gebhart/patrepeval huggingface dataset:
Structure–Activity Relationships of Spectinamide Antituberculosis Agents: A Dissection of Ribosomal Inhibition and Native Efflux Avoidance Contributions (2016)

Spectinamides are a novel class of antitubercular agents with the potential to treat drug-resistant tuberculosis infections. Their antitubercular activity is derived from both ribosomal affinity and their ability to overcome intrinsic efflux mediated by the Mycobacterium tuberculosis Rv1258c efflux pump. This study explores the structure-activity relationships through analysis of 50 targeted spectinamides. Compounds are evaluated for ribosomal translational inhibition, MIC activity in Rv1258c efflux pump deficient and wild type tuberculosis strains, and efficacy in an acute model of tuberculosis infection. The results of this study show a narrow structure-activity relationship, consistent with a tight ribosome-binding pocket and strict structural requirements to overcome native efflux. Rationalization of ribosomal inhibition data using molecular dynamics simulations showed stable complex formation for halogenated spectinamides consistent with the long post antibiotic effects observed. The lead spectinamides identified in this study demonstrated potent MIC activity against MDR and XDR tuberculosis and had desirable antitubercular class specific features including low protein binding, low microsomal metabolism, no cytotoxicity, and significant reductions in bacterial burdens in the lungs of mice infected with M. tuberculosis. The structure-activity relationships detailed here emphasize the need to examine efflux-mediated resistance in the design of antituberculosis drugs and demonstrate that it is possible to overcome intrinsic efflux with synthetic modification. The ability to understand the structure requirements for this class has produced a variety of new substituted spectinamides, which may provide useful alternative candidates and promote the further development of this class.
Terminator-free template-independent enzymatic DNA synthesis for digital information storage (2019)

DNA is an emerging medium for digital data and its adoption can be accelerated by synthesis processes specialized for storage applications. Here, we describe a de novo enzymatic synthesis strategy designed for data storage which harnesses the template-independent polymerase terminal deoxynucleotidyl transferase (TdT) in kinetically controlled conditions. Information is stored in transitions between non-identical nucleotides of DNA strands. To produce strands representing user-defined content, nucleotide substrates are added iteratively, yielding short homopolymeric extensions whose lengths are controlled by apyrase-mediated substrate degradation. With this scheme, we synthesize DNA strands carrying 144 bits, including addressing, and demonstrate retrieval with streaming nanopore sequencing. We further devise a digital codec to reduce requirements for synthesis accuracy and sequencing coverage, and experimentally show robust data retrieval from imperfectly synthesized strands. This work provides distributive enzymatic synthesis and information-theoretic approaches to advance digital information storage in DNA.
Polarization selective diffractive optical elements and applications (1998)

Computer-generated holograms (CGH) fabricated as phase-only optical elements have proven to be useful for various photonic systems applications. Such elements are normally capable of implementing fixed functionality. However, the performances of packaged photonic systems will be further enhanced with availability of CGH elements with multifunctionality in polarization or color, and programmability. We have constructed polarization selective CGH which apply an independent phase profile during readout by horizontal and vertical light polarizations 1 – 3 . These elements are composed of two surface relief etched birefringent substrates joined face to face. We describe the design methodology for arbitrary birefringent substrate and gap materials. We show how these holograms are fabricated with standard microelectronics technology, and discuss the effects of etching and alignment errors on performance. We have demonstrated high diffraction efficiency with a polarization contrast ratio of over 100:1, using a multilevel phase hologram made from two birefringent lithium niobate substrates 2 .
A Randomized, Controlled Trial of In-Home Drinking Water Intervention to Reduce Gastrointestinal Illness (2005)

