] may not be sufficient to maximize yield. Field studies were conducted in 2002, 2003, and 2004 on Sharkey clay soil (very‐fine, smectitic, thermic Chromic Epiaquert) at Stoneville, MS (33°26′ N lat). The objective was to determine the effect of high rates of N applied as a replacement for N2 fixation in nonirrigated and irrigated environments. Eight cultivars ranging from Maturity Group II to IV were planted on 17 Apr. 2002, 2 Apr. 2003, and 25 Mar. 2004. Not all cultivars were evaluated in all 3 yr. Glyphosate herbicide was used in all 3 yr and a non‐glyphosate herbicide treatment was applied in 2002. Cultivars grown in 2003 were also evaluated under an application of 21.3 kg ha−1 of Mn. All cultivar, herbicide, and Mn treatments were evaluated in irrigated and nonirrigated environments with fertilizer N (PlusN treatment) or without fertilizer N (ZeroN treatment). In the PlusN treatment, granular NH4NO3 was surface applied at soybean emergence at rates of 290 kg ha−1 in 2002, 310 kg ha−1 in 2003, and 360 kg ha−1 in 2004. When analyzed over all management practices (years, cultivars, herbicide, and Mn treatments), the PlusN treatment resulted in significantly decreased ureide concentration (57.2 and 53.5% reduction) and significantly increased biomass accumulation (14.1 and 16.7%), N accumulation (12.8 and 28.1%), and seed yield (7.7 and 15.5%) for the irrigated and nonirrigated environments, respectively. The majority of the yield increase in each environment resulted from increased number of seed (9.5% irrigated and 16.2% nonirrigated). These results confirm the sensitivity of N2 fixation to drought and indicate that N2 fixation may limit yield of soybean grown in both irrigated and nonirrigated environments of the midsouthern USA, and that N2 fixation deficiencies occur before the beginning of processes that determine number of seed.
Reducing Nutrient Runoff from Golf Course Fairways Using Grass Buffers of Multiple Heights
Authors: Moss Justin Q. , Bell Gregory E. , Kizer Michael A. , Payton Mark E. , Zhang Hailin , Martin Dennis L.
Published: December 2005

Because golf course fairways often border water features, the potential loss of fertilizer nutrients in surface runoff from fairways can be significant. The objective of this study was to determine if bermudagrass buffers mowed at increasingly higher heights could reduce nutrient runoff from golf course fairways better than bermudagrass buffers mowed at a single height by providing multiple physical barriers to runoff. Grass buffers, 5.5 m long by 12.2 m wide, were positioned perpendicular to 5% slopes at the bottom of six 12.2 by 18.9 m bermudagrass (Cynodon dactylon L.) fairway plots. The buffers on three plots were mowed at a consistent 51 mm height. The remaining buffers included three 1.8 m sections that were mowed at increasingly higher heights of 25, 38, and 51 mm as surface elevation decreased. Runoff from both irrigation and natural rainfall were collected at 5‐min intervals for 1 hr following the initiation of runoff and tested for nutrient concentrations. Irrigation was applied 4 hr after granular urea and triple superphosphate were applied. Graduated buffers of increasing height delayed the initiation of runoff by 4 min during fairway irrigation and by 2 min during natural rainfall events. The graduated buffer resulted in 17% less N, 11% less P, and 19% less runoff volume during 60 min of natural rainfall runoff. The graduated buffer resulted in 18% less N and 14% less P during 60 min of irrigation runoff, and reduced runoff volume by 16%.
Minimum Water Requirements for Creeping, Colonial, and Velvet Bentgrasses under Fairway Conditions
Authors: DaCosta Michelle , Huang Bingru
Published: December 2005

