gebhart/patrepeval huggingface dataset:
Novel m4C modification in type I restriction-modification systems (2016)

We identify a new subgroup of Type I Restriction-Modification enzymes that modify cytosine in one DNA strand and adenine in the opposite strand for host protection. Recognition specificity has been determined for ten systems using SMRT sequencing and each recognizes a novel DNA sequence motif. Previously characterized Type I systems use two identical copies of a single methyltransferase (MTase) subunit, with one bound at each half site of the specificity (S) subunit to form the MTase. The new m4C-producing Type I systems we describe have two separate yet highly similar MTase subunits that form a heterodimeric M1M2S MTase. The MTase subunits from these systems group into two families, one of which has NPPF in the highly conserved catalytic motif IV and modifies adenine to m6A, and one having an NPPY catalytic motif IV and modifying cytosine to m4C. The high degree of similarity among their cytosine-recognizing components (MTase and S) suggest they have recently evolved, most likely from the far more common m6A Type I systems. Type I enzymes that modify cytosine exclusively were formed by replacing the adenine target recognition domain (TRD) with a cytosine-recognizing TRD. These are the first examples of m4C modification in Type I RM systems.
Capacity of MIMO Laser Optical (VLC) Wireless Networks (2015)

In wireless communication systems, the laser optics wireless communication systems becomes more and more popular, such as the visual light communication (VLC) system. In this paper, we have analyzed the capacity of MIMO VLC communication system using Shannon Capacity in general, and provide necessary comments on the VLC system. Simulation results has been given to prove the effectiveness and robust of the MIMO VLC system.
Multiparametric MRI and 18F-DCFPyL PET/CT for detection of locally recurrent prostate cancer after low dose rate brachytherapy (2020)

Abstract Background and purpose: Both multiparametric magnetic resonance imaging (mpMRI) and prostate specific membrane antigen (PSMA)-targeting positron emission tomography (PET) imaging have shown promise in early localization of prostate cancer (PCa) recurrence after primary external beam radiotherapy. Detecting recurrence after brachytherapy for PCa using MRI is significantly hampered by susceptibility artifacts secondary to brachy seeds. Here, we compare the efficacy of 18 F-DCFPyL (2-(3-{1-carboxy-5-[(6- 18 F-fluoro-pyridine-3-carbonyl)-amino]-pentyl}-ureido)-pentanedioic acid) PET/CT versus mpMRI for detecting sites of local recurrence after low dose rate (LDR) brachytherapy for prostate cancer. Materials and methods: A total of 155 patients with a history of recurrent PCa who underwent mpMRI at 3 Tesla and 18 F-DCFPyL PET/CT were retrospectively reviewed. Patients who underwent LDR brachytherapy for PCa and had subsequent biochemical recurrence (BCR) followed by mpMRI and 18 F-DCFPyL PET/CT were included in this study. mpMRI was performed on a 3T scanner with endorectal and surface coils and images were prospectively read by a single expert radiologist. The 18 F-DCFPyL PET/CT scan was prospectively interpreted by two nuclear medicine physicians. Patients underwent targeted biopsy when deemed clinically necessary and specimens were interpreted by an expert GU pathologist. Positivity rates (PR) from mpMRI and 18 F-DCFPyL PET/CT were compared, and pathology results were used to calculate the positive predictive value (PPV) of each imaging modality for detecting PCa recurrence. Results: 15 patients who underwent LDR brachytherapy and had subsequent biochemical failure were imaged with mpMRI and 18 F-DCFPyL PET/CT. 18 non-lymph node lesions were identified on at least one imaging modality. The PR for detection of intraprostatic lesions was 60% (9/15) for both PET/CT and mpMRI, with 3 prostate lesions detected by only one modality. 18 F-DCFPyL PET/CT identified pelvic and extra-pelvic lymph nodes in 8 (53%) patients, while mpMRI noted positive lymph node findings in only 2 (13%) patients. A total of 15 lesions corresponding to 9 patients were targeted for biopsy. The PPV of 18 F-DCFPyL PET/CT and mpMRI for the detection of local recurrence were 84.6% and 71.4%, respectively. For the detection of intraprostatic lesions, 18 F-DCFPyL PET/CT and mpMRI had a PPV of 87.5% and 71.4%, respectively. Conclusion: This case series analysis suggests that 18 F-DCFPyL PET/CT may detect local and regional recurrent PCa after LDR brachytherapy at a higher rate than mpMRI and that it has the potential to detect suspicious pelvic lymph nodes at a much higher rate. Further studies are needed to validate these findings in larger cohorts.
Narrow linewidth power scaling and phase stabilization of 2-<italic>μ</italic>m thulium fiber lasers (2011)

