gebhart/patrepeval huggingface dataset:
Data from Proteomic Markers of DNA Repair and PI3K Pathway Activation Predict Response to the PARP Inhibitor BMN 673 in Small Cell Lung Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Small cell lung carcinoma (SCLC) is an aggressive malignancy affecting nearly 30,000 people annually in the United States. We have previously identified elevated PARP1 levels in SCLC and demonstrated &lt;i&gt;in vitro&lt;/i&gt; sensitivity to the PARP inhibitors AZD 2281 and AG014699. Here, we evaluate activity of a novel, potent PARP inhibitor, BMN 673, and identify markers of response as a basis for developing predictive markers for clinical application.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Inhibition of SCLC proliferation by BMN 673 was assayed &lt;i&gt;in vitro&lt;/i&gt; and effects on tumor growth were measured in SCLC xenograft models. Protein expression and pathway activation was assessed by reverse phase protein array and western blot analysis. PARP inhibition was confirmed using a PAR ELISA.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We demonstrate striking, single agent activity of BMN 673 in SCLC cell lines and xenografts, with single agent BMN 673 exhibiting &lt;i&gt;in vivo&lt;/i&gt; activity similar to cisplatin. Sensitivity to BMN 673 was associated with elevated baseline expression levels of several DNA repair proteins, whereas greater drug resistance was observed in SCLC models with baseline activation of the PI3K/mTOR pathway. Furthermore, we developed and confirmed these data with a novel “DNA repair score” consisting of a group of 17 DNA repair proteins.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Elevated expression of multiple DNA repair proteins, as well as a corresponding “DNA repair protein score,” predict response to BMN 673 in &lt;i&gt;in vitro&lt;/i&gt; SCLC models. These observations complement recent work in which PI3K inhibition sensitizes breast cancer models to PARP inhibition, suggesting cooperation between DNA repair and PI3K pathways. &lt;i&gt;Clin Cancer Res; 19(22); 6322–8. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
What is Academic Freedom? (2022)

This book explores the history of the debate, from 1915 to the present, about the meaning of academic freedom, particularly as concerns political activism on the college campus. The book introduces readers to the origins of the modern research university in the United States, the professionalization of the role of the university teacher, and the rise of alternative conceptions of academic freedom challenging the professional model and radicalizing the image of the university. Leading thinkers on the subject of academic freedom—Arthur Lovejoy, Angela Davis, Alexander Meiklejohn, Edward W. Said, among others—spring to life. What is the relationship between freedom of speech and academic freedom? Should communists be allowed to teach? What constitutes unacceptable political "indoctrination" in the classroom? What are the implications for academic freedom of creating Black Studies and Women's Studies departments? Do academic boycotts, such as those directed against Israel, violate the spirit of academic freedom? The book provides the context for these debates. Instead of opining as a judge, the author discloses the legal, philosophical, political, and semantic disagreements in each controversy. The book will appeal to readers across the social sciences and humanities with interests in scholarly freedom and academic life. The Open Access version of this book, available at www.taylorfrancis.com, has been made available under a Creative Commons Attribution-Non Commercial-No Derivatives 4.0 license.
Catalytic Enantioselective Conia-Ene Reaction (2005)

An enantioselective intramolecular Conia-ene reaction of beta-dicarbonyl compounds and alkynes to afford methylene cyclopentanes is described. The reaction employs a DTBMSegphos-Pd(II)/Yb(III) dual catalyst system that allows for the asymmetric synthesis of all-carbon quaternary centers and generates a product containing an alkene that can be further manipulated.
Haem d1: stereoselective synthesis of the macrocycle to establish its absolute configuration as 2R,7R 1 (1997)

Although the gross structure of haem d1 1 has been established, the absolute stereochemistry at C-2 and C-7 is unknown. An unambiguous stereoselective synthesis of the ester of the metal-free macrocycle corresponding to haem d1 has been completed which establishes the absolute configuration of the natural cofactor as 2R,7R. Haem d1 is thus shown to match stereochemically other biologically important macrocycles, e.g. those involved in the biosynthesis of vitamin B12, which are related to isobacteriochlorins and also display 2R,7R configurations. The synthetic sequence used is based on a new procedure for assembly of the western and eastern building blocks and it serves as an efficient general route for construction of isobacteriochlorins.
Thermal Atomic Layer Etching of Aluminum Oxide (Al2O3) Using Sequential Exposures of Niobium Pentafluoride (NbF5) and Carbon Tetrachloride (CCl4): A Combined Experimental and Density Functional Theory Study of the Etch Mechanism (2021)

