gebhart/patrepeval huggingface dataset:
Ultrathin conductive carbon nanomembranes as support films for structural analysis of biological specimens (2010)

Ultrathin carbon nanomembranes (CNM) have been tested as supports for both cryogenic high-resolution transmission electron microscopy (cryo-EM) as well as atomic force microscopy (AFM) of biological specimens. Purple membrane (PM) from Halobacterium salinarum, a 2-D crystalline monolayer of bacteriorhodopsin (BR) and lipids, was used for this study. Due to their low thickness of just 1.6 nm CNM add virtually no phase contrast to the transmission pattern. This is an important advantage over commonly used amorphous carbon support films which become instable below a thickness of ∼20 nm. Moreover, the electrical conductivity of CNM can be tuned leading to conductive carbon nanomembranes (cCNM). cCNM support films were analyzed for the first time and were found to ideally meet all requirements of cryo-EM of insulating biological samples. A projection map of PM on cCNM at 4 Å resolution has been calculated which proves that the structural integrity of biological samples is preserved up to the high-resolution range. CNM have also proven to be suitable supports for AFM analysis of biological samples. PM on CNM was imaged at molecular resolution and single molecule force spectra were recorded which show no differences compared to force spectra of PM obtained with other substrates. This is the first demonstration of a support film material which meets the requirements of both, cryo-EM and AFM, thus enabling comparative structural studies of biomolecular samples with unchanged sample–substrate interactions. Beyond high-resolution cryo-EM of biological samples, cCNM are attractive new substrates for other biophysical techniques which require conductive supports, i.e. scanning tunneling microscopy (STM) and electrostatic force microscopy (EFM).
Natural killer T cells in lipoprotein metabolism and atherosclerosis (2011)

Cells of both the innate and adaptive immune system participate in the development of atherosclerosis, a chronic inflammatory disorder of medium and large arteries. Natural killer T (NKT) cells express surface markers characteristic of natural killer cells and conventional T cells and bridge the innate and adaptive immune systems. The development and activation of NKT cells is dependent upon CD1d, a MHC-class I-type molecule that presents lipids, especially glycolipids to the T cell receptors on NKT cells. There are two classes of NKT cells; invariant NKT cells that express a semi-invariant T cell receptor and variant NKT cells. This review summarises studies in murine models in which the effect of the activation, overexpression or deletion of NKT cells or only invariant NKT cells on atherosclerosis has been examined.
Controlled/‘living’ radical polymerization of MMA via in situ ATRP process (2000)

Well-defined PMMA with very low polydispersity and α-Et2NCS2 and ω-Cl end groups was synthesized via a novel controlled/‘living’ radical polymerization (in situ ATRP process) using a tetraethylthiuram disulfide (TD)/FeCl3/PPh3 initiating system.
Rescue of the limb deformity in Hammertoe mutant mice by retinoic acid-induced cell death (1997)

Retinoids, used therapeutically primarily in the treatment of skin disorders, are potent teratogens. Several craniofacial, neural tube, and limb defects derive from a selective increase in cell death by retinoic acid in sites of spontaneous programmed cell death. Previously we showed that programmed cell death in the limb was apoptotic, and that the webbing of the foot of the Hammertoe mutant mouse correlates with diminished cell death in these regions of webbing. We therefore examined the effect of the induction of cell death by retinoic acid in normal and mutant limbs. Here we report that exogenously administered retinoic acid enhances cell death in the interdigital and marginal regions of the limb. This cell killing is apoptotic by several criteria. We also report that retinoic acid induces cell death in areas of the Hammertoe limb that display a suppression of cell death during development. This induction of cell death ameliorates the mutant phenotype. These results establish that a genetic defect in cell death can be modified by retinoic acid. Retinoic acid, therefore, may be a signal involved in the regulation of cell death during normal limb development. However, neither the effect of retinoic acid on cell death nor the defect of cell death in Hammertoe correlates with an altered expression pattern of the homeobox-containing Msx genes, the retinoic acid receptor beta gene, or the ability of endogenous retinoic acid to bind its receptors. We conclude that retinoic acid may influence pattern formation and cell death through an indirect mechanism.
A low cost wrist vein sensor for biometric authentication (2016)

