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PubMed2003

Comparing nutrient intake from food to the estimated average requirements shows middle- to upper-income pregnant women lack iron and possibly magnesium.

OBJECTIVE: To determine whether nutrient intake from food alone was adequate across trimesters for middle- to upper-income pregnant women when compared with estimated average requirements (EAR), and to determine whether food intake exceeded the tolerable upper intake level (UL) for any nutrient. DESIGN: Observational study in which pregnant women completed 3-day diet records each month during their pregnancy. Records were analyzed for nutrient content, and usual intake distributions were determined. SUBJECTS/SETTING: Subjects were low-risk women in their first trimester of pregnancy (living in middle- to upper-income households). Ninety-four women were recruited, and sixty-three participated. STATISTICAL ANALYSIS PERFORMED: Nutrient intake data were adjusted to achieve normality by using a power transformation. A mixed model method was used to assess trends in intake over time, and to estimate mean intake and within-subjects and between-subjects variance. The usual intake distribution for each nutrient was determined and compared with the EAR and UL. RESULTS: The probabilities of usual nutrient intake from food being less than the EAR were highest for iron (.91), magnesium (.53), zinc (.31), vitamin B6 (.21), selenium (.20), and vitamin C (.12). Women were not at risk of exceeding the UL from food intake for any nutrient studied. APPLICATIONS/CONCLUSIONS: Study participants did not consume adequate amounts of iron from food to meet the needs of pregnancy, and therefore iron supplementation is warranted in this population. Intake of magnesium was suboptimal using the EAR as a cut-point for adequacy.

Adult↗

PubMed1989

[Biologically active compounds from the aqueous extract of Urtica dioica].

From the water extract of the roots of Urtica dioica (stinging nettle) a polysaccharide fraction was isolated which revealed activity in the carrageenan rat paw edema model and lymphocyte transformation test. Ion exchange chromatography and gel filtration of this fraction afforded 4 different polysaccharides, one of which reduced dose dependent hemolysis in the classical pathway of the complement test. The Urtica dioica lectin (UDA) was reisolated and found to stimulate the proliferation of human lymphocytes.

Animals↗

PubMed2005

Time-resolved optical Kerr-effect investigation on CS2/polystyrene mixtures.

The relaxation dynamics of carbon disulfide are investigated in mixtures with polystyrene (PS) using the time-resolved optical heterodyne-detected optical Kerr effect (OHD-OKE). The data are analyzed using both the model-dependent approach, which assumes four distinct temporal responses, and the model-independent Fourier transform approach, which generates a spectral response that can be compared with results obtained by depolarized Rayleigh scattering. A slow dynamics is observed for the OHD-OKE transient decaying exponentially with a time constant that varies from 1.68 ps for neat CS2 to 3.76 ps for the most concentrated CS2PS mixture. The increase of this time constant accompanies an increase in the viscosity of the mixture, so we can associate this component with the diffusive reorientation process of the induced polarizability anisotropy of the carbon disulfide in the mixture. The short-time nuclear response is characterized in the frequency domain by a broad band that peaks around 30 cm(-1) for neat carbon disulfide, and is associated with a complex relaxation pattern. The vibrational distribution shifts to higher frequencies when the PS concentration is increased in the mixture. This result is discussed in terms of an increase in the interaction strength between the PS phenyl rings and the carbon disulfide molecules.

Journal Article↗

PubMed1977

Reconstitution of thermostable ATPase capable of energy coupling from its purified subunits.

