gebhart/patrepeval huggingface dataset:
Distinguishing 3 classes of corpus callosal abnormalities in consanguineous families (2011)

The data suggest that complete agenesis may be a common end-phenotype, and implicate multiple overlapping pathways in the etiology of CCA.
Polyanionic (Phosphates, Silicates, Sulfates) Frameworks as Electrode Materials for Rechargeable Li (or Na) Batteries (2013)

For more than 20 years, most of the technological achievements for the realization of positive electrodes for practical rechargeable Li battery systems have been devoted to transition metal oxides such as LixMO2 (M = Co, Ni, Mn), LixMn2O4, LixV2O5, or LixV3O8. The first two classes of materials built on close-packed oxygen stacking adopt bidimensional and tridimensional crystal structures, respectively (Figure 1), from which lithium ions may be easily intercalated or extracted in a reversible manner. These oxides are reasonably good ionic and electronic conductors, and lithium insertion/extraction proceeds while operating on the M4+/M3+ redox couple, located between 4 and 5 V versus Li+/Li...
Package Bidding : Vickrey vs. Ascending Auctions (2002)

Encheres par lots : mecanisme de Vickrey ou enchères ascendantes On démontre que les enchères à la Vickrey et les enchères ascendantes par lots ont des propriétés similaires dans le cas où les biens concernés sont des substituts. Dans les autres cas, les mécanismes de Vickrey conservent leurs pro­priétés incitatives, mais conduisent à des prix si bas que le résultat n'appartient pas au noyau de l'économie d'échange concernée. Les enchères à la Vickrey induisent par ailleurs des biais qui affectent les investissements dans les nouvelles technologies. Par contraste, les enchères ascendantes par lots produisent un équilibre qui appartient au noyau de l'économie, sont neutres en matière d'incitations à l'investissement et sont plus simples à comprendre et à gérer pour les participants au mécanisme.
Transglutaminase-2 facilitates extracellular vesicle-mediated establishment of the metastatic niche (2020)

The ability of breast cancer cells to interconvert between epithelial and mesenchymal states contributes to their metastatic potential. As opposed to cell autonomous effects, the impact of epithelial-mesenchymal plasticity (EMP) on primary and metastatic tumor microenvironments remains poorly characterized. Herein we utilize global gene expression analyses to characterize a metastatic model of EMP as compared to their non-metastatic counterparts. Using this approach, we demonstrate that upregulation of the extracellular matrix crosslinking enzyme tissue transglutaminase-2 (TG2) is part of a novel gene signature that only emerges in metastatic cells that have undergone induction and reversion of epithelial-mesenchymal transition (EMT). Consistent with our model system, patient survival is diminished when primary tumors demonstrate enhanced levels of TG2 in conjunction with its substrate, fibronectin. Targeted depletion of TG2 inhibits metastasis, while overexpression of TG2 is sufficient to enhance this process. In addition to being present within cells, we demonstrate a robust increase in the amount of TG2 and crosslinked fibronectin present within extracellular vesicle (EV) fractions derived from metastatic breast cancer cells. Confocal microscopy of these EVs suggests that FN undergoes fibrillogenesis on their surface via a TG2 and Tensin1-dependent process. Upon in vivo administration, the ability of tumor-derived EVs to induce metastatic niche formation and enhance subsequent pulmonary tumor growth requires the presence and activity of TG2. Finally, we develop a novel 3D model of the metastatic niche to demonstrate that conditioning of pulmonary fibroblasts via pretreatment with tumor-derived EVs promotes subsequent growth of breast cancer cells in a TG2-dependent fashion. Overall, our studies illustrate a novel mechanism through which EMP contributes to metastatic niche development and distant metastasis via tumor-derived EVs containing aberrant levels of TG2 and fibrillar FN.
Improving the carboxyamidomethyl ester for subtilisin A-catalysed peptide synthesis (2012)

A series of novel glycine esters was evaluated for efficiency in subtilisin A-CLEA-catalysed peptide synthesis. The reactivity of the easily accessible carboxyamidomethyl (Cam) ester was further enhanced by elongating it with an amino acid residue, thereby creating more recognition space for subtilisin A.
Selecting Informative Contexts Improves Language Model Fine-tuning (2021)