Biometric recognition of an individual can be done based on physiological characteristics such as a face, palmprint, vein, etc. and behavioural characteristics which include gait, keystroke, mouse dynamics, etc. Among the various biometric modalities, the wrist vein recognition has been known for high accuracy, stability and resistance to spoofing. The success of wrist vein biometrics strongly correlates with the quality of the wrist vein image captured using the sensor. In this paper, we present a new wrist vein sensor that can capture a high-quality wrist vein image using Near infrared (NIR) lighting. The NIR lighting employed in this work can emit light in a spectrum of 940nm that in turn is used to illuminate the wrist area of the hand. The presented sensor employs a single camera with a simple physical structure that will further improve the quality of the light to properly illuminate the wrist hand region to capture good quality wrist vein images. Extensive experiments are carried out on our newly collected database comprised of 50 subjects resulting in 100 unique wrist veins. We also present a comprehensive evaluation of nine different state-of-the-art techniques that demonstrated the outstanding performance of the Log-Gabor and Sparse Representation Classifier (SRC) with an EER of 1.63% and the GMR of 94.01 at FMR = 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> %.
On optimal anchor node placement in sensor localization by optimization of subspace principal angles (2008)

In sensor network self-localization, anchor nodes provide a convenient means to disambiguate scene translation and rotation, thereby affording estimates in an absolute coordinate system. However, localization performance depends on the positions of the anchor nodes relative to the unknown-location nodes. Conventional wisdom in the literature is that anchor nodes should be placed around the perimeter of the network. In this paper, we show analytically why this strategy works well universally. We demonstrate that perimeter placement forces the information provided by the anchor constraints to closely align with the subspace that cannot be estimated from inter-node measurements: the subspace of translations and rotations. Examples quantify the efficacy of perimeter placement of anchors.
Epithelial-mesenchymal interactions are required for <i>msx 1</i> and <i>msx 2</i> gene expression in the developing murine molar tooth (1993)

Duplication of the msh-like homeobox gene of Drosophila may be related to the evolution of the vertebrate head. The murine homologues of this gene, msx 1 and msx 2 are expressed in the developing craniofacial complex including the branchial arches, especially in regions of epithelial-mesenchymal organogenesis including the developing tooth. By performing in vitro recombination experiments using homochronic dental and non-dental epithelial and mesenchymal tissues from E10 to E18 mouse embryos, we have found that the maintenance of homeobox gene expression in the tooth is dependent upon tissue interactions. In homotypic recombinants, dental-type tissue interactions occur, leading to expression of both genes in a manner similar to that seen during in vivo development. msx 1 is expressed exclusively in mesenchyme, both in the dental papilla and follicle. msx 2 is expressed in the dental epithelium and only in the mesenchyme of the dental papilla. In heterotypic recombinants, the dental epithelium is able to induce msx 1 expression in non-dental mesenchyme, this potential being lost at the bell stage. In these recombinants msx 2 was induced by presumptive dental epithelium prior to the bud stage but not thereafter. The expression of msx 1 and msx 2 in dental mesenchyme requires the presence of epithelium until the early bell stage. However, whereas non-dental, oral epithelium is capable of maintaining expression of msx 1 in dental mesenchyme throughout tooth development, induction of msx 2 was temporally restricted suggesting regulation by a specific epithelial-mesenchymal interaction related to the inductive events of tooth formation. msx 1 and msx 2, as putative transcription factors, may play a role in regulating the expression of other genes during tooth formation. We conclude that expression of msx 1 in jaw mesenchyme requires a non-specific epithelial signal, whereas msx 2 expression in either epithelium or mesenchyme requires reciprocal interactions between specialized dental cell populations.
A high-performance custom standard-cell CMOS equalizer for telecommunications applications (1987)