Trials have provided conflicting estimates of the risk of gastrointestinal illness attributable to tap water. To estimate this risk in an Iowa community with a well-run water utility with microbiologically challenged source water, the authors of this 2000-2002 study randomly assigned blinded volunteers to use externally identical devices (active device: 227 households with 646 persons; sham device: 229 households with 650 persons) for 6 months (cycle A). Each group then switched to the opposite device for 6 months (cycle B). The active device contained a 1-microm absolute ceramic filter and used ultraviolet light. Episodes of "highly credible gastrointestinal illness," a published measure of diarrhea, nausea, vomiting, and abdominal cramps, were recorded. Water usage was recorded with personal diaries and an electronic totalizer. The numbers of episodes in cycle A among the active and sham device groups were 707 and 672, respectively; in cycle B, the numbers of episodes were 516 and 476, respectively. In a log-linear generalized estimating equations model using intention-to-treat analysis, the relative rate of highly credible gastrointestinal illness (sham vs. active) for the entire trial was 0.98 (95% confidence interval: 0.86, 1.10). No reduction in gastrointestinal illness was detected after in-home use of a device designed to be highly effective in removing microorganisms from water.
The synthesis of poly(ether ether ketone) (PEEK) derived from 1,1-bis(4-hydroxyphenyl)-1-phenyl-2,2,3,3,4,4,4-heptafluorobutane (1995)

Poly(ether ether ketone)s (PEEK) are of interest due to their high thermal stability. Most PEEK materials are prepared by aromatic nucleophilic substitution between an activated aromatic dihalide and an alkali-metal bisphenolate in polar, aprotic solvents. We now report the preparation of a PEEK containing an extended fluorocarbon chain in the bisphenol, analogous to that produced by McGrath, et. al which contained a trifluoromethyl group in the bisphenol, and examine the effect on thermal properties.
Cooling bolocam, a new camera for the future GTM/LMT (1998)

The observations at millimeter wavelength begin to occupy an important role in the modern astronomy. The fast growing up of millimeter--wave bolometer array systems, such as SCUBA on the JCMT, MPfIR on the IRAM telescope or SuZIE on the CSO, have opened a new window that have allowed astronomers to make significant contributions in such diverse fields as the study of primeval galaxies and the early universe, anisotropies in the CMB due to the Sunyaev-Zel'dovich effect and protostars located inside dense molecular clouds. Bolocam is a new millimeter--wave camera with 144 pixels. It will operate at wave lengths centered at 1.1, 1.4 and 2.1 mm with a spatial resolution of 43'' ($\lambda = $1.4~mm) at CSO telescope and 8'' at the LMT/GMT. This camera will have a mapping speed two orders of magnitude larger than any of the previous mentioned cameras. The sensitivity of Bolocam is determined by the cryogenic system. This poster describes the actual stage of the cryogenic system which will cool the Bolocam receivers down to 300mK.
Hybrid Photonic-Plasmonic Waveguides with Ultrathin TiN (2019)

We experimentally demonstrate hybrid photonic-plasmonic waveguides utilizing plasmonic TiN, and index mismatched substrate and superstrate. The design offers lower losses and tighter mode-confinement compared to previously reported long-range surface plasmon polariton waveguides using noble metals. © 2019 The Author(s)
Multilingual Natural Language Processing (1997)

Preview this article: Multilingual Natural Language Processing, Page 1 of 1 < Previous page | Next page > /docserver/preview/fulltext/ijcl.2.1.08gre-1.gif
A Mobile Structured Light System for 3D Face Acquisition (2015)

A mobile sensor based on fringe projection techniques is developed with the goal of acquiring face 3D and color with a smartphone device. The system consists of a portable pico-projector and an Android-based smartphone. The data acquisition, pattern generation. and reconstruction of the final 3D point cloud are all driven by the smartphone. We present results on the root-mean-square error (RMSE) of the sensor and on 3D face matching.
On the efficiency of interference coordination schemes in emerging cellular wireless networks (2008)

