cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Does Correction for Measurement Error Have an Effect on the Structure of Basic Human Values?
Creators: name: Lilleoja, Laur
name: Saris, Willem E.
Publisher: name: European Survey Research Association
Year: 2015
Subjects: measurement error, Schwartz human values scale; equivalence; PVQ-40

description: It is well known fact that survey data contains always measurement errors, which can in different ways bias the results of the analyses (Alwin, 2007). In quantitative research this problem has been usually ignored due lack of quality estimates and complexity of correction procedure. Although this argument is not valid anymore, as there exists a new approach to determine quality of specific question, based on a prediction of the quality using the program SQP2, which in turn allows correcting for measurement error by following a relatively simple procedure (Saris & Revilla, 2015). 
During the recent years, there have been an increasing number of studies researching the structure of basic human values (Schwartz, 1992), which has resulted with improvements in the theory and led to a new 19-factor value model (Schwartz et al., 2012; Saris, Knoppen, & Schwartz, 2013). Although none of recent studies have considered the measurement error, which can potentially also have an effect on the structure. Therefor in this paper we will try to overcome this shortcoming and will be analysing the effect of the correction for measurement error on the structure of basic human values.
We use same representative data from Estonia that was used in study of Lilleoja and Saris (2014), which enables to compare value structures before and after the correction for measurement error. Due to the existence of large ethnic minority in Estonian society, the sample allowed additionally testing the equivalence of the measurement in the two subpopulations after correcting for measurement error. 
This study shows that the correction for measurement error provides additional support for the validity of new value structure and it also shades some new light on the cross-cultural equivalence.
description: Survey Research Methods, Vol 9, No 3 (2015)
Rotochemical Heating in Millisecond Pulsars. Formalism and Non-superfluid case
Creators: name: Fernández, Rodrigo
name: Reisenegger, Andreas
Publisher: name: arXiv
Year: 2005
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Rotochemical heating originates in a departure from beta equilibrium due to spin-down compression in a rotating neutron star. The main consequence is that the star eventually arrives at a quasi-equilibrium state, in which the thermal photon luminosity depends only on the current value of the spin-down power, which is directly measurable. Only in millisecond pulsars the spin-down power remains high long enough for this state to be reached with a substantial luminosity. We report an extensive study of the effect of this heating mechanism on the thermal evolution of millisecond pulsars, developing a general formalism in the slow-rotation approximation of general relativity that takes the spatial structure of the star fully into account, and using a sample of realistic equations of state to solve the non-superfluid case numerically. We show that nearly all observed millisecond pulsars are very likely to be in the quasi-equilibrium state. Our predicted quasi-equilibrium temperatures for PSR J0437-4715 are only 20% lower than inferred from observations. Accounting for superfluidity should increase the predicted value.
description: 34 pages, 8 figures, AASTeX. Accepted for publication in ApJ
Dilaton-gravity, deformations of the minimal string, and matrix models
Creators: name: Turiaci, Gustavo J.
name: Usatyuk, Mykhaylo
name: Weng, Wayne W.
Publisher: name: arXiv
Year: 2020
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: A large class of two-dimensional dilaton-gravity theories in asymptotically AdS$_2$ spacetimes are holographically dual to a matrix integral, interpreted as an ensemble average over Hamiltonians. Viewing these theories as Jackiw-Teitelboim gravity with a gas of defects, we extend this duality to a broader class of dilaton potentials compared to previous work by including conical defects with small deficit angles. In order to do this we show that these theories are equal to the large $p$ limit of a natural deformation of the $(2,p)$ minimal string theory.
description: 48pp. v2: typos corrected and references added
Fairness in Machine Learning
Creators: name: Oneto, Luca
name: Chiappa, Silvia
Publisher: name: arXiv
Year: 2020
Subjects: subject: Machine Learning (cs.LG)
subject: Computers and Society (cs.CY)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: Machine learning based systems are reaching society at large and in many aspects of everyday life. This phenomenon has been accompanied by concerns about the ethical issues that may arise from the adoption of these technologies. ML fairness is a recently established area of machine learning that studies how to ensure that biases in the data and model inaccuracies do not lead to models that treat individuals unfavorably on the basis of characteristics such as e.g. race, gender, disabilities, and sexual or political orientation. In this manuscript, we discuss some of the limitations present in the current reasoning about fairness and in methods that deal with it, and describe some work done by the authors to address them. More specifically, we show how causal Bayesian networks can play an important role to reason about and deal with fairness, especially in complex unfairness scenarios. We describe how optimal transport theory can be used to develop methods that impose constraints on the full shapes of distributions corresponding to different sensitive attributes, overcoming the limitation of most approaches that approximate fairness desiderata by imposing constraints on the lower order moments or other functions of those distributions. We present a unified framework that encompasses methods that can deal with different settings and fairness criteria, and that enjoys strong theoretical guarantees. We introduce an approach to learn fair representations that can generalize to unseen tasks. Finally, we describe a technique that accounts for legal restrictions about the use of sensitive attributes.
