Miracle-dz/UniFAR-FTUs huggingface dataset:
First-principles LDA+U and GGA+U study of cerium oxides : Dependence on the effective U parameter

The electronic structure and properties of cerium oxides CeO2 and Ce2O3 have been studied in the framework of the LDA+ U and GGAPW91 + U implementations of density functional theory. The dependence of selected observables of these materials on the effective U parameter has been investigated in detail. The examined properties include lattice constants, bulk moduli, density of states, and formation energies of CeO2 and Ce2O3. For CeO2, the LDA+ U results are in better agreement with experiment than the GGA+ U results whereas for the computationally more demanding Ce2O3 both approaches give comparable accuracy. Furthermore, as expected, Ce2O3 is much more sensitive to the choice of the U value. Generally, the PW91 functional provides an optimal agreement with experiment at lower U energies than LDA does. In order to achieve a balanced description of both kinds of materials, and also of nonstoichiometric CeO2�x phases, an appropriate choice of U is suggested for LDA+ U and GGA+ U schemes. Nevertheless, an optimum value appears to be property dependent, especially for Ce2O3. Optimum U values are found to be, in general, larger than values determined previously in a self-consistent way.
Resolution of Two Sub-Populations of Conformers and Their Individual Dynamics by Time Resolved Ensemble Level FRET Measurements

Most active biopolymers are dynamic structures; thus, ensembles of such molecules should be characterized by distributions of intra- or intermolecular distances and their fast fluctuations. A method of choice to determine intramolecular distances is based on Förster resonance energy transfer (FRET) measurements. Major advances in such measurements were achieved by single molecule FRET measurements. Here, we show that by global analysis of the decay of the emission of both the donor and the acceptor it is also possible to resolve two sub-populations in a mixture of two ensembles of biopolymers by time resolved FRET (trFRET) measurements at the ensemble level. We show that two individual intramolecular distance distributions can be determined and characterized in terms of their individual means, full width at half maximum (FWHM), and two corresponding diffusion coefficients which reflect the rates of fast ns fluctuations within each sub-population. An important advantage of the ensemble level trFRET measurements is the ability to use low molecular weight small-sized probes and to determine nanosecond fluctuations of the distance between the probes. The limits of the possible resolution were first tested by simulation and then by preparation of mixtures of two model peptides. The first labeled polypeptide was a relatively rigid Pro7 and the second polypeptide was a flexible molecule consisting of (Gly-Ser)7 repeats. The end to end distance distributions and the diffusion coefficients of each peptide were determined. Global analysis of trFRET measurements of a series of mixtures of polypeptides recovered two end-to-end distance distributions and associated intramolecular diffusion coefficients, which were very close to those determined from each of the pure samples. This study is a proof of concept study demonstrating the power of ensemble level trFRET based methods in resolution of subpopulations in ensembles of flexible macromolecules.
Unique functionals and representations of Hecke algebras

Rogawski (1985) used the affine Hecke algebra to model the intertwining operators of unramified principal series representations of p-adic groups. On the other hand, a representation of this Hecke algebra in which the standard generators act by Demazure‐Lusztig operators was introduced by Lusztig (1989) and applied by Kazhdan and Lusztig (1987) to prove the Deligne‐Langlands conjecture. These operators appear in various other contexts. Ion (2006) used them to express matrix coefficients of principal series representations in terms of nonsymmetric Macdonald polynomials, while Brubaker, Bump and Licata (2011) found essentially the same operators underlying recursive relationships for Whittaker functions. Here we explain the role of unique functionals and Hecke algebras in these contexts and revisit the results of Ion from the point of view of Brubaker et al.
Correlated Volume−Energy Fluctuations of Phospholipid Membranes: A Simulation Study

