Comment on "Structural stability of complex hydrides: LiBH(4) revisited".
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Comment↗
Biomedical subjects
D D Johnson
Publications and source records attributed to D D Johnson.
Origin of bulklike structure and bond length disorder of Pt37 and Pt6Ru31 clusters on carbon: comparison of theory and experiment.
We describe a theoretical analysis of the structures of self-organizing nanoparticles formed by Pt and Ru-Pt on carbon support. The calculations provide insights into the nature of these metal particle systems-ones of current interest for use as the electrocatalytic materials of direct oxidation fuel cells-and clarify complex behaviors noted in earlier experimental studies. With clusters deposited via metallo-organic Pt or PtRu(5) complexes, previous experiments [Nashner et al. J. Am. Chem. Soc. 1997, 119, 7760; Nashner et al. J. Am. Chem. Soc. 1998, 120, 8093; Frenkel et al. J. Phys. Chem. B 2001, 105, 12689] showed that the Pt and Pt-Ru based clusters are formed with fcc(111)-stacked cuboctahedral geometry and essentially bulklike metal-metal bond lengths, even for the smallest (few atom) nanoparticles for which the average coordination number is much smaller than that in the bulk, and that Pt in bimetallic [PtRu(5)] clusters segregates to the ambient surface of the supported nanoparticles. We explain these observations and characterize the cluster structures and bond length distributions using density functional theory calculations with graphite as a model for the support. The present study reveals the origin of the observed metal-metal bond length disorder, distinctively different for each system, and demonstrates the profound consequences that result from the cluster/carbon-support interactions and their key role in the structure and electronic properties of supported metallic nanoparticles.
Journal Article↗
Effects of calpastatin and micro-calpain markers in beef cattle on tenderness traits.
The objective of this study was to assess the association of single nucleotide polymorphisms (SNP) developed at the calpastatin (CAST) and mu-calpain (CAPN1) genes with meat tenderness and palatability traits in populations with diverse genetic backgrounds. Three populations were used in the study. One population consisted of Bos taurus that included crossbred animals derived from Hereford, Angus, Red Angus, Limousin, Charolais, Gelbvieh, and Simmental (GPE7; n = 539). Another population consisted of Bos taurus with Bos indicus influence, including crossbred animals from Hereford, Angus, Brangus, Beefmaster, Bonsmara, and Romosinuano (GPE8; n = 580). The third population was Bos indicus and consisted of purebred Brahman (STARS; n = 444). Traits evaluated were meat tenderness measured as Warner-Bratzler shear force (WBSF; kg) at 14 d postmortem, and traits evaluated by trained sensory panels that included tenderness score, juiciness, and flavor intensity. A SNP at the CAST gene had a significant (P < 0.003) effect on WBSF and tenderness score in the GPE7 and GPE8 populations. Animals inheriting the TT genotype at CAST had meat that was more tender than those inheriting the CC genotype. The marker at the CAPN1 gene was significant (P < 0.03) for tenderness score in GPE7 and GPE8. Animals inheriting the CC genotype at CAPN1 had meat that was more tender than those inheriting the TT genotype. Markers at the CAST and CAPN1 genes were associated with flavor intensity in the GPE8 population. Animals inheriting the CC genotype at CAST and the TT genotype at CAPN1 produced steaks with an intense flavor when compared with the other genotypes. An interaction between CAST and CAPN1 was detected (P < 0.05) for WBSF on GPE8. The statistical significance of the interaction is questionable because of the limited number of observations in some cells. Markers developed at the CAST and CAPN1 genes are suitable for use in identifying animals with the genetic potential to produce meat that is more tender.
Animals↗
Removing critical errors for DFT applications to transition-metal nanoclusters: correct ground-state structures of Ru clusters.
