Miracle-dz/UniFAR-FTUs huggingface dataset:
Algorithm 684: C1- and C2-interplation on triangles with quintic and nonic bivariate polynomials

The innovative part of the algorithm is the formulation of a bivariate nonic Hermite polynomial with C2-property [7] contained in modules CBSIDE, CSINSD, and CSHORN. These formulas are of principal value. They describe a twice differentiable polynomial representation on a set of triangles. To be of immediate use, some interfaces were designed, and the new modules were integrated into Renka’s triangle interpolation package [9]. Especially all procedures related to the generation and the handling of triangles are taken or may be taken from that algorithm. Also, the method of derivative estimation is identical with Renka’s global method [S]. The higher derivatives of order n are generated by taking the derivatives of order n 1 as input (n = 2, 3, 4). For the sake of completeness, equivalent routines for Cl-interpolation (once differentiable) are supplied, based on the well known quintic triangular element [l, 3, 41. In general, the Cl-routines are approximately 3 times faster than their C ‘-equivalents and need less memory. The main user interfaces to the package are the routines C2GRID and ClGRID. They interpolate values of a rectangular grid to a given set of irregularly distributed points (scattered data interpolation in two dimensions). Because the array of grid points is scanned for every triangie, the coefficients for each polynomial are computed only once, and the fast evaluation phase of the Taylor representation [7] can be exploited most efficiently. If the mesh lines of the rectangular grid are relatively wide with respect to the irregularly distributed
Hydropathy--a window on the evasion of water.

'Proteome' is currently the word of choice to represent those functioning polypeptides that result from the translation of a gene transcript. Only a small number of the proteins that make up this group have been fully annotated, and researchers worldwide are working to increase this volume. Structure and function are closely related in terms of understanding what these proteins do and how they govern processes within an organism. In the absence of structural information derived from X-ray crystallography or other experimental means, bioinformatics has sought to make up the shortfall by enabling calculations of many parameters that would contribute to an understanding of the final structure of a protein. Hydropathy is one such parameter and is used to determine the hydrophobicity of various regions of the molecule. As a protein is created from the translation of an mRNA template it is subject to a variety of forces, enabling it to fold in a way relevant to its future function. In addition to the chaperone proteins known to aid this process, chemical attractions and interactions between molecules are all seen to influence the final product. One of these forces is the repulsion of water by various hydrophobic residues on the emerging polypeptide chain — indeed many chaperones also function using hydrophobic interactions. Hydrophilic residues are necessary to fill the void. For soluble, globular proteins in particular, the energy required to bury hydrophobic residues is one of the main driving forces behind the folding of the polypeptide molecule. Once folded, these hydrophobic interactions are instrumental in retaining the tertiary structure of the protein. Those regions that repel water are the hydrophobic ones and are calculated in terms of 'hydropathy' — the score generated for a specified region of the protein, taking both the number of hydrophobic and the number of hydrophilic residues into account. Hydrophobicity may be represented by a positive or a negative score depending on the experimental data used to determine it. Such hydrophobic regions may indicate a buried core within the protein structure, or perhaps a feature such as a trans-membrane segment. Computational calculations of the hydropathic nature of a protein from its secondary structure may reveal areas of high hydrophobicity, hinting at possible structural features. The most common programs determine the hydrophobicity of a region based on the calculation of experimentally determined values for each residue — the hydropathy index. A window (a run of adjacent residues within …
Soluble interleukin 2 receptor (sIL‐2R) levels in renal transplant recipients

Abstract: Background: Allograft rejection is associated with T cell activation. T cell activation leads to secretion of soluble IL‐2 receptor and elevated serum soluble IL‐2 receptor (sIL‐2R) levels. However, the clinical implication of individual elevated sIL‐2 receptor levels is unclear. We followed levels of sIL‐2R pre‐ and post‐transplantation to determine if sIL‐2R levels predict rejection episodes or degree of graft function.
The Minimum Satisfiability Problem

This paper shows that a minimization version of satisfiability is strongly NP-hard, even if each clause contains no more than two literals and/or each clause contains at most one unnegated variable. The worst-case and average-case performances of greedy and probabilistic greedy heuristics for the problem are examined, and tight upper bounds on the performance ratio in each case are developed.
Comparison of tuning procedures based on evolutionary algorithm for multi-region fuzzy-logi PID controller for non-linear plant