This paper reports all-atom computer simulations of five phospholipid membranes (DMPC, DPPC, DMPG, DMPS, and DMPSH) with focus on the thermal equilibrium fluctuations of volume, energy, area, thickness, and chain order. At constant temperature and pressure, volume and energy exhibit strong correlations of their slow fluctuations (defined by averaging over 0.5 ns). These quantities, on the other hand, do not correlate significantly with area, thickness, or chain order. The correlations are mainly reported for the fluid phase, but we also give some results for the ordered (gel) phase of two membranes, showing a similar picture. The cause of the observed strong correlations is identified by splitting volume and energy into contributions from tails, heads, and water, and showing that the slow volume−energy fluctuations derive from van der Waals interactions of the tail region; they are thus analogous to the similar strong correlations recently observed in computer simulations of the Lennard-Jones and other simple van der Waals type liquids (U. R. Pedersen et al., Phys. Rev. Lett.2008, 100, 015701). The strong correlations reported here confirm one crucial assumption of a recent theory for nerve signal propagation proposed by Heimburg and Jackson (T. Heimburg and A. D. Jackson, Proc. Natl. Acad. Sci.2005, 102, 9790−9795).
Hydrodynamic stability in accretion disks under the combined influence of shear and density stratification

The hydrodynamic stability of accretion disks is considered. The particular question is whether the combined action of a (stable) vertical density stratification and a (stable) radial dierential rotation gives rise to a new instability for nonax- isymmetric modes of disturbances. The existence of such an instability is not suggested by the well-known Solberg-Hoiland criterion. It is also not suggested by a local analysis for disturbances in general stratifications of entropy and angular momentum which is presented in our Sect. 2. This confirms the results of the Solberg-Hoiland criterion also for nonaxisymmetric modes within the frame of ideal hydrodynamics but only in the frame of a short-wave approximation for small m . A s anecessary condition for stability we find that only conservative external forces are allowed to influence the stable disk. As magnetic forces are never conservative, linear disk instabilities should only exist in the magnetohydrodynamical regime which indeed contains the magnetorotational instability as a much-promising candidate. To overcome some of the used approximations in a numerical approach, the equations of the compressible adiabatic hydro- dynamics are integrated, imposing initial nonaxisymmetric velocity perturbations with m = 1t om = 200. Only solutions with decaying kinetic energy are found. The system always settles in a vertical equilibrium stratification according to pressure balance with the gravitational potential of the central object.
BUREAU OF THE CENSUS

This series contains research reports, written by or in cooperation with staff members of the Statistical Research Division, whose content may be ofinterestto the general statistical research corn munity. The views reflected in these reports are not necessarily those of the Census Bureau nor do they necessarily represent Census Bureau statistical policy or practice. Inquiries may be addressed to the author(s) or the SRD Report Series Coordinator, Statistical Research Division, Bureau ofthe Census, Washington, D.C. 20233.
MTHFR genetic polymorphism increases the risk of preterm delivery.

AIMS This study aimed to investigate the association between the methylene tetrahydrofolate reductase (MTHFR) gene C677T and A1298C polymorphisms and premature delivery susceptibility. METHODS With matched age and gender, 108 premature delivery pregnant women as cases and 108 healthy pregnant women as controls were recruited in this case-control study. The cases and controls had same gestational weeks. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was adopted to analyze C677T and A1298C polymorphisms of the participants. Linkage disequilibrium (LD) and haplotype analysis were conducted by Haploview software. The differences for frequencies of gene type, allele and haplotypes in cases and controls were tested by chi-square test. The relevant risk of premature delivery was represented by odds ratios (ORs) with 95% confidence intervals (95% CIs). RESULTS TT gene type frequency of C677T polymorphsim was higher in cases than the controls (P=0.004, OR=3.077, 95% CI=1.469-6.447), so was allele T (P=0.002, OR=1.853, 95% CI=1.265-2.716). Whereas, CC gene type of A1298C polymorphism had a lower distribution in cases than the controls (P=0.008, OR=0.095, 95% CI=0.012-0.775), so was allele C (P=0.047, OR=0.610, 95% CI=0.384-0.970). Haplotype analysis and linkage disequilibrium test conducted on the alleles of two polymorphisms in MTHFR gene, we discovered that haplotype T-A had a higher distribution in cases, which indicated that susceptible haplotype T-A was the candidate factor for premature delivery. CONCLUSIONS Gene type TT of MTHFR C677T polymorphism might make premature delivery risk rise while gene type CC of A1298C polymorphism might have protective influence on premature delivery.
Facial Twist (Asymmetry) in Isolated Unilateral Coronal Synostosis: Does Premature Facial Suture Fusion Play a Role?

