gebhart/patrepeval huggingface dataset:
Efficacy Analysis of In Situ Synthesis of Nanogold via Copper/Iodonium/Amine/Gold System Under a Visible Light (2021)

. This article presents, for the first time, the kinetics and the general features of a photopolymerization system (under visible light) G1/ Iodonium/ TEA/gold chloride (or A/B/N/G), having initial concentrations of A0, B0, N0 and G0, based on the proposed mechanism of Tar et al. Analytic formulas are developed to explore the new features including: (i) both FRP efficacy and the production of nanogold (NG) are proportional to the relative concentration ratios of (A0+B0+N0)/G0, which may be optimized for maximum efficacy; (ii) the two competing procedure of NG production and efficacy of free radical photopolymerization (FRP) can be tailored for optimal system with nanogold in the polymer matrix;(ii) the FRP efficacy is contributed by 3 components: the coupling of the excited state of copper complex (T) with the radicals (R and S) produced by the iodonium and the amine; (iii) the production of NG is contributed by 2 components: the coupling of T and radical (S) with gold ion; (iv) NG production has a transient state value which is an increasing function of light intensity and the combined concentration ratio [(A0/G0)+(N0/(K'M0). whereas it has a steady-state independent to the light intensity.
Leg Pain May Reveal Vertebral Osteoporosis: Figure 1. (2009)

We report a case of neurological complication related to an osteoporotic vertebral fracture. A 79-year-old woman presented with a 2-month history of worsening radicular pain in her left lower limb. She had no history of trauma, and the pain was most severe in her left buttock, extending along the left posterior thigh and anterior leg. She experienced permanent radicular pain and dysethesia (pins and needles) in the L5 dermatome of the left leg in the standing position, but almost no pain while supine. Her radicular pain had been recently aggravated over a 10-day period before she presented at hospital. When she stood up or walked, the radicular pain became severe, making it impossible to walk continuously for more than 10 to 15 minutes. Questioned on past events that might be related to the compression vertebral fracture, she remembered having experienced one single episode of acute and intense low back pain during a coughing spell related to a viral bronchitis. This episode had occurred 2 weeks preceding the onset of the radicular pain. Neurologic examination revealed moderate hypoesthesia in the L5 dermatome. Deep tendon reflexes were normal. Examination also revealed mild bilateral low back pain. Her height was 160 cm and weight 57 kg; she took no regular medications and was otherwise fit and well. An osteoporotic compression fracture of the L5 vertebral body was visible … Address correspondence to Dr. Sailhan; E-mail: fred.sailhan{at}wanadoo.fr
Preventing Sybil Attacks by Privilege Attenuation: A Design Principle for Social Network Systems (2011)

In Face book-style Social Network Systems (FSNSs), which are a generalization of the access control model of Face book, an access control policy specifies a graph-theoretic relationship between the resource owner and resource access or that must hold in the social graph in order for access to be granted. Pseudonymous identities may collude to alter the topology of the social graph and gain access that would otherwise be forbidden. We formalize Denning's Principle of Privilege Attenuation (POPA) as a run-time property, and demonstrate that it is a necessary and sufficient condition for preventing the above form of Sybil attacks. A static policy analysis is then devised for verifying that an FSNS is POPA compliant (and thus Sybil free). The static analysis is proven to be both sound and complete. We also extend our analysis to cover a peculiar feature of FSNS, namely, what Fong et al. dubbed as Stage-I Authorization. We discuss the anomalies resulted from this extension, and point out the need to redesign Stage-I Authorization to support a rational POPA-compliance analysis.
Non-Peptide Angiotensin II Receptor Antagonists:  Chemical Feature Based Pharmacophore Identification (2003)