Thulium-doped fiber lasers (TFLs) emitting retina-safe 2-μm wavelengths offer substantial power-scaling advantages over ytterbium-doped fiber lasers for narrow linewidth, single-mode operation. This article reviews the design and performance of a pump-limited, 600 W, single-mode, single-frequency TFL amplifier chain that balances thermal limitations against those arising from stimulated Brillouin scattering (SBS). A simple analysis of thermal and SBS limits is anchored with measurements on kilowatt class Tm and Yb fiber lasers to highlight the scaling advantage of Tm for narrow linewidth operation. We also report recent results on active phase-locking of a TFL amplifier to an optical reference as a precursor to further parallel scaling via coherent beam combining.
Global Motion Perception in 2-Year-Old Children: A Method for Psychophysical Assessment and Relationships With Clinical Measures of Visual Function (2013)

Global motion perception can be measured in 2-year-old children using the OKR. This technique is reliable and data from adults suggest that motion coherence thresholds based on the OKR are related to motion perception. Global motion perception was related to stereoacuity in children.
Antibacterial mechanisms identified through structural systems pharmacology (2013)

The structural systems pharmacology framework presented in this study was shown to be effective in the prediction of molecular mechanisms of antibacterial compounds. The study provides a promising proof of principle for such an approach to antibacterial development and raises specific molecular and systemic hypotheses about antibacterials that are amenable to experimental testing. This framework, and perhaps also the specific predictions of antibacterials, is extensible to developing antibacterial treatments for pathogenic E. coli and other bacterial pathogens.
Clinical and Genomic Characterization of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer: A Multi-institutional Prospective Study (2018)

Purpose The prevalence and features of treatment-emergent small-cell neuroendocrine prostate cancer (t-SCNC) are not well characterized in the era of modern androgen receptor (AR)-targeting therapy. We sought to characterize the clinical and genomic features of t-SCNC in a multi-institutional prospective study. Methods Patients with progressive, metastatic castration-resistant prostate cancer (mCRPC) underwent metastatic tumor biopsy and were followed for survival. Metastatic biopsy specimens underwent independent, blinded pathology review along with RNA/DNA sequencing. Results A total of 202 consecutive patients were enrolled. One hundred forty-eight (73%) had prior disease progression on abiraterone and/or enzalutamide. The biopsy evaluable rate was 79%. The overall incidence of t-SCNC detection was 17%. AR amplification and protein expression were present in 67% and 75%, respectively, of t-SCNC biopsy specimens. t-SCNC was detected at similar proportions in bone, node, and visceral organ biopsy specimens. Genomic alterations in the DNA repair pathway were nearly mutually exclusive with t-SCNC differentiation ( P = .035). Detection of t-SCNC was associated with shortened overall survival among patients with prior AR-targeting therapy for mCRPC (hazard ratio, 2.02; 95% CI, 1.07 to 3.82). Unsupervised hierarchical clustering of the transcriptome identified a small-cell-like cluster that further enriched for adverse survival outcomes (hazard ratio, 3.00; 95% CI, 1.25 to 7.19). A t-SCNC transcriptional signature was developed and validated in multiple external data sets with > 90% accuracy. Multiple transcriptional regulators of t-SCNC were identified, including the pancreatic neuroendocrine marker PDX1. Conclusion t-SCNC is present in nearly one fifth of patients with mCRPC and is associated with shortened survival. The near-mutual exclusivity with DNA repair alterations suggests t-SCNC may be a distinct subset of mCRPC. Transcriptional profiling facilitates the identification of t-SCNC and novel therapeutic targets.
Translational Pharmacologic Efficacy Studies of Glial Growth Factor 2 (GGF2) in Spinal Cord Injury Models and in the Veterinary Clinical Setting (2013)

