gebhart/patrepeval huggingface dataset:
Abstract 837: Preclinical development of ELU001: A folate receptor alpha (FRα)-targeted C’Dot drug conjugate (CDC) for the treatment of brain metastases (2023)

Abstract Antibody-drug conjugates (ADCs) exhibit limited efficacy against brain malignancies due to their inability to cross the blood-brain barrier (BBB) and penetrate into solid tumors. In clinical imaging studies C’Dots readily crossed tumor-disrupted BBB and penetrated across/localized in tumors in the brain avoiding healthy brain. CDCs are ultra-small (6-7 nm) nanoparticles with a silica core coated by short polyethylene glycol chains conjugated to up to 80 small payload and targeting moieties, creating highly potent and avid agents. CDCs’ small size mediates rapid renal clearance leading to limited exposure to healthy tissues. ELU001 is a potent anti-FRα CDC with an average of 21 exatecan topoisomerase-1 inhibitor payload molecules and 13 folic acid targeting molecules on its surface. ELU001 is currently in a dose escalation trial in patients with systemic solid tumor indications that have the potential to overexpress FRα. Early signs of activity with a manageable safety profile have been seen across antigen expression levels. ELU001 exhibits in vitro potency in the sub/low nanomolar range against cancer cell lines that express 3+, 2+ or 1+ levels of FRα. In studies performed in immunodeficient mice bearing intracranial NCI-H2228-luc bioluminescent non-small cell lung cancer tumors, ELU001 was observed to penetrate across disrupted BBB and localize in tumors. Microscopic analysis revealed that ELU001 distributed throughout the tumors but not into the healthy brain. Treatment with a single cycle of ELU001 Q3Dx3 in mice bearing either early (Day 7) or late (Day 14) brain tumors was well tolerated and resulted in significant reduction in tumor burden measured by bioluminescence as well as a prolonged survival benefit. Retreatment of these animals resulted in an additional decrease in tumor burden. These results suggest that ELU001 may have promise for the treatment of metastatic brain tumors that are difficult to treat with currently available agents. Citation Format: Gregory P. Adams, Tin Khor, Feng Chen, Kai Ma, Marion Scocca, Aranapakam Venkatesan, Cathy Reddick, Mary Hilgart, Thomas Gardinier, Fei Wu, Melik Turker, Peiming Chen, Vaibhav Patel, Eliel Bayever. Preclinical development of ELU001: A folate receptor alpha (FRα)-targeted C’Dot drug conjugate (CDC) for the treatment of brain metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 837.
Role of nutritional factors in pathogenesis of cancer (2018)

Diet and nutrition are crucial factors throughout the complete life course in the promotion and upholding of good health. It has always been accepted that our defencelessness to infection and disease was influenced by diet and environmental as well as genetic factors. Nutrition is coming to the front position as a principle modifiable determinant of chronic disease, with scientific confirmation with time more supporting the view that alterations in diet have strong effects, equally positive as well as negative, on health throughout life. For the most part notably, nutritional adjustments may not only influence present health but also determine whether or not an individual will develop chronic non-communicable diseases like cancer. Diet is a blend of protective, mutagenic, and carcinogenic agents; the majority of them are metabolized by the enzymes of biotransformation process. Genetic polymorphisms that alter protein expression or else the function of these enzymes can change the risk of developing cancer. The scientific community has identified numerous naturally occurring materials in plant food with the power to resolve possible carcinogens. A few of these nutrients and natural phytochemicals look for toxins and usher them from the body before they can cause cell damage that may lead to cancer. Others give the impression to make it easier for the body to make repairs at the cellular level. At a standstill, others may help bring to an end cancer cells from reproducing. Even after a cell begins to experience damage that can lead to cancer, what you eat and drink, and how you live can still help short-circuit the cancer process. It is thought that a diet containing defensive micronutrients as well as carcinogens and mutagens may adapt the risk of cancer development, particularly in genetically susceptible individuals.
Experimental comparison between optical spectroscopy and laser-ultrasound generation in polymer-matrix composites (2001)