The paper presents a comparison of tuning procedures for a multi-region fuzzy-logic controller used for nonlinear process control. This controller is composed of local PID controllers and fuzzy-logic mechanism that aggregates local control signals. Three off-line tuning procedures are presented. The first one focuses on separate tuning of local PID controllers gains in the case when the parameters of membership functions of fuzzy-logic mechanism are know a priori. The second one consists of two major steps. In the first step, the local PID controllers gains are calibrated and in the next step the parameters of membership functions of fuzzy-logic mechanism are tuned. The third one focuses on tuning of PID controllers gains and membership functions parameters jointly. These procedures exploit evolutionary algorithm to optimize the performance of the multi-region fuzzy-logic controller with respect to integral quality criterion such as Integral Absolute Error (IAE). Effectiveness of these procedures is verified based on a well known from literature continuous nonlinear pH neutralization reactor model. For comparison a single PID controller tuned for specific work point is also taken into account.
Effects of m-nisoldipine on the activity and mRNA expression of four CYP isozymes in rats

Abstract 1. For the first time, a systemic in vivo investigation was employed to evaluate the potential effects of m-nisoldipine on activities of rat cytochrome P450 enzymes (CYP1A2, CYP2C11, CYP2D1 and CYP3A1) by both cocktail probe drugs and the quantitative real-time reverse-transcription polymerase chain reaction (RT-qPCR). 2. m-Nisoldipine-treated and blank control groups were respectively administered m-nisoldipine at the dosage of 2.5, 5 and 12.5 mg/kg and CMC-Na solution for 15 days consecutively, then they were given the probe drugs of caffeine, diclofenac, dextromethorphan and midazolam (all probes were 5 mg/kg) by p.o. The blood samples were collected at different times for liquid chromatography coupled with mass spectrometry (LC-MS) analysis. The corresponding pharmacokinetic parameters were applied to evaluate the effects of m-nisoldipine on the four CYP isoforms in vivo. In addition, RT-qPCR was performed to determine the effects of m-nisoldipine on the mRNA expression of CYPs in rat liver. Results indicated that high dose and middle dose of m-nisoldipine showed significant effects on all four CYPs and CYP2C11, respectively. Moreover, for CYP2D1 and CYP1A2, there were no significant effects found at either low or middle dose of m-nisoldipine. 3. This study could provide not only experimental evidence for potential clinical application of m-nisoldipine but also a practical strategy for assessing CYP-mediated drug–drug interactions.
Birth Cohort and the Black-White Achievement Gap: The Roles of Access and Health Soon After Birth;

One literature documents a significant, black-white gap in average test scores, while another finds a substantial narrowing of the gap during the 1980’s, and stagnation in convergence after. We use two data sources – the Long Term Trends NAEP and AFQT scores for the universe of applicants to the U.S. military between 1976 and 1991 – to show: 1) the 1980’s convergence is due to relative improvements across successive cohorts of blacks born between 1963 and the early 1970’s and not a secular narrowing in the gap over time; and 2) the across-cohort gains were concentrated among blacks in the South. We then demonstrate that the timing and variation across states in the AFQT convergence closely tracks racial convergence in measures of health and hospital access in the years immediately following birth. We show that the AFQT convergence is highly correlated with post-neonatal mortality rates and not with neonatal mortality and low birth weight rates, and that this result cannot be explained by schooling desegregation and changes in family background. We conclude that investments in health through increased access at very early ages have large, long-term effects on achievement, and that the integration of hospitals during the 1960’s affected the test performance of black teenagers in the 1980’s. Kenneth Y. Chay Jonathan Guryan Bhashkar Mazumder Department of Economics Booth School of Business Federal Reserve Bank of Chicago Brown University University of Chicago 230 S. Lasalle Street Box B 5807 S. Woodlawn Avenue Chicago, IL 60604 Providence, RI 02912 Chicago, IL 60637 bmazumde@frbchi.org and NBER and NBER kenneth_chay@brown.edu jonathan.guryan@chicagobooth.edu
Segmental marking as a cue in auditory voice identification of telephone speech