Knowledge of water use requirements of various grass species is important for identifying grasses that persist with reduced water inputs and also for developing efficient irrigation management practices. This study was designed to examine minimum water requirements for maintaining acceptable quality fairways established to creeping (Agrostis stolonifera L.), colonial (A. capillaris L.) and velvet (A. canina L.) bentgrasses. Field experiments were conducted from July to November in 2002 and 2003. Plots were irrigated at four levels of irrigation on the basis of the percentage of actual evapotranspiration determined with minilysimeters (ETa): 100, 80, 60, and 40% ETa replacement. Turf performance was evaluated by measuring visual turf quality (TQ), canopy spectral parameters, canopy photosynthetic rates (Pn), and soil moisture status. Results generally demonstrated that irrigating at 100% ETa was not necessary to maintain acceptable TQ and physiological processes and that the minimum water requirements depended on species and time of year. Colonial bentgrass required irrigating at 80 to 100% ETa, while creeping and velvet bentgrasses required 60 to 80% ETa to maintain acceptable turf performance in the summer of 2002. During the summer treatment period in 2003, however, irrigating at 60% ETa was sufficient for all three species. Irrigating at 40% ETa in the fall treatment period in both 2002 and 2003 was sufficient to maintain acceptable TQ, canopy Pn, and comparable canopy growth parameters to plots receiving 100% ETa. The results from this study demonstrate the potential for significant water and monetary savings by utilizing deficit irrigation practices on bentgrass species used for golf course fairways.
Analysis of Genetic Diversity in Rough Bluegrass Determined by RAPD Markers
Authors: Rajasekar Shanmugam , Fei Shui‐hang , Christians Nick E.
Published: December 2005

Information on genetic variation in rough bluegrass (Poa trivialis L.), a cool‐season grass that is grown for sports fields and lawns, is needed. The objective of this study was to assess genetic variation in 27 accessions of rough bluegrass obtained from the National Plant Germplasm System (NPGS) by random amplified polymorphic DNA (RAPD) markers. Fifteen of the 80 primers screened generated 64 highly repeatable polymorphic bands. A dendrogram constructed on the basis of the Unweighted Pair Group Method with Arithmetic Average (UPGMA) clustering algorithm revealed that 26 of 27 accessions formed two distinct clusters. Genetic similarity coefficients calculated from the RAPD data ranged from 0.07 to 0.74 with the lowest value of 0.07 measured between PI 254908, PI 594396, PI 250982, and PI 229782 from Iraq, the USA, Yugoslavia, and Iran, respectively. The highest value of 0.74 was measured between PI 225826, PI 289643, and PI 592521 from Denmark, Spain, and the USA, respectively. The cophenetic correlation coefficient (r) was 0.90, indicative of a very good fit between the data matrix and the resulting cluster analysis. Principal coordinate analysis (PCO) clearly grouped 26 accessions on the two axes, with a single accession that did not cluster with the others. The PCO clustering pattern corresponded well with the dendrogram. PI 254908 from Iraq did not cluster with any other accessions, either in the dendrogram or on the basis of the PCO.
Selection in Cultivar Trials—Is It Ignorable?
Authors: Piepho Hans‐Peter , Möhring Jens
Published: December 2005

Crop cultivar registration requires multienvironment trials for assessing the value for cultivation and use (VCU). The series of trials usually extends across 3 yr, with some cultivars being discarded each year. Selection gives rise to a missing‐data or drop‐out pattern that is not completely random. The present paper studies the effect of drop‐out on the validity of mixed model procedures such as REML and BLUP. It is shown on the basis of the pertinent statistical theory and simulations that selection is ignorable providing that all data used in the selection process are included in the analysis. Simulations show that REML is preferable to ML and BLUP is preferable to BLUE. It is suggested that cultivar registration authorities can benefit from multivariate mixed model analyses comprising all traits on which selection is based.
Fertilizer Source and Soil Aeration Effects on Runoff Volume and Quality
Authors: Franklin D. H. , Cabrera M. L. , Calvert V. H.
Published: December 2005