In this paper, the efficiencies of different interference coordination schemes are evaluated for emerging wireless networks and the possible impact on intra-cell scheduling is studied through extensive simulations. The results show that pure fractional frequency reuse can provide similar improvement in the cell-edge throughput compared to power coordinated counterpart at a less cost in terms of overall throughput. Moreover, it can provide fairer distribution of throughput in both central as well as cell-edge areas. However, this scheme can not mange asymmetrical changes in the distribution of users across different cells in the entire system. As a result, a power coordination mechanism would be still necessary on top of such flexible frequency reuse schemes.
Effects of Age and Genetic Variations in VKORC1 , CYP2C9 and CYP3A4 on the phenprocoumon dose in Pediatric Patients (2018)

Our study reveals that age and genetic variations explain a significant part of the variability in phenprocoumon dose requirement in pediatric patients.
Transcriptional profiling of matched biopsies reveals molecular determinants of enzalutamide resistance. (2022)

5058 Background: Castration-resistant prostate cancer (CRPC) is the lethal form of the disease. One of the principal therapies in CRPC is the potent androgen receptor (AR) signaling inhibitor enzalutamide (enza). Most patients benefit from enza, but disease progression is nearly universal. A variety of resistance mechanisms have been described by comparing enza-naïve and enza-resistant tumors. However, these results are largely from different groups of patients and do not provide information on the changes induced by enza within a given patient. Lineage plasticity—most commonly-exemplified by loss of AR signaling and switch from a luminal to an alternate differentiation program—is a particularly aggressive resistance mechanism. Importantly, lineage plasticity appears to be increasing in incidence since more widespread use of potent AR signaling inhibitors such as enza. To improve our understanding of resistance mechanisms induced by enza treatment, we analyzed the transcriptomes of matched metastatic CRPC patient biopsies obtained prior to treatment and at the time of disease progression. Methods: All biopsies were obtained as part of the Stand Up 2 Cancer/Prostate Cancer Foundation-funded West Coast Dream Team, a prospective, IRB-approved protocol focused on understanding the biology of metastatic CRPC. We identified 21 patients for whom matched tumor biopsies with RNA-seq were available prior to starting treatment with enza and at the time of progression while still taking enza. Results: Our RNA-seq analysis demonstrates that the majority of progression tumors cluster with their baseline pair, suggesting that enza does not markedly change the tumor transcriptome in most cases. Three of 21 patients showed evidence of lineage plasticity at progression by gene expression analysis. By analyzing the RNA-seq data, we identified pathways linked to stemness that were more activated in baseline tumors from patients whose progression tumors underwent lineage plasticity. Furthermore, we identified a gene signature enriched in these baseline tumors that was associated with risk of lineage plasticity after enza treatment. We determined that high expression of this signature was strongly associated with poor survival from the time of AR signaling inhibitor treatment in independent patient samples, suggesting this signature is linked to poor patient outcome. Conclusions: Enza-resistant tumors are heterogeneous. Most tumors do not undergo significant transcriptional changes at progression vs. baseline. Matching recent reports, approximately 15% of tumors underwent lineage plasticity upon progression. Our work implicates a gene program that may predispose tumors to enza-induced lineage plasticity. Finally, the gene signature we identified may be a marker of lineage plasticity risk and tumor aggressiveness in CRPC prior to the initiation of AR signaling inhibitor therapy.
Stability of an inclined, pneumatically‐transported system of particles (2016)