Richard Antonello, Nicole Beckage, Javier Turek, Alexander Huth. Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2021.
ChemInform Abstract: STEREOCONTROLLED SYNTHESIS OF SUBSTITUTED 2‐ALKOXYTETRAHYDROPYRANS FROM MESO‐2,4‐DIMETHYLGLUTARIC ANHYDRIDE (1983)

Abstract Aus dem Dimethylglutarsäureanhydrid (I) erhält man nach Hydrolyse zu (IIa) das Säurechlorid (IIb), aus dem mit Organometallverbindungen die Ketone (IIIa)‐(IIIc) hergestellt werden.
An Identity Privacy Preserving IoT Data Protection Scheme for Cloud Based Analytics (2019)

Efficient protection of huge amount of IoT produced data is key for wide scale data analytic services. The most efficient way is to use pure symmetric encryption as that allows both fast decryption at the analytic engine side as well as energy efficient encryption at the IoT side. However, symmetric encryption can only be performed if there is a way to directly map an encrypted object to the correct key. Typically, such mapping require a unique IoT identity, which constitute a privacy problem. In this paper, we present an IoT identity protection scheme for symmetric IoT data encryption. We give basic security definitions for this problem setting, present a new construction and give security proofs of security level achieved with the construction. Performance figures for a proof of concept implementation are also given. The new scheme gives a fair trade-off between identity privacy and complexity.
COHERENT INJECTION OF MICROCAVITIES POLARITON THROUGH TWO PHOTON EXCITATION (2012)

We present a technique based on a two-photon absorption process. We coherently inject polaritons in planar or pillar microcavities, being in resonance and with a well defined in plane wavevector (k) and show polariton laser.
Mixture theory modeling for characterizing solute transport in breast tumor tissues (2018)

Solute transport is modeled using mixture theory, applied to the nanoparticle accumulation and concentration decay in the tissue space for different vascular configurations. A comparison of a single capillary configuration (SBC) with two parallel cylindrical blood vessels (2 BC) and a lymph vessel parallel to a blood vessel (BC_LC) embedded in the tissue cylinder is performed for five solute molecular weights between 0.1 kDa and 70 kDa. We found that the presence of a second capillary reduces the extravascular concentration compared to a single capillary and this reduction is enhanced by the presence of a lymph vessel. Co-current flow direction between two adjacent vessels led to nonhomogeneous nanoparticle distribution for larger particle sizes in the tissue space, while smaller particles (0.1 kDa and 3 kDa) showed the propensity to get trapped locally in the tissue during counter-current flow. Varying the intercapillary distance with respect to vessel diameter shows a deviation of 10-30 % concentration for 2 BC and 45-60% concentration for BC_LC configuration compared to the reference SBC configuration. Finally, we introduce a non-dimensional time scale that captures the concertation as a function of the transport and geometric parameters. We find that the peak solute concentration in the tissue space occurs at a non-dimensional time, T_peak^* = 0.027+/-0.018, irrespective of the solute size, tissue architecture, and microvessel flow direction. This suggests that if indeed such a universal time scale holds, the knowledge of this time would allow estimation of the time window at which solute concentration in tissue peaks. Hence this can aid in the design of future therapeutic efficacy studies as an example for triggering drug release or laser excitation in the case of photothermal therapies.
ChemInform Abstract: Hydrogenation Processes in the Synthesis of Perfumery Ingredients (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Maternal Acceptance of the Fetus: True Human Tolerance (2007)

Induction and maintenance of immunologic tolerance in humans remains a desirable but elusive goal. Therefore, understanding the physiologic mechanisms of regulation of immune responses is highly clinically relevant for immune-mediated diseases (e.g., autoimmunity and asthma/allergy) and for cell and organ transplantation. Acceptance of the fetus, which expresses paternally inherited alloantigens, by the mother during pregnancy is a unique example of how the immune system reshapes a destructive alloimmune response to a state of tolerance. Understanding the complex mechanisms of fetomaternal tolerance has important implications for developing novel strategies to induce immunologic tolerance in humans in general and for prevention of spontaneous abortion in at-risk populations in particular.
Introduction (2017)

