gebhart/patrepeval huggingface dataset:
Supplementary material and methods re-revised from <i>WRN</i> Promoter CpG Island Hypermethylation Does Not Predict More Favorable Outcomes for Patients with Metastatic Colorectal Cancer Treated with Irinotecan-Based Therapy (2023)

&lt;p&gt;Detailed description of material and methods used&lt;/p&gt;
Emerging business models in frontier contexts (2017)

Two in-depth case studies of new business models at the frontiers of innovation are presented. The first case study examines the move to make the vast stores of, often publically held, data available to firms and others in order to provide a basis for new forms of value creation and, potentially, new types of business model. The second case is a detailed case study of an organisation that emerged specifically to create and supply a new class of product – a user-developed version of the Android smartphone operating system. The case explores the foundation and development of the CyanogenMod project, and how the collective development of its products, takes place in concert with its large and active user base. Unlike many more traditional firms CyanogenMod represents a new organisational form – the User Organisation – in which extensive volunteer labour has been drawn into the core of its operations.
Figure S1 from Arginine Depletion Therapy with ADI-PEG20 Limits Tumor Growth in Argininosuccinate Synthase–Deficient Ovarian Cancer, Including Small-Cell Carcinoma of the Ovary, Hypercalcemic Type (2023)

&lt;p&gt;ASS1 immunohistochemistry in 15 cases of SCCOHT. Different areas (small cell, large cell, rhabdoid) are represented for some cases. Representative cores for each area for each case are shown. Final histoscore for each case is the highest score among all areas.&lt;/p&gt;
Single-mode/multimode waveguide electro-optic grating coupler modulator (1995)

A waveguide electro-optic grating coupler modulator based on a single straight channel waveguide and an interdigital modulation electrode structure on an electro-optic substrate, has been reported. Both single-mode and multimode operations are possible. Preliminary experiments have demonstrated the modulation on a proton exchanged LiNbO3 waveguide device. Modulation performed on other electro-optic waveguides, such as GaAs, LiTaO3, and EO polymers, are also possible.
Pourquoi consacrer une séance thématique au concept «une seule santé» ? (2015)

Jestin André, Davoust Bernard. Pourquoi consacrer une séance thématique au concept «une seule santé» ?. In: Bulletin de l'Académie Vétérinaire de France tome 168 n°3, 2015. p. 223.
Enantioselective Organocatalytic Reduction of β‐Trifluoromethyl Nitroalkenes: An Efficient Strategy for the Synthesis of Chiral β‐Trifluoromethyl Amines (2015)

An efficient organocatalytic stereoselective reduction of β-trifluoromethyl-substituted nitroalkenes, mediated by 3,5-dicarboxylic ester-dihydropyridines (Hantzsch ester type), has been successfully developed. A multifunctional thiourea-based (S)-valine derivative was found to be the catalyst of choice, promoting the reaction in up to 97% ee. The methodology has been applied to a wide variety of substrates, leading to the formation of differently substituted precursors of enantiomerically enriched β-trifluoromethyl amines. The mechanism of the reaction and the mode of action of the metal-free catalytic species were computationally investigated; on the basis of DFT transition-state (TS) analysis, a model of stereoselection was also proposed.
Preclinical in vitro and in vivo pharmacokinetic properties of danicamtiv, a new targeted myosin activator for the treatment of dilated cardiomyopathy (2020)