Laser ultrasound is a technique based on lasers to generate and detect ultrasound. The generation mechanism involves several parameters among which one of the most important is the optical penetration depth. This letter presents a comparison between the amplitude of ultrasonic waves generated by an optical parametric oscillator and optical penetration depth spectra measured by photoacoustic spectroscopy in the 3.0 to 3.5 μm wavelength range for three different composite samples. The laser-ultrasound amplitude spectra closely track the photoacoustic spectra. The results presented in this letter experimentally demonstrate why the 3.0–3.5 μm wavelength range generates more efficiently generates ultrasonic waves in the ultrasonic frequency range of interest for the inspection of polymer-matrix composites than the 10.6 μm wavelength of the CO2 laser.
Surprising robustness of a unit cell: isomorphism in caesium 18-crown[6] complexes with aromatic polycarboxylate anions (2010)

Reaction in solution and in the solid state of 18-crown[6] with Cs2CO3 and 5-substituted isophthalic acids yields the new organic–inorganic complexes 18-crown[6]·Cs[OH-isoH] (2), 18-crown[6]·Cs[CH3-isoH] (3), 18-crown[6]·Cs[Br-isoH] (4), 18-crown[6]·Cs[OCH3-isoH] (5), 18-crown[6]·Cs[NO2-isoH] (6) and 18-crown[6]·Cs[tert-Butyl-isoH] (8), which have all been characterized by X-ray diffraction. All compounds except the latter are isomorphous, in spite of the size, shape and chemical nature of the substituent and its ability to form hydrogen bonds.
Ge[sub 2]Sb[sub 2]Te[sub 5] Charge Trapping Nanoislands with High-k Blocking Oxides for Charge Trap Memory (2009)

Charge trap memory capacitors using (GST) nanoislands as charge storage media were fabricated. The GST nanoislands were prepared by plasma-enhanced cyclic chemical vapor deposition on a 6 nm thick tunneling layer. A 16 nm thick or 40 nm thick film was used as the blocking oxide (BO). A shift in the flatband voltage in the capacitance–voltage test was achieved when the GST nanoislands were interposed between the and BOs, highlighting the feasibility of memory applications. The charges were trapped at the interface between the GST and BOs. Stable charge retention up to was observed.
Molecular modeling of the interaction between heparan sulfate and cellular growth factors: Bringing pieces together (2011)

Heparan sulfate is a polysaccharide belonging to the glycaminoglycan family. It interacts with numerous proteins of the extracellular matrix, in particular cellular growth factors. The number of experimental protein-heparin sulfate complexes obtained by crystallography or nuclear magnetic resonance is limited. Alternatively, computational approaches can be employed. Generally, they restrain the conformation of the glycosidic rings and linkages in order to reduce the complexity of the problem. Modeling the interaction between protein and heparan sulfate is indeed challenging because of the large size of the fragment needed for a strong binding, the flexibility brought by the glycosidic rings and linkages and the high density of negative charges. We propose a two-step method based on molecular docking and molecular dynamics simulation. Molecular docking allows exploring the positioning of a rigid heparin sulfate fragment on the protein surface. Molecular dynamics refine selected docking models by explicitly representing solvent molecules and not restraining the polysaccharide backbone. The interaction of a hexamer of heparin sulfate was studied in interaction with fibroblast growth factor 2 and stromal cell-derived factor 1α. This approach shed light on the plasticity of the growth factors interacting with heparan sulfate. This approach can be extended to the study of other protein/glycosaminoglycan complexes.
Vaxign: The First Web-Based Vaccine Design Program for Reverse Vaccinology and Applications for Vaccine Development (2010)

Vaxign is the first web-based vaccine design system that predicts vaccine targets based on genome sequences using the strategy of reverse vaccinology. Predicted features in the Vaxign pipeline include protein subcellular location, transmembrane helices, adhesin probability, conservation to human and/or mouse proteins, sequence exclusion from genome(s) of nonpathogenic strain(s), and epitope binding to MHC class I and class II. The precomputed Vaxign database contains prediction of vaccine targets for >70 genomes. Vaxign also performs dynamic vaccine target prediction based on input sequences. To demonstrate the utility of this program, the vaccine candidates against uropathogenic Escherichia coli (UPEC) were predicted using Vaxign and compared with various experimental studies. Our results indicate that Vaxign is an accurate and efficient vaccine design program.
Synergistic effects of intracoronary infusion of autologous bone marrow-derived mesenchymal stem cells and revascularization procedure on improvement of cardiac function in patients with severe ischemic cardiomyopathy (2021)