As ruthenium plays an important role in heterogeneous catalysis, understanding the structural and electronic properties of Ru clusters is crucial to advancement of technology. Because of its efficiency, density functional theory (DFT) calculations are often utilized in nanoscience, but careful validation is necessary. Recently, small, nonmetallic Ru(n) clusters were reported by Zhang et al. [J. Phys. Chem. B 2004, 108, 2140] to form unusual square and cubic ground-state structures within DFT by treating the exchange-correlation (XC) functional at the level of general-gradient-corrected approximation (GGA). For such clusters, we show that the calculated, energetically preferred structures are sensitive to which XC functional is used and whether relativistic effects are included. We find that a hybrid XC functional with partially exact exchange, such as PBE0, corrects the Ru2 magnetic moment, bond length, and dissociation energy in agreement with experiment and high-level quantum chemistry calculations and changes the Ru4 ground-state structure to a tetrahedron, instead of a square. The change in structural preference is explained by the corrections to the electronic structure of a Ru atom, where the relative position of majority spin s level is shifted with respect to e(g) levels. We also find that standard nonrelativistic DFT-GGA gives similar results to relativistic DFT-PBE0, i.e., relative shifting of s level, but not for the right reasons. Our results again stress the need to validate an XC functional before application to transition-metal nanoclusters.
Journal Article↗
Assessment of single nucleotide polymorphisms in genes residing on chromosomes 14 and 29 for association with carcass composition traits in Bos indicus cattle.
Objective of this study was to assess the association of SNP in the diacylglycerol O-acyltransferase 1 (DGAT1), thyroglobulin (TG), and micromolar calcium-activated neutral protease (CAPN1) genes with carcass composition and meat quality traits in Bos indicus cattle. A population of Brahman calves (n = 479) was developed in central Florida from 1996 to 2000. Traits analyzed were ADG, hip height, slaughter weight, fat thickness, HCW, marbling score, LM area, estimated KPH fat, yield grade, retail yield, sensory panel tenderness score, carcass hump height, and cooked meat tenderness measured as Warner-Bratzler shear force at 7, 14, and 21 d postmortem. Single nucleotide polymorphisms previously reported in the TG and DGAT1 genes were used as markers on chromosome 14. Two previously reported and two new SNP in the CAPN1 gene were used as markers on chromosome 29. One SNP in CAPN1 was uninformative, and another one was associated with tenderness score (P < 0.05), suggesting the presence of variation affecting meat tenderness. All three informative SNP at the CAPN1 gene were associated with hump height (P < 0.02). The TG marker was associated with fat thickness and LMA (P < 0.05), but not with marbling score. No significant associations of the SNP in the DGAT1 gene were observed for any trait. Allele frequencies of the SNP in TG and CAPN1 were different in this Brahman population than in reported allele frequencies in Bos taurus populations. The results suggest that the use of molecular marker information developed in Bos taurus populations to Bos indicus populations may require development of appropriate additional markers.
Animals↗
A new single nucleotide polymorphism in CAPN1 extends the current tenderness marker test to include cattle of Bos indicus, Bos taurus, and crossbred descent.
The three objectives of this study were to 1) test for the existence of beef tenderness markers in the CAPN1 gene segregating in Brahman cattle; 2) test existing CAPN1 tenderness markers in indicus-influenced crossbred cattle; and 3) produce a revised marker system for use in cattle of all subspecies backgrounds. Previously, two SNP in the CAPN1 gene have been described that could be used to guide selection in Bos taurus cattle (designated Markers 316 and 530), but neither marker segregates at high frequency in Brahman cattle. In this study, we examined three additional SNP in CAPN1 to determine whether variation in this gene could be associated with tenderness in a large, multisire American Brahman population. One marker (termed 4751) was associated with shear force on postmortem d 7 (P < 0.01), 14 (P = 0.015), and 21 (P < 0.001) in this population, demonstrating that genetic variation important for tenderness segregates in Bos indicus cattle at or near CAPN1. Marker 4751 also was associated with shear force (P < 0.01) in the same large, multisire population of cattle of strictly Bos taurus descent that was used to develop the previously reported SNP (referred to as the Germplasm Evaluation [GPE] Cycle 7 population), indicating the possibility that one marker could have wide applicability in cattle of all subspecies backgrounds. To test this hypothesis, Marker 4751 was tested in a third large, multisire cattle population of crossbred subspecies descent (including sire breeds of Brangus, Beefmaster, Bonsmara, Romosinuano, Hereford, and Angus referred to as the GPE Cycle 8 population). The highly significant association of Marker 4751 with shear force in this population (P < 0.001) confirms the usefulness of Marker 4751 in cattle of all subspecies backgrounds, including Bos taurus, Bos indicus, and crossbred descent. This wide applicability adds substantial value over previously released Markers 316 and 530. However, Marker 316, which had previously been shown to be associated with tenderness in the GPE Cycle 7 population, also was highly associated with shear force in the GPE Cycle 8 animals (P < 0.001). Thus, Marker 316 may continue to be useful in a variety of populations with a high percentage of Bos taurus backgrounds. An optimal marker strategy for CAPN1 in many cases will be to use both Markers 316 and 4751.
