Hartree-Fock-Bogoliubov theory versus local-density approximation for superfluid trapped fermionic atoms

We investigate a gas of superfluid fermionic atoms trapped in two hyperfine states by a spherical harmonic potential. We propose a new regularization method to remove the ultraviolet divergence in the Hartree-Fock-Bogoliubov equations caused by the use of a zero-range atom-atom interaction. Compared with a method used in the literature, our method is simpler and has improved convergence properties. Then we compare Hartree-Fock-Bogoliubov calculations with the semiclassical local-density approximation. We observe that for systems containing a small number of atoms shell effects, which cannot be reproduced by the semiclassical calculation, are very important. For systems with a large number of atoms at zero temperature the two calculations are in quite good agreement, which, however, is deteriorated at non-zero temperature, especially near the critical temperature. In this case the different behavior can be explained within the Ginzburg-Landau theory.Comment: 12 pages, 8 figures, revtex; v2: references and clarifying remarks adde

Utilization of glycerin byproduct derived from soybean oil biodiesel as a carbon source for heterologous protein production in Pichia pastoris

AbstractCrude glycerol, also known as glycerin, is the main byproduct of the biodiesel industry. It has been estimated that up to 40,000tons of glycerin will be produced each year by 2020. This study evaluated the value-added use of crude glycerol derived from soybean biodiesel preparation as a carbon source for heterologous protein production using the yeast Pichia pastoris. Eleven glycerin samples were obtained by methanolysis of soybean oil using different acids or bases as catalysts. Cell growth experiments showed that crude glycerol containing either potassium or sodium hydroxide resulted in 1.5–2 times higher final cell densities when compared to glycerol P.A. Finally, crude glycerol containing sodium hydroxide was successfully utilized for constitutive heterologous α-amylase production in P. pastoris. This study demonstrated that crude glycerol without any purification steps may be directly used as carbon source for protein production in P. pastoris

Elastic Tensor of Sr2_2RuO4_4

The six independent elastic constants of Sr$_2$RuO$_4$ were determined using resonant ultrasound spectroscopy on a high-quality single-crystal specimen. The constants are in excellent agreement with those obtained from pulse-echo experiments performed on a sample cut from the same ingot. A calculation of the Debye temperature using the measured constants agrees well with values obtained from both specific heat and M\"{o}ssbauer measurements.Comment: 4 pages, 2 figures, 2 tables, submitted to PR

Regulacija puta razgradnje pentoza s pomoću gena izoliranih iz plijesni Aspergillus niger

The aim of this study was to obtain a better understanding of the pentose catabolism in Aspergillus niger and the regulatory systems that affect it. To this end, we have cloned and characterised the genes encoding A. niger L-arabitol dehydrogenase (ladA) and xylitol dehydrogenase (xdhA), and compared the regulation of these genes to other genes of the pentose catabolic pathway. This demonstrated that activation of the pathway depends on two transcriptional regulators, the xylanolytic activator (XlnR) and an unidentified L-arabinose specific regulator (AraR). These two regulators affect those genes of the pentose catabolic pathway that are related to catabolic conversion of their corresponding inducers (D-xylose and L-arabinose, respectively).Istraživanje je provedeno radi boljeg razumijevanja puta razgradnje pentoza plijesni Aspergillus niger i regulacijskih sustava koji na njega utječu. Klonirani su i karakterizirani geni koji kodiraju L-arabitol dehidrogenazu (ladA) i ksilitol dehidrogenazu (xdhA) plijesni A. niger, te uspoređeni s ostalim genima koji reguliraju put razgradnje pentoza. Otkriveno je da aktivacija puta razgradnje ovisi o dva regulatora transkripcije gena, tj. aktivatoru razgradnje D-ksiloze (XlnR) i regulatoru ekspresije gena pri razgradnji L-arabinoze (AraR)

Branched chain amino acids are associated with metabolic complications in liver transplant recipients