Thermal relaxation in metal films limited by diffuson lattice excitations of amorphous substrates
Creators: name: Baeva, E. M.
name: Titova, N. A.
name: Veyrat, L.
name: Sacépé, B.
name: Semenov, A. V.
name: Goltsman, G. N.
name: Kardakova, A. I.
name: Khrapai, V. S.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Here we examine the role of the amorphous insulating substrate in the thermal relaxation in thin NbN, InO$_x$, and Au/Ni films at temperatures above 5 K. The studied samples are made up of metal bridges on an amorphous insulating layer lying on or suspended above a crystalline substrate. Noise thermometry was used to measure the electron temperature $T_e$ of the films as a function of Joule power per unit of area $P_{2D}$. In all samples, we observe the dependence $P_{2D}\propto T_e^n$ with the exponent $n\simeq 2$, which is inconsistent with both electron-phonon coupling and Kapitza thermal resistance. In suspended samples, the functional dependence of $P_{2D}(T_e)$ on the length of the amorphous insulating layer is consistent with the linear $T$-dependence of the thermal conductivity, which is related to lattice excitations (diffusons) for the phonon mean free path smaller than the dominant phonon wavelength. Our findings are important for understanding the operation of devices embedded in amorphous dielectrics.
description: 9 pages, 5 figures
Large Component QCD and Theoretical Framework of Heavy Quark Effective Field Theory
Creators: name: Wu, Yue-Liang
Publisher: name: arXiv
Year: 2005
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Based on a large component QCD derived directly from full QCD by integrating over the small components of quark fields with $|{\bf p}| < E + m_Q$, an alternative quantization procedure is adopted to establish a basic theoretical framework of heavy quark effective field theory (HQEFT) in the sense of effective quantum field theory. The procedure concerns quantum generators of Poincare group, Hilbert and Fock space, anticommutations and velocity super-selection rule, propagator and Feynman rules, finite mass corrections, trivialization of gluon couplings and renormalization of Wilson loop. The Lorentz invariance and discrete symmetries in HQEFT are explicitly illustrated. Some new symmetries in the infinite mass limit are discussed. Weak transition matrix elements and masses of hadrons in HQEFT are well defined to display a manifest spin-flavor symmetry and $1/m_Q$ corrections. A simple trace formulation approach is explicitly demonstrated by using LSZ reduction formula in HQEFT, and shown to be very useful for parameterizing the transition form factors via $1/m_Q$ expansion. As the heavy quark and antiquark fields in HQEFT are treated on the same footing in a fully symmetric way, the quark-antiquark coupling terms naturally appear and play important roles for simplifying the structure of transition matrix elements, and for understanding the concept of `dressed heavy quark' - hadron duality. In the case that the `longitudinal' and `transverse' residual momenta of heavy quark are at the same order of power counting, HQEFT provides a consistent approach for systematically analyzing heavy quark expansion in terms of $1/m_Q$. Some interesting features in applications of HQEFT to heavy hadron systems are briefly outlined.
description: 59 pages, RevTex, no figures, published version
Weak gravity on a $Λ$CDM background
Creators: name: Gannouji, Radouane
name: Perivolaropoulos, Leandros
name: Polarski, David
name: Skara, Foteini
Publisher: name: arXiv
Year: 2020
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We consider Horndeski modified gravity models obeying stability, velocity of gravitational waves $c_T$ equals $c$ and quasistatic approximation (QSA) on subhorizon scales. We assume further a $Λ$CDM background expansion and a monotonic evolution on the cosmic background of the $α$ functions as $α_i= α_{i0}~a^s$ where $i=M,B$, $a$ is the scale factor and $α_{i0}$ ($α_{M0}, α_{B0}$), $s$ are arbitrary parameters. We show that the growth and lensing reduced (dimensionless) gravitational couplings $μ\equiv G_{\rm growth}/G$, $Σ\equiv G_{\rm lensing}/G$ exhibit the following generic properties today: $Σ_0 < 1$ for all viable parameters, $μ_0<1$ (weak gravity today) is favored for small $s$ while $μ_0>1$ is favored for large $s$. We establish also the relation $μ\geq Σ$ at all times. Taking into account the $fσ_8$ and $E_G$ data constrains the parameter $s$ to satisfy $s\lesssim 2$. Hence these data select essentially the weak gravity regime today ($μ_0<1$) when $s<2$, while $μ_0>1$ subsists only marginally for $s\approx 2$. At least the interval $0.5\lesssim s \lesssim 2$ would be ruled out in the absence of screening. We consider further the growth index $γ(z)$ and identify the $(α_{M0},α_{B0},s)$ parameter region that corresponds to specific signs of the differences $γ_0-γ_0^{ΛCDM}$, and $γ_1-γ_1^{ΛCDM}$, where $γ_0\equiv γ\bigl|_{z=0}$ and $γ_1\equiv \frac{{\rm d}γ}{\rm d z}\bigl|_{z=0}$. In this way important information is gained on the past evolution of $μ$. We obtain in particular the signature $γ_0>γ_0^{ΛCDM}$ for $s<2$ in the selected weak gravity region.
description: 14 pages, 2 figures
Screening and molecular characterization of lethal mutations of human homogentisate 1, 2 dioxigenase
Creators: name: Parth Sarthi Sen Gupta
name: Islam, Rifat Nawaz UI
name: Sahini Banerjee
name: Arnab Nayek
name: Rana, Malay Kumar
name: Bandyopadhyay, Amal Kumar
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer
subject: 60506 Virology
subject: Computational Biology