The present investigation seeks to assess to what extent some Dutch phonemes can serve as cues in auditory voice identification of telephone speech. Four Dutch consonants, /x/, /r/, /s/ and /p/, occurring in three different contexts in 24 monosyllabic words, were selected on the basis of their different auditory interspeaker variability. The words were pronounced by 16 speakers in two guises, ordinary ehest voice and falsetto. Although none of the consonants appeared to perform significantly better, an interaction was found between type of consonant and position in the word. It also appears that the confidence ratings assigned to the responses vary significan tly as a function of the type of consonant and its position in the word.
Binding Conformation of 2-Oxoamide Inhibitors to Group IVA Cytosolic Phospholipase A2 Determined by Molecular Docking Combined with Molecular Dynamics

The group IVA cytosolic phospholipase A(2) (GIVA cPLA(2)) plays a central role in inflammation. Long chain 2-oxoamides constitute a class of potent GIVA cPLA(2) inhibitors that exhibit potent in vivo anti-inflammatory and analgesic activity. We have now gained insight into the binding of 2-oxoamide inhibitors in the GIVA cPLA(2) active site through a combination of molecular docking calculations and molecular dynamics simulations. Recently, the location of the 2-oxoamide inhibitor AX007 within the active site of the GIVA cPLA(2) was determined using a combination of deuterium exchange mass spectrometry followed by molecular dynamics simulations. After the optimization of the AX007-GIVA cPLA(2) complex using the docking algorithm Surflex-Dock, a series of additional 2-oxoamide inhibitors have been docked in the enzyme active site. The calculated binding affinity presents a good statistical correlation with the experimental inhibitory activity (r(2) = 0.76, N = 11). A molecular dynamics simulation of the docking complex of the most active compound has revealed persistent interactions of the inhibitor with the enzyme active site and proves the stability of the docking complex and the validity of the binding suggested by the docking calculations. The combination of molecular docking calculations and molecular dynamics simulations is useful in defining the binding of small-molecule inhibitors and provides a valuable tool for the design of new compounds with improved inhibitory activity against GIVA cPLA(2).
Molecular Underpinnings of Fe(III) Oxide Reduction by Shewanella Oneidensis MR-1

In the absence of O2 and other electron acceptors, the Gram-negative bacterium Shewanella oneidensis MR-1 can use ferric [Fe(III)] (oxy)(hydr)oxide minerals as the terminal electron acceptors for anaerobic respiration. At circumneutral pH and in the absence of strong complexing ligands, Fe(III) oxides are relatively insoluble and thus are external to the bacterial cells. S. oneidensis MR-1 and related strains of metal-reducing Shewanella have evolved machinery (i.e., metal-reducing or Mtr pathway) for transferring electrons from the inner-membrane, through the periplasm and across the outer-membrane to the surface of extracellular Fe(III) oxides. The protein components identified to date for the Mtr pathway include CymA, MtrA, MtrB, MtrC, and OmcA. CymA is an inner-membrane tetraheme c-type cytochrome (c-Cyt) that belongs to the NapC/NrfH family of quinol dehydrogenases. It is proposed that CymA oxidizes the quinol in the inner-membrane and transfers the released electrons to MtrA either directly or indirectly through other periplasmic proteins. A decaheme c-Cyt, MtrA is thought to be embedded in the trans outer-membrane and porin-like protein MtrB. Together, MtrAB deliver the electrons through the outer-membrane to the MtrC and OmcA on the outmost bacterial surface. MtrC and OmcA are the outer-membrane decaheme c-Cyts that are translocated across the outer-membrane by the bacterial type II secretion system. Functioning as terminal reductases, MtrC and OmcA can bind the surface of Fe(III) oxides and transfer electrons directly to these minerals via their solvent-exposed hemes. To increase their reaction rates, MtrC and OmcA can use the flavins secreted by S. oneidensis MR-1 cells as diffusible co-factors for reduction of Fe(III) oxides. Because of their extracellular location and broad redox potentials, MtrC and OmcA can also serve as the terminal reductases for soluble forms of Fe(III). In addition to Fe(III) oxides, Mtr pathway is also involved in reduction of manganese oxides and other metals. Although our understanding of the Mtr pathway is still far from complete, it is the best characterized microbial pathway used for extracellular electron exchange. Characterizations of the Mtr pathway have made significant contributions to the molecular understanding of microbial reduction of Fe(III) oxides.
Similarity and difference in the mechanisms of neonatally induced tolerance and cyclophosphamide-induced tolerance in mice.