Background:Unilateral coronal synostosis (UCS) often causes notable facial twist in affected patients. This condition occurs when the midface deviates toward the synostotic side, and the lower face deviates away from the synostotic side. The exact underlying mechanism for this phenomenon remains unclear. It has been proposed that premature fusion of facial sutures may play a role in the formation of facial twist. The purpose of this study was to determine whether asymmetrical facial suture fusion is present in patients with UCS. Methods:A single-center retrospective study was designed. Our study group consisted of 23 patients with a confirmed diagnosis of isolated UCS. Our control group consisted of 17 age-matched patients with deformational plagiocephaly and 11 normocephalic control subjects. The computed tomography scans of the faces were examined for the presence of facial suture fusions on both synostotic and nonsynostotic sides. All results with P < 0.05 were considered statistically significant. Results:We found an increased incidence of fusion of the frontomaxillary, nasofrontal, and nasomaxillary sutures on the side of synostosis in UCS when compared with the nonsynostotic side and when compared with patients with deformational plagiocephaly or normocephalic patients. Conclusions:Asymmetrical premature fusion of facial sutures can potentially be contributing to the facial twist that is seen in patients with UCS.
Distributed memory implementation of multigrid methods for groundwater flow problems with rough coefficients

In this paper we present parallel solvers for large linear systems arising from the finite-element discretization of three-dimensional groundwater flow problems. We have tested our parallel implementations on the Intel Paragon XP/S 150 supercomputer using up to 1024 parallel processors. Our solvers are based on multigrid and Krylov subspace methods. Our goal is to combine powerful algorithms and current generation high performance computers to enhance the capabilities of computer models for groundwater modeling. We demonstrate that multigrid can be a scalable algorithm on distributed memory machines. We demonstrate the effectiveness of parallel multigrid based solvers by solving problems requiring more than 64 million finite-elements in less than a minute. Our results show that multigrid as a stand alone solver works best for problems with smooth coefficients, but for rough coefficients it is best used as a preconditioner for a Krylov method.
Relationship between Bleomycin hydrolase and Apolipoprptein E genes in Alzheimer patients in Northwest of Iran

Background and Aims: Alzheimer's disease (AD) is the most common and devastating neurodegenerative disease of the elderly. Several studies indicated a relationship between different genes and AD. Bleomycin hydrolase (BLMH) and the Apolipoprotein E (ApoE) gene allele epsilon4 (E4) known as genetic risk factors for late-onset AD in sporadic cases. We have analyzed the association between the Apo E and BLMH polymorphisms in AD and control group in Northwest of Iran. Methods: EDTA blood from 62 AD and 65 controls were collected and DNA was extracted. The genes were amplified with SSCP-PCR for BLMH and RFLP-PCR for ApoE and allelic frequencies were performed. Then the results compared between AD cases and control group by chisquared test. Results: Apo E4 and BLMH alleles frequencies are %8.33 Control, %18.33 AD and %20 Control, %36 AD respectively. Conclusion: According with our result, no association was observed between carrying the G allele of BLMH gene and AD in epsilon4 negative groups but carrying the epsilon4 allele is a dose-dependent risk factor for the AD and decrease the age of symptom onset (p < 0.05). Finally when considering the ApoE and BLMH polymorphisms alone, ApoE4 status is the best predictor of AD. [Seyed Mahmoud Tabatabaei. Relationship between Bleomycin hydrolase and Apolipoprptein E genes in Alzheimer patients in Northwest of Iran. Life Sci J 2012;9(4):4338-4340]. (ISSN: 1097-8135). http://www.lifesciencesite. com. 650
The Rx Gene from Potato Controls Separate Virus Resistance and Cell Death Responses