Purified dicyclohexylcarbodiimide-sensitive ATPase (TF0-F1) from thermophilic bacterium PS3 is composed of a water soluble part with ATP hydrolytic activity (TF1) and a water insoluble moiety (TF0). All of the five subunits (alpha, beta, gamma, delta, and epsilon) of TF1 were isolated. TF1 was reconstituted from the five subunits, which catalyzed an ATP-32Pi exchange and an ATP-driven enhancement of fluorescence of 1-anilinonaphthalene-8-sulfonate, when adsorbed on proteoliposome inlaid with TF0 (TF3-vesicles). Subunit epsilon and/or delta became firmly bound to TF0-vesicles and there was no preferential sequence in the binding. Both subunits were required for binding of the remaining subunits of TF1 to TF0-vesicles, but they did not modify the high H+ -permeability of TF0-vesicles. The addition of gamma but they did not modify the high H+-permeability of TFO-vesicles. The addition of gamma subunit together with epsilon and delta subunits caused a marked decrease of H+ -permeability of TF0-vesicles, similar to that induced by TF1. We conclude tentatively that the epsilon and delta subunits connect TF0 and the other subunits forming a part of a proton pathway, gamma is a gate of proton flow coupled to ATP hydrolysis (or synthesis), and alpha and beta subunits contain the active site for energy transformation. A possible model of subunit structure of TF1 is proposed.

Adenosine Triphosphatases↗

PubMed2000

Stereoisomeric specificity of the retinoid cycle in the vertebrate retina.

Understanding of the stereospecificity of enzymatic reactions that regenerate the universal chromophore required to sustain vision in vertebrates, 11-cis-retinal, is needed for an accurate molecular model of retinoid transformations. In rod outer segments (ROS), the redox reaction involves all-trans-retinal and pro-S-NADPH that results in the production of pro-R-all-trans-retinol. A recently identified all-trans-retinol dehydrogenase (photoreceptor retinol dehydrogenase) displays identical stereospecificity to that of the ROS enzyme(s). This result is unusual, because photoreceptor retinol dehydrogenase is a member of a short chain alcohol dehydrogenase family, which is often pro-S-specific toward their hydrophobic alcohol substrates. The second redox reaction occurring in retinal pigment epithelium, oxidation of 11-cis-retinol, which is largely catalyzed by abundantly expressed 11-cis-retinol dehydrogenase, is pro-S-specific to both 11-cis-retinol and NADH. However, there is notable presence of pro-R-specific activities. Therefore, multiple retinol dehydrogenases are involved in regeneration of 11-cis-retinal. Finally, the cellular retinaldehyde-binding protein-induced isomerization of all-trans-retinol to 11-cis-retinol proceeds with inversion of configuration at the C(15) carbon of retinol. Together, these results provide important additions to our understanding of retinoid transformations in the eye and a prelude for in vivo studies that ultimately may result in efficient pharmacological intervention to restore and prevent deterioration of vision in several inherited eye diseases.

Alcohol Oxidoreductases↗

PubMed2004

Tissue distribution of AU-rich mRNA-binding proteins involved in regulation of mRNA decay.

Short lived cytokine and proto-oncogene mRNAs are destabilized by an A+U-rich element (ARE) in the 3'-untranslated region. Several regulatory proteins bind to AREs in cytokine and proto-oncogene mRNAs, participate in inhibiting or promoting their rapid degradation of ARE mRNAs, and influence cytokine expression and cellular transformation in experimental models. The tissue distribution and cellular localization of the different AU-rich binding proteins (AUBPs), however, have not been uniformly characterized in the mouse, a model for ARE mRNA decay. We therefore carried out immunoblot and immunohistochemical analyses of the different AUBPs using the same mouse tissues. We show that HuR protein, a major AUBP that stabilizes the ARE mRNAs, is most strongly expressed in the thymus, spleen (predominantly in lymphocytic cells), intestine, and testes. AUF1 protein, a negative regulator of ARE mRNA stability, displayed strong expression in thymus and spleen cells within lymphocytic cells, moderate expression in the epithelial linings of lungs, gonadal tissues, and nuclei of most neurons in the brain, and little expression in the other tissues. Tristetraprolin, a negative regulator of ARE mRNA stability, displayed a largely non-overlapping tissue distribution with AUF1 and was predominantly expressed in the liver and testis. KH-type splicing regulatory protein, a presumptive negative regulator of ARE mRNA stability, was distributed widely in murine organs. These results indicate that HuR and AUF1, which functionally oppose each other, have generally similar distributions, suggesting that the balance between HuR and AUF1 is likely important in control of short lived mRNA degradation, lymphocyte development, and/or cytokine production, and possibly in certain aspects of neurological function.