Minimizing runoff losses from grasslands may benefit the producer and abate potential eutrophication of aquatic systems. This study was conducted to evaluate the effects of fertilizer source and soil aeration on the volume and quality of runoff from grassed plots. Sixteen tall fescue [Festuca arundinaceaSchreb.]–bermudagrass [Cynodon dactylonL.] plots were established on Altavista sandy‐loam soil (fine‐loamy, mixed, semiactive, thermic Aquic Hapludults) in Georgia, USA. Two fertilizer sources (inorganic fertilizer [IF] and broiler litter [BL]) and two aeration treatments (aerated and nonaerated) were factorially combined to generate four experimental treatments. Broiler litter was applied at 1765 kg dry matter ha−1and IF was applied to match nutrient rates applied with BL (36 kg available N ha−1, 39 kg P ha−1, 60 kg K ha−1). Simulated rainfall was applied immediately after fertilizer application and 1 mo later. Runoff samples were analyzed for dissolved reactive phosphorus (DRP), total Kjeldahl phosphorus (TKP), and ammonium (NH4–N). In the first runoff event, plots fertilized with IF lost more TKP than plots fertilized with BL (3.4 vs. 1.1 kg P ha−1). In contrast, plots fertilized with BL lost more NH4–N than plots fertilized with IF (1.4 vs. 0.6 kg N ha−1). These results support the use of different weighting factors for BL and IF when assessing their potential for contaminating surface runoff. Aeration numerically reduced runoff volume by 27%, though not significantly, in the first runoff event (P= 0.16), but did not affect runoff volume 1 mo later. Aeration did not affect the mass losses of DRP, TKN, and NH4–N. These results indicate that aeration of hayed grasslands on these soils would not be expected to significantly affect the volume and quality of surface runoff.
Assessing Change in Soil‐Site Productivity of Intensively Managed Loblolly Pine Plantations
Authors: Eisenbies M. H. , Burger J. A. , Aust W. M. , Patterson S. C. , Fox T. R.
Published: December 2005

Intensively managed forests are among the most important sources of wood fiber and timber in the southern United States. There is a great deal of concern that wet‐weather harvesting disturbances might diminish long‐term soil‐site productivity. Determining the true effect of harvesting disturbance and silvicultural treatments on long‐term productivity of pine plantations is difficult because growth and yield are affected by changes in climate, silviculture, and genetics. Change in productivity rank among treatments was used as a new approach to evaluate harvest disturbance effects on changes in soil‐site quality because it is less influenced by the confounding factors that affect tree growth. Three 20‐ha loblolly pine (Pinus taeda L.) plantations were subjected to combinations of wet‐ and dry‐weather harvesting and mechanical site preparations. Wet‐weather harvesting had no discernable effect at the operational scale (3.3 ha) compared to dry harvesting on changes in soil‐site quality when standard site preparation methods were used; however, results based on change in rank for site index indicated that the combination of wet harvesting and flat planting diminished productivity. Polypedon‐scale (0.008 ha) investigations indicated that silviculture, inherent site factors, and disturbance affected drainage and changes in soil‐site productivity. This study showed that the industrial practice of bedding maintained site productivity of wet‐weather harvested stands on wet pine flats. These results are potentially important to nonindustrial private landowners whose plantations are not commonly bedded before replanting.
Litter Quality and Climate Decouple Nitrogen Mineralization and Productivity in Chilean Temperate Rainforests
Authors: Joshi Amishi B. , Vann David R. , Johnson Arthur H.
Published: December 2005