Thermal atomic layer etching (ALEt) of amorphous Al2O3 was performed by alternate exposures of niobium pentafluoride (NbF5) and carbon tetrachloride (CCl4). The ALEt of Al2O3 is observed at temperatures from 380 to 460 degrees C. The etched thickness and the etch rate were determined using spectroscopic ellipsometry and verified by X-ray reflectivity. The maximum etch rate of about 1.4 A/cycle and a linear increase of the removed film thickness with the number of etch cycles were obtained at a temperature of 460 degrees C. With the help of density functional theory calculations, an etch mechanism is proposed where NbF5 converts part of the Al2O3 surface into an AlF3 or aluminum oxyfluoride layer, which upon reacting with CCl4 is converted into volatile halide-containing byproducts, thus etching away the converted portion of the material. Consistent with this, a significant surface fluorine content of about 55 at. % was revealed when the elemental depth profile analysis of a thick NbF5-treated Al2O3 layer was performed by X-ray photoelectron spectroscopy. The surface morphology of the reference, pre-, and postetch Al2O3 surfaces was analyzed using atomic force microscopy and brightfield transmission electron microscopy. Moreover, it is found that this process chemistry is able to etch Al2O3 selectively over silicon dioxide (SiO2) and silicon nitride (Si3N4).
Niobcarbid - Ein vergessener Hartstoff für den Verschleißschutz in offenen und geschlossenen Tribosystemen (2015)

Das tribologische Profil von binderlosem NbC und mit 8% bzw. mit 12% Cobalt oder 12% Fe3Al gebundenem NbC wird unter unidirektionaler Gleitreibung (v= 0,1-10 m/s, T= 22°C und 400°C) und unter oszillierender Gleitreibung vergleichend gegenuber Ingenieurkeramiken und Hartmetallen dargestellt. Zusatzlich werden die 4-Punkt-Biegebruchfestigkeit, elastische Eigenschaften (E,G) bis 1.000�C die lastabhangige Mikroharte sowie die Phasenzusammensetzung und Gefugestrukturen vorgestellt. Die Verschleiskoeffizienten des binderlosen NbC lagen bei T unterhalb von 10-6 mm³/N?m, wahrend diejenigen der cobaltgebundenen NbCs mit ansteigender Gleitgeschwindigkeit von 2-4 10-6 mm³/N?m bei 0,1 m/s auf 5-7 10-7 mm³/N.m bei 10 m/s abnahmen. Die Verschleiskoeffizienten bei 400°C lagen fur die NbCs generell unterhalb von 10-6 mm³/N.m. Das tribologische Lasttragevermogen im Trockenlauf, ausgedruckt als PV-Wert, nimmt mit ansteigender Gleitgeschwindigkeit auf 100 W/mm² zu. Bedingt durch die geringe Loslichkeit von NbC in Legierungen offenbarten erste Zerspanversuche mit verschiedenen Stahlen eine gegenuber WC-basierten Schneidstoffen signifikant angehobene Zerspanungsvolumina. Somit offenbart NbC in offenen und geschlossenen Tribosystemen Anwendungspotentiale.
Metal ions in ribozyme folding and catalysis (2000)

Current research is reshaping basic theories regarding the roles of metal ions in ribozyme function. No longer viewed as strict metalloenzymes, some ribozymes can access alternative catalytic mechanisms depending on the identity and availability of metal ions. Similarly, reaction conditions can allow different folding pathways to predominate, with divalent cations sometimes playing opposing roles.
Numerical Simulation for Quasi-Brittle Interface Fracture in Cementitious Bi-material System (2001)

Peer Reviewed
Patterning and etch challenges for future DRAM and other high aspect ratio memory device fabrication (2013)