The mechanisms of cyclophosphamide (CP)-induced tolerance were investigated by comparing with those of neonatally induced tolerance. When C3H/He Slc (C3H; H-2k, Mls-1b) mice were given i.v. either AKR/J Sea (AKR; H-2k, Mls-1a) or (AKR x C3H)F1 (AKC3F1; H-2k, Mls-1a/b) spleen cells and treated i.p. with CP 2 days later, a long-lasting skin allograft tolerance to AKR was induced in each case without any signs of graft-vs-host disease (GVHD). However, typical signs of GVHD were observed in the C3H mice neonatally tolerized with AKR spleen cells, but not in those tolerized with AKC3F1 spleen cells. The expression of TCR V beta 6, which is strongly correlated with the reactivity to Mls-1a Ag (of donor AKR origin), in the periphery was quite different between the two types of tolerant C3H mice. Namely, in the lymph nodes of the C3H mice tolerized with AKR spleen cells and CP, only CD4(+)-V beta 6+, but not CD8(+)-V beta 6+, T cells selectively disappeared, whereas both of them were abrogated in the lymph nodes of the C3H mice neonatally tolerized of AKR. By contrast, in the thymus of the two types of tolerant C3H mice, both CD4+CD8- and CD4-CD8+ single-positive thymocytes expressing TCR V beta 6 were clonally deleted, suggesting that the thymic involvement was the same in each type of tolerance. These results suggest that the preferential disappearance of the CD4(+)-V beta 6+ T cells (of host origin) and the effector T cells of GVHD (of donor origin) occurred only in the periphery of the C3H mice tolerized with AKR spleen cells plus CP and was attributable to the destruction of Ag-stimulated T cells by the CP treatment. In contrast, the intrathymic clonal deletion of immature V beta 6+ T cells was a common mechanism for both of the tolerance induction systems.
Generalization and the evolution of symmetry preferences

Biological displays are often symmetrical, and there is growing evidence that receivers are sensitive to these symmetries. One explanation for the evolution of such sensitivity is that symmetry reflects the quality of the signaller. An alternative is that the sensitivity may arise as a by–product of general properties of biological recognition systems. In line with the latter idea, simulations of the recognition process based on simple, artificial neural networks have suggested that generalization can give rise to preferences for particular symmetrical stimuli. However, it is not clear from these studies exactly how the preferences emerge, and to what extent the results are relevant to biological recognition systems. Here, we employ a different class of recognition models (gradient interaction models) to demonstrate more clearly how generalization can generate a preference for symmetrical variants of a display. We also point out that the predictions of the gradient interaction and network–based models regarding the effects of generalization closely match the results from empirical studies of stimulus control. Our analysis demonstrates that the effects of generalization cannot be ignored when studying the evolution of symmetry preferences and symmetric signals.
Greenland mass balance from GRACE

We use 22 monthly GRACE (Gravity Recovery and Climate Experiment) gravity fields to estimate the linear trend in Greenland ice mass during 2002–2004. We recover a decrease in total ice mass of 82 ± 28 km3 of ice per year, consistent with estimates from other techniques. Our uncertainty estimate is dominated by the effects of GRACE measurement errors and errors in our post glacial rebound (PG) correction. The main advantages of GRACE are that it is sensitive to the entire ice sheet, and that it provides mass estimates with only minimal use of supporting physical assumptions or ancillary data.
Title Glycosylated porphyra-334 and palythine-threonine from the terrestrialcyanobacterium nostoc commune

