gebhart/patrepeval huggingface dataset:
Flexible structure alignment by chaining aligned fragment pairs allowing twists (2003)

We have developed the Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT), a new method for structural alignment of proteins. The FATCAT approach simultaneously addresses the two major goals of flexible structure alignment; optimizing the alignment and minimizing the number of rigid-body movements (twists) around pivot points (hinges) introduced in the reference protein. In contrast, currently existing flexible structure alignment programs treat the hinge detection as a post-process of a standard rigid body alignment. We illustrate the advantages of the FATCAT approach by several examples of comparison between proteins known to adopt different conformations, where the FATCAT algorithm achieves more accurate structure alignments than current methods, while at the same time introducing fewer hinges.
ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation (1994)

Abstract An efficient methodology, further referred to as ICM, for versatile modeling operations and global energy optimization on arbitrarily fixed multimolecular systems is described. It is aimed at protein structure prediction, homology modeling, molecular docking, nuclear magnetic resonance (NMR) structure determination, and protein design. The method uses and further develops a previously introduced approach to model biomolecular structures in which bond lengths, bond angles, and torsion angles are considered as independent variables, any subset of them being fixed. Here we simplify and generalize the basic description of the system, introduce the variable dihedral phase angle, and allow arbitrary connections of the molecules and conventional definition of the torsion angles. Algorithms for calculation of energy derivatives with respect to internal variables in the topological tree of the system and for rapid evaluation of accessible surface are presented. Multidimensional variable restraints are proposed to represent the statistical information about the torsion angle distributions in proteins. To incorporate complex energy terms as solvation energy and electrostatics into a structure prediction procedure, a “double‐energy” Monte Carlo minimization procedure in which these terms are omitted during the minimization stage of the random step and included for the comparison with the previous conformation in a Markov chain is proposed and justified. The ICM method is applied successfully to a molecular docking problem. The procedure finds the correct parallel arrangement of two rigid helixes from a leucine zipper domain as the lowest‐energy conformation (0.5 Å root mean square, rms, deviation from the native structure) starting from completely random configuration. Structures with antiparallel helixes or helixes staggered by one helix turn had energies higher by about 7 or 9 kcal/mol, respectively. Soft docking was also attempted. A docking procedure allowing side‐chain flexibility also converged to the parallel configuration starting from the helixes optimized individually. To justdy an internal coordinate approach to the structure prediction as opposed to a Cartesian one, energy hypersurfaces around the native structure of the squash seeds trypsin inhibitor were studied. Torsion angle minimization from the optimal conformation randomly distorted up to the rms deviation of 2.2 Å or angular rms deviation of l0° restored the native conformation in most cases. In contrast, Cartesian coordinate minimization did not reach the minimum from deviations as small as 0.3 Å or 2°. We conclude that the most promising detailed approach to the protein‐folding problem would consist of some coarse global sampling strategy combined with the local energy minimization in the torsion coordinate space. © 1994 by John Wiley & Sons, Inc.
Comparison of JPEG and SPIHT image compression algorithms using objective quality measures (2009)

In this paper, a comparative study of JPEG and SPIHT compression algorithms is presented. A set of objective picture quality measures like peak signal to noise ratio (PSNR), maximum difference (MD), least mean square error (LMSE), structural similarity index (SSIM) and picture quality scale(PQS) are used to measure the picture quality and comparison is done based upon the results of these quality measures. Different kind of standard test images are assessed with different compression ratios. SPIHT based compression achieves better results as compared to JPEG for all compressions.
Introduction The Common Experience (2002)

The ways in which African American teachers think about their practice became clear to me over a four-year period (1994–98) in which I directed a professional development center I founded at Emory University called the Center for Urban Learning/Teaching and Urban Research in Education and Schools (CULTURES). The chapters in this book all share a common setting and background. The teachers who are the focus of the case studies were participants in the CULTURES program, and most of the chapter authors assisted in the planning and implementing of the professional development curriculum.KeywordsProfessional DevelopmentAfrican American StudentDiverse StudentResponsive PedagogyWhite TeacherThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Rapid characterization of protein productivity and production stability of CHO cells by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (2011)

The biopharmaceutical industry has been in pursuit of strategies which can isolate stable and high-producing cell lines. The whole cell mass spectrometry method by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) is a rapid and simple method for cell characterization based on the differences in the fingerprints of the mass spectra. This work describes how the method was evaluated for the application of screening for stable and high-producing clones from a panel of recombinant Chinese hamster ovary (CHO) cell lines. Detectable m/z values and their relative intensities were collected and processed by partial least squares (PLS). To reduce the errors introduced by the preparation method and spectra noise, high intensity preliminary data was selected and the number of variables introduced was validated by leave-one-out cross-validation. The differences in recombinant protein productivity and titer were revealed by PLS regression with promising results. Partial least-squares discriminant analysis (PLS-DA) was applied to differentiate stable and unstable cell lines as traditional stability testing would require several months involving numerous continuous passages. Results confirmed that the whole cell MALDI-TOF method can be a powerful method for routine monitoring of bioprocesses and study can be further developed by extending the number of the cell lines tested to establish a recombinant cell line database.
Qualitative Assessment of Scleral Shape Patterns Using a New Wide Field Ocular Surface Elevation Topographer (2017)