Current challenges are outlined for masking materials that enable future high aspect ratio (AR&gt; 25) etch requirements. At such high aspect ratios, and 20nm to 30nm feature sizes, ion energy flux loss due to sidewall collisions, feature gap necking, polymerization, and feature charging in deep via-like structures has driven etch process conditions into very high bias voltage regimes. At these ion energies (keV), lateral removal of mask material due to faceting is the dominating mask erosion mechanisms. Using carbon as our baseline hard mask film, we present here normalized performance comparisons of 13 alternative films. We demonstrate that feature CD changes that correlate to lateral mask loss on the test structure also correlate to lateral mask loss on a real patterned structure and that we can therefore use these test structures as a tool for hard mask film evaluation without having the capability to pattern the hard mask under investigation. We propose that such test structures can be a valuable tool for film development as they relate to hard mask applications in dry etch patterning, and should be used in future development efforts rather than the more classical methods of blanket etch rate analysis. Such test structures can also be used to study film etch properties in general and we show that they are capable of capturing ARDE and sputter redeposition phenomena. Correlations between surface loss/addition as a function of sidewall position are presented and results of in-practice applications are shown. Key issues for future hard mask film implementation are discussed from the perspective of photo patterning, dry etching, wet etching, and integration.
Directional visible light communication signal enhancement using a varifocal micromirror with four degrees of freedom (2016)

We present the use of a micromirror to dynamically improve an optical wireless communications link. The signal-to-noise ratio (SNR) is improved by directing the output of a 675 nm laser diode modulated at 10 MHz toward a receiver and by varying the divergence of the output beam using a varifocal, tip-tilt-piston micromirror. The SNR has a dynamic range of 30 dB for a diffuse source, all by optimizing the overall shape and direction of the mirror.
Anatomically interpretable deep learning of brain age captures domain-specific cognitive impairment (2023)

The gap between chronological age (CA) and biological brain age, as estimated from magnetic resonance images (MRIs), reflects how individual patterns of neuroanatomic aging deviate from their typical trajectories. MRI-derived brain age (BA) estimates are often obtained using deep learning models that may perform relatively poorly on new data or that lack neuroanatomic interpretability. This study introduces a convolutional neural network (CNN) to estimate BA after training on the MRIs of 4,681 cognitively normal (CN) participants and testing on 1,170 CN participants from an independent sample. BA estimation errors are notably lower than those of previous studies. At both individual and cohort levels, the CNN provides detailed anatomic maps of brain aging patterns that reveal sex dimorphisms and neurocognitive trajectories in adults with mild cognitive impairment (MCI, <i>N</i> = 351) and Alzheimer's disease (AD, <i>N</i> = 359). In individuals with MCI (54% of whom were diagnosed with dementia within 10.9 y from MRI acquisition), BA is significantly better than CA in capturing dementia symptom severity, functional disability, and executive function. Profiles of sex dimorphism and lateralization in brain aging also map onto patterns of neuroanatomic change that reflect cognitive decline. Significant associations between BA and neurocognitive measures suggest that the proposed framework can map, systematically, the relationship between aging-related neuroanatomy changes in CN individuals and in participants with MCI or AD. Early identification of such neuroanatomy changes can help to screen individuals according to their AD risk.
A NEW AUTOMOBILE CRASH SENSOR TESTER. FRONTAL CRASH SAFETY TECHNOLOGIES FOR THE 90'S (1991)

This paper examines how crash sensors are tested and describes a new general purpose impact machine which can be used. It describes the pulse shapes in common use (haversine and half sine), pulse accuracy, longitudinal and cross-axis vibrations and pulse durations and how this machine performs these tests. Other tests including pulse angularity, temperature, vibration and other environmental tests. Finally, this paper discusses available sensor test equipment from the standpoint of pulse accuracy, data acquisition accuracy, pulse amplitude and duration capability, coast or dwell capability, the ability to simulate an actual crash pulse, ability to impose cross axis vibrations and the ability to test against a mathematical model.
Cellular Immune Responses to ESAT-6 Discriminate between Patients with Pulmonary Disease Due toMycobacterium aviumComplex and Those with Pulmonary Disease Due toMycobacterium tuberculosis (1999)

ESAT-6 (for 6-kDa early secreted antigenic target) is a secreted antigen found almost exclusively in organisms of the Mycobacterium tuberculosis complex. We compared in vitro gamma interferon (IFN-gamma) responses by peripheral blood mononuclear cells to this antigen in patients with pulmonary disease due to either Mycobacterium avium complex (MAC) or Mycobacterium tuberculosis with those in healthy, skin test-negative, control subjects. Significant IFN-gamma responses to ESAT-6 were detected in 16 (59%) of 27 M. tuberculosis pulmonary disease patients, 0 (0%) of 8 MAC disease patients, and 0 (0%) of 8 controls. Significant IFN-gamma responses to M. tuberculosis purified protein derivative were detected in 23 (85%) of 27 M. tuberculosis disease patients, 2 (25%) of 8 MAC disease patients, and 5 (63%) of 8 healthy controls. M. avium sensitin was recognized in 24 (89%) of 27 M. tuberculosis disease patients, 4 (50%) of 8 MAC disease patients, and 1 (13%) of 8 controls. IFN-gamma responses to ESAT-6 are specific for disease due to M. tuberculosis and are not observed in patients with MAC disease or in healthy controls.
Evaluation of serological lateral flow assays for severe acute respiratory syndrome coronavirus-2 (2021)