Animals↗
Reliable first-principles alloy thermodynamics via truncated cluster expansions.
In alloys cluster expansions (CE) are increasingly used to combine first-principles electronic-structure calculations and Monte Carlo methods to predict thermodynamic properties. As a basis-set expansion in terms of lattice geometrical clusters and effective cluster interactions, the CE is exact if infinite, but is tractable only if truncated. Yet until now a truncation procedure was not well defined and did not guarantee a reliable truncated CE. We present an optimal truncation procedure for CE basis sets that provides reliable thermodynamics. We then exemplify its importance in Ni3V, where the CE has failed unpredictably, and now show agreement to a range of measured values, predict new low-energy structures, and explain the cause of previous failures.
Journal Article↗
Lichtenstein vs anterior preperitoneal prosthetic mesh placement in open inguinal hernia repair: a prospective, randomized trial.
Male veterans with unilateral primary inguinal hernia, classified intraoperatively as Gilbert Type III or IV, were randomized to subaponeurotic (Lichtenstein, n=126) or preperitoneal (Read-Rives, n=121) repair under general or spinal anesthesia. The two groups of patients were comparable in age, body weight index, comorbidities, and size and type of hernia. Of the 247 patients enrolled, 224 were followed for at least 2 years (median 82 months, range 24-110 months), 16 were lost to follow-up, and seven died from causes unrelated to the surgery. The average operative time of the Read-Rives repair was 9 min longer than that of the Lichtenstein repair. There were no wound infections, and the frequencies of other short- and long-term complications were low and similar in the two groups. Six patients developed hernia recurrence, five in the Lichtenstein group (4.3%), and one in the Read-Rives group (<1%), ( P=0.21). Both anterior repairs are associated with low postoperative morbidity and recurrence rates. The Lichtenstein repair is technically easier and less time consuming. There is no statistically significant difference in the recurrence rate between the two repairs.
Adolescent↗
Effect of sire on mu- and m-calpain activity and rate of tenderization as indicated by myofibril fragmentation indices of steaks from Brahman cattle.
The objectives of this study were to assess the influence of sire on mu- and m-calpain activities, to evaluate the relationships of activities of these enzymes to other traits related to beef palatability, and to assess the influence of sire on the rate of tenderization (as measured by myofibril fragmentation index [MFI]) in Brahman longissimus muscle. Brahman calves (n = 87), sired by nine bulls, were born, weaned, fed, and slaughtered in central Florida. Traits evaluated were mu- and m-calpain activities and MFI after 1, 7, 14, and 21 d of aging. Other traits were analyzed to determine their associations with mu- and m-calpain activity and MFI, including calpastatin activity, percentage of raw and cooked lipids, Warner-Bratzler shear force (WBSF) values after 7, 14, and 21 d of aging, and sensory panel rating of tenderness, juiciness, and connective tissue amount after 14 d of aging. Data were analyzed using a model with sire, sex, year, and slaughter group (calves of the same sex slaughtered on the same date) as fixed effects, and adjusted to a constant adjusted 12th-rib fat thickness. Sire affected mu-calpain activity (P < 0.04), calpastatin activity (P < 0.01), d-14 MFI (P < 0.02), d-7 WBSF (P < 0.05), d-14 WBSF (P < 0.04), and sensory panel juiciness score (P < 0.01), but not (P < 0.75) m-calpain activity. Measures of tenderness and palatability were generally moderately to strongly correlated (both simple and residual correlations) with calpastatin and m-calpain activity. Myofibril fragmentation index residuals (adjusted for all model components except sire) after all aging periods were fitted using nonlinear regression to the exponential curve (MFI(i) = kappa0 + kappa1 exp[kappa2 t(i)] + epsilon(i), where t(i) represents aging in days, k0 is ultimate MFI after aging, kappa1 is the difference between initial and ultimate MFI, kappa2 is the rate of increase in MFI, and epsilon(i) is the error term associated with the ith observation, assumed to be independent and identically distributed normally). Sires had different estimates and combinations of estimates, which were used to plot MFI change with time. These curves visually differed for sires and suggested that postmortem tenderization extent and rate differ as well. Use of a combination of these estimated parameters in a selection/carcass sorting program represents an alternative consideration for tenderization improvement programs.