Background: Obesity, dyslipidemia and type 2 diabetes (T2D) contribute substantially to increased cardiovascular morbidity and mortality in patients after orthotopic liver transplantation (OLTx). Elevated plasma branched chain amino acids (BCAA) are linked to metabolic disturbances and cardiovascular disease (CVD) risk profiles in several non-OLTx populations. Methods: Cross-sectional analysis of liver transplant recipients from TransplantLines, a single-center biobank and cohort study. BCAA plasma levels were measured by means of nuclear-magnetic resonance spectroscopy. CVD and cardiometabolic factors were collected by using data from electronic patient records. Associations were determined between BCAA plasma levels and T2D, Metabolic Syndrome (MetS), CVD as well as mTOR inhibition in liver transplant recipients. Results: 336 Patients were divided into sex-stratified tertiles of total BCAA. MetS (P &lt; 0.001) and T2D (P = 0.002) were significantly more frequent in subjects in the highest BCAA tertile. In logistic regression analyses, the multivariable adjusted odds ratio (OR) per 1 standard deviation increase in BCAA was 1.68 (95%CI: 1.18–2.20, P = 0.003) for MetS and 1.60 (95%CI: 1.14–2.23, P = 0.006) for T2D. Use of Sirolimus (mTOR inhibitor) was significantly associated with higher BCAA plasma levels, independent of age, sex, time after OLTx, MetS and other immunosuppressive medication (adjusted P = 0.002). Conclusion: Elevated BCAA plasma levels are associated with T2D, MetS and use of Sirolimus in liver transplant recipients. BCAA plasma levels may represent a valuable biomarker for cardiometabolic complications after OLTx.</p

Branched chain amino acids are associated with metabolic complications in liver transplant recipients

Background: Obesity, dyslipidemia and type 2 diabetes (T2D) contribute substantially to increased cardiovascular morbidity and mortality in patients after orthotopic liver transplantation (OLTx). Elevated plasma branched chain amino acids (BCAA) are linked to metabolic disturbances and cardiovascular disease (CVD) risk profiles in several non-OLTx populations. Methods: Cross-sectional analysis of liver transplant recipients from TransplantLines, a single-center biobank and cohort study. BCAA plasma levels were measured by means of nuclear-magnetic resonance spectroscopy. CVD and cardiometabolic factors were collected by using data from electronic patient records. Associations were determined between BCAA plasma levels and T2D, Metabolic Syndrome (MetS), CVD as well as mTOR inhibition in liver transplant recipients. Results: 336 Patients were divided into sex-stratified tertiles of total BCAA. MetS (P &lt; 0.001) and T2D (P = 0.002) were significantly more frequent in subjects in the highest BCAA tertile. In logistic regression analyses, the multivariable adjusted odds ratio (OR) per 1 standard deviation increase in BCAA was 1.68 (95%CI: 1.18–2.20, P = 0.003) for MetS and 1.60 (95%CI: 1.14–2.23, P = 0.006) for T2D. Use of Sirolimus (mTOR inhibitor) was significantly associated with higher BCAA plasma levels, independent of age, sex, time after OLTx, MetS and other immunosuppressive medication (adjusted P = 0.002). Conclusion: Elevated BCAA plasma levels are associated with T2D, MetS and use of Sirolimus in liver transplant recipients. BCAA plasma levels may represent a valuable biomarker for cardiometabolic complications after OLTx.</p

Impact of measured versus estimated glomerular filtration rate-based screening on living kidney donor characteristics:A study of multiple cohorts