description: Alkaptonuria (AKU) is an autosomal recessive disorder, which is caused by a site-specific mutation(s) and thus, impaired the function of Homogentisate-1, 2-dioxygenase (HGD), an essential enzyme for the catabolism of phenylalanine and tyrosine. Among frameshift, intronic, splice-site and missense mutations, the latter has been the most common form of genetic variations for the disease. How do the acquired mutations in HGD correlate with the disease? Systematic staged-screening of some sixty-five mutations, which are known to have a relation with the disease, by GVGD, SIFT, SNAP, PANTHER, SDM, PHD-SNP, Meta-SNP, Pmut and Mutpred methods, showed that mutations, W60G, A122D and V300G are potentially related with the severity of AKU. Detailed analyses on molecular docking and molecular dynamics simulation (MDS) of these mutants against the wild-type HGD reveal the loss of structural and molecular dynamic properties of the enzyme. Further, the observed conformational flexibility in mutants at targeted peptide segments seems to have a relation with the impairment of the function of HGD. Taken together, the study involves a designed computational methodology to analyse the disease-associated nsSNPs for AKU, the knowledge of which seems to have potential applications in drug therapies for the disease in particular and other similar systems in general. Communicated by Ramaswamy H. Sarma
Landau-Zener transitions in qubits controlled by electromagnetic fields
Creators: name: Wubs, Martijn
name: Saito, Keiji
name: Kohler, Sigmund
name: Kayanuma, Yosuke
name: Hanggi, Peter
Publisher: name: arXiv
Year: 2005
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We investigate the influence of a dipole interaction with a classical radiation field on a qubit during a continuous change of a control parameter. In particular, we explore the non-adiabatic transitions that occur when the qubit is swept with linear speed through resonances with the time-dependent interaction. Two classical problems come together in this model: the Landau-Zener and the Rabi problem. The probability of Landau-Zener transitions now depends sensitively on the amplitude, the frequency and the phase of the Rabi interaction. The influence of the static phase turns out to be particularly strong, since this parameter controls the time-reversal symmetry of the Hamiltonian. In the limits of large and small frequencies, analytical results obtained within a rotating-wave approximation compare favourably with a numerically exact solution. Some physical realizations of the model are discussed, both in microwave optics and in magnetic systems.
description: 12 pages, 5 figures
Analyzing exception flow in Java (tm) programs
Creators: name: Robillard, Martin P.
Publisher: name: University of British Columbia
Year: 2009

description: Exception handling mechanisms provided by programming languages are intended to ease the difficulty of developing robust software systems. Using these mechanisms, a software developer can describe the exceptional conditions a module might raise, and the response of the module to exceptional conditions that may occur as it is executing. Creating a robust system from such a localized view requires a developer to reason about the flow of exceptions across modules. The use of unchecked exceptions, and in object-oriented languages, subsumption, makes it difficult for a software developer to perform this reasoning manually. In this thesis, I describe an approach for analyzing the flow of exceptions in Java source code to produce views of the exception structure. The approach is supported by a tool called Jex. I demonstrate how Jex can help a developer identify program points where exceptions are caught accidentally, where there is an opportunity to add finer-grain recovery code, and where error handling policies are not being followed.
Letter from The Springs Citizens Advisory Committee Chairman to Town of East Hampton, October 31, 1979
Creators: name: Hollenbeck, Frank B.
Publisher: name: Town of East Hampton
Year: 1979
Subjects: East Hampton
Committees
Meetings
Town meetings
Municipal government
Municipal officials
Correspondence

description: This letter is from Frank B Hollenbeck of the Springs Citizens Advisory Committee to Mrs. Mary Fallon, Supervisor of the Town of East Hampton, October 31, 1979.
description: This material was lent to the Long Island Collection by the Springs Historical Society Library for digitization purposes.
Dances
Creators: name: Ochurte, Rufino
name: Mixco, Mauricio J.
Publisher: name: California Language Archive, University of California, Berkeley
Year: 2021
Subjects: subject: klb