Animals↗

PubMed2002

Comparative analysis of the biochemical and immunohistochemical determination of hormone receptors in invasive breast carcinoma influence of the tumor-stroma ratio.

Tumor samples obtained from 106 primary breast cancer patients were examined biochemically (DCCA) and immunohistochemically (IHC) for estrogen (ER) and progesterone receptors (PR) to assess a quantitative relationship between both assays and to study the influence of the tumor-stroma ratio on this quantitative relationship. We used a model of logit transformation of IHC values (% of positive cells) and logarithmic transformation of DCCA values (fmol receptor/mg cytosolic protein). Tumors were subdivided into three categories according to the tumor-stroma ratio (more (t > s), equal amounts (t = s) or less (t < s) tumor than stroma), and the influence of the tumor-stroma ratio was studied using multiple regression analysis. We report a mathematical relationship between the results of the biochemical and immunohistochemical assays for the determination of ER status and PR status in primary breast cancer patients (ER: log DCCA(fmol/mg) = 0.369 logit (IHC(%pos cells)) + 2.328 (r = 0.573; p < 0.0001); PR: log DCCA (fmol/mg) = 0.474 logit (IHC(%pos cells)) + 0, 00 (r = 0.634; p < 0.0001)). In tumors overexpressing ER immunohistochemically (>10% nuclear positivity), median ER-DCCA is significantly higher if the tumor-stroma ratio is greater than 1. As these patients respond to hormonal treatment, depending on the degree of expression of both receptors, this study suggests that the biochemical assay be avoided because this technique is hampered by false-negative or falsely low results due to the loss of morphological information on the tumor-stroma ratio.

Biochemistry↗

PubMed2026

Immunogenicity and safety of prophylactic HPV vaccines in people living with HIV: A systematic review and meta-analysis.

Human papillomavirus (HPV) is a major global public health concern, causing genital warts and cancers of the cervix, anus, oropharynx, vulva, and penis. People living with HIV (PLWH) face a disproportionately elevated burden of HPV infection and HPV-related malignancies due to chronic immunosuppression. We conducted a systematic review and meta-analysis searching six databases from January 2006 to June 2026 without language restrictions. Twenty-five studies were included in the systematic review; 12 independent studies (N = 1,493 for HPV16) were included in the quantitative meta-analysis. Using a DerSimonian-Laird random-effects model with logit transformation, pooled seroconversion rates were: HPV16 97.8% (95% CI: 94.9-99.1%; I2 = 89.6%; 15 datasets), HPV18 94.2% (95% CI: 86.1-97.7%; I2 = 95.8%; 13 datasets), HPV6 97.0% (95% CI: 93.7-98.6%; I2 = 66.1%; 10 studies), and HPV11 97.1% (95% CI: 90.5-99.1%; I2 = 95.5%; 10 studies). CD4 count was the most consistently reported modifier of immunogenic response: HPV16 seroconversion was 98.5% in PLWH with CD4 > 350 cells/μL vs. 71.1% in those with CD4 ≤ 200 cells/μL (ACTG A5240). All three vaccine generations demonstrated high immunogenicity. Two doses of the nonavalent vaccine were non-inferior to three doses in virologically suppressed women (Papillon RCT). No vaccine-related serious adverse events were reported. GRADE certainty of evidence was moderate for HPV16, HPV6, and HPV11, and low for HPV18. Prophylactic HPV vaccination achieves high seroconversion rates across all vaccine generations in PLWH. CD4 count significantly modifies vaccine response, underscoring the importance of vaccination before severe immunosuppression develops. These findings support current international recommendations advocating HPV vaccination for all PLWH.