Animals↗
Effects of implant regimens (trenbolone acetate-estradiol administered alone or in combination with zeranol) and vitamin D3 on fresh beef color and quality.
In the first oftwo experiments, 123 calf-fed steers were used over a 2-yr period to evaluate the effects of trenbolone acetate (TBA)-based implants administered alone or in combination with zeranol implants on fresh beef muscle quality, color, and physiological maturity of the carcass. Implant treatments decreased (P < 0.05) a* values (d 0 and d 3 of retail display) and b* values (d 0, d 1, and d 3 of retail display) after 14 d of aging. Carcasses from cattle initially implanted with Revalor-S and reimplanted with Revalor-S on d 60 of the finishing period showed increased lean and bone maturity scores and ash content of the 9th to 11th thoracic buttons and Warner-Bratzler shear force values (WBS) compared to those initially implanted with Ralgro and subsequently reimplanted with Revalor-S or control cattle. In addition, implants decreased (P < 0.05) marbling, percentage of the carcasses grading Choice, and kidney, pelvic, and heart fat (KPH). Implant treatments increased (P < 0.05) ADG, hot carcass weights, and longissimus muscle (LM) area. In the second experiment over a 2-yr period, 166 steers fed as yearlings were allotted to one of two implant treatments and one of two vitamin D3 preharvest supplementation treatments. Implanted steers had heavier (P < 0.05) final body weights and higher (P < 0.05) ADG, less (P < 0.05) KPH fat, and larger (P < 0.05) LM. Also, implanted steers had more (P < 0.05) advanced bone maturity scores, higher (P < 0.05) ash content of the 9th to 11th thoracic buttons, and higher (P < 0.05) WBS values on 5-d postmortem loin steaks. Vitamin D3 feeding decreased (P < 0.05) final live weight, ADG (P < 0.05), and LM (P < 0.05), but did not significantly improve WBS values. In Experiment 2, neither implant treatment nor vitamin D3 supplementation had significant effects on L*, a*, or b* values of muscles in steaks before or during simulated retail display.
Administration, Oral↗
Estimated genetic parameters for palatability traits of steaks from Brahman cattle.
Heritabilities and genetic and phenotypic correlations were estimated from carcass and beef palatability data collected from Brahman calves (n = 504) born in central Florida from 1996 to 2000. Traits evaluated included Warner-Bratzler shear force (after 7, 14, and 21 d of aging), panel tenderness score, connective tissue amount, juiciness, flavor intensity, and off flavor (after 14 d of aging), percentages of raw and cooked lipids, and milligrams per gram of muscle calpastatin activity. Parameters were estimated using an animal model and derivative-free restricted maximum likelihood procedures. Estimated heritabilities for d 7, 14, and 21 shear force were 0.14,0.14, and 0.06, respectively, indicating that improvement in these traits by selection would be slow. Estimated heritabilities of sensory panel attributes were 0.11, 0.12, 0.05, 0.04, and 0.01 for tenderness, connective tissue amount, juiciness, flavor intensity, and off flavor, respectively. The estimated heritabilities for percentages of raw and cooked lipids, and calpastatin activity were 0.34, 0.17, and 0.07, respectively. Most of the estimated genetic correlations among palatability traits and for palatability traits with fat thickness, marbling score, and loin muscle area were consistent with other estimates from the literature. Results indicated that improvement in tenderness based on selection for favorable shear force, sensory panel tenderness, or calpastatin activity would be slow; therefore, postslaughter intervention programs should also be considered.
Animals↗
Absolute TiN(111) step energies from analysis of anisotropic island shape fluctuations.
In situ high-temperature (1165-1248 K) scanning tunneling microscopy was used to measure fluctuations around the equilibrium shape of two-dimensional vacancy islands on TiN(111) terraces. From the equilibrium shape, the ratio of the two <110> step energies was found to be 0.72 +/- 0.02. Combining this with the results of an exact approach for analysis of shape fluctuations, applicable to highly anisotropic islands, we obtain absolute values for step energies and step stiffnesses as a function of orientation.