description: See Kiliwa Texts: "When I have Donned My Crest of Stars" (University of Utah Press, 1983), p. 138 for transcription, segmentation, glossing, and translation of this story.
Greedy Optimization Provably Wins the Lottery: Logarithmic Number of Winning Tickets is Enough
Creators: name: Ye, Mao
name: Wu, Lemeng
name: Liu, Qiang
Publisher: name: arXiv
Year: 2020
Subjects: subject: Machine Learning (cs.LG)
subject: Optimization and Control (math.OC)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: Despite the great success of deep learning, recent works show that large deep neural networks are often highly redundant and can be significantly reduced in size. However, the theoretical question of how much we can prune a neural network given a specified tolerance of accuracy drop is still open. This paper provides one answer to this question by proposing a greedy optimization based pruning method. The proposed method has the guarantee that the discrepancy between the pruned network and the original network decays with exponentially fast rate w.r.t. the size of the pruned network, under weak assumptions that apply for most practical settings. Empirically, our method improves prior arts on pruning various network architectures including ResNet, MobilenetV2/V3 on ImageNet.
On Quantum Effects Near a Black Hole Singularity
Creators: name: Qadir, Asghar
name: Siddiqui, Azad A.
Publisher: name: arXiv
Year: 2008
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: It is pointed out that the claim made by Joshi and Joshi [1], has not been rigorously demonstrated by them. A simpler and more correct proof is provided.
description: Perprint of the AS-ICTP
Ferrofluidic Manipulator: Automatic Manipulation of Non-magnetic Microparticles at Air-Ferrofluid Interface
Creators: name: Cenev, Zoran
name: Harischandra, P. A. Diluka
name: Nurmi, Seppo
name: Latikka, Mika
name: Hynninen, Ville
name: Ras, Robin H. A.
name: Timonen, Jaakko V. I.
name: Zhou, Quan
Publisher: name: arXiv
Year: 2021
Subjects: subject: Robotics (cs.RO)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: Manipulation of small-scale matter is a fundamental topic in micro- and nanorobotics. Numerous magnetic robotic systems have been developed for the manipulation of microparticles in an ambient environment, liquid as well as on the air-liquid interface. These systems move intrinsically magnetic or magnetically tagged objects by inducing a magnetic torque or force. However, most of the materials found in nature are non-magnetic. Here, we report a ferrofluidic manipulator for automatic two-dimensional manipulation of non-magnetic objects floating on top of a ferrofluid. The manipulation system employs eight centimeter-scale solenoids, which can move non-magnetic particles by deforming the air-ferrofluid interface. Using linear programming, we can control the motion of the non-magnetic particles with a predefined trajectory of a line, square, and circle with a precision of 25.1+/-19.5 um, 34.4+/-28.4 um and 33.4+/-26.6 um, respectively. The ferrofluidic manipulator is versatile with the materials and the shapes of the objects under manipulation. We have successfully manipulated particles made of polyethylene, polystyrene, a silicon chip, and poppy and sesame seeds. This work shows a promising venue for the manipulation of living and non-living matter at the air-liquid interface.
description: 9 pages, 8 figures
Identification of hot spot residues on serine-arginine protein kinase-1 by molecular dynamics simulation studies
Creators: name: Anshuman Chandra
name: Nainee Goyal
name: Imteyaz Qamar
name: Nagendra Singh
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Serine-arginine protein kinase-1 (SRPK1) is a highly specific kinase that recognizes serine-arginine dipeptide repeats and phosphorylates SR rich splicing factor ASF/SF2 in a cell-cycle regulated manner. SRPK1 processively phosphorylates serine residues on its substrate ASF/SF2. Elevated expression pattern of both SRPK1 and ASF/SF2 and their association with various carcinomas have established SRPK1 as a potent target for drug design against cancers. In order to develop specific inhibitors the binding of ASF/SF2 to SRPK1 is desired to be selectively interrupted. We have performed molecular dynamics simulation studies on crystal structure of SRPK1 complex with ASF/SF2. The ASF/SF2 acquired a stable binding on the surface of SRPK1 with strong attractive forces. Analysis revealed that there was no major position shifting of the core β-sheet region within the catalytic site of SRPK1 when present in the state of ASF/SF2 bound in comparison to apo form. Global motions of SRPK1 indicated that major stable structural changes occurred after the substrate binding. The interactions between SRPK1 and ASF/SF2 were examined and calculated during molecular dynamics simulation of 1 µs. Molecular dynamics study indicated Arg84, Lys85, Leu86, Lys174, Tyr227 and Leu479 residues of SRPK1 as essential hot spots involved in the stable binding with substrate. Structural analysis of the binding affinity and hot spot investigation provided significant information on ASF/SF2 binding which may also be considered for designing of the novel specific inhibitors of SRPK1 for the applications in cancer therapy. Communicated by Ramaswamy H. Sarma
Conformational flexibility correlates with glucose tolerance for point mutations in β-glucosidases – A computational study
Creators: name: Lima, Leonardo Henrique Franca De
name: Fernandez-Quintéro, Monica
name: Rocha, Rafael Eduardo Oliveira
name: Mariano, Diego César Batista
name: Melo-Minardi, Raquel Cardoso De
name: Liedl, Klaus Roman
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified

description: β-glucosidases (EC 3.2.1.21) have been described as essential to second-generation biofuel production. They act in the last step of the lignocellulosic saccharification, cleaving the β-1,4 glycosidic bonds in cellobiose to produce two molecules of glucose. However, β-glucosidases have been described as strongly inhibited by glucose, causing an increment of cellobiose concentration. Also, cellobiose is an inhibitor of other enzymes used in this process, such as exoglucanases and endoglucanases. Hence, the engineering of thermostable and glucose-tolerant β-glucosidases has been targeted by many studies. In this study, we performed high sampling accelerated molecular dynamics for a wild glucose-tolerant GH1 β-glucosidase (Bgl1A), a wild non-tolerant (Bgl1B), and a set of glucose-tolerant Bgl1B’s mutants: V302F, N301Q/V302F, F172I, V227M, G246S, T299S, and H228T. Our results suggest that point mutations promissory to induce glucose tolerance trend to enhance the mobility of the flexible loops around the active site. Mutations affected B and C loops regions, and an αβ-hairpin motif between them. Conformational clusters and free energy landscape profiles suggest that the mobility acquired by mutants allows a higher closure of the substrate channel. This closure is compatible with a higher impedance for glucose entrance and stimulus of its withdrawal. Based on mutants’ structural analyses, we inferred that both the direct stereochemical effect on the glucose path and the changes in the mobility affect glucose tolerance. We hope these results be useful for the rational design of glucose-tolerant and industrially promising enzymes.
Identification of new potential cyclooxygenase-2 inhibitors: insight from high throughput virtual screening of 18 million compounds combined with molecular dynamic simulation and quantum mechanics
Creators: name: Leily Heidarpoor Saremi
name: Ebrahimi, Ali
name: Lagzian, Milad
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer

description: The cyclooxygenase isoenzymes (COX-1 and COX-2) have a critical role in inflammation, fever, and pain. In contrary to COX-1, COX-2 is specifically expressed in inflamed tissues. Because of the subtle difference between both enzyme active sites, targeting COX-2 represents an efficient strategy for the development of novel inhibitors against inflammation with fewer side effects. In order to identify potential inhibitors of COX-2, more than 18,000,000 small molecules were retrieved from the ZINC database and virtually screened against it with a gradual increase in the precision through combined multistep docking. The results were sorted according to the rank-by-rank, induced-fit docking, and MM-GBSA evaluation. Subsequently from the final hit list, two top hits along with an approved selective inhibitor (celecoxib) were further investigated by the molecular dynamics (MD) simulations. The results were indicated that ZINC16934653 and ZINC40484701 demonstrate the highest affinity for the COX-2 binding pocket. Both ligands were bound to the important active-site residues, which are necessary for the correct orientation of inhibitors inside the binding cavity. Their binding free energies were comparable to celecoxib. 100 ns MD simulation is revealed that ZINC40484701 is more preferred in comparison with ZINC16934653 and celecoxib. In addition, non-covalent interactions between the compounds and key residues located in 6 Å distance from the COX-2 binding site show similar patterns of bonding by the reduced density gradient and the independent gradient model. Therefore, ZINC40484701 can be a potential candidate for further in vitro and in vivo analysis after lead-optimization efforts. Communicated by Ramaswamy H. Sarma
Observation of magnetization reversal in epitaxial Gd0.67Ca0.33MnO3 thin films
Creators: name: MA, Yanwei
name: Guilloux-Viry, M.
name: Barahona, P.
name: Pena, O.
name: Moure, C.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: High quality epitaxial thin films of Gd0.67Ca0.33MnO3 have been deposited onto (100) SrTiO3 substrates by pulsed-laser deposition. Enhanced properties in comparison with bulk samples were observed. The magnetic transition temperature (Tc) of the as-grown films is much higher than the corresponding bulk values. Most interestingly, magnetization measurements performed under small applied fields, exhibit magnetization reversals below Tc, no matter whether the film is field-cooled (FC) or zero-field-cooled (ZFC). A rapid magnetization reversal occurs at 7 K when field cooled, while as for the ZFC process the magnetization decreases gradually with increasing temperatures, taking negative values above 7 K and changing to positive values again, above 83 K. In higher magnetic fields the magnetization does not change sign. The reversal mechanism is discussed in terms of a negative exchange f-d interaction and magnetic anisotropy, this later enhanced by strain effects induced by the lattice mismatch between the film and the substrate.
description: 16 pages, 4 figures
Elucidation of molecular interactions between human γD-crystallin and quercetin, an inhibitor against tryptophan oxidation
Creators: name: Shiwani Rana
name: Sharat Sarmah
name: Atanu Singha Roy
name: Ghosh, Kalyan Sundar
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Molecular Biology
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer

description: Different post-translational changes in eye lens crystallin proteins contribute towards the development of cataract. We have studied in vitro oxidative modification of tryptophan (Trp) residues of human γD-crystallin (HGD) towards formation of N-formylkynurenine (NFK) associated with cataractogenesis. This oxidation was found to be inhibited by quercetin at relatively low concentration. Interactions between quercetin and HGD were further studied using fluorescence techniques. Binding and quenching constants were determined as ∼104 M−1. Static quenching of fluorescence due to HGD–quercetin complex formation at ground state was confirmed by finding excited state life time of Trp residues. Energy transfer occurred between the protein and quercetin. Hydrogen bonding and/or van der Waals interactions were involved between HGD and quercetin. Synchronous and three-dimensional fluorescence along with far-UV CD studies suggested no major conformational alterations occurred in HGD due to quercetin binding. Experimental observations were supported by the docking results. Communicated by Ramaswamy H. Sarma
A Strain-Resolved Metagenomic Study of H2S-Induced Changes in Anaerobic Biofilms - MAGs collection
Creators: name: De Bernardini, Nicola
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 310703
subject: Microbial ecology
classificationCode: 310704
subject: Microbial genetics

description: MAGs published in the context of the paper: From Microbial Heterogeneity to Evolutionary Insights: A Strain-Resolved Metagenomic Study of H2S-Induced Changes in Anaerobic Biofilms
Glucose driven self-sustained electro-Fenton platform for remediation of 2,4-dichlorophenoxy herbicide contaminated water
Creators: name: Aravind, Priyadharshini
name: Vasudevan, Subramanyan
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Developmental Biology

description: As electrochemical oxidation technologies are energy-intensive, they are sparsely included in wastewater treatment plants. This study demonstrates a self-reliable glucose driven-electro-Fenton (GD-EF) system for decontamination of 2,4-dichlorophenoxy (2,4-D) herbicides without the supply of external current or voltage. It incorporates a cathode (graphite) which accepts electrons from abiotic glucose oxidation at anode (Pt/Ti or BDD or PbO2/Cu/Ti) and generates in situ H2O2. For the first time, the ability of Pt/Ti, BDD, and PbO2/Cu/Ti anodes in GD-EF and their influence on 2,4-D decontamination rate have been studied. Pt/Ti and PbO2/Cu/Ti exhibited maximum power densities of 60.42 and 219.3 µW cm−2, respectively than BDD (2.418 µW cm−2). Even though Pt/Ti fuel cell exhibited lower power density than the PbO2/Cu/Ti – fuel cell, it had a faster 2,4-D degradation rate of k = 18 × 10−3 s−1. The generated cathodic potential of −0.275 mV vs. Ag/AgCl in the Pt/Ti-fuel cell was sufficient to produce 23 mg L−1h−1 of H2O2. The high performance liquid chromatography analysis reveals the complete transformation of 2,4-D in 540 min and its degradation by 95% in 1080 min. This finding paves the way for greener decontamination of bio-recalcitrant herbicides with zero electrochemical energy consumption.
Sex and Marriage
Creators: name: Ochurte, Rufino
name: Mixco, Mauricio J.
Publisher: name: California Language Archive, University of California, Berkeley
Year: 2021
Subjects: subject: klb