Chemical feature based pharmacophore models were elaborated for angiotensin II receptor subtype 1 (AT(1)) antagonists using both a quantitative and a qualitative approach (Catalyst HypoGen and HipHop algorithms, respectively). The training sets for quantitative model generation consisted of 25 selective AT(1) antagonists exhibiting IC(50) values ranging from 1.3 nM to 150 microM. Additionally, a qualitative pharmacophore hypothesis was derived from multiconformational structure models of the two highly active AT(1) antagonists 4u (IC(50) = 0.2 nM) and 3k (IC(50) = 0.7 nM). In the case of the quantitative model, the best pharmacophore hypothesis consisted of a five-features model (Hypo1: seven points, one hydrophobic aromatic, one hydrophobic aliphatic, a hydrogen bond acceptor, a negative ionizable function, and an aromatic plane function). The best qualitative model consisted of seven features (Hypo2: 11 points, two aromatic rings, two hydrogen bond acceptors, a negative ionizable function, and two hydrophobic functions). The obtained pharmacophore models were validated on a wide set of test molecules. They were shown to be able to identify a range of highly potent AT(1) antagonists, among those a number of recently launched drugs and some candidates presently undergoing clinical tests and/or development phases. The results of our study provide confidence for the utility of the selected chemical feature based pharmacophore models to retrieve structurally diverse compounds with desired biological activity by virtual screening.
High‐Temperature Morphological Evolution of Lithographically Introduced Cavities in Silicon Carbide (2001)

Internal cavities of controlled geometry and crystallography were introduced in 6 H silicon carbide single crystals by combining lithographic methods, ion‐beam etching, and solid‐state diffusion bonding. The morphologic evolution of these internal cavities (negative crystals) in response to anneals of up to 128 h duration at 1900°C was examined using optical microscopy. Surface energy anisotropy and faceting had a strong influence on the geometric and kinetic characteristics of evolution. Decomposition of {1210} cavity edges into {101 x } facets was observed after 16 h anneals, indicating that {1210} faces are not components of the Wulff shape. The shape evolution kinetics of penny‐shaped cavities were also investigated. Experimentally observed evolution rates decreased much more rapidly with those predicted by a model in which surface diffusion was assumed to be rate limiting. This suggested that the development of facets and the associated loss of ledges and terraces during the initial stages of evolution resulted in an evolution process limited by the nucleation rate of attachment/detachment sites (ledges) on the facets.
Physiological changes induced by the quaternary ammonium compound benzyldimethyldodecylammonium chloride on Pseudomonas fluorescens (2011)

BDMDAC is an effective biocide against P. fluorescens. It binds by ionic and hydrophobic interactions to the cell membrane, causing changes in membrane properties and function, as manifested by phenomena such as cellular disruption and loss of membrane integrity with consequent leakage of essential intracellular constituents.
Abstract 5425: Quantitative determination of fibroblast growth factor receptor inhibitor-AZD4547 using HPLC analysis in a mouse model of ultraviolet B (UVB)-induced skin carcinogenesis (2022)

Abstract Cutaneous squamous cell carcinoma (cSCC) is the second most common form of skin cancer affecting more than two million Americans annually. Cumulative sun exposure plays a leading role in the pathogenesis of cSCC. In our previous studies, topical application of Fibroblast growth factor receptor (FGFR) inhibitor AZD4547 was associated with a significant reduction in Ultraviolet B-induced (UVB)-induced acute skin changes such as epidermal hyperplasia and hyperproliferation. Further, chronic, topical application of AZD4547 was associated with significant inhibition in UVB-induced tumor incidence and multiplicity. Unfortunately, oral administration of FGFR inhibitors in clinical trials for solid tumors is associated with notable side effects such as hyperphosphatemia, diarrhea, decreased appetite, fatigue, and liver dysfunction. Therefore, our objective was to investigate whether topical administration of AZD4547 could potentially circumvent systemic absorption, leading to a low toxicity profile. Accordingly, mice were topically administered AZD4547 (400ug/200ul acetone) followed by exposure to UVB three times a week for two weeks. Blood was collected at the end of the study. AZD4547 was extracted using methanol extraction and concentrated using a Savant SpeedVac system. Samples were reconstituted in 25% acetone/75% water solution and analyzed using Reverse-phase HPLC (Shimadzu) with a Zorbax Eclipse C18 3.5-µm 4.6x100mm analytical column operated at ambient temperature and gradient elution using trifluoroacetic acid (TFA) (Mobile A) and 0.1% TFA in Acetonitrile. Data from HPLC analysis demonstrated non-appreciable absorption of AZD4547 (blood levels only from 108-358nM) suggesting that the topical application of AZD4547 was not systemically absorbed and the effect of treatment was restricted to the local skin tissue. Based on the efficacy and low systemic absorption profile, AZD4547 could potentially be utilized as a topical agent to both prevent and treat UVB-induced cSCC. Citation Format: Rema Anisha Kandula, Katherine Claire Babin, Brian Latimer, Kenneth Mc Martin, Lauren Linquest, Tara Moore-Medlin, Megha A. Thakur, Alok R. Khandelwal, John DiGiovanni, Cherie-Ann O. Nathan. Quantitative determination of fibroblast growth factor receptor inhibitor-AZD4547 using HPLC analysis in a mouse model of ultraviolet B (UVB)-induced skin carcinogenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5425.
Basic Study on Anti-bacterial Urethral Catheter (2000)