Dilated cardiomyopathy (DCM) is a disease of the myocardium defined by left ventricular enlargement and systolic dysfunction leading to heart failure.Danicamtiv, a new targeted myosin activator designed for the treatment of DCM, was characterised in in vitro and in vivo preclinical studies.Danicamtiv human hepatic clearance was predicted to be 0.5 mL/min/kg from in vitro metabolic stability studies in human hepatocytes. For human, plasma protein binding was moderate with a fraction unbound of 0.16, whole blood-to-plasma partitioning ratio was 0.8, and danicamtiv showed high permeability and no efflux in a Caco-2 cell line.Danicamtiv metabolism pathways in vitro included CYP-mediated amide-cleavage, N-demethylation, as well as isoxazole- and piperidine-ring-opening.Danicamtiv clearance in vivo was low across species with 15.5, 15.3, 1.6, and 5.7 mL/min/kg in mouse, rat, dog, and monkey, respectively. Volume of distribution ranged from 0.24 L/kg in mouse to 1.7 L/kg in rat. Oral bioavailability ranged from 26% in mouse to 108% in dog.Simple allometric scaling prediction of human plasma clearance, volume of distribution, and half-life was 0.64 mL/min/kg, 0.98 L/kg, and 17.7 h, respectively.Danicamtiv preclinical attributes and predicted human pharmacokinetics supported advancement toward clinical development.
RETRACTED: Identification of metabolites of brexpiprazole in human urine for use in monitoring patient compliance (2017)

Brexpiprazole (Rexulti®) is an atypical antipsychotic prescribed for the treatment of schizophrenia. While therapeutic drug monitoring (e.g., blood testing) for adherence to prescription paradigms has been the norm, urine drug testing is increasing in popularity. Here, we identify major metabolites of brexpiprazole in urine that could be used in monitoring patient compliance. Urine samples from patients prescribed brexpiprazole were collected and analyzed using liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOF) to identify brexpiprazole metabolites present in urine. The carboxylic acid metabolite, OPC-3952, was found to be the most abundant metabolite of brexpiprazole present in urine. While this result is consistent with qualitative results determined in plasma, the quantitative results observed in urine are different from these earlier reports. The use of OPC-3952 in urine, as an indicator of compliance, provides a potential avenue for improved monitoring of patients who have been prescribed brexpiprazole.
Integrative study of pandemic A/H1N1 influenza infections: design and methods of the CoPanFlu-France cohort (2012)

The large amount of data collected throughout the follow-up will permit a multidisciplinary study of influenza infections. Additional data is being collected and analyzed in this ongoing cohort. The longitudinal analysis of these households will permit integrative analyses of complex phenomena such as individual, collective and environmental risk factors of infection, routes of transmission, or determinants of the immune response to infection or vaccination.
Long-term Follow-Up of Patients with Heart Failure and Reduced Ejection Fraction Receiving Autonomic Regulation Therapy in the ANTHEM-HF Pilot Study (2020)

In a 42-month follow-up, ART was durable, safe, and was associated with beneficial effects on LVEF and 6-min walk distance. Long term, chronic, open-loop ART continued to be well-tolerated in patients with HFrEF. The open label, randomized, controlled, ANTHEM-HFrEF Pivotal Study is currently underway to further evaluate ART in patients with advanced HF.
Effects of deprotonation efficiency of protected units on line edge roughness and stochastic defect generation in chemically amplified resist processes for 11 nm node of extreme ultraviolet lithography (2014)

The deprotonation of polymer radical cations plays an important role in the acid generation in chemically amplified resists upon exposure to ionizing radiation. In this study, the effects of the deprotonation efficiency of protected units of a resist polymer on line edge roughness (LER) and stochastic defect generation were investigated. The suppression of stochastic effects is essential for the realization of high-volume production of semiconductor devices with an 11 nm critical dimension using extreme ultraviolet (EUV) lithography. By increasing the deprotonation efficiency, the chemical contrast (latent image quality) was improved; however, the protected unit number fluctuation did not significantly change. Consequently, LER and the probability of stochastic defect generation were reduced. This effect was prominent when the protection ratio was close to 100%.
1108. High Rate of Anti-Tumor Immune Responses in a Phase 1 Clinical Trial of Adenoviral-Interferon-Beta Gene Transfer for Malignant Mesothelioma (MM) and Malignant Pleural Effusions (MPE) (2006)

