bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vertebrate gene finding from multiple-species alignments using a two-level strategy
Authors: Carter David , Durbin Richard 
Published: August 2006

Abstract
Background
One way in which the accuracy of gene structure prediction in vertebrate DNA sequences can be improved is by analyzing alignments with multiple related species, since functional regions of genes tend to be more conserved.

Results
We describe DOGFISH, a vertebrate gene finder consisting of a cleanly separated site classifier and structure predictor. The classifier scores potential splice sites and other features, using sequence alignments between multiple vertebrate species, while the structure predictor hypothesizes coding transcripts by combining these scores using a simple model of gene structure. This also identifies and assigns confidence scores to possible additional exons. Performance is assessed on the ENCODE regions. We predict transcripts and exons across the whole human genome, and identify over 10,000 high confidence new coding exons not in the Ensembl gene set.

Conclusion
We present a practical multiple species gene prediction method. Accuracy improves as additional species, up to at least eight, are introduced. The novel predictions of the whole-genome scan should support efficient experimental verification.
JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions
Authors: Allen Jonathan E , Majoros William H , Pertea Mihaela , Salzberg Steven L 
Published: August 2006

Abstract
Background
Predicting complete protein-coding genes in human DNA remains a significant challenge. Though a number of promising approaches have been investigated, an ideal suite of tools has yet to emerge that can provide near perfect levels of sensitivity and specificity at the level of whole genes. As an incremental step in this direction, it is hoped that controlled gene finding experiments in the ENCODE regions will provide a more accurate view of the relative benefits of different strategies for modeling and predicting gene structures.

Results
Here we describe our general-purpose eukaryotic gene finding pipeline and its major components, as well as the methodological adaptations that we found necessary in accommodating human DNA in our pipeline, noting that a similar level of effort may be necessary by ourselves and others with similar pipelines whenever a new class of genomes is presented to the community for analysis. We also describe a number of controlled experiments involving the differential inclusion of various types of evidence and feature states into our models and the resulting impact these variations have had on predictive accuracy.

Conclusion
While in the case of the non-comparative gene finders we found that adding model states to represent specific biological features did little to enhance predictive accuracy, for our evidence-based 'combiner' program the incorporation of additional evidence tracks tended to produce significant gains in accuracy for most evidence types, suggesting that improved modeling efforts at the hidden Markov model level are of relatively little value. We relate these findings to our current plans for future research.
On Euclidean designs
Authors: Bajnok Béla 
Published: August 2006

Abstract
A Euclidean t-design, as introduced by Neumaier and Seidel (1988), is a finite set 𝒳 ⊂ ℝ
n
with a weight function w : 𝒳 → ℝ+ for which

holds for every polynomial ƒ of total degree at most t; here R is the set of norms of the points in 𝒳, Wr
is the total weight of all elements of 𝒳 with norm r, Sr
is the n-dimensional sphere of radius r centered at the origin, and

is the average of ƒ over Sr
. Neumaier and Seidel (1988), as well as Delsarte and Seidel (1989), also proved a Fisher-type inequality |𝒳| ≥ N(n, |R|, t) (assuming that the design is antipodal if t is odd). For fixed n and |R| we have N(n, |R|, t) = O(t

n−1).
This paper contains two main results. First, we provide a recursive construction for Euclidean t-designs in ℝ
n
. Namely, we show how to use certain Gauss–Jacobi quadrature formulae to ‘lift’ a Euclidean t-design in ℝ
n−1 to a Euclidean t-design in ℝ
n
, preserving both the norm spectrum R and the weight sum Wr
for each r ∈ R. For fixed n and |R| this construction yields a design of size O(t

n−1); however, the coefficient of t

n−1 here is significantly greater than it is in N(n, |R|, t).
A Euclidean design with exactly N(n, |R|, t) points is called tight; in both of the above mentioned papers it was conjectured that a tight Euclidean design with t ≥ 4 must be a spherical design, that is, |R| = 1 and w is constant on 𝒳. Bannai and Bannai (2003) disproved this conjecture by exhibiting an example for the parameters, (n, |R|, t) = (2,2,4). Here we construct tight Euclidean designs for n = 2 and every t and |R| with |R| ≤

.
Carnot spaces and the k-stein condition
Authors: Druetta María J 
Published: August 2006

Abstract
A riemannian manifold M with associated Jacobi operators R
X
(R
X

Y = R(Y, X) X), X in TM, is said to be k-stein, k ≥ 1, if there exists a function μk
on M such that tr(R
k