Humans↗

PubMed2005

Online correction for respiratory motion: evaluation of two different imaging geometries.

One aim of adaptive radiotherapy (ART) is the observation of organ motion followed by a subsequent adaptation of the treatment plan. One way of achieving this goal is a kV x-ray source mounted at a linear accelerator in combination with a flat-panel imager. Two imaging hardware configurations were evaluated for their potential for online tracking and the subsequent correction of organ motion by using fluoroscopic images: x-ray tube positioned with (A) 90 degrees and (B) 180 degrees offset to the MV beam. For one lung case two IMRT plans with five coplanar beams and the table positioned at 0 degrees were optimized for two multileaf collimators (MLCs) with 10 mm and 2.75 mm leaf width. Respiratory motion, modelled by rigid transformation in the lungs, was investigated for different amplitudes. The 3D dose distributions for different cases (no movement, uncorrected movement, correction for the movement perpendicular to the respective kV beam) were evaluated with the help of dose volume histograms (DVHs) and a modified conformity (Baltas et al 1998 Int. J. Radiat. Oncol. Biol. Phys. 40 515-24) and coverage index using the 90% isodose. For the corrected treatment plans the influence of the observed displacement vector caused by organ movement was accounted for by a respective displacement of the target point. For the simulated movement with a small amplitude (3 mm) in the anterior-posterior (AP) direction the dose distributions resulting from the correction of the displacement vector using imaging system A or B showed similar results for both systems and were in good agreement with the dose distribution of the static (not moving) patient. Increasing the amplitude in the AP direction to 6 mm or even 9 mm leads for both amplitudes and both MLCs to almost the same conformity and coverage index as the static dose distribution if imaging system B is used for the online correction. For the dose distribution obtained with correction based on imaging system A the deviation between the optimal and the corrected dose distribution is increasing with increasing amplitude. For the MLC with the smaller leaf width the difference between the optimal and the corrected dose distributions is always significantly larger than for the less conformal dose distributions created by the MLC with the 10 mm leaves. These results can be explained by the fact that system A cannot observe movement in the AP-LR plane perpendicular to the MV beam and therefore cannot correct for these movements whereas system B only fails to observe the motion in the beam direction which for photon irradiation has less impact on the dose distribution.

Body Burden↗

PubMed2025

PharaCon: a new framework for identifying bacteriophages via conditional representation learning.

MOTIVATION: Identifying bacteriophages (phages) within metagenomic sequences is essential for understanding microbial community dynamics. Transformer-based foundation models have been successfully employed to address various biological challenges. However, these models are typically pre-trained with self-supervised tasks that do not consider label variance in the pre-training data. This presents a challenge for phage identification as pre-training on mixed bacterial and phage data may lead to information bias due to the imbalance between bacterial and phage samples. RESULTS: To overcome this limitation, we proposed a novel conditional BERT framework that incorporates label classes as special tokens during pre-training. Specifically, our conditional BERT model attaches labels directly during tokenization, introducing label constraints into the model's input. Additionally, we introduced a new fine-tuning scheme that enables the conditional BERT to be effectively utilized for classification tasks. This framework allows the BERT model to acquire label-specific contextual representations from mixed sequence data during pre-training and applies the conditional BERT as a classifier during fine-tuning, and we named the fine-tuned model as PharaCon. We evaluated PharaCon against several existing methods on both simulated sequence datasets and real metagenomic contig datasets. The results demonstrate PharaCon's effectiveness and efficiency in phage identification, highlighting the advantages of incorporating label information during both pre-training and fine-tuning. AVAILABILITY AND IMPLEMENTATION: The source code and associated data can be accessed at https://github.com/Celestial-Bai/PharaCon.

Bacteriophages↗

PubMed1997

Time-frequency spectral analysis of heart rate variability during induction of general anaesthesia.