We measured litter quality, N mineralization, air and soil temperatures, soil moisture, and aboveground net primary production (ANPP) at 18 plots in three forest types typical of full‐stature forests found on western slopes of the Cordillera de Piuchué (CP) on Isla de Chiloé in southern Chile. The primary objectives were to examine the range of net N mineralization across forest types that have different vegetation and litter composition, assess probable controls on mineral N production and leaching, and to determine if the relationship between N mineralization and ANPP was similar to that observed in cool temperate northern hemisphere forests. Average annual litter lignin/N ratios were high in the evergreen montane broadleaf forest plots (50:1) and very high in the montane conifer plots (80:1). Net N mineralization during the summer months was correspondingly low (1.2 and 2.2 kg ha−1, respectively). The high litter lignin content and associated low rate of N mineralization can explain the extremely low concentrations of mineral N in soils and upland streams of this region. In the broadleaf evergreen coastal forest plots, lignin/N ratio was lower (23:1) and N mineralized was considerably greater over the same measurement period than in the montane forest plots (14 kg ha−1). In contrast to findings in many cool temperate northern hemisphere forests, ANNP in the broadleaf forest type was high (average 11.1 Mg ha−1 yr−1) in spite of the low net N mineralization rates, and ANPP and net N mineralized were not correlated. Net N mineralization was best correlated with litter quality, soil temperature, and soil moisture content, and ANPP was best correlated with growing degree days.
Cross‐Reference System for Translating Between Genetic Soil Classification of China and Soil Taxonomy
Authors: Shi X. Z. , Yu D. S. , Warner E. D. , Sun W. X. , Petersen G. W. , Gong Z. T. , Lin H.
Published: December 2005

Soil classification systems are not consistent among countries or organizations thereby hindering the communication and organizational functions they are intended to promote. The development of translations between systems will be critical for overcoming the gap in understanding that has resulted from the lack of a single internationally accepted classification system. This paper describes the application of a process that resulted in the translation of the Genetic Soil Classification of China (GSCC) to Soil Taxonomy (ST). A brief history of soil classification in China is also provided to familiarize readers with GSCC and its origins. Genetic Soil Classification of China is the attribute base for the recently assembled digital form of the 1:1 000 000 soil map of The People's Republic of China. The translation between GSCC and ST was based on profile, chemical, and physical descriptions of 2540 soil series. First, the 2540 soil series were classified to their equivalent soil order, suborder, great group, and subgroup according to ST and GSCC subgroup descriptors. Order names for both classification systems were then linked to corresponding map units in the 1:1 000 000 digital soil map of China using a geographic information system (GIS). Differences in classification criteria and in the number of orders of the two systems (there are more GSCC orders than ST orders) meant that each GSCC order could possibly be assigned to more than one ST order. To resolve the differences, the percent correspondence in area between orders was determined and used as the criterion for assigning GSCC orders to ST orders. Some percentages of correspondence were low so additional processing was used to improve the assignment process. The GSCC suborders were then matched with ST orders. When the area for each order was summarized, the percentage of correspondence increased except for two subgroups in the Ferrasols order.
Development and Evaluation of Iron‐Coated Tubes that Indicate Reduction in Soils
Authors: Jenkinson B. J. , Franzmeier D. P.
Published: December 2005

Soil drainage conditions are important to land use decisions. Traditionally, anaerobic conditions induced by poor drainage have been evaluated by observing soil color related to Fe and Mn oxides, using α, α‐dipyridyl dye, measuring dissolved O2, and measuring EH We believe that there is further need for a device that is scientifically sound and easy to use. Therefore, our goals were to develop and test a device that mimics natural soil processes, visually indicates soil reduction, and is robust. Our concept was to coat a rod or tube with a colored soil mineral that dissolves on reduction, insert the device into a soil, remove it after a few weeks or longer, and observe if some of the coating had been lost. If the coating was not dissolved, no reduction occurred, but if it was dissolved, reducing conditions must have prevailed. After trying several kinds of coatings and tubes, we chose ferrihydrite (FH) coating on polyvinyl chloride (PVC) pipe. We call the device an Indicator of Reduction in Soils (IRIS). As the study progressed we added semi‐quantitative interpretations by measuring depleted areas using a digital camera and image analysis. We tested IRIS tubes in the lab and in soils in Indiana, Minnesota, and North Dakota, and concluded they performed as expected. Reduction rates increased between February and April and were related to increasing soil temperature, turnover (flux) of soil OC, and content (inventory) of OC. Reduction rates decreased after April, presumably because the nutrient supply for microbes decreased.
Soil Microbial Responses to Potassium‐Based Black Liquor from Straw Pulping
Authors: Xiao C. , Fauci M. , Bezdicek D. F. , McKean W. T. , Pan W. L.
Published: December 2005