The history of organometallic catalysis begun with a surprising discovery by the German chemist Otto Roelen at Ruhrchemie in Oberhausen. He is the true pioneer in this entire field, and he would clearly have deserved an early Nobel Prize. Before 1938, when the landmark “oxo synthesis” was discovered by Otto Roelen (“hydroformylation”, “Roelen reaction”), homogeneous catalysis had received only occasional mention. Otto Roelen's initial investigations into homogeneous coordination catalysts in oxo synthesis proved a source of much frustration. The intense activity associated with hydroformylation and oxo catalysts, with carbonylations as described by Reppe, and with Ziegler's “borderline case”, the low-pressure polyethylene synthesis, highlighted the recognition of this new special type of catalysis. This chapter tabulates the strengths and weaknesses of both methods, makes it easy to differentiate homogeneous from the older, successful heterogeneous catalysis. It also presents an overview of the key concepts discussed in this book.
Abstract 1702: Cancer stem cell marker DCLK1 correlates with tumorigenic immune infiltrates in the colon and gastric adenocarcinoma microenvironments (2020)

Abstract Immunotherapy that has proved efficacy in several solid cancers plays a partial role in improving clinical outcomes of advanced gastrointestinal (GI) cancers. There is an unmet need to find new immune-related therapeutic targets. Doublecortin-like kinase 1 (DCLK1) marks tuft cells which are recognized as cancer initiating cells and regulators of the type II immune response, and has been studied for its role in many cancers including colon and gastric cancers, but its role in tumor immunity remains unexplored. In the current study, we analyzed colon and gastric cancer RNA sequencing data from 283 and 415 patients respectively from The Cancer Genome Atlas (TCGA). High DCLK1 expression predicted the worse clinical outcomes in colon and gastric cancer patients and correlated with increased immune and stromal components. Further analysis indicated that DCLK1was strongly linked to infiltration of multiple immune cell types, especially TAMs and Tregs, and strongly correlated with increased CD8+ T cell inhibitors TGFB1 and CXCL12 and their receptors, suggesting it may contribute to TAM-mediated inhibition of CD8+ T cells. Interestingly, we found that DCLK1 was a prognostic biomarker in left-sided colon cancer which has worse outcomes and demonstrates a reduced response to existing immunotherapies. In conclusion, our results demonstrate that DCLK1 is linked with functional regulation of the tumor microenvironment and may have potential as a prognostic biomarker and adjuvant target to promote immunotherapy sensitivity in colon and gastric cancer patients. Citation Format: Dongfeng Qu, Xiangyan Wu, Nathaniel Weygant, Jun Peng, Courtney Houchen. Cancer stem cell marker DCLK1 correlates with tumorigenic immune infiltrates in the colon and gastric adenocarcinoma microenvironments [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1702.
Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition (2019)

Renal medullary carcinoma (RMC) is a rare and deadly kidney cancer in patients of African descent with sickle cell trait. We have developed faithful patient-derived RMC models and using whole-genome sequencing, we identified loss-of-function intronic fusion events in one <i>SMARCB1</i> allele with concurrent loss of the other allele. Biochemical and functional characterization of these models revealed that RMC requires the loss of <i>SMARCB1</i> for survival. Through integration of RNAi and CRISPR-Cas9 loss-of-function genetic screens and a small-molecule screen, we found that the ubiquitin-proteasome system (UPS) was essential in RMC. Inhibition of the UPS caused a G2/M arrest due to constitutive accumulation of cyclin B1. These observations extend across cancers that harbor <i>SMARCB1</i> loss, which also require expression of the E2 ubiquitin-conjugating enzyme, <i>UBE2C</i>. Our studies identify a synthetic lethal relationship between <i>SMARCB1</i>-deficient cancers and reliance on the UPS which provides the foundation for a mechanism-informed clinical trial with proteasome inhibitors.
High-Power (>300 mW) On-Chip Laser With Passively Aligned Silicon-Nitride Waveguide DBR Cavity (2020)