Journal Article↗
Estimated genetic parameters for carcass traits of Brahman cattle.
Heritabilities and genetic and phenotypic correlations were estimated from feedlot and carcass data collected from Brahman calves (n = 504) in central Florida from 1996 to 2000. Data were analyzed using animal models in MTDFREML. Models included contemporary group (n = 44; groups of calves of the same sex, fed in the same pen, slaughtered on the same day) as a fixed effect and calf age in days at slaughter as a continuous variable. Estimated feedlot trait heritabilities were 0.64, 0.67, 0.47, and 0.26 for ADG, hip height at slaughter, slaughter weight, and shrink. The USDA yield grade estimated heritability was 0.71; heritabilities for component traits of yield grade, including hot carcass weight, adjusted 12th rib backfat thickness, loin muscle area, and percentage kidney, pelvic, and heart fat were 0.55, 0.63, 0.44, and 0.46, respectively. Heritability estimates for dressing percentage, marbling score, USDA quality grade, cutability, retail yield, and carcass hump height were 0.77, 0.44, 0.47, 0.71, 0.5, and 0.54, respectively. Estimated genetic correlations of adjusted 12th rib backfat thickness with ADG, slaughter weight, marbling score, percentage kidney, pelvic, and heart fat, and yield grade (0.49, 0.46, 0.56, 0.63, and 0.93, respectively) were generally larger than most literature estimates. Estimated genetic correlations of marbling score with ADG, percentage shrink, loin muscle area, percentage kidney, pelvic, and heart fat, USDA yield grade, cutability, retail yield, and carcass hump height were 0.28, 0.49, 0.44, 0.27, 0.45, -0.43, 0.27, and 0.43, respectively. Results indicate that sufficient genetic variation exists within the Brahman breed for design and implementation of effective selection programs for important carcass quality and yield traits.
Animals↗
Classical density functional theory of freezing in simple fluids: numerically induced false solutions.
Density functional theory (DFT) has provided many insights into the freezing of simple fluids. Several analytical and numerical solution have shown that the DFT provides an accurate description of freezing of hard spheres and their mixtures. Compared to other techniques, numerical, grid-based algorithms for solving the DFT equations have more variational freedom and are capable of describing subtle behavior, as that seen in mixtures with multipeaked density profiles. However the grid-based approach is sensitive to the coarseness of the mesh employed. Here we summarize how the granularity of the mesh affects the freezing point within the DFT. For coarse meshes, we show that the freezing point is masked by numerically induced false minima of the DFT grand potential. These false minima are removed when a fine enough grid is used to represent properly the density profiles. Our results suggest that others using such grid-based methods have focused on such numerical artifacts that have little to do with real phenomena.
Journal Article↗
Long-term resource variation and group size: a large-sample field test of the Resource Dispersion Hypothesis.
BACKGROUND: The Resource Dispersion Hypothesis (RDH) proposes a mechanism for the passive formation of social groups where resources are dispersed, even in the absence of any benefits of group living per se. Despite supportive modelling, it lacks empirical testing. The RDH predicts that, rather than Territory Size (TS) increasing monotonically with Group Size (GS) to account for increasing metabolic needs, TS is constrained by the dispersion of resource patches, whereas GS is independently limited by their richness. We conducted multiple-year tests of these predictions using data from the long-term study of badgers Meles meles in Wytham Woods, England. The study has long failed to identify direct benefits from group living and, consequently, alternative explanations for their large group sizes have been sought. RESULTS: TS was not consistently related to resource dispersion, nor was GS consistently related to resource richness. Results differed according to data groupings and whether territories were mapped using minimum convex polygons or traditional methods. Habitats differed significantly in resource availability, but there was also evidence that food resources may be spatially aggregated within habitat types as well as between them. CONCLUSIONS: This is, we believe, the largest ever test of the RDH and builds on the long-term project that initiated part of the thinking behind the hypothesis. Support for predictions were mixed and depended on year and the method used to map territory borders. We suggest that within-habitat patchiness, as well as model assumptions, should be further investigated for improved tests of the RDH in the future.
Animals↗
Bone collagen cross-links: a convergent synthesis of (+)-deoxypyrrololine.