Our group recently completed a Phase 1 trial of intrapleural interferon-beta gene transfer of Ad.huIFNbeta (Biogen-IDEC) in 10 patients with MM and MPE. Vector doses of 9x1011 and 3x1012 viral particles were used. Here, we report the anti-tumor immunologic responses observed. The presence of a catheter within the pleural space allowed us to monitor the response to Ad gene transfer in 7 patients who had pleural effusions. Interestingly, the presence of the vector did not elicit a marked cellular infiltrate in the pleural space. The average fold-increase in total leukocytes (comparing pre-instillation to the peak count in the next four days) was 3.3 fold. Detectable levels of INFbeta (from 200 pg/ml to 160 ng/ml) were found in all but two patients. Intrapleural levels of cytokines (IL-6, IL-1, IL-10, VEGF, MCP-1, IL-8, RANTES, and IFNgamma) were highly variable at baseline and after response to gene transfer. Some patients had dramatic increases in IL-6 levels after gene transfer, while others did not. The only other cytokine to show an increase in multiple patients was the chemokine RANTES. Levels of serum cytokines were also monitored. Only 4 patients showed low levels of serum levels of IL-6. Low levels of IL-8 and MCP-1 were also detected in serum after gene transfer. Humoral responses to the mesothelioma tumor antigens SV40 Virus Large T-antigen (SV40-Tag) and mesothelin were evaluated by using sera from before and after gene transfer to immunoblot purified proteins. One patient had a strong increase in antibody response to SV40-Tag after gene transfer. We also evaluated anti-mesothelin antibody reactivity using an ELISA assay. Four patients had significant baseline levels of anti-mesothelin antibodies. Two patients had a marked increase in levels after therapy. Additionally, we analyzed serum to identify new or increased intensity bands on extracts of mesothelioma, lung cancer, or ovarian cancer cell lines. The sera from six of eight patients examined recognized new antigens in the post-treatment samples. Utilizing stimulated PBMCs from the patient as effectors, chromium release assays showed cytotoxic effects against an HLA- matched in vitro tumor cell line in one patient of six tested. Tetramer analysis was performed in the two HLA-A2+ patients, with one showing staining with survivin and SV40-Tag tetramers. In summary, injection of one intrapleural dose of Ad.IFNbeta induced clear evidence of humoral and/or cellular anti-tumor immune responses in 8 of the 10 patients studied. Of particular interest were antibody responses against SV40-Tag and mesothelin. Future studies will determine if these anti-tumor immune reactions correlate to clinical responses.
Investigation and Mitigation of Shunts for Higher Efficiency Epitaxial GaSb/GaSb and GaSb/GaAs Solar Cells (2017)

Multi-junction cells using GaAs/GaSb interface misfit arrays for metamorphic growth can achieve comparable efficiency to conventional inverted metamorphic multijunction cells without the need for costly graded buffer layers. In this work, GaSb single junction cells were grown via molecular beam epitaxy on both GaSb and GaAs substrates to compare homoepitaxial and heteroepitaxial GaSb material quality. The homoepitaxial cell achieved 4.1% efficiency under 1 sun AM1.5g while the IMF cell achieved 0.70%. The IMF cell had higher non-radiative dark current likely caused by defects related to the mismatched growth. Lock-in thermography was used to explore shunt causing defects and sidewall shunting was passivated by dielectric deposition on device sidewalls. Homoepitaxial cells with sidewalls passivated by Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> had ~5× higher average shunt resistance compared to unpassivated devices. Reverse bias thermograms indicated that MBE-related defects filled with front grid metal were the cause of device-crippling shunts which lowered device yield and limited growth of large-area devices.
JoinABLe: Learning Bottom-up Assembly of Parametric CAD Joints (2022)

Physical products are often complex assemblies combining a multitude of 3D parts modeled in computer-aided design (CAD) software. CAD designers build up these assemblies by aligning individual parts to one another using constraints called joints. In this paper we introduce JoinABLe, a learning-based method that assembles parts together to form joints. JoinABLe uses the weak supervision available in standard parametric CAD files without the help of object class labels or human guidance. Our results show that by making network predictions over a graph representation of solid models we can outperform multiple baseline methods with an accuracy (79.53%) that approaches human performance (80%). Finally, to support future research we release the Fusion 360 Gallery assembly dataset, containing assemblies with rich information on joints, contact surfaces, holes, and the underlying assembly graph structure.
Microemulsion mediated synthesis of nanocrystalline BaTiO3: possibilities, potential and perspectives (2006)