Background Most transplant centers in the Netherlands use estimated glomerular filtration rate (eGFR) for evaluation of potential living kidney donors. Whereas eGFR often underestimates GFR, especially in healthy donors, measured GFR (mGFR) allows more precise kidney function assessment, and therefore holds potential to increase the living donor pool. We hypothesized that mGFR-based donor screening leads to acceptance of donors with lower predonation eGFR than eGFR-based screening. Methods In this longitudinal cohort study, we compared eGFR (CKD-EPI) before donation in one center using mGFR-based screening (mGFR-cohort, n = 250) with two centers using eGFR-based screening (eGFR-cohort1, n = 466 and eGFR-cohort2, n = 160). We also compared differences in eGFR at five years after donation. Results Donor age was similar among the cohorts (mean±standard deviation (SD) mGFR-cohort 53 ±10 years, eGFR-cohort1 52±13 years, P = 0.16 vs. mGFR-cohort, and eGFR-cohort2 53±9 years, P = 0.61 vs. mGFR-cohort). Estimated GFR underestimated mGFR by 10±12 mL/ min/1.73m2 (mean±SD), with more underestimation in younger donors. In the overall cohorts, mean±SD pre-donation eGFR was lower in the mGFR-cohort (91±13 mL/min/ 1.73m2) than in eGFR-cohort1 (93±15 mL/min/1.73m2, P<0.05) and eGFR-cohort2 (94±12 mL/min/1.73m2, P<0.05). However, these differences disappeared when focusing on more recent years, which can be explained by acceptance of more older donors with lower predonation eGFR over time in both eGFR-cohorts. Five years post-donation, mean±SD eGFR was similar among the centers (mGFR-cohort 62±12 mL/min/1.73m2, eGFR-cohort1 61±14 mL/min/1.73m2, eGFR-cohort2 62±11 mL/min/1.73m2, P = 0.76 and 0.95 vs. mGFR-cohort respectively). In the mGFR-cohort, 38 (22%) donors were excluded from donation due to insufficient mGFR with mean±SD mGFR of 71±9 mL/min/1.73m2. Conclusions Despite the known underestimation of mGFR by eGFR, we did not show that the routine use of mGFR in donor screening leads to inclusion of donors with a lower pre-donation eGFR. Therefore eGFR-based screening will be sufficient for the majority of the donors. Future studies should investigate whether there is a group (e.g. young donors with insufficient eGFR) that might benefit from confirmatory mGFR testing

Regulacija puta razgradnje pentoza s pomoću gena izoliranih iz plijesni Aspergillus niger

The aim of this study was to obtain a better understanding of the pentose catabolism in Aspergillus niger and the regulatory systems that affect it. To this end, we have cloned and characterised the genes encoding A. niger L-arabitol dehydrogenase (ladA) and xylitol dehydrogenase (xdhA), and compared the regulation of these genes to other genes of the pentose catabolic pathway. This demonstrated that activation of the pathway depends on two transcriptional regulators, the xylanolytic activator (XlnR) and an unidentified L-arabinose specific regulator (AraR). These two regulators affect those genes of the pentose catabolic pathway that are related to catabolic conversion of their corresponding inducers (D-xylose and L-arabinose, respectively).Istraživanje je provedeno radi boljeg razumijevanja puta razgradnje pentoza plijesni Aspergillus niger i regulacijskih sustava koji na njega utječu. Klonirani su i karakterizirani geni koji kodiraju L-arabitol dehidrogenazu (ladA) i ksilitol dehidrogenazu (xdhA) plijesni A. niger, te uspoređeni s ostalim genima koji reguliraju put razgradnje pentoza. Otkriveno je da aktivacija puta razgradnje ovisi o dva regulatora transkripcije gena, tj. aktivatoru razgradnje D-ksiloze (XlnR) i regulatoru ekspresije gena pri razgradnji L-arabinoze (AraR)

An exact expression to calculate the derivatives of position-dependent observables in molecular simulations with flexible constraints

In this work, we introduce an algorithm to compute the derivatives of physical observables along the constrained subspace when flexible constraints are imposed on the system (i.e., constraints in which the hard coordinates are fixed to configuration-dependent values). The presented scheme is exact, it does not contain any tunable parameter, and it only requires the calculation and inversion of a sub-block of the Hessian matrix of second derivatives of the function through which the constraints are defined. We also present a practical application to the case in which the sought observables are the Euclidean coordinates of complex molecular systems, and the function whose minimization defines the constraints is the potential energy. Finally, and in order to validate the method, which, as far as we are aware, is the first of its kind in the literature, we compare it to the natural and straightforward finite-differences approach in three molecules of biological relevance: methanol, N-methyl-acetamide and a tri-glycine peptideComment: 13 pages, 8 figures, published versio