Rx-mediated extreme resistance against potato virus X in potato does not involve a necrotic hypersensitive response at the site of initial infection and thereby differs from the more usual type of disease resistance in plants. However, the Rx protein is structurally similar to products of disease resistance genes conferring the hypersensitive response. We show in both Nicotiana spp and potato that Rx has the potential to initiate a cell death response but that extreme resistance is separate and epistatic to necrosis. These data indicate that cell death and pathogen arrest are separate disease resistance responses in plants.
Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data.

A novel fine structure mapping method for quantitative traits is presented. It is based on Bayesian modeling and inference, treating the number of quantitative trait loci (QTLs) as an unobserved random variable and using ideas similar to composite interval mapping to account for the effects of QTLs in other chromosomes. The method is introduced for inbred lines and it can be applied also in situations involving frequent missing genotypes. We propose that two new probabilistic measures be used to summarize the results from the statistical analysis: (1) the (posterior) QTL intensity, for estimating the number of QTLs in a chromosome and for localizing them into some particular chromosomal regions, and (2) the locationwise (posterior) distributions of the phenotypic effects of the QTLs. Both these measures will be viewed as functions of the putative QTL locus, over the marker range in the linkage group. The method is tested and compared with standard interval and composite interval mapping techniques by using simulated backcross progeny data. It is implemented as a software package. Its initial version is freely available for research purposes under the name Multimapper at URL http://www.rni. helsinki.fi/mjs.
Alpha 2 giardin is an assemblage A-specific protein of human infective Giardia duodenalis

SUMMARY Of the 7 genetic assemblages of the parasite Giardia duodenalis only 2 (A and B) are known to cause infections in humans. These assemblages have been characterized in detail at the genomic level but few studies have examined differences in the proteins expressed. Employing one and two-dimensional PAGE we have identified an assemblage A-specific protein of human infective G. duodenalis; alpha 2 giardin. The protein difference was evident using both electrophoretic techniques. Alpha 2 giardin is known to be a structural protein and associates with the caudal flagella and the plasma membrane; however, its exact function is unknown. Although several proteins unique to assemblage B were also observed, we were unable to identify these proteins due to a lack of genomic data available for assemblage B isolates. Together, these proteins represent distinct phenotypic differences between the human infective assemblages of G. duodenalis and support the need to revise the taxonomy of this parasite.
Mutant epidermal growth factor receptor signaling down-regulates p27 through activation of the phosphatidylinositol 3-kinase/Akt pathway in glioblastomas.

Alterations of the epidermal growth factor receptor (EGFR) gene are common in some forms of cancer and the most frequent is a deletion of exons 2-7. We have previously shown that this mutant receptor, called DeltaEGFR, confers enhanced tumorigenicity to glioblastoma cells through elevated proliferation and reduced apoptotic rates of the tumor cells in vivo. To understand the molecular mechanisms that underlie DeltaEGFR-enhanced proliferation, we examined the gene products that control cell cycle progression. We found that levels of the cyclin-dependent kinase (CDK) inhibitor, p27, were lower in U87MG.DeltaEGFR tumors than in parental U87MG or control U87MG.DK tumors. Consequently, CDK2-cyclin A activity was also elevated, concomitant with the RB protein hyperphosphorylation. In addition, activated phosphatidylinositol 3-kinase (PI3-K) and phosphorylated Akt levels were also elevated in the U87MG.DeltaEGFR tumors. U87MG.DeltaEGFR cells failed to arrest in G(1) in response to serum starvation in vitro and while maintaining high levels of PI3-K activity and hyperphosphorylated RB. Treatment of U87MG.DeltaEGFR cells with LY294002, a PI3-K inhibitor, caused reduced levels of phosphorylated Akt and concomitantly up-regulated levels of p27. Expression of a kinase dead dominant-negative Akt mutant in the U87MG.DeltaEGFR cells similarly resulted in up-regulation of p27 and down-regulation of tumorigenicity in vivo. These results suggest that the constitutively active DeltaEGFR can enhance cell proliferation in part by down-regulation of p27 through activation of the PI3-K/Akt pathway. This pathway may represent another therapeutic target for treatment of those aggressive glioblastomas expressing DeltaEGFR.
The monaural nuclei of the lateral lemniscus in an echolocating bat: parallel pathways for analyzing temporal features of sound