Abstract The present study gives an overview on the potential, possibilities and perspectives that the synthesis of functional materials, such as BaTiO 3 , with microemulsions as the reaction medium offers. Well defined nanocrystalline particles in the form of powders for further ceramic processing, as well as stable colloidal dispersions for the preparation of coatings may be obtained. The paper describes the formation, phase behaviour and stabilization of microemulsions and related water/oil/surfactant systems that may be used as a nanoreactor during particle formation. The reaction principles of microemulsion mediated synthesis are outlined and some examples of structural aspects, revealing size effects in these systems are implemented using advanced characterization techniques, such as Raman spectroscopy. Finally, the preparation of mesoscopic layers, covering the thickness gap between thin film and thick film technology, is demonstrated.
Source-pull measurements using reverse six-port reflectometers with application to MESFET mixer design (1994)

A new experimental technique using six-port reflectometers, operated in reverse configuration, suitable for source-pull device characterization is reported. Analytical analysis and experimental verification show that using the six-port in reverse configuration allows the impedance of the test port of the six-port junction to be measured. This measurement technique is suitable for the design of low noise amplifiers and of active nonlinear circuits such as FET mixers and power amplifiers. This measurement technique has been used for the first time to study: 1) The effect of the LO and RF impedances of the input matching circuit of a MESFET gate mixer on the LF output power and conversion gain. 2) The effect of the phase of a LO offset short circuit presented to the MESFET output on the DC power efficiency and the conversion gain of the gate mixer. Experimental results of a NE-72084 GaAs MESFET gate mixer demonstrate that by presenting to the MESFET the optimum input RF and LO impedances and the right phase for the LO offset short-circuit at the output, 2.5 dB conversion gain can be achieved with a 2.5 times reduction of DC power consumption as compared to conventional design approaches.<<ETX>>
Multimodal Precision Imaging of Pulmonary Nanoparticle Delivery in Mice: Dynamics of Application, Spatial Distribution, and Dosimetry (2019)

Targeted delivery of nanomedicine/nanoparticles (NM/NPs) to the site of disease (e.g., the tumor or lung injury) is of vital importance for improved therapeutic efficacy. Multimodal imaging platforms provide powerful tools for monitoring delivery and tissue distribution of drugs and NM/NPs. This study introduces a preclinical imaging platform combining X-ray (two modes) and fluorescence imaging (three modes) techniques for time-resolved in vivo and spatially resolved ex vivo visualization of mouse lungs during pulmonary NP delivery. Liquid mixtures of iodine (contrast agent for X-ray) and/or (nano)particles (X-ray absorbing and/or fluorescent) are delivered to different regions of the lung via intratracheal instillation, nasal aspiration, and ventilator-assisted aerosol inhalation. It is demonstrated that in vivo propagation-based phase-contrast X-ray imaging elucidates the dynamic process of pulmonary NP delivery, while ex vivo fluorescence imaging (e.g., tissue-cleared light sheet fluorescence microscopy) reveals the quantitative 3D drug/particle distribution throughout the entire lung with cellular resolution. The novel and complementary information from this imaging platform unveils the dynamics and mechanisms of pulmonary NM/NP delivery and deposition for each of the delivery routes, which provides guidance on optimizing pulmonary delivery techniques and novel-designed NM for targeting and efficacy.
Design requirements and reference trajectory generation for a copier paperpath (2002)