X
) = μk
|X|2k
for all X in TM. We study the k-stein condition on Lie groups of Iwasawa type and in particular in those which are Carnot spaces. We show that a Carnot space which is k-stein for some k > 1 is necessarily a Damek–Ricci space; Damek–Ricci spaces are Einstein and 2-stein and they are not k-stein for any k ≥ 3, unless they are symmetric. Moreover, we show that a harmonic Lie group of Iwasawa type which is 3-stein is a symmetric space of noncompact type and rank one.
Entropy of the geodesic flow for metric spaces and Bruhat–Tits buildings
Authors: Leuzinger Enrico 
Published: August 2006

Abstract
Let (X, dX
) be a geodesically complete Hadamard space endowed with a Borel-measure μ. Assume that there exists a group Γ of isometries of X which acts totally discontinuously and cocompactly on X and preserves μ. We show that the topological entropy of the geodesic flow on the space of (parametrized) geodesics of the compact quotient Γ\X is equal to the volume entropy of μ (if X satisfies a certain local uniformity condition). This extends a result of Manning for riemannian manifolds of nonpositive curvature to the singular case. The result in particular holds for Bruhat–Tits buildings, for which we also compute the entropy explicitly.
Physicochemical and Mineralogical Characterization of Soil–Saprolite Cores from a Field Research Site, Tennessee
Authors: Moon Ji‐Won , Roh Yul , Phelps Tommy J. , Phillips Debra H. , Watson David B. , Kim Young‐Jin , Brooks Scott C. 
Published: August 2006

ABSTRACTSite characterization is an essential initial step in determining the feasibility of remedial alternatives at hazardous waste sites. Physicochemical and mineralogical characterization of U‐contaminated soils in deeply weathered saprolite at Area 2 of the DOE Field Research Center (FRC) site, Oak Ridge, TN, was accomplished to examine the feasibility of bioremediation. Concentrations of U in soil–saprolite (up to 291 mg kg−1in oxalate‐extractable Uo) were closely related to low pH (ca. 4–5), high effective cation exchange capacity without Ca (64.7–83.2 cmolckg−1), amorphous Mn content (up to 9910 mg kg−1), and the decreased presence of relative clay mineral contents in the bulk samples (i.e., illite 2.5–12 wt. %, average 32 wt. %). The pH of the fill material ranged from 7.0 to 10.5, whereas the pH of the saprolite ranged from 4.5 to 8. Uranium concentration was highest (about 300 mg kg−1) at around 6 m below land surface near the saprolite–fill interface. The pH of ground water at Area 2 tended to be between 6 and 7 with U concentrations of about 0.9 to 1.7 mg L−1These site specific characteristics of Area 2, which has lower U and nitrate contamination levels and more neutral ground water pH compared with FRC Areas 1 and 3 (ca. 5.5 and <4, respectively), indicate that with appropriate addition of electron donors and nutrients bioremediation of U by metal reducing microorganisms may be possible.
Distribution of Uranium Contamination in Weathered Fractured Saprolite/Shale and Ground Water
Authors: Phillips D. H. , Watson D. B. , Roh Y. , Mehlhorn T. L. , Moon J.‐W. , Jardine P. M. 
Published: August 2006

ABSTRACTThe objective of this study was to determine how structure, stratigraphy, and weathering influence fate and transport of contaminants (particularly U) in the ground water and geologic material at the Department of Energy (DOE) Environmental Remediation Sciences Department (ERSD) Field Research Center (FRC). Several cores were collected near four former unlined adjoining waste disposal ponds. The cores were collected, described, analyzed for U, and compared with ground water geochemistry from surrounding multilevel wells. At some locations, acidic U‐contaminated ground water was found to preferentially flow in small remnant fractures weathering the surrounding shale (nitric acid extractable U [UNA] usually < 50 mg kg−1) into thin (<25 cm) Fe oxide‐rich clayey seams that retain U (UNA 239 to 375 mg kg−1). However, greatest contaminant transport occurs in a 2 to 3 m thick more permeable stratigraphic transition zone located between two less permeable, and generally less contaminated zones consisting of (i) overlying unconsolidated saprolite (UNA < 0.01 to 200 mg kg−1) and (ii) underlying less‐weathered bedrock (UNA generally < 0.01 to 7 mg kg−1). In this transition zone, acidic (pH < 4) U‐enriched ground water (U of 38 mg L−1) has weathered away calcite veins resulting in greater porosity, higher hydraulic conductivity, and higher U contamination (UNA 106 to 745 mg kg−1) of the weathered interbedded shale and sandstone. These characteristics of the transition zone produce an interval with a high flux of contaminants that could be targeted for remediation.
Sorption–Desorption of Carbamazepine from Irrigated Soils
Authors: Williams C. F. , Williams C. F. , Adamsen F. J. 
Published: August 2006