Abstract : The work performed under this grant evaluated the efficacy of Glial Growth Factor 2 (GGF2), a member for the neuregulin family, as a spinal cord injury (SCI) therapeutic. The research expanded on previous work and extended these studies to determine if GGF2 should be advanced into human clinical studies for SCI. GGF2 s optimal dosage was examined using a model of rodent SCI and testing several dose levels delivered either subcutaneously (SC) or intravenously (IV). Optimized dosing was determined to be by a SC route, and subsequent studies evaluated recovery of function by monitoring bladder function, muscle volume changes, and motor function in SCI rodent models of various severities. Additionally, safety and tolerability was explored in naive canines, and followed by a clinical trial for safety in dogs with SCI.
ChemInform Abstract: Total Synthesis of (+)‐Aloperine. Use of a Nitrogen‐Bound Silicon Tether in an Intramolecular Diels—Alder Reaction. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
14 Retrotransposon Reverse Transcription (1993)

During the past decade, it has become evident that genes encoding putative reverse transcriptases (RTs) are widespread genomic residents. Potential RT-coding domains have been identified in genes inhabiting a variety of genomic niches within animal, plant, protozoan, fungal, and even eubacterial cells. The existence of extensive sequence data has led to a number of studies of the evolutionary relationships among RT-encoding elements and speculations about the origin of this enzyme in a pre-DNA world, preceding the prokaryotic/eukaryotic divergence (Temin 1985; Darnell and Doolittle 1986; Wintersberger and Wintersberger 1987; Varmus 1989). This chapter concentrates on the available evidence for the existence of RTs encoded by three broad groups of transposable elements as well as evidence suggesting that these elements transpose through an RNA-mediated mechanism. These three groups of elements, collectively called “retrotransposons,” differ from the much more extensively studied retroviruses in a number of ways, most conspicuously by their apparent inability to be transferred horizontally. Given the impossibility of discussing all of the large number of sequenced transposons thought to encode RT, this chapter concentrates on those systems that have proved to be most amenable to experimental dissection of the detailed mechanisms involved in transposon reverse transcription. Recent comprehensive reviews of these genomic elements can be found elsewhere (Boeke 1988; Berg and Howe 1989; Echalier 1989; Boeke and Sandmeyer 1991), and more specialized reviews are referenced in the text under specific topics. A list of structural features of the elements discussed in this chapter is presented in Table 1. The wide...
JANUS (2012)

This paper addresses the problem of reducing unnecessary conflicts in optimistic synchronization. Optimistic synchronization must ensure that any two concurrently executing transactions that commit are properly synchronized. Conflict detection is an approximate check for this condition. For efficiency, the traditional approach to conflict detection conservatively checks that the memory locations mutually accessed by two concurrent transactions are accessed only for reading.
Influence of impact load‐temperature conformity on toughening of poly(vinyl chloride) by core‐shell rubber particles (2008)

Abstract The work focused on the elucidation of several key parameters in toughening poly(vinyl chloride) (PVC) by the methyl methacrylate–butadiene–styrene (MBS) core‐shell particles. Accordingly, blends containing various weight percent of the MBS particles were prepared and characterized by dilute solution viscometry, dynamic light scattering, dynamic mechanical thermal analysis, transmission electron microscopy, and temperature variable impact test. The results showed PVC/MBS solution miscibility in almost all compositions with their maximum thermodynamic affinities at about 17 and 67 wt % of MBS in tetrahydrofurane (THF). In addition, MBS weight percent increase in its blend with the PVC above 10 led to severe impact energy raise with eventual leveling at about 17 wt %. Furthermore, blend toughness and its components miscibility in solution increased in parallel up to 20 wt % of MBS particles. On the other hand, blend toughness declined with test temperature decrease toward impact modifier core T g at about −30°C even for the sample with 20 wt % of the MBS particles. Finally, the brittle‐ductile transition of the blend containing 20 wt % of the MBS particles comparison with its matrix tan δ‐temperature correlation implied 2500 J/m impact energy equivalence with 90°C sample temperature rise in secondary relaxation activation. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
DeepRing: Protecting Deep Neural Network With Blockchain (2019)