We have examined the spectral components of heart rate variability (HRV) during induction of anaesthesia with thiopentone, tracheal intubation and subsequent inhalation of isoflurane-nitrous oxide. Commonly used spectral analysis methods such as fast Fourier transformation or autoregressive modelling require stationary data and are not suitable for the rapidly changing HRV data in this period. An advanced spectral analysis method, time-frequency analysis, which can treat non-stationary data, was used in this study. Multiple spectra were generated to demonstrate the time-related spectral components of HRV. Mid-frequency power (MF, 0.08-0.15 Hz), high-frequency power (HF, 0.15-0.5 Hz) and MF/HF ratio at baseline, after induction (before intubation), immediately after intubation and during maintenance periods were calculated and compared. MF and HF powers decreased after induction and were reduced further in the maintenance period but MF/HF ratio remained unchanged after induction. Immediately after intubation MF and HF powers did not differ significantly from the immediate pre-intubation values, but MF/HF ratio did.

Adult↗

PubMed1998

Clonal analysis of urothelial carcinomas in C3H/HeN<-->BALB/c chimeric mice treated with N-butyl-N-(4-hydroxybutyl)nitrosamine.

The histological background for multifocal and metachronous development of urothelial carcinomas remains equivocal, although accumulated genetic evidence suggests monoclonal origin of multiple urothelial carcinomas. Clonal development of various preneoplastic and neoplastic urothelial lesions of C3H<-->BALB/c chimeric mice induced by N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN) was immunohistochemically investigated using a C3H strain-specific antibody. All tumor masses induced in the mice treated with 0.05% BBN for 20 weeks were composed of neoplastic cells of a single parental type, which is indicative of monoclonal lesions. Three of 10 animals harbored two or more separate carcinomas of different clonal type, which is indicative of multicentric development applicable in this model. Using DNAs derived from urothelial carcinomas and tumor-adjacent urothelium of chimeric mice, polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis and direct sequencing were performed for p53 gene exons 5-7. p53 mutations were identified in four of 11 (36%) dysplasias and non-invasive carcinomas (carcinoma in situ and pTa tumor) and 13 of 22 (59%) invasive carcinomas. Only in a single case were identical p53 mutations found in separate urinary bladder carcinomas. In contrast to the random distribution of urothelial proliferating units in chimeric mice without chemical supplement, invasive carcinomas in BBN-treated mice were accompanied by widely-distributed preneoplastic and neoplastic lesions of the same clonality, which occasionally had frequent foci of microinvasion. This is indicative of lateral clonal expansion of the clones, which precedes the bulk of invasive carcinomas. Thus, two aspects of 'field change' of the urothelium became evident in this model: either independent transformation events or lateral clonal expansion might, respectively, result in multicentric and monoclonal carcinoma development in the urinary tract.

Animals↗

PubMed1993

Mitochondrial phylogeny of the endemic mouthbrooding lineages of cichlid fishes from Lake Tanganyika in eastern Africa.