ABSTRACTTh anti‐seizure medication carbamazepine is often found in treated sewage effluent and environmental samples. Carbamazepine has been shown to be very persistent in sewage treatment, as well as ground water. Due to environmental persistence, irrigation with sewage effluent could result in carbamazepine contamination of surface and ground water. To determine the potential for leaching of carbamazepine, a series of adsorption and desorption batch equilibrium experiments were conducted on irrigated soils. It was found that carbamazepine adsorption to biosolid‐amended (T) soils had aKDof 19.8 vs. 12.6 for unamended soil. Based on adsorption, carbamazepine leaching potential would be categorized as low. During desorption significant hysteresis was observed andKDincreased for both soils. Desorption isotherms also indicate a potential for irreversibly bound carbamazepine in the T soil. Results indicate that initial removal of carbamazepine via adsorption from irrigation water is significant and that desorption characteristics would further limit the mobility of carbamazepine through the soil profile indicating that carbamazepine found in sewage effluent used for irrigation has a low leaching potential.
Bias of Tedlar Bags in the Measurement of Agricultural Odorants
Authors: Trabue Steven L. , Anhalt Jennifer C. , Zahn James A. 
Published: August 2006

ABSTRACTOdor regulations typically specify the use of dynamic dilution olfactometery (DDO) as a method to quantify odor emissions, and Tedlar bags are the preferred holding container for grab samples. This study was conducted to determine if Tedlar bags affect the integrity of sampled air from animal operations. Air samples were collected simultaneously in both Tedlar bags and Tenax thermal desorption tubes. Sample sources originated from either a hydrocarbon‐free air tank, dynamic headspace chamber (DHC), or swine‐production facility, and were analyzed by gas chromatography–mass spectrometry–olfactometry (GC–MS–O). Several background contaminants were identified from Tedlar bags, which included the odorous compoundsN,N‐dimethyl acetamide (DMAC), acetic acid, and phenol. Samples from the DHC demonstrated that recovery of malodor compounds was dependent on residence time in the Tedlar bag with longer residence time leading to lower recovery. After 24 h of storage, recovery of C3–C6volatile fatty acids (VFA) averaged 64%, 4‐methylphenol and 4‐ethylphenol averaged 10%, and indole and 3‐methylindole were below the detection limits of GC–MS–O. The odor activity value (OAV) of grab samples collected in Tedlar bags were 33 to 65% lower following 24 h of storage. These results indicate that significant odorant bias occurs when using Tedlar bags for the sampling of odors from animal production facilities.
Change in Soluble Phosphorus in Soils following Fertilization is Dependent on Initial Mehlich‐3 Phosphorus
Authors: Bond C. Ryan , Maguire R. O. , Havlin J. L. 
Published: August 2006

ABSTRACTThere is a lack of information on how fertilization and initial Mehlich‐3 phosphorus (M3P) interact to affect water soluble P (WSP) in soils. Our objectives were to (i) quantify the relationship between WSP and M3P for four textural diverse benchmark soils of North Carolina (NC) and (ii) quantify the change in WSP concentrations following P additions to soils over a wide range of initial M3P. Soils known to represent a wide range in M3P were collected from an Autryville loamy sand (loamy, siliceous, subactive, thermic Arenic Paleudults), Wasda muck (fine‐loamy, mixed, semiactive, acid, thermic Histic Humaquepts), Georgeville silt loam (fine, kaolinitic, thermic Typic Kanhapludults), and Pacolet sandy clay loam (fine, kaolinitic, thermic Typic Kanhapludults) and analyzed for M3P, Fe, Al, and WSP. An incubation study was also conducted where four samples representing a range in M3P from each series were fertilized at rates of 150 and 300 kg P ha−1, and WSP was measured at 1, 7, and 21 d after fertilization. The Wasda muck exhibited a change point at 115 mg P kg−1 across a broad range of M3P concentrations (60–238 mg kg−1) while Autryville, Georgeville, and Pacolet series (with ranges in M3P of 32–328, 119–524, 0–1034 mg P kg−1, respectively) maintained linear relationships between WSP and M3P. For the fertilized soils, significant increases in WSP occurred regardless of P rate. Yet, WSP concentrations were greater in soils with greater initial M3P. Thus, these data suggest that shifting animal waste applications to fields of relatively lower M3P concentrations would have an immediate impact on reducing risk for P losses, if all other factors are equal.
Use of Beryllium‐7 to Document Soil Redistribution following Forest Harvest Operations
Authors: Schuller Paulina , Iroumé Andrés , Walling Desmond E. , Mancilla Héctor B. , Castillo Alejandra , Trumper Rosa E. 
Published: August 2006