Sodium‐based black liquor from fiber pulping for papermaking creates challenging waste disposal issues. By substituting NaOH with KOH in the pulping process, the resulting black liquors may be land applied as an environmentally beneficial disposal alternative. Incubation studies examined the effect of KOH‐based black liquor on soil pH, electrical conductivity (EC), microbial biomass, CO2evolution, and soil enzyme activities in a silt loam soil. Amended soils with black liquor at rates up to 67.2 mL kg−1soil, corresponding to 1200 kg K ha−1were incubated at 24°C for 60 d. Increasing application rates increased soil pH, indicating that black liquor has potential as a fluid liming material. Soil EC increased with black liquor application rates, but only up to 1.04 dS m−1, suggesting that black liquor application at these rates would not cause a salinity problem. Carbon dioxide evolution rate peaked at 2 d of incubation, and then gradually declined until the end of incubation. Metabolic quotient significantly increased with increasing application rates. Soil microbial biomass, CO2evolution, dehydrogenase, β‐glucosidase, and arylsulfatase activities generally increased with increasing application rates throughout the incubation period. In contrast, increasing soil pH with KOH alone generally decreased CO2evolution and soil dehydrogenase, β‐glucosidase, and arylsulfatase activities, indicating that this liquor effects in increasing soil microbial activity were possibly attributable to organic constituents contained in this liquor rather than its high pH.
Citrus Water Uptake Dynamics on a Sandy Florida Entisol
Authors: Morgan K. T. , Obreza T. A. , Scholberg J. M. S. , Parsons L. R. , Wheaton T. A.
Published: December 2005

Florida citrus trees must be irrigated to reach maximum production due to low soil water‐holding capacity. In a highly urbanizing state with limited water resources, improved understanding of soil water uptake dynamics is needed to optimize irrigation volume and timing. The objectives of this study were: (i) estimate mature citrus daily evapotranspiration (ETc) from changes in soil water content (), (ii) calculate citrus crop coefficients (Kc) from ETc and reference evapotranspiration (ETo), (iii) determine the relationship of soil water stress coefficient (Ks) to , and (iv) evaluate how ETc was related to root length density. In a 25‐mo field study using mature Hamlin orange [Citrus sinensis (L.) Osbeck] trees, ETc averaged 1137 mm yr1, and estimated Kc ranged between 0.7 and 1.1. Day of year explained more than 88% of the variation in Kc when was near field capacity. The value of Ks decreased steadily from 1.0 at field capacity ( = 0.072 cm3 cm3) to approximately 0.5 at 50% available soil water depletion ( = 0.045 cm3 cm3). Roots were concentrated in the top 15 cm of soil under the tree canopy (0.71 to 1.16 cm roots cm3 soil), where maximum soil water uptake was about 1.3 mm3 mm root1 d1 at field capacity, decreasing quadratically as decreased. Estimating daily plant water uptake and resulting soil water depletion based on root length density distribution would provide a reasonable basis for a citrus soil water balance model.
Need for a Soil‐Based Approach in Managing Nitrogen Fertilizers for Profitable Corn Production
Authors: Mulvaney R. L. , Khan S. A. , Ellsworth T. R.
Published: December 2005