Mycosporine-like amino acids (MAAs) are water-soluble UV-absorbing pigments, and structurally different MAAs have been identified in eukaryotic algae and cyanobacteria. In this study novel glycosylated MAAs were found in the terrestrial cyanobacterium Nostoc commune (N. commune). An MAA with an absorption maximum at 334 nm was identified as a hexose-bound porphyra-334 derivative with a molecular mass of 508 Da. Another MAA with an absorption maximum at 322 nm was identified as a two hexose-bound palythine-threonine derivative with a molecular mass of 612 Da. These purified MAAs have radical scavenging activities in vitro, which suggests multifunctional roles as sunscreens and antioxidants. The 612-Da MAA accounted for approximately 60% of the total MAAs and contributed approximately 20% of the total radical scavenging activities in a water extract, indicating that it is the major water-soluble UV-protectant and radical scavenger component. The hexose-bound porphyra-334 derivative and the glycosylated palythine-threonine derivatives were found in a specific genotype of OPEN ACCESS Mar. Drugs 2013, 11 3125 N. commune, suggesting that glycosylated MAA patterns could be a chemotaxonomic marker for the characterization of the morphologically indistinguishable N. commune. The glycosylation of porphyra-334 and palythine-threonine in N. commune suggests a unique adaptation for terrestrial environments that are drastically fluctuating in comparison to stable aquatic environments.
Analysis of Multiple Ethyl Methanesulfonate-Mutagenized Caenorhabditis elegans Strains by Whole-Genome Sequencing

Whole-genome sequencing (WGS) of organisms displaying a specific mutant phenotype is a powerful approach to identify the genetic determinants of a plethora of biological processes. We have previously validated the feasibility of this approach by identifying a point-mutated locus responsible for a specific phenotype, observed in an ethyl methanesulfonate (EMS)-mutagenized Caenorhabditis elegans strain. Here we describe the genome-wide mutational profile of 17 EMS-mutagenized genomes as assessed with a bioinformatic pipeline, called MAQGene. Surprisingly, we find that while outcrossing mutagenized strains does reduce the total number of mutations, a striking mutational load is still observed even in outcrossed strains. Such genetic complexity has to be taken into account when establishing a causative relationship between genotype and phenotype. Even though unintentional, the 17 sequenced strains described here provide a resource of allelic variants in almost 1000 genes, including 62 premature stop codons, which represent candidate knockout alleles that will be of further use for the C. elegans community to study gene function.
SNaPshot reveals high mutation and carrier frequencies of 15 common hearing loss mutants in a Chinese newborn cohort

Genetic causes account for more than half of congenital hearing loss cases. The most frequent mutations found in non‐syndromic hearing loss patients occur in GJB2 and SLC26A4. Mitochondrial genome mutations are also prevalent. However, the frequency of common hearing loss mutations in the Chinese population has not yet been well estimated. Here, we implemented the SNaPshot genotyping method to investigate the carrier frequency of 15 commonly reported hearing loss mutations in GJB2, SLC26A4 and the mitochondrial genome based on a cohort of 5800 neonates in China. Up to 15.9% (923/5800) of the newborns carry at least one mutant allele. The top three were GJB2‐c.109G>A, GJB2‐c.235delC, and SLC26A4‐c.919A>G, with notably high carrier frequencies of 1/10, 1/53 and 1/62 respectively, and mt‐7444G>A with 1/141 was the most frequent allele in the mitochondrial genome. In this cohort, 0.48% (28/5800) of neonates were genetically diagnosed with hearing loss, from which seven cases failed an OAE test. This is the first epidemiological study of non‐syndromic hearing loss in Chinese newborns indicating a notably high carrier frequency (1 per 6.3 newborns) among these 15 mutant alleles. Our carrier frequency data also aid in effective risk assessment and genetic counseling for hearing loss patients in the Chinese population.
Failure to attain adult comprehension of intentions in Japanese children with severe to profound mental retardation

Pre-linguistic children with severe to profound mental retardation were compared to matched infants without disabilities in regard to attaining adult comprehension of the child's communicative intentions by repairing communication and accepting correct interpretations. The results showed no group difference in the rate of repair, but the types of repair produced were different between the two groups. The children with mental retardation were offered fewer interpretations to their initiations and repairs, and accepted these at a far lower rate compared to the infants. Adults responded to intentions of these children at far higher rates compared to the normally developing infants, even when they repaired the adult's comprehension failure. The relationship between the type of repair, type of intended effect in communication, and an adult's response to a child's initiation and repair are discussed. The need for some compensatory strategy to help these children operate with some junior version of the Gricean cycle is suggested.