Of the three cichlid species flocks in eastern Africa, Lake Tanganyika harbors the oldest species assemblage, which is also the most diverse morphologically and behaviorally. For 12 species (20 individuals) of 12 genera of the tribe Ectodini, 852 bp from two segments (cytochrome b and control region) of the mitochondrial genome were sequenced. In addition, orthologous sequences were obtained from eight species (11 individuals) representing other mouthbrooding lineages from Lake Tanganyika. Comparisons of sequence divergences revealed that the single Tanganyikan tribe Ectodini appears to be approximately five times older than the whole Lake Malawi cichlid species flock, suggesting that the radiation of the Tanganyikan mouthbrooding lineages took place long before the species flocks of Lakes Malawi and Victoria evolved. Seven of nine surveyed tribes of Tanganyikan cichlids appear to be approximately equally divergent, and this seems to corroborate the hypothesis of a rapid simultaneous formation of lineages at an early stage in the history of the Lake Tanganyika species flock. The close genetic relationship between the endemic Tropheus lineage and a nonendemic "Haplochromine," Astatotilapia burtoni, indicates that members of the tribe Tropheini may be the sister group of the cichlid flocks of Lakes Malawi and Victoria. The phylogenetic analyses demonstrate the monophyly of the Ectodini and identify the Cyprichromini as their sister group among the Tanganyikan cichlids. Within the tribe Ectodini the molecular data suggest both a branching pattern different than that previously proposed and a subdivision of the Ectodini into four clades, instead of the two originally described. The previously postulated model of morphological transformations believed to be responsible for the drastically different types of ecological specialization found among the Ectodini might therefore be in need of reinterpretation. Characters immediately related to foraging and nutrition seem to be particularly prone to homoplasy, even among members of a single lineage of cichlid fishes.

Africa, Eastern↗

PubMed2006

Medicine of senescence or managing a hospital system: the resistible rise of geriatric medicine in the State of Victoria.

This paper investigates the conditions in which geriatric medicine emerged in the state of Victoria between the late 1950s and the late 1970s. It shows how, in transforming a charity model of care into a medical model of service, nascent geriatricians were caught up in the shifting balance of responsibilities between state and Commonwealth governments in funding health services and care for the aged, and in the efforts of a small segment of the Australian medical profession to establish an organisational setting and professional context for social medicine. In Victoria, the potential for doctors to circumvent bureaucratic and professional limitations on their work lay in their relationship with their institutional committees of management whose members were drawn from the general community. The paper argues that pioneer 'geriatricians' failed to establish a field of practice that met all the needs they discerned in their patient group because they could not change community ideas about appropriate responses to old age infirmity.

Aged↗

PubMed1997

Evolution of male tail development in rhabditid nematodes related to Caenorhabditis elegans.

The evolutionary pathway that has led to male tails of diverse morphology among species of the nematode family Rhabditidae was reconstructed. This family includes the well-studied model species Caenorhabditis elegans. By relating the steps of male tail morphological evolution to the phenotypic changes brought about by developmental mutations induced experimentally in C. elegans, the goal is to identify genes responsible for morphological evolution. The varying morphological characters of the male tails of several rhabiditid species have been described previously (Fitch and Emmons, 1995, Dev. Biol. 170:564-582). The developmental events preceding differentiation of the adult structures have also been analyzed; in many cases the origins of varying adult morphological characters were traced to differences during ontogeny. In the present work, the evolutionary changes producing these differences were reconstructed in the context of the four possible phylogenies supported independently by sequences of 18S ribosomal RNA genes (rDNA). Two or more alternative states were defined for 36 developmental and adult morphological characters. These characters alone do not provide sufficient data to resolve most species relationships; however, when combined with the rDNA characters, they provide stronger support for one of the four rDNA phylogenies. Assuming a model of ordered transformations for multistate developmental characters generally results in greater resolution. Transformations between character states can be assigned unequivocally by parsimony to unambiguous branches for most of the characters. Correlations are thereby revealed for some of the developmental characters, indicating a probability of a shared developmental or genetic regulatory pathway. Four of the unequivocal character state changes on unambiguously supported branches closely resemble the phenotypic changes brought about by known mutations in C. elegans. These mutations define genes that are known to act in genetic regulatory hierarchies controlling pattern formation, differentiation, and morphogenesis. Although these studies are still at an early stage, these results strongly suggest that parallel studies of developmental mutants in C. elegans and of morphological and developmental evolution among related nematodes will help define genetic changes underlying the evolution of form.

Animals↗

PubMed1993

Microencapsulation of recombinant cells: a new delivery system for gene therapy.