A high-performance CMOS programmable amplitude equalizer has been implemented with a dynamic range greater than 100 dB and supply rejection greater than 60 dB at 1 kHz from both supplies. This was accomplished using a balanced architecture. A nonreturn-to-zero sample-and-hold circuit is proposed that is also parasitic-insensitive. The circuits are implemented using a standard-cell methodology.
Alpha-amylase gene of thermophilic Streptomyces sp. TO1: nucleotide sequence, transcriptional and amino acid sequence analysis (1998)

The nucleotide sequence of a 1860-bp region encoding a thermostable K-amylase of Streptomyces sp. TO1 was determined. Frame analysis revealed the presence of a 1359-bp long open reading frame (amy TO1) encoding a 453 amino acid protein with a deduced M r of 49 kDa. Northern blot analysis revealed that amy TO1 gene was expressed as approximately 1.5-kbp monocistronic transcript in both SL1326/pLM1 and Streptomyces sp. TO1 strains. Primer extension experiments indicated that the transcriptional start site lies 30 bp upstream of the ATG start codon, and allowed the identification of 335 (TTGCTG) and 310 (TACGCG) eubacterial-like promoter sequences. Amy TO1 exhibits strong amino acid identities with those from other Streptomyces species with a maximum of 78% with S. thermoviolaceus K-amylase. Nevertheless, subtle amino acid changes such as the substitution of four conserved residues found at similar positions in other Streptomyces K-amylases by proline residues, and the substitution of three conserved hydrophilic amino acids by hydrophobic ones in Amy TO1 might account for the thermostable properties of Amy TO1.
Improved bacterial baby machine: application to Escherichia coli K-12 (1992)

Exponentially growing derivatives of Escherichia coli K-12 were immobilized onto the surfaces of nitrocellulose membrane filters which had been coated with poly-D-lysine. The cells attached firmly to the surfaces, and when flushed with culture medium, the immobilized cells continued to divide and newborn cells were released into the effluent. Cell cycle parameters were examined with the technique, and it was found that K-12 derivatives possessed differing values for interdivision times, C, D, and average cell sizes when grown in the same culture media. It was also found that the cells released from immobilized populations of one culture consisted of two predominant size classes: newborn cells of unit size with single nucleoids and newborn cells of double this unit size. The results demonstrated that K-12 derivatives can be used in the baby machine culture technique to examine all aspects of the cell cycle of this organism. Furthermore, the yield of newborn cells was about fivefold greater than that obtained previously with cultures of strain B/r immobilized onto uncoated membranes.
Three‐dimensional model of a substrate‐bound SARS chymotrypsin‐like cysteine proteinase predicted by multiple molecular dynamics simulations: Catalytic efficiency regulated by substrate binding (2004)

Severe acute respiratory syndrome (SARS) is a contagious and deadly disease caused by a new coronavirus. The protein sequence of the chymotrypsin-like cysteine proteinase (CCP) responsible for SARS viral replication has been identified as a target for developing anti-SARS drugs. Here, I report the ATVRLQ(p1)A(p1')-bound CCP 3D model predicted by 420 different molecular dynamics simulations (2.0 ns for each simulation with a 1.0-fs time step). This theoretical model was released at the Protein Data Bank (PDB; code: 1P76) before the release of the first X-ray structure of CCP (PDB code: 1Q2W). In contrast to the catalytic dyad observed in X-ray structures of CCP and other coronavirus cysteine proteinases, a catalytic triad comprising Asp187, His41, and Cys145 is found in the theoretical model of the substrate-bound CCP. The simulations of the CCP complex suggest that substrate binding leads to the displacement of a water molecule entrapped by Asp187 and His41, thus converting the dyad to a more efficient catalytic triad. The CCP complex structure has an expanded active-site pocket that is useful for anti-SARS drug design. In addition, this work demonstrates that multiple molecular dynamics simulations are effective in correcting errors that result from low-sequence-identity homology modeling.
Fidelity of dose delivery at high dose rate of volumetric modulated arc therapy in a truebeam linac with flattening filter free beams (2012)