ABSTRACTRapid and reliable methods for documenting soil erosion associated with forest harvest operations are needed to support the development of best management practices for soil and water conservation. To address this need, the potential for using 7Be measurements to estimate patterns and amounts of soil redistribution associated with individual post‐harvest events was explored. The 7Be technique, which was originally developed for use on agricultural land, was employed to estimate soil redistribution associated with a period of heavy rainfall within a harvested forest area located in the Lake Region of Chile (39°44′7″ S, 73°10′39″ W; 22% slope; and mean annual rainfall 2300 mm yr−1). The results provided by the 7Be technique were validated against direct measurements of soil gain or loss during the same period obtained using erosion pins. The information produced by the two approaches was similar. The results of this study demonstrate the potential for using 7Be measurements to document event‐based erosion in recently harvested forest areas.
Preferential Flow Estimates to an Agricultural Tile Drain with Implications for Glyphosate Transport
Authors: Stone Wesley W. , Wilson John T. 
Published: August 2006

ABSTRACTAgricultural subsurface drains, commonly referred to as tile drains, are potentially significant pathways for the movement of fertilizers and pesticides to streams and ditches in much of the Midwest. Preferential flow in the unsaturated zone provides a route for water and solutes to bypass the soil matrix and reach tile drains faster than predicted by traditional displacement theory. This paper uses chloride concentrations to estimate preferential flow contributions to a tile drain during two storms in May 2004. Chloride, a conservative anion, was selected as the tracer because of differences in chloride concentrations between the two sources of water to the tile drain, preferential and matrix flow. A strong correlation between specific conductance and chloride concentration provided a mechanism to estimate chloride concentrations in the tile drain throughout the storm hydrographs. A simple mixing analysis was used to identify the preferential flow component of the storm hydrograph. During two storms, preferential flow contributed 11 and 51% of total storm tile drain flow; the peak contributions, 40 and 81%, coincided with the peak tile drain flow. Positive relations between glyphosate [N‐(phosphonomethyl)glycine] concentrations and preferential flow for the two storms suggest that preferential flow is an important transport pathway to the tile drain.
Sorption and Degradation of Pesticides in Nursery Recycling Ponds
Authors: Lu Jianhang , Wu Laosheng , Newman Julie , Faber Ben , Merhaut Donald J. , Gan Jianying 
Published: August 2006

ABSTRACTKnowledge of pesticide distribution and persistence in nursery recycling pond water and sediment is critical for preventing phytotoxicity of pesticides during water reuse and to assess their impacts to the environment. In this study, sorption and degradation of four commonly used pesticides (diazinon, chlorpyrifos, chlorothalonil, and pendimethalin) in sediments from two nursery recycling ponds was investigated. Results showed that diazinon and chlorothalonil were moderately sorbed [KOC (soil organic carbon distribution coefficient) from 732 to 2.45 × 103 mL g−1] to the sediments, and their sorption was mainly attributable to organic matter content, whereas chlorpyrifos and pendimethalin were strongly sorbed (KOC ≥ 7.43 × 103 mL g−1) to the sediments, and their sorption was related to both organic matter content and sediment texture. The persistence of diazinon and chlorpyrifos was moderate under aerobic conditions (half‐lives = 8 to 32 d), and increased under anaerobic conditions (half‐lives = 12 to 53 d). In contrast, chlorothalonil and pendimethalin were quickly degraded under aerobic conditions with half‐lives < 2.8 d, and their degradation was further enhanced under anaerobic conditions (half‐lives < 1.9 d). The strong sorption of chlorpyrifos and pendimethalin by the sediments suggests that the practice of recycling nursery runoff would effectively retain these compounds in the recycling pond, minimizing their offsite movement. The prolonged persistence of diazinon and chlorpyrifos, however, implies that incidental spills, such as overflows caused by storm events, may contribute significant loads of such pesticides into downstream surface water bodies.
A kinetic method for para-nitrophenol determination based on its inhibitory effect on the catalatic reaction of catalase
Authors: Mureşanu Claudia , Copolovici Lucian , Pogącean Florina 
Published: August 2006