The therapeutic potential of somatic gene therapy has been extensively investigated in recent years, yet its slow progression into the clinical setting can be attributed to problems associated with the inability to achieve efficient gene transfers, to obtain sustained level of expression of the transfected gene, and the necessity to avoid immunorejection after transplantation. Here we report on an alternate strategy in gene therapy that overcomes all three problems by immunoisolating genetically modified cells in a biocompatible membrane, thereby introducing a system that can provide sustained delivery of the desired gene product. As a model, mouse fibroblasts transformed with the human growth hormone gene (Ltk-GH) were encapsulated with an alginate-poly-L-lysine-alginate membrane. Long-term in vitro studies showed that the encapsulation of the cells was physiologically compatible with growth and survival of the cells. Furthermore, there was a unique pattern of secretion of the human protein by the encapsulated cells: there was a phase of steady increase in the secretion of the human growth hormone by each cell, followed by a plateau phase. The most convincing evidence of the feasibility of this strategy was provided by the in vivo study: Balb-c mice transplanted with encapsulated Ltk-GH cells had detectable serum levels of human growth hormone (hGH) for the duration of the study (115 days). Moreover, encapsulated cells recovered from a recipient 1 year after the transplantation continued to secrete high levels of hGH in culture.

Alginates↗

PubMed2001

Nitrogen fertilizer rate and crop management effects on nitrate leaching from an agricultural field in central Pennsylvania.

Eighteen pan lysimeters were installed at a depth of 1.2 m in a Hagerstown silt loam soil in a corn field in central Pennsylvania in 1988. In 1995, wick lysimeters were also installed at 1.2 m depth in the same access pits. Treatments have included N fertilizer rates, use of manure, crop rotation (continuous corn, corn-soybean, alfalfa-corn), and tillage (chisel plow-disk, no-till). The leachate data were used to evaluate a number of nitrate leaching models. Some of the highlights of the 11 years of results include the following: 1) growing corn without organic N inputs at the economic optimum N rate (EON) resulted in NO3--N concentrations of 15 to 20 mg l(-1) in leachate; 2) use of manure or previous alfalfa crop as partial source of N also resulted in 15 to 20 mg l(-1) of NO3--N in leachate below corn at EON; 3) NO3--N concentration in leachate below alfalfa was approximately 4 mg l(-1); 4) NO3--N concentration in leachate below soybeans following corn was influenced by fertilizer N rate applied to corn; 5) the mass of NO3--N leached below corn at the EON rate averaged 90 kg N ha(-1) (approx. 40% of fertilizer N applied at EON); 6) wick lysimeters collected approximately 100% of leachate vs. 40-50% collected by pan lysimeters. Coefficients of variation of the collected leachate volumes for both lysimeter types were similar; 7) tillage did not markedly affect nitrate leaching losses; 8) tested leaching models could accurately predict leachate volumes and could be calibrated to match nitrate leaching losses in calibration years, but only one model (SOILN) accurately predicted nitrate leaching losses in the majority of validation treatment years. Apparent problems with tested models: there was difficulty estimating sizes of organic N pools and their transformation rates, and the models either did not include a macropore flow component or did not handle macropore flow well.

Agriculture↗

PubMed2001

Constant pressure molecular dynamics on a hypercylinder.

A Lagrangian formalism for variable-cell-shape molecular dynamics is derived from first principles. It is based on consideration of a crystal as arranged on the surface of hypercylinder in an extended coordinate frame. The artificial curvature along the additional degrees of freedom upsets the balance of forces acting on every atom in a periodically repeating cell. Since the distance between atoms is not the metric tensor the proposed method provides an essential simplification of the equations of motion compared to those of Parinello and Rahman approach. The Lagrangian of the system eliminates the cell orientation from the dynamics, thus avoiding symmetry-breaking effects and physically irrelevant cell rotation. The change from a fully flexible cell to an isotropically flexible cell is realized within the same computational framework. Simulations for the transformation of a model He lattice under isotropic applied pressure are used to illustrate the application of this method.

Journal Article↗