We provide a public resource of the accuracy of select lateral flow assays with potential for home testing. The cost-effectiveness, scalable manufacturing process, and suitability for self-testing makes LFAs an attractive option for monitoring disease prevalence and assessing vaccine responsiveness. Our web tool provides an easy-to-use interface to demonstrate the impact of prevalence and test accuracy on the positive predictive values.
Synthesis, Characterization, and Analytical Applications of a New Composite Cation Exchange Material Acetonitrile Stannic(IV) Selenite: Adsorption Behavior of Toxic Metal Ions in Nonionic Surfactant Medium (2011)

Abstract A composite cation exchange material acetonitrile stannic(IV) selenite was prepared under different experimental conditions. The ion exchange capacity of the material was improved from 0.75 to 1.83 meq g−1 in comparison to its inorganic counterpart, stannic selenite. The material was characterized on the basis of X-ray, TGA, FTIR, and SEM studies. Ion-exchange capacity, pH titration, elution behavior, and distribution studies were also carried out to determine the preliminary ion-exchange properties of the material. Furthermore, it was investigated that this ion exchange material has a good reusability after 8 times regeneration. The sorption behavior of metal ions was studied in nonionic surfactants namely triton x-100 and tween. On the basis of distribution coefficient studies, several binary separations of metal ions viz- Pb2+-Th4+, Ni2+-Th4+, Ni2+-Zn2+, Cu2+-Ce4+, Al3+-Bi3+, and Al3+Zn2+ was achieved on the packed column of this ion exchange material. The practical applicability of this cation-exchanger was demonstrated in the separation of Th4+ from a synthetic mixture of Th4+, Ca2+, Sr2+, Ni2+, and Mg2+ as well as Cu2+ and Zn2+ from a brass alloy sample. Thus, all the studies suggest that acetonitrile stannic(IV) selenite has excellent potential for the removal of metal ionic pollutant species from aqueous media effectively. Keywords: acetonitrile stannic(IV) seleniteheavy metalsnonionic surfactantsorganic-inorganic ion exchange materialselective separationsynthesis ACKNOWLEDGEMENTS The authors would like to acknowledge A.M.U., Aligarh, India and the Research Centre, College of Science, King Saud University, Riyadh, Saudi Arabia for their support to carry out this research work. Notes A-10% acetonitrile, Sc-0.1 M stannic chloride, St-0.1 M sodium selenite. *IEC-Ion exchange capacity. a Average of three replicate determinations. a Average of three replicate determinations. a Average of three replicate determinations.
Distribution of corticotropin‐releasing factor (CRF) receptor binding in the mouse brain using a new, high‐affinity radioligand, [125I]‐PD‐Sauvagine (2017)

The corticotropin-releasing factor (CRF) family of peptides includes CRF and three urocortins, which signal through two distinct G-protein coupled receptors, CRF<sub>1</sub> and CRF<sub>2</sub> . Although the cellular distribution of CRF receptor expression has been well characterized at the mRNA level, the localization of receptor protein, and, by inference, of functional receptors, has been limited by a lack of reliable immunohistochemical evidence. Recently, a CRF-related peptide, termed PD-sauvagine, was isolated from the skin of the frog, Pachymedusa dacnicolor, and validated as a high-affinity ligand for CRF receptor studies. A radiolabeled analog, [<sup>125</sup> I]-PD-sauvagine, with high signal-to-noise ratio, was used in autoradiographic studies to map the distribution of CRF receptor binding sites in the mouse brain. Through the use of receptor-deficient mice and subtype-specific antagonists, CRF<sub>1</sub> and CRF<sub>2</sub> binding sites were isolated, and found to be readily reconcilable with regional patterns of mRNA expression. Binding site distributions within a given structure sometimes differed from mRNA patterns, however, particularly in laminated structures of the isocortex, hippocampus, and cerebellum, presumably reflecting the trafficking of receptors to their operational homes on neuronal (mostly dendritic) processes. Binding patterns of [<sup>125</sup> I]-PD-sauvagine provided independent assessments of controversial receptor localizations, failing to provide support for CRF<sub>1</sub> expression in central autonomic components of the limbic forebrain, the locus coeruleus and cerebellar Purkinje cells, or for CRF<sub>2</sub> in any aspect of the cerebellar cortex. Though lacking in ideal resolution, in vitro binding of the PD-sauvagine radioligand currently provides the most sensitive and accurate available tool for localizing CRF receptors in rodent brain.
Low-Noise Avalanche Photodiodes for Midwave Infrared (2 to 5 um) Applications (2005)