A linear stability analysis is performed on the base‐state solution describing a pneumatically‐transported system inclined at an angle θ. One of two modes was found to be dominant, depending on the tilting angle: a low‐shear mode whose voidage eigenmode remains nearly symmetric from 0° &lt; θ ≤ θ c , and a “boundary layer” mode for θ &gt; θ c , marked by significant asymmetry throughout the domain and a high level of shear inside the thin regions adjacent to the walls. The critical angle θ c increases with the amount of momentum and energy lost to particle–wall friction and collisions, respectively. The time‐evolution of the latter mode, superimposed onto the base‐state solution, reveals an alternating train of dense and dilute regions near the top of the domain, which agrees qualitatively with the development and propagation of bubbles in inclined systems observed in experiment. An analytic solution corresponding to a vertical system with a uniform base state was also derived to identify the instability mechanisms responsible for a class of non‐oscillatory transverse waves which exist in both vertical and tilted particle systems. © 2016 American Institute of Chemical Engineers AIChE J , 62: 2248–2258, 2016
An NMR Method To Identify Nondestructively Chemical Compounds Bound to a Single Solid-Phase-Synthesis Bead for Combinatorial Chemistry Applications (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTAn NMR Method To Identify Nondestructively Chemical Compounds Bound to a Single Solid-Phase-Synthesis Bead for Combinatorial Chemistry ApplicationsSusanta K. Sarkar, Ravi S. Garigipati, Jerry L. Adams, and Paul A. KeiferView Author Information SmithKline Beecham Pharmaceuticals 709 Swedeland Road King of Prussia, Pennsylvania 19406 Varian NMR Instruments, 3120 Hansen Way Palo Alto, California 94304 Cite this: J. Am. Chem. Soc. 1996, 118, 9, 2305–2306Publication Date (Web):March 6, 1996Publication History Received21 July 1995Published online6 March 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja952434dhttps://doi.org/10.1021/ja952434drapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views475Altmetric-Citations110LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Combinatorial chemistry,Mathematical methods,Nuclear magnetic resonance spectroscopy,Organic polymers,Probes Get e-Alerts
Correction: MiR-34a/c-Dependent PDGFR-α/β Downregulation Inhibits Tumorigenesis and Enhances TRAIL-Induced Apoptosis in Lung Cancer (2022)

[This corrects the article DOI: 10.1371/journal.pone.0067581.].
Rethinking Machine Vision Time of Flight With GHz Heterodyning (2017)

Time-of-flight (ToF) 3-D cameras like the Microsoft Kinect, are prevalent in computer vision and computer graphics. In such devices, the power of an integrated laser is amplitude modulated at megahertz frequencies and demodulated using a specialized imaging sensor to obtain subcentimeter range precision. To use a similar architecture and obtain micrometer range precision, this paper incorporates beat notes. To bring telecommunications ideas to correlation ToF imaging, we study a form of “cascaded Time of Flight”which uses a hertz-scale intermediate frequency to encode high-frequency pathlength information. We show synthetically and experimentally that a bulk implementation of opto-electronic mixers offers: 1) robustness to environmental vibrations; 2) programmability; and 3) stability in frequency tones. A fiberoptic prototype is constructed, which demonstrates 3-μm range precision over a range of 2 m. A key contribution of this paper is to study and evaluate the proposed architecture for use in machine vision.
Using only the DC current information to detect stator turn faults in automotive claw-pole alternators (2011)

The stator turn fault is an important type of fault in automotive claw-pole alternators. In a typical vehicle electric system, however, it is difficult to access the AC current or voltage information of the claw-pole alternator, making conventional sequence-component-based fault detectors useless. This paper analyzes the effects of a full-bridge rectifier on the three-phase unbalanced system. A novel stator turn fault detector was proposed using only the alternator output current measurement. The performance of the stator turn-fault detector is demonstrated both by finite-element simulation and by extensive experimental results. The effect of the winding layout on stator turn fault detection is also discussed. Although the fault detector is originally proposed for claw-pole alternators, it is also applicable to most poly-phase AC generators with a DC link rectifier.
Preparation of arsenic sulfide thin films for integrated optical elements by spiral bar coating (2014)

We report on the preparation of thin As35S65 films from their amine based solutions by a spiral bar coating technique on flexible PET substrates and the direct writing of subwavelength surface corrugated gratings with a period of 350 nm into these films by excimer laser interference lithography. The structural and optical properties of bar coated As35S65 glass are investigated in detail and compared with those of samples fabricated by vacuum thermal evaporation. The polarization dependent spectral filtering properties of the guided mode resonance devices built by the waveguiding thin films and the surface relief gratings written by a single laser pulse are presented finally.
Supplementary Figure S2 from Relationship of Gene Expression and Chromosomal Abnormalities in Colorectal Cancer (2023)