Presents an approach to introducing closed loop control in a copier paperpath in order to achieve robust, high-speed media handling. The basic idea exploits periodicity in the relative position of correctly fed sheets and their corresponding images. It is shown that the periodic behavior allows to design polynomial position reference trajectories for sheets as a function of their initial position error. Only longitudinal position errors are considered. By measuring sheet positions and using closed loop control to track the reference trajectories, position errors can be successfully removed. In addition to the reference trajectories, the paper also offers a design strategy that minimizes the required paperpath length while satisfying given bounds on sheet velocities and accelerations. Two examples, each with different initial error bounds, illustrate the design algorithm.
Inverse designed extended depth of focus meta‐optics for broadband imaging in the visible (2021)

We report an inverse-designed, high numerical aperture (∼0.44), extended depth of focus (EDOF) meta-optic, which exhibits a lens-like point spread function (PSF). The EDOF meta-optic maintains a focusing efficiency comparable to that of a hyperboloid metalens throughout its depth of focus. Exploiting the extended depth of focus and computational post processing, we demonstrate broadband imaging across the full visible spectrum using a 1 mm, f/1 meta-optic. Unlike other canonical EDOF meta-optics, characterized by phase masks such as a log-asphere or cubic function, our design exhibits a highly invariant PSF across ∼290 nm optical bandwidth, which leads to significantly improved image quality, as quantified by structural similarity metrics.
Back Cover: Analysis of Powders Containing Illicit Drugs Using Magnetic Levitation (Angew. Chem. Int. Ed. 2/2020) (2019)

A powdered mixture is separated into its five components in a non-polar paramagnetic solution in a 2.5 cm high cuvette inside a magnetic levitation device. As shown by J. S. Bozenko, G. M. Whitesides et al. in their Research Article on page 874, the method separates the compounds based on their different densities in the linear density gradient formed in the solution. The levitating compounds (image was taken with crossed polarizers) are common polar adulterants and diluents used to cut illicit drugs.
Methods for the Detection and Characterization of Silica Colloids by Microsecond spICP-MS (2016)

The rapid development of nanotechnology has led to concerns over their environmental risk. Current analytical techniques are underdeveloped and lack the sensitivity and specificity to characterize these materials in complex environmental and biological matrices. To this end, single particle ICP-MS (spICP-MS) has been developed in the past decade, with the capability to detect and characterize nanomaterials at environmentally relevant concentrations in complex environmental and biological matrices. However, some nanomaterials are composed of elements inherently difficult to quantify by quadrupole ICP-MS due to abundant molecular interferences, such as dinitrogen ions interfering with the detection of silicon. Three approaches aimed at reducing the contribution of these background molecular interferences in the analysis of (28)Si are explored in an attempt to detect and characterize silica colloids. Helium collision cell gases and reactive ammonia gas are investigated for their conventional use in reducing the signal generated from the dinitrogen interference and background silicon ions leaching from glass components of the instrumentation. A new approach brought on by the advent of microsecond dwell times in single particle ICP-MS allows for the detection and characterization of silica colloids without the need for these cell gases, as at shorter dwell times the proportion of signal attributed to a nanoparticle event is greater relative to the constant dinitrogen signal. It is demonstrated that the accurate detection and characterization of these materials will be reliant on achieving a balance between reducing the contribution of the background interference, while still registering the maximum amount of signal generated by the particle event.
Analysis of Spontaneous Deletions and Gene Amplification in the lac Region of Escherichia coli (1983)

Spontaneous rearrangements, such as large deletions and duplications, have important implications for the structure of the genome. It is therefore of great interest to analyze these events at the molecular level. We have previously described the distribution of spontaneous mutations in the lacI gene of Escherichia coli (Farabaugh et al. 1978). Approximately 15% of the observed I− mutations resulted from deletions. We analyzed 12 deletions at the DNA sequence level (Fig. 1) and found that 7 of these occurred at short repeats of 5 or 8 bp. All of the deletions examined arose in a recA+ background and ranged in length from 9 bp to 123 bp. Subsequently, deletions between short repeated sequences have been demonstrated in bacteriophage T7 (Studier et al. 1979), bacteriophage T4 (Pribnow et al. 1981), and E. coli (Brake et al. 1978; Fedoroff 1979; Ghosal and Saedler 1979; Ross et al. 1979; Post et al. 1980;...