In echolocating bats, three cell groups in the lateral lemniscus are conspicuous for their large size and high degree of differentiation. These cell groups are the intermediate nucleus (INLL), columnar nucleus (VNLLc), and multipolar cell area (VNLLm). All receive projections from the contralateral cochlear nucleus. Previous anatomical studies suggest the hypothesis that these nuclei are important for analyzing the temporal structure of sound. To investigate this possibility, we recorded responses of single units in the INLL, VNLLc, and VNLLm of Eptesicus fuscus. The results show that each cytoarchitectural division contains a complete tonotopic representation. Certain response properties are common to all three nuclei. First, virtually all units are monaural. Second, all are broadly tuned to frequency; their average Q10dB value of 9.1 is considerably lower than values measured in the inferior colliculus of Eptesicus. Third, most units have little or no spontaneous activity. Fourth, all have short integration times, responding robustly to stimuli less than 5 msec in duration. The broad tuning, lack of spontaneous activity, and short integration time all make these neurons well suited for the accurate encoding of temporal information. Although there are many similarities, there are also important differences among nuclei. The clearest evidence of specialization is in VNLLc. Neurons here are more broadly tuned than those in INLL or VNLLm, have no spontaneous activity, and always respond with one spike per stimulus. The latency of the spike is precisely locked to the stimulus onset, with variability from trial to trial as low as 0.03 msec. In addition, the latency remains constant over large variations in frequency or intensity. In INLL and VNLLm, response patterns are about equally distributed between tonic, chopping, and phasic; there are no single-spike constant-latency responses of the type seen in VNLLc, although some choppers and pausers do respond with constant first-spike latency. The results indicate that VNLLc is specialized to encode very precisely the onset of sound; the other nuclei may encode ongoing properties of a sound.
Unusual Susceptibility of a Multidrug-Resistant Yeast Strain to Peptidic Antifungals

ABSTRACT The susceptibility of Saccharomyces cerevisiae JG436 multidrug transporter deletion mutant, Δpdr5, to several antifungal agents was compared to that of JG436-derived JGCDR1 and JGCaMDR1 transformants, harboring the CDR1 and CaMDR1 genes, encoding the main drug-extruding membrane proteins ofCandida albicans. The JGCDR1 and JGCaMDR1 yeasts demonstrated markedly diminished susceptibility to the azole antifungals, terbinafine and cycloheximide, while that to amphotericin B was unchanged. Surprisingly, JGCDR1 but not JGCaMDR1 cells showed enhanced susceptibility to peptidic antifungals, rationally designed compounds containing inhibitors of glucosamine-6-phosphate synthase. It was found that these antifungal oligopeptides, as well as model oligopeptides built of proteinogenic amino acids, were not effluxed from JGCDR1 cells. Moreover, they were taken up by these cells at rates two to three times higher than by JG436. The tested oligopeptides were rapidly cleaved to constitutive amino acids by cytoplasmic peptidases. Studies on the mechanism of the observed phenomenon suggested that an additive proton motive force generated by Cdr1p stimulated uptake of oligopeptides into JGCDR1 cells, thus giving rise to the higher antifungal activity of FMDP [N3-(4-methoxyfumaroyl)-l-2,3-diaminopropanoic acid]-peptides.