In order to develop a new anti-bacterial urethral catheter, we studied anti-bacterial and antiadherent coating material suitable for silicon catheters. Several aspects of various silver compounds were examined, including anti-bacterial activity, chemical property and toxicity. Among silver citrate, silver phosphate and silver oxide, which were found to have excellent anti-bacterial activities, silver citrate was regarded as the material of choice for anti-bacterial coating in terms of durable activity and biological safety. It was also found that several surfactants inhibited bacterial adherence to the surface of silicon catheters. Among them soybean lecithin exhibited excellent anti-adherent activity in a dose dependent manner. Finally, a mixture of silver citrate, soybean lecithin and liquid silicon at the ratio of 2: 2: 8 was regarded as an ideal anti-bacterial coating materialfor silicon catheters.
Evaluation of ER/PR and HER2 status by RNA sequencing in tissue core biopsies from preoperative clinical trial specimens. (2011)

46 Background: Next-generation sequencing for measuring RNA (RNASeq) offer increased sensitivity, dynamic range and provide unbiased detection of all transcripts. To evaluate the clinical utility of such methods, we sequenced entire transcriptomes from fresh-frozen biopsies in a cohort of 120 patients enrolled on a preoperative therapy trial receiving carboplatin, nab paclitaxel and either bevacizumab (HER2-) or trastuzumab (HER2+). Methods: Total RNA was extracted and amplified from frozen breast core biopsies and libraries constructed using TruSeq (Illumina). Sequencing was performed on the Illumina GAII platform. 75bp reads were mapped using Tophat and transcript abundance in FPKM units (Fragments per kilo-base of mRNA per million reads) calculated using Cufflinks. CLIA approved assays were performed for ER, PR, HER2 (IHC+/- FISH) on patient tumors. Four tumors from each subtype (ER +ve/HER2 -ve; HER2 +ve; ER/HER2 -ve) were analyzed for correlation with clinical status. PAM50 classification will be provided for verification of molecular subtypes. Results: RNA-Seq library construction/sequencing were successful in 12/12 samples with 50-90% reads mapped. ER +ve tumors ranged in FPKM values from 1.76-22.67 and ER -ve tumors ranged from 0.00-0.79. i.e. ER RNASeq measurements can separate clinical ER status. HER2 +ve tumors ranged in FPKM values from 2.62-21.71 and HER2 -ve tumors from 0.21-1.79. Of note, 7/8 HER2 -ve tumors ranged from 0.21-0.87 with one ‘outlier’ at 1.79±0.3. This outlier was HER2 IHC 2+, FISH ratio 1.1 with 45% of tumor cells with polysomy chromosome 17. Correspondence of ER/PR and HER2 status with molecular subtyping by PAM50 analysis will be presented. Conclusions: RNASeq has potential to provide in depth analysis of the breast cancer transcriptome and a single analysis test for standard markers. In addition, RNASeq may uncover unexpected expression patterns in conventionally-defined HER2 -ve tumors. If reproducible in larger datasets, this technology may provide both standard and novel information previously unavailable to oncologists and their patients.
Sex pheromone of the tsetse species, Glossina austeni : isolation and identification of natural hydrocarbons, and bioassay of synthesized compounds (2005)