description: See Kiliwa Texts: "When I have Donned My Crest of Stars" (University of Utah Press, 1983), p. 150 for transcription, segmentation, glossing, and translation of this story.
GOYA Survey: U and B Number Counts in the Groth-Westphal Strip
Creators: name: Eliche-Moral, M. C.
name: Balcells, M.
name: Prieto, M.
name: Garcia-Dabo, C. E.
name: Erwin, P.
name: Cristobal-Hornillos, D.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present U and B galaxy differential number counts from a field of ~900 arcmin^2, based on GOYA Survey imaging of the HST Groth-Westphal strip. Source detection efficiency corrections as a function of the object size have been applied. A variation of the half-exposure image method has been devised to identify and remove spurious detections. Achieved 50% detection efficiencies are 24.8 mag in U and 25.5 mag in B in the Vega system. Number count slopes are d log (N)/dm = 0.50 +/- 0.02 for B=21.0-24.5, and d log (N)/dm = 0.48 +/- 0.03 for U=21.0-24.0. Simple number count models are presented that simultaneously reproduce the counts over 15 mag in U and B,and over 10 mag in K_s, using a Lambda-dominated cosmology and SDSS local luminosity functions. Only by setting a recent z_f ~ 1.5 formation redshift for early-type, red galaxies do the models reproduce the change of slope observed at Ks = 17.5 in NIR counts. A moderate optical depth (tau_B = 0.6) for all galaxy types ensures that the recent formation for ellipticals does not leave a signature in the U or B number counts, which are featureless at intermediate magnitudes. No ad-hoc disappearing populations are needed to explain the counts if number evolution is introduced using an observationally-based z-evolution of the merger fraction.
description: 30 pages, 13 figures, 13 tables. Accepted for publication in ApJ. Formatted with emulateapj, using lscape package
Identification of New Potential Cyclooxygenase-2 Inhibitors: Insight from High Throughput Virtual Screening of 18 Million Compounds Combined with Molecular Dynamic Simulation and Quantum Mechanics
Creators: name: Leily Heidarpoor Saremi
name: Ebrahimi, Ali
name: Lagzian, Milad
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer

description: The cyclooxygenase isoenzymes (COX-1 and COX-2) have a critical role in inflammation, fever, and pain. In contrary to COX-1, COX-2 is specifically expressed in inflamed tissues. Because of the subtle difference between both enzyme active sites, targeting COX-2 represents an efficient strategy for the development of novel inhibitors against inflammation with fewer side effects. In order to identify potential inhibitors of COX-2, more than 18,000,000 small molecules were retrieved from the ZINC database and virtually screened against it with a gradual increase in the precision through combined multistep docking. The results were sorted according to the rank-by-rank, induced-fit docking, and MM-GBSA evaluation. Subsequently from the final hit list, two top hits along with an approved selective inhibitor (celecoxib) were further investigated by the molecular dynamics (MD) simulations. The results were indicated that ZINC16934653 and ZINC40484701 demonstrate the highest affinity for the COX-2 binding pocket. Both ligands were bound to the important active-site residues, which are necessary for the correct orientation of inhibitors inside the binding cavity. Their binding free energies were comparable to celecoxib. 100 ns MD simulation is revealed that ZINC40484701 is more preferred in comparison with ZINC16934653 and celecoxib. In addition, non-covalent interactions between the compounds and key residues located in 6Å distance from the COX-2 binding site show similar patterns of bonding by the reduced density gradient and the independent gradient model. Therefore, ZINC40484701 can be a potential candidate for further in vitro and in vivo analysis after lead-optimization efforts.
Impact of glioblastoma multiforme associated mutations on the structure and function of MAP/Microtubule affinity regulating kinase 4
Creators: name: Naqvi, Ahmad Abu Turab
name: Deeba Shamim Jairajpuri
name: Hussain, Afzal
name: Hasan, Gulam Mustafa
name: Alajmi, Mohamed F.
name: Md. Imtaiyaz Hassan
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Computational Biology

description: MAP/Microtubule affinity regulating kinase 4 (MARK4) plays an important role in the regulation of microtubule dynamics by phosphorylation of tau protein. A higher expression of MARK4 is observed in the glioblastoma multiforme (GBM) cell lines. We identified eight synonymous and non-synonymous (ns) mutations in the MARK4 gene related to GBM in The Cancer Genome Atlas (TCGA) consortium. Out of these, three ns mutations were found in the catalytic domain of the protein (Lys231Asn, Tyr247His and Arg265Gln), were selected to see the possible deleterious effects on the structure and function using the cutting-edge in-silico tools. In addition, molecular dynamics simulation, principal component analysis, dynamic cross correlation matrix analysis and correlation network analysis were performed to gain insights into the conformation of the MARK4 and its mutants. We found that, Tyr247His shows a maximum deleterious impact, reflected from structural deviation in comparison to Lys231Asn and Arg265Gln. In conclusion, Tyr247His mutant of MARK4 has relatively higher chances of affecting the structure and function of the protein thus leading to abnormal MARK4 activity which is associated to GBM.
A Measurement of the Quadrupole Power Spectrum in the Clustering of the 2dF QSO Survey
Creators: name: Yamamoto, Kazuhiro
name: Nakamichi, Masashi
name: Kamino, Akinari
name: Bassett, Bruce A.
name: Nishioka, Hiroaki
Publisher: name: arXiv
Year: 2005
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We report a measurement of the quadrupole power spectrum in the two degree field (2dF) QSO redshift (2QZ) survey. The analysis uses an algorithm parallel to that for the estimation of the standard monopole power spectrum without first requiring computation of the correlation function or the anisotropic power spectrum. The error on the quadrupole spectrum is rather large but the best fit value of the bias parameter from the quadrupole spectrum is consistent with that from previous investigations of the 2dF data.
description: 12pages, accepted by PASJ
Protein binding and antioxidant studies of diimine based emissive surfactant–ruthenium(II) complexes
Creators: name: S. Nehru
name: S. Veeralakshmi
name: S. Kalaiselvam
name: S. P. Subin David
name: J. Sandhya
name: S. Arunachalam
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer

description: Biophysical interaction of amphiphilic fluorescent surfactant–ruthenium(II) complexes and its precursor ruthenium(II) complexes with drug carrying proteins such as bovine and human serum albumins (BSA and HSA) have been studied through the UV-visible absorption, fluorescence and circular dichroism spectroscopic techniques to correlate the impact of head and tail groups of the metallosurfactants towards the designing of metallodrugs for the biomedical applications. The obtained results showed that both precursor– and surfactant–ruthenium(II) complexes interact with BSA/HSA via ground state protein–complex formation and their quenching follows the static mechanism. The extent of protein quenching and binding parameters resulted that the surfactant–ruthenium(II) complexes effectively interact with protein compared to their precursor–ruthenium(II) complexes, and also those interaction have greatly influenced by the change in the head group size compared to change in the tail group length. Interestingly on increasing the temperature, the protein–complex binding strength was decreased for the precursor–ruthenium(II) complexes, those increased for the surfactant–ruthenium(II) complexes, probably due to the respective involvement of electrostatic and hydrophobic interactions as supported by the thermodynamics of protein–complex interaction. Moreover, the results from UV–visible, synchronous and circular dichroism studies confirmed the occurrence of conformational and micro environmental changes in BSA/HSA upon binding with these complexes. It is also noted that HSA has more binding affinity with surfactant–ruthenium(II) complexes compared to BSA. The free radical scavenging ability against DPPH, ABTS, NO and superoxide free radical assays suggested that surfactant–ruthenium(II) complexes have better free radical scavenging ability compared to precursor–ruthenium(II) complexes. Communicated by Ramaswamy H. Sarma.
Elucidation of molecular interactions between human γD-crystallin and quercetin, an inhibitor against tryptophan oxidation
Creators: name: Shiwani Rana
name: Sharat Sarmah
name: Atanu Singha Roy
name: Ghosh, Kalyan Sundar
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Marine Biology
subject: Cancer

description: Different posttranslational changes in eye lens crystallin proteins contribute towards the development of cataract. We have studied in vitro oxidative modification of tryptophan (Trp) residues of human γD-crystallin (HGD) towards formation of N-formylkynurenine (NFK) associated with cataractogenesis. This oxidation was found to be inhibited by quercetin at relatively low concentration. Interactions between quercetin and HGD were further studied using fluorescence techniques. Binding and quenching constants were determined as ∼104 M-1. Static quenching of fluorescence due to HGD-quercetin complex formation at ground state was confirmed by finding excited state life time of Trp residues. Energy transfer occurred between the protein and quercetin. Hydrogen bonding and/or van der Waals interactions were involved between HGD and quercetin. Synchronous and three-dimensional fluorescence along with far-UV CD studies suggested no major conformational alterations occurred in HGD due to quercetin binding. Experimental observations were supported by the docking results.
Evaluation of the dual-process approach for in-situ groundwater arsenic removal
Creators: name: Wang, Sheng-Wei
name: Pan, Shu-Yuan
name: Kao, Yu-Hsuan
name: Kim, Hyunook
name: Fan, Chihhao
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Physiology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Computational Biology

description: While the worldwide distribution of geogenic arsenic (As)-affected groundwater is highly overlapped with the areas with abundant groundwater, utilization of As-contained groundwater is an inevitable compromise in those areas where surface water is not enough for irrigation. Since the occurrence of As in groundwater is often accompanied by high iron (Fe) contents, the facilitation of As and Fe precipitation without adding additional oxidizers and adsorbents is considered an environmental-friendly approach to removing As in groundwater. In the present study, the oxidation/filtration dual-process with sprinkling height of 25 cm and 120 kg filter media efficiently increased the dissolved oxygen (DO) concentration (0.36–1.52 mg/L) and oxidation–reduction potential (ORP) (24–63 mV), which facilitated the formation of Fe oxides and As co-precipitation. The correlation of As removal efficiencies with their respective flow rates indicated that a decrease in groundwater Fe and an increase of Fe in sands and gravels filters as the flow rate increased evidenced the rapid oxidation of Fe to form the Fe hydroxides. In a 40-hour continuous aeration/filtration operation, As and Fe concentrations in groundwater were reduced by 79.5% and 64.88% within 40 hrs, respectively. The ease of filter replacement and cost-effectiveness in operation can be the major attractions and innovations for future field practices.