Abstract : Report developed under STTR contract for topic AF04-T021. We have developed a mid-wave infrared (MWIR) avalanche photodiode (APD) based on a GaInAs/GaAsSb superlattice absorption region that is compatible with InP substrates. This superlattice structure exhibits a photodetection cutoff wavelength of approximately 2.5 microns when lattice-matched to InP, and our calculations show the introduction of compensated strain can provide cutoff wavelengths as long as -5 microns. Using the lattice-matched superlattice in a p-i-n structure, we have demonstrated 43% quantum efficiency at 2.23 microns, a low dark current density of 1E-5 A/sq cm, and a peak detectivity of 7E10 cm (Hz/W)(exp 1/2), all at a temperature of 200 K, accessible using thermoelectric coolers. By incorporating this superlattice into an APD structure with an InP multiplication region, we have fabricated 160 micron diameter MWIR APDs exhibiting a gain of 50 and an operating dark current of less than 100 nA at 240 K. Smaller 36 micron diameter devices of the same structure exhibit sub-nanoampere dark currents below approximately 225 K.
117. Trends in Four-class HIV Drug Resistance in Treatment-experienced Patients in the United States (2021)

Abstract Background Despite the availability of potent antiretroviral therapy, only 56% of people living with HIV in the US were virally suppressed in 2018. Drug resistance can hinder suppression, especially among treatment-experienced patients, in whom the prevalence of 4-class drug resistance (4CR) is unknown. Methods Genotypic results of PhenoSense GT® Plus Integrase (Monogram Biosciences, South San Francisco, CA) obtained from Apr 2014 to Dec 2020 were used to assign susceptibility to nucleos(t)ide reverse transcriptase, non-nucleoside reverse transcriptase, integrase, and protease inhibitors (NRTIs, NNRTI, INIs, and PIs). Data were analyzed using summary statistics, 2 proportion Z test, one-way ANOVA and Tukey-Kramer; p &amp;lt; 0.05 was significant. Results Among 13,651 patients with 15,372 tests, median age was 43 years; most had HIV-1 subtype B infection (95.09%), followed by AG (1.32%). Among 12,303 patients with only one test, 4CR prevalence was 1.55%. Among 1,348 patients with more than one test, 4CR was seen in 3.64% of patients, and in 4.60% if cumulative resistance reports were assembled for each patient. Patients with 4CR were significantly older than those with less resistance. The incidence of 4CR fluctuated, with a decline from 2.61% of patients tested in 2014 to 1.38% in 2017, an increase to 2.36% in 2018, and a decline to 1.56% in 2020. Among patients with more than one test, 21.01% gained resistance to a drug in a new class over an average of 19.5 months. Most new resistance each year was to NNRTIs, followed by NRTIs, INIs, and PIs. The incidence of PI resistance declined for PIs from 13.34% of patients tested in 2014 to 11.82% in 2020, but increased for INIs from 14.56% in 2014 to 16.49% in 2020. The regimen expected to be suppressive in the greatest proportion of patients was dolutegravir + darunavir/cobicistat (94.51%). Conclusion The prevalence of 4CR has declined over time, but remains clinically relevant, particularly in older patients who may struggle with adherence due to complex regimens, comorbidities and polypharmacy. New drug classes may benefit this group. The concurrent increase in INI and decline in PI resistance may reflect changes in prescribing practices. Drug resistance may be underestimated unless cumulative resistance is determined. Disclosures Dusica Curanovic, PhD, Monogram Biosciences (Employee) Johnny Lai, BS, Monogram Biosciences (Employee, Shareholder) Christos J. Petropoulos, PhD, Monogram Biosciences (Employee, Shareholder) Charles M. Walworth, MD, Monogram Biosciences (Employee, Shareholder)