A convergent total synthesis of (+)-deoxypyrrololine (Dpl, 4), a putative cross-link of bone collagen, is described starting from a commercially available L-glutamic acid derivative, (4S)-5-(tert-butoxy)-4-[(tert-butoxycarbonyl)amino]-5- oxopentanoic acid (16). Condensation of aldehyde (S)-(-)-17 with nitro compound (S)-(-)-27, both of which were prepared from a common precursor (S)-16, gave the alpha-hydroxynitro compound 28, which upon acetylation afforded alpha-acetoxynitro compound 14 in good yield. Subsequent condensation and cyclization of alpha-acetoxynitro compound 14 with benzyl isocyanoacetate (15) in the presence of DBU in THF gave the key pyrrole intermediate (S,S)-(-)-12 in 57% yield. N-Alkylation of pyrrole (S,S)-(-)-12 with iodide (S)-(-)-13 using t-BuOK in THF afforded the 2-benzyloxycarbonyl-1,3,4-substituted pyrrole derivative (-)-29 in 42% yield. Removal of the protective groups in (-)-29 followed by hydrogenolysis and decarboxylation afforded the cross-link (+)-Dpl (4) in good overall yield. The synthesis of an analogue (S)-(+)-24 and formation of a novel tetrahydroindole derivative (-)-31 are also described.
Amino Acids↗
Growth, puberty, and carcass characteristics of Brahman-, Senepol-, and Tuli-sired F1 Angus bulls.
Postweaning growth, sexual development, libido, and carcass data were collected from two consecutive calf crops using 31 Brahman x Angus (B x A), 41 Senepol x Angus (S x A), and 38 Tuli x Angus (T x A) F1 bulls. Following weaning (by mid-September) and preconditioning, at the start of the study (late September) bulls were fed concentrate (three times each week at a rate equivalent to 4.5 kg/d) on bahiagrass pasture for approximately 250 d. At the start of the study and at 28-d intervals, BW, hip height, and scrotal circumference (SC) were measured. Concurrently at 28-d intervals, when the SC of a bull was > or = 23 cm, semen collection was attempted using electroejaculation. Ejaculates were evaluated for presence of first spermatozoa (FS), 50 x 10(6) sperm with at least 10% motility (PU), and 500 x 10(6) sperm with at least 50% motility (PP). After all bulls reached PP they were subjected to two libido tests. Carcass data were collected on all bulls (n = 110) and Warner-Bratzler shear (WBS) force values were assessed on a subset (n = 80). For both years, B x A bulls were heavier (P < 0.05) and taller (P < 0.05) than S x A and T x A bulls at the start and end of the study. However, breed type did not influence (P > 0.10) gain in BW or hip height during the study. Scrotal circumference of T x A bulls was larger (P < 0.05) than that of B x A or S x A bulls at the start of the study, but there was no effect (P > 0.10) of breed type by the end of the study. At PU and PP, B x A bulls were older (P < 0.05), heavier (P < 0.05), and taller (P < 0.05) and had larger (P < 0.05) SC than S x A and T x A bulls. Tuli x Angus bulls were younger (P < 0.05) than S x A bulls at PU and PP but had similar SC. Libido scores tended (P < 0.10) to be lower for B x A than for S x A and T x A bulls. Breed type affected (P < 0.05) carcass traits; B x A bulls had the heaviest (P < 0.05) hot carcass weight, greatest (P < 0.05) dressing percentage, larger (P < 0.05) longissimus muscle area than S x A bulls, and higher (P < 0.05) USDA yield grade than T x A bulls but greatest (P < 0.05) WBS force values. Breed type did not affect (P > 0.10) USDA quality grade. In conclusion, tropically adapted F1 bulls produced from Senepol (Bos taurus) and Tuli (Sanga) sires bred to Angus cows in Florida had lighter BW, shorter hip heights, and smaller carcasses than those from Brahman sires but reached puberty earlier and had higher libido scores and lower WBS force values.
Adaptation, Physiological↗
Synthesis of immunoreagents for detection of deoxypyrrololine, a cross-link of bone collagen.
Two immunogens (5,6) and two probes (fluorescent 7 and chemiluminescent 8) were prepared from benzyl ester (-)-10. These immunoreagents (5,6 and 7,8) are useful for detection of collagen cross-link (+)-deoxypyrrololine (Dpl, 4), and for development of assays for osteoporosis.
Amino Acids↗