MSCs infusion significantly improves LV function in ICM patients. MSCs infusion plus concurrent revascularization procedure worked synergistically to improve cardiac function in patients with severe ICM.
Diaminoterephthalate–α-lipoic acid conjugates with fluorinated residues (2019)

Two bifunctional diaminoterephthalate (DAT) fluorescence dyes were prepared in a three-step sequence including one deprotection reaction. One functional unit is α-lipoic acid (ALA) for binding the dye to gold surfaces. It was introduced to the DAT scaffold by an amidation reaction. The other functional unit is a <i>para</i>-(trifluoromethyl)benzyl group for facile detection of the surface-bound material by X-ray photoelectron spectroscopy (XPS). This residue was introduced by reductive amination of the DAT scaffold with the respective benzaldehyde derivative. In one compound (60% yield over three steps) the ALA unit is directly bound to the DAT as a relatively electron-withdrawing amide. In solution (CH<sub>2</sub>Cl<sub>2</sub>), this material shows strong fluorescence (quantum yield 57% with emission at 495 nm, absorption maximum at 420 nm). The other compound (57% yield over three steps) possesses a propylene spacer between the ALA and the DAT units for electronic decoupling, thus, bathochromic shifts are observed (absorption at 514 nm, emission at 566 nm). The quantum yield is, however, lower (4%). Self-assembled monolayers on a gold surface of both compounds were prepared and characterized by high-resolution XPS of the C 1s, O 1s, S 2p, N 1s and F 1s emissions. The high signal-to-noise ratios of the F 1s peaks indicated that trifluoromethylation is an excellent tool for the detection of surface-bound materials by XPS.
Massage decreases aggression in preschool children: a long‐term study (2008)

Daily touching by massage lasting for 5-10 min could be an easy and inexpensive way to decrease aggression among preschool children.
Valorisation of lignocellulose waste streams (2010)

Although second generation bioethanol starts being produced at industrial scale, considerable improvement is still required for commercial viability. Up to now, the substrates that can be used are very limited. Most interesting substrates (e.g. wood or cellulose containing waste products) cannot be used because: 1) The process of pretreatment and hydrolysis (to liberate fermentable sugars) is too expensive or inefficient 2) The fermentable hydrolysate contains too many inhibitors. In a TETRA project, a grant programme to stimulate innovation in Flemish companies through technology transfer, we are comparing several pretreatment and hydrolysis conditions of lignocellulosic waste and energy crops. When a hydrolysate is obtained with at least 5% fermentable sugars, fermentation experiments are performed. A range of Saccharomyces cerevisiae strains is being tested and pre-culture and fermentation conditions are modified in order to find the best combination. From our first series of experiments it is clear that: 1) With some substrates it is very difficult to obtain a hydrolysate that contains sufficient fermentable sugars 2) Even with a mild treatment, the hydrolysate still contains inhibitory compounds 3) The different yeast strains tested with flax hydrolysate exhibited a very different fermentation pattern. Most strains were able to ferment the sugars to the same extend, but the rate of fermentation strongly depended on the strain 4) Pre-culture of the yeast (shaking flasks) in the presence of flax hydrolysate did not affect the yield of the pre-culture, but had a clear effect on the subsequent fermentation. Conclusion: from our first results it is clear that by screening a collection of different substrates, evaluating different pretreatment methods, screening a large set of yeast strains and optimizing the pre-culture and fermentation conditions, we may be able to produce second generation bioethanol from different substrates in an economically viable way.
Privacy preserving encrypted phonetic search of speech data (2017)

This paper presents a strategy for enabling speech recognition to be performed in the cloud whilst preserving the privacy of users. The approach advocates a demarcation of responsibilities between the client and server-side components for performing the speech recognition task. On the client-side resides the acoustic model, which symbolically encodes the audio and encrypts the data before uploading to the server. The server-side then employs searchable encryption to enable the phonetic search of the speech content. Some preliminary results for speech encoding and searchable encryption are presented.
Viral PB1-F2 and host IFN-γ guide ILC2 and T cell activity during influenza virus infection (2022)