Several computer vision applications such as object detection and face recognition have started to completely rely on deep learning based architectures. These architectures, when paired with appropriate loss functions and optimizers, produce state-of-the-art results in a myriad of problems. On the other hand, with the advent of "blockchain", the cybersecurity industry has developed a new sense of trust which was earlier missing from both the technical and commercial perspectives. Employment of cryptographic hash as well as symmetric/asymmetric encryption and decryption algorithms ensure security without any human intervention (i.e., centralized authority). In this research, we present the synergy between the best of both these worlds. We first propose a model which uses the learned parameters of a typical deep neural network and is secured from external adversaries by cryptography and blockchain technology. As the second contribution of the proposed research, a new parameter tampering attack is proposed to properly justify the role of blockchain in machine learning.
Comparison of the Performance of CoP-Coated and Pt-Coated Radial Junction n+p-Silicon Microwire-Array Photocathodes for the Sunlight-Driven Reduction of Water to H2(g) (2015)

The electrocatalytic performance for hydrogen evolution has been evaluated for radial-junction n(+)p-Si microwire (MW) arrays with Pt or cobalt phosphide, CoP, nanoparticulate catalysts in contact with 0.50 M H2SO4(aq). The CoP-coated (2.0 mg cm(-2)) n(+)p-Si MW photocathodes were stable for over 12 h of continuous operation and produced an open-circuit photovoltage (Voc) of 0.48 V, a light-limited photocurrent density (Jph) of 17 mA cm(-2), a fill factor (ff) of 0.24, and an ideal regenerative cell efficiency (ηIRC) of 1.9% under simulated 1 Sun illumination. Pt-coated (0.5 mg cm(-2)) n(+)p-Si MW-array photocathodes produced Voc = 0.44 V, Jph = 14 mA cm(-2), ff = 0.46, and η = 2.9% under identical conditions. Thus, the MW geometry allows the fabrication of photocathodes entirely comprised of earth-abundant materials that exhibit performance comparable to that of devices that contain Pt.
Designing auditory interactions for PDAs (1995)

This panel addresses issues in designing audio-based user interactions for small, personal computing devices, or PDAs. One issue is the nature of interacting with an auditory PDA and the interplay of affordances and form factors. Another issue is how both new and traditional metaphors and interaction concepts might be applied to auditory PDAs. The utility and design of nonspeech cues are discussed, as are the aesthetic issues of persona and narrative in designing sounds. Also discussed are commercially available sound and speech components and related hardware tradeoffs. Finally, the social implications of auditory interactions are explored, including privacy, fashion and novel social interactions.
Measurement of the Frictional Force between PVA Roller Brushes and Semiconductor Wafers with Various Films Immersed in Chemicals (2016)

To better understanding the lubrication condition between a polyvinyl acetal (PVA) brush and cleaning surfaces, we measured the frictional force between the PVA roller brushes and the semiconductor wafers with various films immersed in chemicals. The frictional force showed different tendencies depending on the combination of chemicals and surface films. Especially, the large fluctuation of friction force was observed under the combination of Cu and NH 4 OH.
Hydrolysis of peptides by carboxypeptidase A: equilibrium trapping of the ES2 intermediate (1986)

The cobalt absorption and electron paramagnetic resonance (EPR) spectra of cobalt carboxypeptidase undergo unique variations on formation of catalytic peptide and ester intermediates as previously recorded in cryoenzymologic experiments employing rapid-scanning spectroscopy and cryotrapping [Geoghegan, K. F., Galdes, A., Martinelli, R. A., Holmquist, B., Auld, D.S., & Vallee, B. L. (1983) Biochemistry 22, 2255-2262]. We here describe a means of stabilizing these intermediates, which we have termed "equilibrium trapping". It allows peptide intermediates to be observed for longer periods (much greater than 1 min) at ambient as well as subzero temperatures. The reaction intermediate with the rapidly turned over peptide substrate Dns-Ala-Ala-Phe is trapped when the cobalt enzyme (greater than 10 microM) has catalyzed the attainment of chemical equilibrium between high concentrations of the hydrolysis products Dns-Ala-Ala, 10 mM, and L-phenylalanine, 50 mM, and the product of their coupling Dns-Ala-Ala-Phe. Under these conditions, Dns-Ala-Ala-Phe is present in the equilibrated substrate-product reaction mixture at a level that exceeds the one predicted on the basis of K'eq for hydrolysis of this substrate and is close to the enzyme concentration. Other pairs of peptide hydrolysis products yield similar results. Visible absorption and EPR spectra of the cobalt enzyme show that the synthesized peptide binds to the active site in the mode previously recognized as the ES2 catalytic intermediate in peptide hydrolysis. Equilibrium trapping of the ES2 intermediate allows analysis of its physicochemical properties by methods that could not be employed readily under cryoenzymological conditions, e.g., circular dichroic and magnetic circular dichroic spectra.(ABSTRACT TRUNCATED AT 250 WORDS)
Normal sensitivity to acute pain, but increased inflammatory hyperalgesia in mice lacking the nociceptin precursor polypeptide or the nociceptin receptor (2003)