Copulatory responses of male Glossina austeni (Newstead) (Diptera: Glossinidae), that were elicited after contact with frozen female tsetse, were not observed after solvent washing of cuticular lipids. Chromatographic analysis of extracts from laboratory-reared and field-collected G. austeni females yielded natural hydrocarbons that were highly stimulatory to males. Most of this activity was produced by compounds in the alkene fraction. Gas chromatograms (GC) contained five natural alkenes; these were separated by preparative GC for bioassays conducted in Tanzania. The two major alkenes were identified using gas chromatography-mass spectrometry (GC-MS) to be 13,17-dimethyltritriacont-1-ene and 13,17-dimethylpentatriacont-1-ene, after the samples had undergone derivatization using dimethyl disulphide and saturation with deuterium. These alkenes and natural alkanes were quantified from G. austeni of both sexes from laboratory and field samples to confirm that their presence was consistent in this species. Trials of synthetic samples resulted in the order of biological activity for the stereoisomers of 13,17-dimethyltritriacont-1-ene as follows: S,R-33:1 > R,S- 33:1 > S,S-33:1 > R,R-33:1. Dose-response data showed an ED(50) at 5 microg per treated, solvent-washed male decoy. Of the four stereoisomers of 13,17-dimethylpentatriacont-1-ene, R,R-35:1 showed the most activity. This is the first report of alkene-induced sexual activity in males of the genus Glossina.
Fabrication of Metallized Nanopores in Silicon Nitride Membranes for Single‐Molecule Sensing (2010)

The fabrication and characterization of a metallized nanopore structure for the sensing of single molecules is described. Pores of varying diameters (>10 nm) are patterned into free-standing silicon nitride membranes by electron-beam lithography and reactive ion etching. Structural characterization by transmission electron microscopy (TEM) and tomography reveals a conical pore shape with a 40 degrees aperture. Metal films of Ti/Au are vapor deposited and the pore shape and shrinking are studied as a function of evaporated film thickness. TEM tomography analysis confirms metalization of the inner pore walls as well as conservation of the conical pore shape. In electrical measurements of the transpore current in aqueous electrolyte solution, the pores feature very low noise. The applicability of the metallized pores for stochastic sensing is demonstrated in real-time translocation experiments of single lambda-DNA molecules. We observe exceptionally long-lasting current blockades with a fine structure of distinct current levels, suggesting an attractive interaction between the DNA and the PEGylated metallic pore walls.
Physiology of Left Ventricular Septal Pacing and Left Bundle Branch Pacing (2022)

Following the recognition of the adverse effects of right ventricular pacing, alternative permanent pacing strategies aiming to maintain a synchronous ventricular contraction have been sought. The quest for the optimal pacing site has recently led to several promising and rapidly emerging new pacing strategies, such as left ventricular septal pacing and left bundle branch pacing. In both animal and human studies, these pacing strategies seem to maintain electrical and mechanical activation of the left ventricle to a (near)physiologic level. However, more studies on the long-term effects of both strategies are needed.
Study of Wake-Blade Interactions in a Transonic Compressor Using Flow Visualization and DPIV (2001)

Flow-field interactions are studied in a high-through-flow, axial-flow transonic compressor using Digital Particle Image Velocimetry (DPIV). Measurement of instantaneous velocities in two-dimensional (2D) planes in the main flow direction allows characterization of the unsteadiness of spatial structures from an upstream blade row and their interaction with the downstream rotor. The measurement system is specially designed for a large transonic environment, which introduces conditions that differ from those generally encountered by traditional DPIV systems. Viewing windows on the compressor housing are used to allow optical access, and the design of a special optical probe permits laser-sheet delivery through one of the wake generators (WG). The system is synchronized with the blade passage and is remotely monitored and controlled. Through flow visualization and instantaneous and ensemble-averaged quantities, it clearly captures the interactions of the wake with the potential field of the rotor leading edge (LE) and its bow shock, vortex shedding, vortex-blade synchronization, wake chopping, and boundary-layer flow at the housing for several configurations.
Cytoskeleton-dependent Membrane Domain Segregation during Neutrophil Polarization (2001)

On treatment with chemoattractant, the neutrophil plasma membrane becomes organized into detergent-resistant membrane domains (DRMs), the distribution of which is intimately correlated with cell polarization. Plasma membrane at the front of polarized cells is susceptible to extraction by cold Triton X-100, whereas membrane at the rear is resistant to extraction. After cold Triton X-100 extraction, DRM components, including the transmembrane proteins CD44 and CD43, the GPI-linked CD16, and the lipid analog, DiIC(16), are retained within uropods and cell bodies. Furthermore, CD44 and CD43 interact concomitantly with DRMs and with the F-actin cytoskeleton, suggesting a mechanism for the formation and stabilization of DRMs. By tracking the distribution of DRMs during polarization, we demonstrate that DRMs progress from a uniform distribution in unstimulated cells to small, discrete patches immediately after activation. Within 1 min, DRMs form a large cap comprising the cell body and uropod. This process is dependent on myosin in that an inhibitor of myosin light chain kinase can arrest DRM reorganization and cell polarization. Colabeling DRMs and F-actin revealed a correlation between DRM distribution and F-actin remodeling, suggesting that plasma membrane organization may orient signaling events that control cytoskeletal rearrangements and, consequently, cell polarity.
Application of Two Methods to Determine Killing ofStreptococcus pneumoniaeby Various Fluoroquinolones (2006)