Functional plasticity of innate lymphoid cells (ILCs) and T cells is regulated by host environmental cues, but the influence of pathogen-derived virulence factors has not been described. We now report the interplay between host interferon (IFN)-γ and viral PB1-F2 virulence protein in regulating the functions of ILC2s and T cells that lead to recovery from influenza virus infection of mice. In the absence of IFN-γ, lung ILC2s from mice challenged with the A/California/04/2009 (CA04) H1N1 virus, containing nonfunctional viral PB1-F2, initiated a robust IL-5 response, which also led to improved tissue integrity and increased survival. Conversely, challenge with Puerto Rico/8/1934 (PR8) H1N1 virus expressing fully functional PB1-F2, suppressed IL-5<sup>+</sup> ILC2 responses, and induced a dominant IL-13<sup>+</sup> CD8 T cell response, regardless of host IFN-γ expression. IFN-γ-deficient mice had increased survival and improved tissue integrity following challenge with lethal doses of CA04, but not PR8 virus, and increased resistance was dependent on the presence of IFN-γR<sup>+</sup> ILC2s. Reverse-engineered influenza viruses differing in functional PB1-F2 activity induced ILC2 and T cell phenotypes similar to the PB1-F2 donor strains, demonstrating the potent role of viral PB1-F2 in host resistance. These results show the ability of a pathogen virulence factor together with host IFN-γ to regulate protective pulmonary immunity during influenza infection.
High resolution tumor targeting in living mice by means of multispectral optoacoustic tomography (2012)

The current study demonstrates the high potential of MSOT to broadly impact the fields of tumor diagnostics and preclinical drug development.
In vivo synergistic activity of a CAZyme cassette from <i>Acidothermus cellulolyticus</i> significantly improves the cellulolytic activity of the <i>C. bescii</i> exoproteome (2017)

The use of microbial cells to convert plant biomass directly to fuels and chemicals is referred to as consolidated bioprocessing (CBP). Members of the bacterial genus, Caldicellulosiruptor (Gram-positive, anaerobic hyperthermophiles) are capable of deconstructing plant biomass without enzymatic or chemical pretreatment. This is accomplished by the production and secretion of free, multi-domain enzymes that outperform commercial enzyme cocktails on some substrates. Here, we show that the exoproteome of Caldicellulosiruptor bescii may be enhanced by the heterologous expression of enzymes from Acidothermus cellulolyticus that act synergistically to improve sugar release from complex substrates; as well as improve cell growth. In this work, co-expression of the A. cellulolyticus Acel_0615 β-glucanase (GH6 and GH12) and E1 endoglucanase (GH5) enzymes resulted in an increase in the activity of the exoproteome on Avicel; as well as an increase in growth of C. bescii on Avicel compared to the parental strain or the strain expressing the β-glucanase alone. Our ability to engineer the composition and effectiveness of the exoproteome of these bacteria provides insight into the natural mechanism of plant cell wall deconstruction, as well as future directions for improving CBP. Biotechnol. Bioeng. 2017;114: 2474-2480. © 2017 Wiley Periodicals, Inc.
Identification, Synthesis, and Strategy For Minimization of Potential Impurities Observed In Raltegravir Potassium Drug Substance (2012)

Multiple sources of anticipated degradation and process impurities of raltegravir potassium drug substance observed during the laboratory optimization and later during its bulk synthesis are described in this article. The impurities were monitored by UPLC, and their structures are tentatively assigned on the basis of fragmentation patterns in LC–MS and NMR spectroscopy. Most of the impurities are synthesized, and their assigned constitutions were confirmed by co-injection in UPLC. In addition to the formation, synthesis, and characterization, strategy for minimizing these impurities to the level accepted by ICH is also described. We feel that our study will be helpful to the generic industry for obtaining chemically pure raltegravir potassium.
Determinants of worldwide antibiotic resistance dynamics across drug-bacterium pairs: a multivariable spatial-temporal analysis using ATLAS (2023)

Independent research Pfizer Global Medical Grant and ANR Labex IBEID.
Integration of amorphous ferromagnetic oxides with multiferroic materials for room temperature magnetoelectric spintronics (2020)