Background and Objectives: Objective was to examine new findings regarding conjunctival/scleral shape mapped with a novel wide field elevation topography device and software, to propose a new classification system for scleral shape. Methods: The Scleral Shape Study Group (SSSG) collaborated on this research. Data was collected from 152 eyes of prospective scleral lens patients utilizing a new topography device and software specifically designed to measure and map the sclera out to as much as 22 mm. Circumferential scleral plots of sagittal height vs. meridian at 14, 15 and 16mm diameters from the corneal center were generated for each eye. Scleral shape patterns were reviewed in all cases and classified according to recurring characteristics. Results: Twelve eyes were excluded from the analysis due to incomplete data. Of the remaining 140 eyes, 8 (5.7%), of the plots were primarily spherical (Group 1) and 40 (28.6%) were primarily regularly toric, largely conforming to a toric (Sin2) curve with approximately 180° periodicity or interval between elevation to elevation or depression to depression (Group 2). Fifty-seven cases (40.7%) had asymmetric depressions (or steep areas) or asymmetric elevations (or flat areas) which were classified as Group 3. The remaining 35 cases (26%) had a recognizable toric pattern with elevations and depressions but they were irregularly spaced or did not have the customary 180° periodicity (Group 4). Conclusion: A new classification of conjunctival/scleral shape is presented based upon data now available through wide field elevation topography, which could be helpful in scleral lens fitting and potentially soft lens fitting as the landing zone of these lenses are beyond the corneal borders.
Microsatellite instability and loss of heterozygosity in breast cancer. (1994)

Microsatellite instability (MSI) has been described in colorectal and other cancers. The purpose of this study was to determine the presence of MSI in breast cancer and to correlate its occurrence with clinicopathological parameters. For microsatellite markers we examined mono-, di-, tri-, and tetranucleotide repeats that, due to their polymorphic nature, may also be used to investigate loss of heterozygosity. In 20 paired breast cancer-peripheral blood DNA samples we identified four tumors (20%) with somatic MSI. All four tumors were stage I or II, grade 1 or 2, and estrogen receptor positive. To study MSI in relation to tumor progression we also examined paired DNA samples from two ipsilateral and three contralateral breast cancers, as well as two matched tumor-metastatic lymph node specimens. None of these seven cases showed MSI, but two of the contralateral tumors revealed allelic loss of polymorphic repeats. These data suggest that MSI is an early event in mammary tumorigenesis while loss of heterozygosity may occur at a later stage.
Current Status of Newer Carbapenems (2009)

We included in our review: ertapenem, biapenem, panipenem, doripenem, tebipenem pivoxil and tomopenem.
Effect of Gold Nanorod Surface Chemistry on Cellular Response (2011)

Gold nanorods (GNRs) stabilized with cetyltrimethylammonium bromide (CTAB) and GNR functionalized via a ligand exchange method with either thiolated polyethylene glycol (PEG(5000)) or mercaptohexadecanoic acid (MHDA) were investigated for their stability in biological media and subsequent toxicological effects to HaCaT cells. GNR-PEG and GNR-MHDA exhibited minimal effects on cell proliferation, whereas GNR-CTAB reduced cell proliferation significantly due to the inherent toxicity of the cationic surfactant to cells. Cell uptake studies indicated relatively low uptake for GNR-PEG and high uptake for GNR-MHDA. Reverse transcriptase polymerase chain reaction (RT-PCR) revealed that GNR-PEG induced less significant and unique changes in the transcription levels of 84 genes related to stress and toxicity compared to GNR-MHDA. The results demonstrate that, although cell proliferation was not affected by both particles, there is a significant difference in gene expression in GNR-MHDA exposed cells, suggesting long-term implications for chronic exposure.
XXVI.—The alkaloids of ipecacuanha. Part III (1918)

F. L. Pyman, J. Chem. Soc., Trans., 1918, 113, 222 DOI: 10.1039/CT9181300222
Computerized Automated Quantification of Subcutaneous and Visceral Adipose Tissue From Computed Tomography Scans: Development and Validation Study (2016)

The results described in this paper confirm the accuracy and reliability of the proposed method. The method is expected to be both convenient and useful in the clinical evaluation and study of obesity in patients who require SAT and VAT measurements.
Crystal Structure of Microbial Transglutaminase fromStreptoverticillium mobaraense (2002)