Minimum inhibitory concentration (MIC) testing measures the lowest drug concentration that prevents microbial growth using an inoculum of 10(5) colony forming units/ml (cfu/ml) whereas the mutant prevention concentration (MPC) (inoculum approximately 10(10) cells) defines the antimicrobial drug concentration threshold that would require an organism to possess two simultaneous mutations for continued growth in the presence of the drug. The rates at which multidrug-resistant Streptococcus pneumoniae [MDRSP] were killed by the respiratory fluoroquinolones, gatifloxacin, gemfloxacin, levofloxacin and moxifloxacin, were compared based on the MIC and MPC drug concentrations and at inocula ranging from 10(6)-10(9) cfu/ml. The MIC drug concentration failed to eradicate all viable cells whereas the MPC drug concentration resulted in 99.9% to 100% cellular reduction following 12-24 hours of drug exposure. MPC values against S. pneumoniae were different for each fluoroquinolone. The MPC drug concentration prevents the selection of multidrug-resistant or fluoroquinolone-resistant S. pneumoniae. The value of dosing of antimicrobial agents based on MPC thresholds results in a rapid reduction in viable cells--even at higher inocula which are more reflective of organism burden in pneumonia. The rapid reduction in viable cells observed at MPC drug concentrations may not only have an impact on preventing the selection of resistant mutants but may also help explain the rapid symptom resolution seen with new fluoroquinolones since these agents lead to little or low release of cell contents which are known to drive the inflammatory response.
Cascade of Two $W$ -Band Helical-Waveguide Gyro-TWTs With High Gain and Output Power: Concept and Modeling (2017)

In order to realize a high-power (100 s of kilowatts at the W-band) wideband microwave amplifier, we suggest to use a cascade of two gyrotron traveling-wave tubes (gyro-TWTs), one of which possesses a relatively high gain (40-50 dB) while the other provides a high output power at a moderate (15-20 dB) gain. Both gyro-TWTs are assumed to use helically corrugated waveguides and operate at the second cyclotron harmonic. A principal scheme of such an amplifier chain is discussed, including issues on the microwave input, output, and transmission between the tubes. Computer modeling of the beam-wave interaction using CST Particle Studio PIC Solver shows the possibility of achieving of 200-370-kW output power with 8-10-GHz bandwidth when driving by a 50-mW input source at the W-band.
Increased ID2 Levels in Adult Precursor B Cells as Compared with Children Is Associated with Impaired Ig Locus Contraction and Decreased Bone Marrow Output (2013)

Precursor B cell production from bone marrow in mice and humans declines with age. Because the mechanisms behind are still unknown, we studied five precursor B cell subsets (ProB, PreBI, PreBII large, PreBII small, immature B) and their differentiation-stage characteristic gene expression profiles in healthy individual toddlers and middle-aged adults. Notably, the composition of the precursor B cell compartment did not change with age. The expression levels of several transcripts encoding V(D)J recombination factors were decreased in adults as compared with children: RAG1 expression was significantly reduced in ProB cells, and DNA-PKcs, Ku80, and XRCC4 were decreased in PreBI cells. In contrast, TdT was 3-fold upregulated in immature B cells of adults. Still, N-nucleotides, P-nucleotides, and deletions were similar for IGH and IGK junctions between children and adults. PreBII large cells in adults, but not in children, showed highly upregulated expression of the differentiation inhibitor, inhibitor of DNA binding 2 (ID2), in absence of changes in expression of the ID2-binding partner E2A. Further, we identified impaired Ig locus contraction in adult precursor B cells as a likely mechanism by which ID2-mediated blocking of E2A function results in reduced bone marrow B cell output in adults. The reduced B cell production was not compensated by increased proliferation in adult immature B cells, despite increased Ki67 expression. These findings demonstrate distinct regulatory mechanisms in B cell differentiation between adults and children with a central role for transcriptional regulation of ID2.