Nociceptin/orphanin FQ (N/OFQ) is the endogenous agonist of the N/OFQ peptide receptor (NOP receptor). It is released from a larger precursor polypeptide, called prepro-nociceptin (ppN/OFQ) from which, in addition to N/OFQ, other biologically active neuropeptides may be derived. Increasing evidence indicates that exogenous application of N/OFQ to the central nervous system of mice and rats induces pro- and antinociceptive effects depending on the dose and site of administration. Much less is known about a potential contribution of endogenous N/OFQ to pain control. Here, we have used a genetic approach to address this topic. Mice deficient in either the NOP receptor (NOP-R-/- mice) or the N/OFQ precursor polypeptide (ppN/OFQ-/- mice) or both (double knockout mice) were compared with wild-type littermates in animal models of acute and tonic pain. Nociceptive responses to acute noxious heat of all three types of mutant mice were indistinguishable from those of wild-type mice. Accordingly, nociceptive behaviour was very similar in the early phase of the formalin test. However, NOP-R-/-, ppN/OFQ-/- and double knockout mice showed markedly stronger nociceptive responses during prolonged nociceptive stimulation in the second phase of the formalin test and significantly lower thermal pain thresholds in inflamed tissue after zymosan A injection. These results indicate that N/OFQ contributes significantly to endogenous pain control during prolonged nociceptive stimulation but does not affect acute pain sensitivity. Among the three types of mutant mice nociceptive behaviour was nearly identical, indicating that the lack of other potential ppN/OFQ products in the ppN/OFQ-/- mice was apparently without effect on the nociceptive phenotype.
Quantitative buffy coat analysis. A new laboratory tool functioning as a screening complete blood cell count (1983)

We have developed a system for the quantitative analysis of the buffy coat in centrifuged whole blood samples. This analysis, performed in a modified microhematocrit tube, provides a hematocrit value, total WBC count, platelet count, and a separation of the leukocyte population into granulocytes and nongranulocytes. All results are available within 15 minutes and correlate well with existing methods. The system is expected to provide a rapid means of performing a complete blood cell count in a physician's office.
Preparation of high-Tc superconducting Bi-Sr-Ca-Cu-O films by organometallic chemical vapor deposition using second-generation fluorocarbon-based precursors (1991)

High-Tc superconducting Bi-Sr-Ca-Cu-O thin films with good electrical properties and smooth surface morphologies have been prepared by low-pressure organometallic chemical vapor deposition using the new fluorocarbon-based precursors Sr(hexafluoroacetylacetonate)2⋅tetraglyme and Ca(hexafluoroacetylacetonate)2⋅triglyme together with Cu(acetylacetonate)2 and triphenylbismuth [Bi(C6H5)3]. The fluorinated precursors are air-stable and exhibit high, stable volatility even after prolonged heating. X-ray diffraction measurements reveal that the films deposited at 650 °C contain some fluoride phases but no high-Tc phases. However, post-annealing in oxygen produces films composed predominantly of the Bi2Sr2CaCu2Ox phase with high preferential orientation of the crystallite c axes perpendicular to the substrate surface. Four-probe resistivity measurements indicate the onset of film superconductivity at ∼100 K and zero resistivity achieved at 73 K.
TOTAL KNEE ARTHROPLASTY IN PATIENTS WITH LYMPHOEDEMA: A MATCHED COHORT STUDY (2018)

Introduction In the lower extremity, lymphedema is characterized by fluid buildup and swelling which can lead to fibrosis of the skin and recurring soft-tissue infections. Risk factors include obes...
Supplementary Table 1, Figures 1-4, Methods from Nrdp1-Mediated Regulation of ErbB3 Expression by the Androgen Receptor in Androgen-Dependent but not Castrate-Resistant Prostate Cancer Cells (2023)

Supplementary Table 1, Figures 1-4, Methods from Nrdp1-Mediated Regulation of ErbB3 Expression by the Androgen Receptor in Androgen-Dependent but not Castrate-Resistant Prostate Cancer Cells