The crystal structure of a microbial transglutaminase from Streptoverticillium mobaraense has been determined at 2.4 A resolution. The protein folds into a plate-like shape, and has one deep cleft at the edge of the molecule. Its overall structure is completely different from that of the factor XIII-like transglutaminase, which possesses a cysteine protease-like catalytic triad. The catalytic residue, Cys(64), exists at the bottom of the cleft. Asp(255) resides at the position nearest to Cys(64) and is also adjacent to His(274). Interestingly, Cys(64), Asp(255), and His(274) superimpose well on the catalytic triad "Cys-His-Asp" of the factor XIII-like transglutaminase, in this order. The secondary structure frameworks around these residues are also similar to each other. These results imply that both transglutaminases are related by convergent evolution; however, the microbial transglutaminase has developed a novel catalytic mechanism specialized for the cross-linking reaction. The structure accounts well for the catalytic mechanism, in which Asp(255) is considered to be enzymatically essential, as well as for the causes of the higher reaction rate, the broader substrate specificity, and the lower deamidation activity of this enzyme.
An Improved Fabrication Technique For Applying Coatings To Optical Fiber Waveguides (1977)

Optical fibers must be coated as they are drawn to protect their inherent strength from handling abuse. In order to maintain high strength over the entire length of a fiber it is imperative that the coating be applied without damaging the fiber surface at any point. The coating must completely encapsulate the fiber and in the ideal case would concentrically surround it. A concentric coating is especially desirable for silicone-clad fibers1,2 in order to achieve low connector losses.
Self-Accelerating CO Sorption in a Soft Nanoporous Crystal (2013)

Carbon monoxide (CO) produced in many large-scale industrial oxidation processes is difficult to separate from nitrogen (N2), and afterward, CO is further oxidized to carbon dioxide. Here, we report a soft nanoporous crystalline material that selectively adsorbs CO with adaptable pores, and we present crystallographic evidence that CO molecules can coordinate with copper(II) ions. The unprecedented high selectivity was achieved by the synergetic effect of the local interaction between CO and accessible metal sites and a global transformation of the framework. This transformable crystalline material realized the separation of CO from mixtures with N2, a gas that is the most competitive to CO. The dynamic and efficient molecular trapping and releasing system is reminiscent of sophisticated biological systems such as heme proteins.
An Initialization Scheme of Hurricane Models by Vortex Specification (1993)

A scheme is presented to improve the representation of a tropical cyclone in the initial condition of a high-resolution hurricane model. In the proposed method, a crudely resolved tropical cyclone in the large-scale analysis is replaced by a vortex that is properly specified for use in the prediction model. Appropriate filters are used to remove the vortex from the large-scale analysis so that a smooth environmental field remains. The new specified bogus vortex takes the form of a deviation from this environmental held so that it can be easily merged with the latter field at the correct position. The specified vortex consists of both axisymmetric and asymmetric components. The symmetric component is generated by the time integration of an axisymmetric version of the hurricane prediction model. This ensures dynamical and thermodynamical consistency in the vortex structure, including the moisture field, and also compatibility of the vortex with the resolution and physics of the hurricane model. In the course of the integration of the axisymmetric model, the tangential wind component is gradually forced to a target wind profile determined from observational information and empirical knowledge. This makes the symmetric vortex a good approximation to the corresponding real tropical cyclone. The symmetric flow thus produced is used to generate an asymmetric wind field by the time integration of a simplified barotropic vorticity equation, including the beta effect. The asymmetric wind field, which can make a significant contribution to the vortex motion, is then added to the symmetric flow. After merging the specified vortex with the environmental flow, the mass field is diagnosed from the divergence equation with an appropriately controlled time tendency. The wind field remains unchanged at this step of initialization. Since the vortex specified by the proposed method is well adapted to the hurricane prediction model, problems of initial adjustment and false spinup of the model vortex, a long-standing difficulty in the dynamical prediction of tropical cyclones, are alleviated. It is anticipated that the improvement of the initial conditions can reduce the error in hurricane track forecasting and extend the feasibility of tropical cyclone forecasting to intensity change.
Factors affecting the measurement of photochromic lens performance (2016)

The principles, characteristics, and measurement methodology of photochromism of plastic ophthalmic lenses are briefly introduced and discussed. The factors influencing measurement variation and accuracy, including the preconditioning process, measurement device, and procedure, were investigated on ophthalmic photochromic lenses covering both photocasting and photocoating lens technologies. By design of experiment, factors affecting the measurements were studied using a photochromic measurement rig with reference to ISO 8980‐3 requirements. Experimental results prove the necessity for a lens preconditioning process prior to measurement. The excitation light source in the photochromic measurement rig has the greatest impact on measurement variation from the device perspective, while lens temperature is the key environmental factor. On the basis of the investigation, recommendations are made for reducing measurement variations and improving result accuracy.
Capturing CO2 from combustion flue gases with a carbonation calcination loop. Experimental results and process development (2009)