The purpose of this study is to assess fidelity of radiation delivery between high and low dose rates of the flattening filter free (FFF) modes of a new all-digital design medical linear accelerator (Varian TrueBeam™), particularly for plans optimized for volumetric modulated arc therapy (VMAT). Measurements were made for the two energies of flattening filter free photon beams with a Varian TrueBeam™ linac: 6 MV (6 XFFF) at 400 and 1400 MU/min, and 10 MV (10 XFFF) at 400 and 2400 MU/min. Data acquisition and analysis was performed with both ionization chambers and diode detector system Delta(4), for square radiation fields and for 8 VMAT treatment plans optimized for SBRT treatment of lung tumors. For the square fields, a percent dose difference between high and low dose rate of the order of 0.3-0.4% for both photon energies was seen with the ionization chambers, while the contribution to the difference from ion recombination was found to be negligible. For both the VMAT and square-field deliveries, the Delta(4) showed the same average percent dose difference between the two dose rates of ~0.8% and ~0.6% for 10 MV and 6 MV, respectively, with the lower dose rate values giving the greater measured dose compared to the high dose rate. Thus, the VMAT deliveries introduced negligible dose differences between high and low dose rate. Finally, reproducibility of dose measurements was good for both energies.
An analysis of the effects of radio‐frequency interference on packaged junction‐field‐effect transistors (1990)

Abstract Radio‐frequency signals may be picked up from the environment and interfere with a low‐frequency circuit. A computer‐aided method of predicting the resulting effects of this interference on the junction‐field‐effect transistors is presented in this paper. The method presented provides a convenient and simple means of analyzing the conducted‐susceptibility problem in a low‐frequency circuit. In our analysis, the parasitic components of the package are taken into account. The variation of the equivalent input‐noise voltage with the gate‐bias voltage and the decrease of the rectification factor with the increase of frequency are illustrated. The predicted results show good agreement with the experimental data.
Heart Failure and Risk of Dementia and Alzheimer Disease (2006)

Heart failure is associated with an increased risk of dementia and Alzheimer disease in older adults. Antihypertensive drug therapy may partially counteract the risk effect of heart failure on dementia disorders.
Content-Adaptive Resolution Control To Improve Video Coding Efficiency (2018)

Aiming at improved rate-distortion (R-D) performance, this paper presents a machine-learning based solution for the run-time video resolution adaptation problem. The proposed approach utilizes neural networks that leverage a complexity feature extracted from the video frames topredict a quantization parameter (QP) for downscaled video targeting the same bitrate as the native video. The peak signal to noise ratio (PSNR) is also predicted for both the native and downscaled resolutions, and the one that leads to the highest PSNR is selected. Experimental results show that \quad the proposed adaptive approach achieves significant improvements in R-D performance compared to using a fixed resolution.
Measuring the Web. (1996)

Abstract “When you can measure what you are speaking about, and express it in numbers, you know something about it; but when you cannot express it in numbers, your knowledge is of a meager and unsatisfactory kind; it may be the beginning of knowledge, but you have scarcely in your thoughts advanced to the state of science.” — Lord Kelvin This paper presents some difficult qualitative questions concerning the Web, and attempts to provide some partial quantitative answers to them. It uses the numbers in these answers to drive some 3-D visualizations of localities in the Web.
Photophysical Properties of ZnS Nanoclusters with Spatially Localized Mn<sup>2+</sup> (1996)

The synthesis and photophysical characterization of nanometer-size ZnS with and without Mn2+ are reported. Without Mn2+, the ZnS nanoclusters emit in the blue upon ultraviolet excitation. ZnS doped with 1−5% Mn2+ (presumably in Zn2+ sites) yields the orange emission observed for bulk Zn:Mn phosphors but with greatly reduced emissive lifetimes. ZnS with surface-bound Mn2+, in contrast, emits in the ultraviolet with even shorter lifetimes. Thus, the physical location of Mn2+ in the ZnS nanocluster determines its optical properties.
Genetic Variation and Relationships among Cultivated, Wild, and Semiwild Soybean (2004)