Abstract
The inhibitory effect of para-nitrophenol on the catalytic reaction of catalase was investigated. Michaelis-Menten kinetic parameters were determined from Lineweaver-Burk plots obtained in the absence or in the presence of the inhibitor. The inhibitor pattern, revealed by the Lineweaver-Burk plots, suggested a fully mixed inhibition mechanism. Spectrophotometric monitoring of the indicator reaction:
$$H_2 O_2 \xrightarrow{{catalase,para - nitrophenol}}H_2 O + \tfrac{1}{2}O_2 $$
in conjunction with initial rate measurements was employed for the kinetic determination of the inhibitor. Calibration plots of initial rate vs. para-nitrophenol concentration were linear in the concentration range 0.9·10−5–2.5·10−5 mol/L and the detection limit was 3·10−6 mol/L (417 μg/L) para-nitrophenol. Interferences from other phenolic compounds like orto-cresole, meta-and orto-nitrophenol were observed.
Oxygen detection using yttria-stabilized zirconia thin films doped with platinum
Authors: Dimitrov Dimitre , Dushkin Ceco 
Published: August 2006

Abstract
Yttria stabilized zirconia (YSZ) thin films are obtained using both spray-pyrolysis and dip-coating. The ability of YSZ films incorporated with platinum nanospecies (Pt-YSZ) to detect oxygen is compared with that of pure YSZ thin films using a new experimental setup. With this system, the surface electrical resistance of the films as a function the oxygen content is measured at a fixed temperature. In addition, the effects of thermal annealing on the oxygen sensitivity of the films are observed. Platinum doped samples, Pt-YSZ, show different kinetics of carrier diffusion as compared to pure YSZ samples.
New computer program to calculate the symmetry of molecules
Authors: Ashrafi Ali , Ahmadi Mohammad 
Published: August 2006

Abstract
In this paper we, present some MATLAB and GAP programs and use them to find the automorphism group of the Euclidean graph of the C80 fullerence with connectivity and geometry of Ih symmetry point group. It is proved that this group has order 120 and is isomorphic to Ih≊Z2×A5, where Z2 is, a cyclic group of order 2 and A5 is the alternating group on five symbols.
Molecule dynamics and combined QM/MM study on one-carbon unit transfer reaction catalyzed by GAR transformylase
Authors: Qiao Qing-An , Jin Yueqing , Cai Zhengting , Qu Rongjun , Yang Chuanlu , Wang Meishan 
Published: August 2006

Abstract
Both a molecule dynamic study and a combined quantum mechanics and molecule mechanics (QM/MM) study on Glycinamide ribonucleotide transformylase (GAR Tfase) catalytic mechanism are presented. The results indicate a direct one-carbon unit transfer process but not a stepwise mechanism in this reaction. The residues near the active center can fix the cofactor (N10-formyltetrahydrofolate) and GAR in proper relative positions by a H-bond network. The transition state and the minimum energy pathway are located on the potential energy surface. After all the residues (including H2O molecules) are removed from the system the activation energy has increased from 145.1 kJ/mol to 243.3 kJ/mol, and the formly transfer reaction is very hard to achieve. The interactions between coenzyme, GAR and residues near the reactive center are discussed as well.
Synthesis, structural and conformational study of selected N-substituted phthalimides
Authors: Iriepa Isabel , Javier Villasante F. , Gálvez Enrique , Herrera Antonio , Sánchez Angel , Cano Felix 
Published: August 2006

Abstract
This paper synthesizes N-substituted phthalimides derived from nitrogen heterocycles as potential 5-HT4 ligands by using the Mitsunobu reaction. Conformational studies of some of the new compounds have been conducted using 1H and 13C-NMR spectroscopy. Proton and carbon resonances were achieved through the application of one-dimensional selective NOE, two-dimensional NMR techniques-homonuclear COSY-45, NOESY and heteronuclear 1H-13C HMQC correlated spectroscopy- and double resonance experiments. The crystal structure of compound 1 was determined by X-ray diffraction.