A room temperature amorphous ferromagnetic oxide semiconductor can substantially reduce the cost and complexity associated with utilizing crystalline materials for spintronic devices. We report a new material (Fe<sub>0.66</sub>Dy<sub>0.24</sub>Tb<sub>0.1</sub>)<sub>3</sub>O<sub>7-x</sub> (FDTO), which shows semiconducting behavior with reasonable electrical conductivity (~500 mOhm-cm), an optical band-gap (2.4 eV), and a large enough magnetic moment (~200 emu/cc), all of which can be tuned by varying the oxygen content during deposition. Magnetoelectric devices were made by integrating ultrathin FDTO with multiferroic BiFeO<sub>3</sub>. A strong enhancement in the magnetic coercive field of FDTO grown on BiFeO<sub>3</sub> validated a large exchange coupling between them. Additionally, FDTO served as an excellent top electrode for ferroelectric switching in BiFeO<sub>3</sub> with no sign of degradation after ~10<sup>10</sup> switching cycles. RT magneto-electric coupling was demonstrated by modulating the resistance states of spin-valve structures using electric fields.
Leveraging Immunopeptidomics To Study and Combat Infectious Disease (2021)

T cells must recognize pathogen-derived peptides bound to major histocompatibility complexes (MHCs) in order to initiate a cell-mediated immune response against an infection, or to support the development of high-affinity antibody responses. Identifying antigens presented on MHCs by infected cells and professional antigen-presenting cells (APCs) during infection may therefore provide a route toward developing new vaccines. Peptides bound to MHCs can be identified at whole-proteome scale using mass spectrometry-a technique referred to as "immunopeptidomics." This technique has emerged as a powerful tool for identifying potential vaccine targets in the context of many infectious diseases. In this review, we discuss the contributions immunopeptidomic studies have made to understanding antigen presentation and T cell priming in the context of infection and the potential for immunopeptidomics to inform the development of vaccines to address pressing global health problems in infectious disease.
Implementing a Second-Level Observation Unit at a Large Academic Medical Center (2021)

Supplemental digital content is available in the text.
Ultra-Fine Pitch Stencil Printing for a Low Cost and Low Temperature Flip-Chip Assembly Process (2007)

This paper presents the results of a packaging process based on the stencil printing of isotropic conductive adhesives (ICAs) that form the interconnections of flip-chip bonded electronic packages. Ultra-fine pitch (sub-100-mum), low temperature (100degC), and low cost flip-chip assembly is demonstrated. The article details recent advances in electroformed stencil manufacturing that use microengineering techniques to enable stencil fabrication at apertures sizes down to 20mum and pitches as small as 30mum. The current state of the art for stencil printing of ICAs and solder paste is limited between 150-mum and 200-mum pitch. The ICAs-based interconnects considered in this article have been stencil printed successfully down to 50-mum pitch with consistent printing demonstrated at 90-mum pitch size. The structural integrity or the stencil after framing and printing is also investigated through experimentation and computational modeling. The assembly of a flip-chip package based on copper column bumped die and ICA deposits stencil printed at sub-100-mum pitch is described. Computational fluid dynamics modeling of the print performance provides an indicator on the optimum print parameters. Finally, an organic light emitting diode display chip is packaged using this assembly process
Microstructural characterization of polypropene surfaces using grazing incidence X-ray diffraction (1998)

The grazing incidence X-ray diffraction was applied for characterizing the crystalline structure of the outermost layer of polypropene sheets. Even in the outermost surface layer within about 5 nm, the crystalline structure of the a form was confirmed by the X-ray diffraction patterns. The values of a and c for the crystal lattice dimension were almost constant in spite of the variation of surface layer crystallinity, whereas the value of b for the surface layer decreased with increasing crystallinity or decreasing comonomer content of polypropene. This suggests that the density of the crystal increased as a function of crystallinity. Additionally, the value of b for the surface layer was smaller than that of the bulk. It was concluded that the lattice distortion can be ascribed to the residual stress caused by the molding pressure under the higher super-cooling rate.
A case of type AB thymoma with atypical histological features: Is atypical type AB thymoma an acceptable variant of thymoma? (2021)

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