Nitrogen fertilization for corn (Zea mays L.) production has relied extensively on yield‐based recommendations that were developed to represent regional averages, yet are routinely applied to individual fields, on the assumption that fertilizer N serves as the major supply for crop N uptake. Using data from 102 on‐farm N‐response studies, an evaluation was conducted of the Illinois proven‐yield (PY) method for accuracy and economic profitability on a site‐by‐site basis. As additional objectives, the Illinois soil N test (ISNT) was evaluated for detecting whether N fertilization was economical, and for quantifying crop response to N fertilization relative to soil and management factors. For 18% of the site‐years studied, N recommendations by the PY method were accurate to within 20 kg ha−1, whereas 13% were underfertilized by 25 to 129 kg ha−1 (60 kg ha−1 on average) at a current cost of $5 to $170 ha−1 ($75 ha−1 on average), and 69% were overfertilized by 21 to 235 kg ha−1 (103 kg ha−1 on average) at a cost of $12 to $130 ha−1 ($57 ha−1 on average). The latter group included 30 site‐years that were completely nonresponsive to N fertilization, all but two of which were predicted by site‐average ISNT values assuming a critical test level of 230 mg kg−1 This level was exceeded for 19 of 69 responsive site‐years, mostly during 2001–2003 when corn followed soybean (Glycine max L. Merr.) with high plant populations. A higher critical test level would have been required under such conditions, owing to more extensive residue inputs that would promote microbial N immobilization, and increased crop uptake of mineralized soil N. The ISNT was significantly related to crop N requirement, and was the most powerful predictor of error in PY recommendations (P < 0.001).
Soil Solution Sampling for Organic Acids in Rice Paddy Soils
Authors: Angeles Olivyn R. , Johnson Sarah E. , Buresh Roland J.
Published: December 2005

Low molecular weight organic acids (OA), which are intermediates in the anaerobic decomposition of straw incorporated into submerged soils, have been implicated in causing toxicity to young rice (Oryza sativa L.) seedlings. The objective of this study was to develop a method for measuring OA in soil solution in field and greenhouse studies. Three methods of soil solution sampling were evaluated: zero‐tension displacement (ZTD), variable‐tension centrifugation (CFG), and medium‐tension suction sampling through porous tubes (PT). All solution samples were analyzed for OA by high performance liquid chromatography (HPLC) using an ion exclusion column. Use of cation exchange membrane resin strips during sample collection to sorb interfering cations improved OA recovery. Comparison between sampling methods of the OA concentration in soil solution extracted from soil amended with reagent OA was as follows: PT = CFG >> ZTD. Variables between methods that could cause artifacts in OA measurement were tested systematically: solution pH after sampling, headspace gas pressure during sampling, and sorption to sand or soil layers. No artifact effects were observed, and it was concluded that the tension methods sampled a different fraction of soil solution than the zero‐tension method. Since the tension methods extracted a higher concentration of OA, they are recommended for studies comparing treatment effects on OA production. However, it was beyond the scope of this study to determine which soil solution fraction is more relevant to OA toxicity studies with rice seedlings. Between the two tension methods, PT was more convenient for repeated sampling from the same location compared to the destructive nature of centrifugation.
Acid‐base Characteristics of Soils in the Adirondack Mountains, New York
Authors: Sullivan Timothy J. , Fernandez Ivan J. , Herlihy Alan T. , Driscoll Charles T. , McDonnell Todd C. , Nowicki Nancy A. , Snyder Kai U. , Sutherland James W.
Published: December 2005

It is believed that atmospheric deposition of S and N in the Adirondack Mountains of New York has depleted soil‐base cation pools, reduced soil base saturation (BS), and contributed to enhanced acidification of soils and surface waters. However, data to determine changes in soil characteristics are generally lacking. It is expected that soil acid‐base status will improve as acidic deposition declines in response to atmospheric emissions controls. We studied edaphic characteristics at 199 locations within 44 statistically selected Adirondack lake‐watersheds, plus 26 additional watersheds that are included in long‐term lakewater monitoring programs. The statistically selected watersheds were chosen to be representative of Adirondack watersheds containing lakes larger than 1 ha and deeper than 1 m that have lakewater acid neutralizing capacity (ANC) less than or equal to 200 μmolc L−1 Results of soil analyses were extrapolated to the watersheds of 1320 low ANC lakes. In general, the concentrations of exchangeable base cations, base saturation, and soil pH were low. More than 75% of the target lakes received drainage from watersheds having average B horizon exchangeable Ca concentrations < 0.52 cmolc kg−1, base saturation < 10.3%, and pH (H2O) < 4.5. Variations in the effective cation exchange capacity in both O and B horizons were closely correlated with soil organic matter content. These data provide a baseline against which to compare future changes in regional soil chemistry, and provide input data for aquatic and terrestrial effects models intended to project future changes in surface water chemistry, biological conditions, and forest health.