Supplementary Figure S2 from Relationship of Gene Expression and Chromosomal Abnormalities in Colorectal Cancer
Targeted Inactivation of the Mouse Locus Encoding Coagulation Factor XIII-A: Hemostatic Abnormalities in Mutant Mice and Characterization of the Coagulation Deficit (2002)

Blood coagulation factor XIII (FXIII) promotes cross-linking of fibrin during blood coagulation; impaired clot stabilization in human genetic deficiency is associated with marked pathologies of major clinical impact, including bleeding symptoms and deficient wound healing. To investigate the role of FXIII we employed homologous recombination to generate a targeted deletion of the inferred exon 7 of the FXIII-A gene. FXIII transglutaminase activity in plasma was reduced to about 50% in mice heterozygous for the mutant allele, and was abolished in homozygous null mice. Plasma fibrin gamma-dimerization was also indetectable in the homozygous deficient animals, confirming the absence of activatable FXIII. Homozygous mutant mice were fertile, although reproduction was impaired. Bleeding episodes, hematothorax, hematoperitoneum and subcutaneous hemorrhage in mutant mice were associated with reduced survival. Arrest of tail-tip bleeding in FXIII-A deficient mice was markedly and significantly delayed; replacement of mutant mice with human plasma FXIII (Fibrogammin P) restored bleeding time to within the normal range. Thrombelastography (TEG) experiments demonstrated impaired clot stabilization in FXIII-A mutant mice, replacement with human FXIII led to dose-dependent TEG normalization. The mutant mice thus reiterate some key features of the human genetic disorder: they will be valuable in assessing the role of FXIII in other associated pathologies and the development of new therapies.
Comparison of analytic and numerical results for the mean cluster density in continuum percolation (1990)

Recently a number of techniques have been developed for bounding and approximating the important quantities in a description of continuum percolation models, such as 〈nc〉/ρ̄, the mean number of clusters per particle. These techniques include Kirkwood–Salsburg bounds, and approximations from cluster enumeration series of Mayer–Montroll type, and the scaled-particle theory of percolation. In this paper, we test all of these bounds and approximations numerically by conducting the first systematic simulations of 〈nc〉/ρ̄ for continuum percolation. The rigorous Kirkwood–Salsburg bounds are confirmed numerically in both two and three dimensions. Although this class of bounds seems not to converge rapidly for higher densities, averaging an upper bound with the corresponding lower bound gives an exceptionally good estimate at all densities. The scaled-particle theory of percolation is shown to give extremely good estimates for the density of clusters in both two and three dimensions at all densities below the percolation threshold. Also, partial sums of the virial series for 〈nc〉 are shown numerically to give extremely tight upper and lower bounds for this quantity. We argue that these partial sums may have similar bounding properties for a general class of percolation models.
Ionic conditions for the cleavage of the tRNA-like structure of turnip yellow mosaic virus by the catalytic RNA of RNase P. (1988)

The 3'-end of the RNA genome of turnip yellow mosaic virus can form a pseudoknotted tRNA-like structure that can be recognized by several tRNA-specific enzymes. We have found that the catalytic RNA component of Bacillus subtilis RNase P can cleave this structure in unusually low ionic strength buffers at a site analogous to the 5'-end of an aminoacyl stem of a tRNA. Most other precursors can only be processed under low ionic strength conditions if the RNase P holoenzyme is used; processing by the catalytic RNA component alone requires a higher ionic strength buffer. The cleavage of the turnip yellow mosaic virus tRNA-like structure demonstrates the importance of the substrate in determining the optimal buffer conditions for this reaction and also shows that high ionic strength buffers are not always necessary for cleavage by the catalytic RNA.