Some annual Glycine accessions are intermediate between the standard phenotypes of Glycine max (L.) Merr. and Glycine soja Sieb. & Zucc. and have been labeled semiwild. Few studies have examined both the genetic and phenotypic relationships among G. soja, G. max, and semiwild-types by combining morphological traits and DNA markers. The objectives of this research were to quantify genetic variation within G. soja, G. max, and semiwild accessions; to investigate the relationships among the G. soja, G. max, and semiwild accessions; and to examine the relationships among phenotypes on the basis of morphological traits and genotypes on the basis of DNA markers. Ninety-two semiwild, G. soja, and G. max accessions from the USDA Soybean Germplasm Collection were evaluated for 20 phenotypic traits and with 137 RAPD markers. Mahalanobis distances and a Jaccard genetic similarity matrix were calculated for phenotypic traits and DNA data, respectively. Nonhierarchical and hierarchical clustering as well as multidimensional scaling (MDS) were used to evaluate relationships among semiwild, G. soja, and G. max accessions. Principal component analysis was applied to identify the morphological traits that were most significant in separating the three groups. For the accessions examined, unique RAPD markers were found for each taxonomic type. Three clusters defined by either phenotypic or DNA data are highly consistent and strongly corresponded to G. soja, G. max, and semiwild classifications. On the basis of the analysis of RAPD data, G. soja accessions have the greatest genetic diversity and semiwild accessions the least. Glycine max and semiwild accessions are more closely related to each other than to G. soja accessions. These data will be useful in helping to define a core collection of annual Glycine
Synthesis of Pyrrolidine Analogues of <i>N</i>‐Acetylneuraminic Acid as Potential Sialidase Inhibitors (1990)

Abstract The pyrrolidine derivatives 3 , 4 , and 5 were prepared from the methyl ester 7 of Neu2en5Ac via lie pyrrolidine‐borane adduct 33 . They inhibit Vibrio cholerae sialidase competitively with K i = 4. 4 10 −3 M, 5. 3 10 −3 M, and 4. 0 10 −2 M, respectively. Benzylation of 7 gave the fully O ‐benzylated 8 besides 9, 10 , and 11. Ozonolysis and reduction with NaBH 4 of 8 and 9 gave the 1, 4‐diols 12 and 15 , the hydroxy acetates 13 and 16 , and the furanoses 14 and 17 ( Scheme 1 ), respectively. The diol 12 was selectively protected (→ 19 → 20 → 23 ) and transformed into the azide 27 by a Mitsunobu reaction. Selective base‐catalysed deprotection of the diacetate 22 , obtained from 12 , was hampered by an easy acetyl‐group migration. The mesylate 28 proved unstable. The azide 27 was transformed via 29 into the ketone 30 ( Scheme 2 ). Hydrogenation of 30 gave the dihydropyrrole 31 and, hence, the pyrrole 32. The adduct 33 was obtained from 30 by a Staudinger reaction (→31) and reduction with LiBH 4 /HBF 4 . It was transformed into the pyrroudine 34 . The structure of 34 was established by X‐ray analysis. Reductamination of the pyrrolidine‐borane adduct with glyoxylic acid gave 40 and, hence, 3. N ‐Alkylation afforded 44 and, hence, the phosphonate 4. The acid 5 was obtained from 33 by acylation (→ 47 ) and deprotection ( Scheme 4 ).
Inference Degradation of Active Information Fusion within Bayesian Network Models (2008)

Bayesian networks have been extensively used in active information fusion that selects the best sensor based on expected utility calculation. However, inference degradation happens when the same sensors are selected repeatedly over time if the applied strategy is not well designed to consider the history of sensor engagement. This phenomenon decreases fusion accuracy and efficiency, in direct conflict to the objective of information integration with multiple sensors. This paper provides mathematical scrutiny of the inference degradation problem in the popular myopia planning. It examines the generic dynamic Bayesian network models and shows experimentation results for mental state recognition tasks. It also discusses the candidate solutions with initial results. The inference degradation problem is not limited to the discussed fusion tasks and may emerge in variants of sensor planning strategies with more global optimization approach. This study provides common guidelines in information integration applications for information awareness and intelligent decision.