Post-combustion carbonate looping processes are based on the capture of CO2 from the flue gases of an existing power plant in a circulating fluidized bed (CFB) reactor of CaO (the carbonator) at around 650 ∘C. The calcination of CaCO3 in a new oxy-fired experimental results from a small test facility (30 kWt) operated in continuous mode using two interconnected CFB reactors as carbonator and calciner. Capture efficiencies between 70 and 97% have been obtained under realistic flue gas conditions in the carbonator reactor. The similarity between process conditions and those existing in CFBC power plants should allow a rapid scaling up of this technology.
Decision support system for localizing prostate cancer based on multiparametric magnetic resonance imaging (2012)

This DSS provides a cancer probability map for peripheral zone prostate tumors based on endorectal MP-MRI. These cancer probability maps can potentially aid radiologists in accurately localizing peripheral zone prostate cancers for planning targeted biopsies, focal therapy, and follow up for active surveillance.
Identification of the Active Site Nucleophile in the Thermostable β-Glycosidase from the Archaeon <i>Sulfolobus solfataricus</i> Expressed in <i>Escherichia coli</i> (1997)

Sulfolobus solfataricus beta-glycosidase expressed in Escherichia coli was fully inactivated at 65 degrees C, according to pseudo-first-order kinetics, by [3H]conduritol B epoxide (DL-1,2 anhydro-myo-inositol) synthesized as the active site directed inhibitor by a slight modification of Legler's procedure [Legler, G. (1977) Methods Enzymol. 46, 368-381]. The determination of kinetic constants for the inactivation showed that the process took place through the formation of a stabilized inhibitor-enzyme intermediate. Inactivation and reactivation studies suggested that the inhibitor-enzyme intermediate complex was formed more rapidly and hydrolyzed at a lower rate than it was for other glycosidases. Moreover, the stoichiometry of the binding, determined by electrospray mass spectrometric analysis, revealed that one molecule of the inhibitor was covalently bound to each enzyme subunit. The binding site for [3H]conduritol B epoxide was identified by the isolation and partial sequence analysis of the radioactive peptide obtained by cyanogen bromide and pepsin digests. Electrospray tandem mass analysis of the labeled peptide showed that the inhibitor was covalently bound to E387. This result, in agreement with data obtained from sequence alignments of S. solfataricus beta-glycosidase with other gluco- and galactosidases of the glycosyl hydrolase family 1 [Henrissat, B. (1991) Biochem. J. 280, 309-316], indicates that the conserved E387 is the nucleophilic amino acid residue in the active site of the enzyme.
Glycoproteins M and N of Pseudorabies Virus Form a Disulfide-Linked Complex (1998)

Genes homologous to the herpes simplex virus UL49.5 open reading frame are conserved throughout the Herpesviridae. In the alphaherpesvirus pseudorabies virus (PrV), the UL49.5 product is an O-glycosylated structural protein of the viral envelope, glycoprotein N (gN) (A. Jöns, H. Granzow, R. Kuchling, and T. C. Mettenleiter, J. Virol. 70:1237-1241, 1996). For functional characterization of gN, a gN-negative PrV mutant, PrV-gNbeta, and the corresponding rescuant, PrV-gNbetaR, were constructed, gN-negative PrV was able to productively replicate on noncomplementing cells, and one-step growth in cell culture was only slightly reduced compared to that of wild-type PrV. However, penetration was significantly delayed. In indirect immunofluorescence assays with rabbit serum directed against baculovirus-expressed gN, specific staining of wild-type PrV-infected cells occurred only after permeabilization of cells, whereas live cells failed to react with the antiserum. This indicates the lack of surface accessibility of gN in the plasma membrane of a PrV-infected cell. Western blot analyses and radioimmunoprecipitation experiments under reducing and nonreducing conditions led to the discovery of a heteromeric complex composed of gM and gN. The complex was stable in the absence of 2-mercaptoethanol but dissociated after the addition of the reducing agent, indicating that the partners are linked by disulfide bonds. Finally, gN was absent from gM-negative PrV virions, whereas gM was readily detected in virions in the absence of gN. Thus, gM appears to be required for virion localization of gN.
Respiratory systems and respiratory adaptations in larvae and pupae of Diptera (1944)

Each year the study of Diptera reveals some new and often unexpected facts concerning the mode of life of their early stages. The rich entomological literature dealing with this subject clearly shows that the diversity of conditions under which the larvae of this order of insects live surpasses that of any other order of the Animal Kingdom.