We demonstrate a high-power on-chip 1550-nm laser implemented by passive flip-chip integration of a curved-channel, double-pass InGaAsP/InP slab-coupled optical waveguide amplifier (SCOWA) onto a photonic integrated circuit (PIC) containing a silicon nitride (SiN) waveguide and distributed Bragg reflector (DBR) grating. The combined chip-scale SCOW external cavity laser (SCOWECL) has single mode emission with 312 mW of optical power at a drive current of 2.5 A, and exhibits a side mode suppression ratio (SMSR) of 55 dB, peak photon conversion efficiency (PCE) of 10%, low relative-intensity noise (RIN) of ~160 dB/Hz, and an integrated linewidth of 192 kHz. Additionally, we demonstrate a multi-wavelength SCOWECL array comprised of four SCOWAs coupled to SiN-waveguide DBR gratings. The four-element array generates 80 mW per channel when the SCOWAs are driven in parallel (1.25 A/channel) with ~1-nm wavelength spacing centered at 1533 nm. We describe the fabrication and hybrid integration processes. The measured SCOWA-to-waveguide coupling loss is estimated to be 1.6 +/-1.0 dB which agrees well with the simulation.
Effects of Fungal-derived High Molecular Weight Chitosan on 5-Fluorouracil-induced Adverse Reactions (2008)

The effects of fungal-derived high molecular weight chitosan (HMWC) on the prevention of 5-fluorouracil (5-FU)-induced side-effects were studied in a sarcoma-bearing mice model. 5-FU (12.5mg/kg) was gargled into the mice with or without HMWC (25, 75, and 150mg/kg) every 12 h for consecutive 8 or 16 days in different experiments. The HMWC (25—150 mg/kg) exerted no toxicity and did not interfere with the anti-tumor activity of 5-FU on sarcoma-bearing mice. HMWC in a higher dose (150 mg/kg) partially protected 5-FU-induced cytotoxicity on peripheral leukocytes, lymphocytes, and bone marrow CD-19 positive cells. HMWC reversed the 5-FU suppression of intestine sucrase activity and attenuated the 5-FU-induced diarrhea. Bone marrow cells micronucleus and DNA comet assays demonstrated that HMWC significantly reversed 5-FU-induced genome toxicity to marrow cells. These results suggested that fungal-derived HMWC attenuated the 5-FU-induced bone marrow and gastrointestinal toxicity, and has the potential for clinical applications in the future.
An Empirical Analysis of Backward Compatibility in Machine Learning Systems (2020)

In many applications of machine learning (ML), updates are performed with the goal of enhancing model performance. However, current practices for updating models rely solely on isolated, aggregate performance analyses, overlooking important dependencies, expectations, and needs in real-world deployments. We consider how updates, intended to improve ML models, can introduce new errors that can significantly affect downstream systems and users. For example, updates in models used in cloud-based classification services, such as image recognition, can cause unexpected erroneous behavior in systems that make calls to the services. Prior work has shown the importance of "backward compatibility" for maintaining human trust. We study challenges with backward compatibility across different ML architectures and datasets, focusing on common settings including data shifts with structured noise and ML employed in inferential pipelines. Our results show that (i) compatibility issues arise even without data shift due to optimization stochasticity, (ii) training on large-scale noisy datasets often results in significant decreases in backward compatibility even when model accuracy increases, and (iii) distributions of incompatible points align with noise bias, motivating the need for compatibility aware de-noising and robustness methods.
hADA2a and hADA3 are required for acetylation, transcriptional activity and proliferative effects of beta-catenin (2008)

AbstractBeta-catenin is the key transcriptional activator of the Wnt pathway important for development and tissue homeostasis of multicellular organisms. Its deregulation contributes to many human cancers. The beta-catenin transcriptional activator complex continues to be defined, but already contains several proteins with chromatin remodeling activity. Here we show that two members of histone acetyltransferase complexes without enzymatic activity, hADA2a and hADA3, are required for full activity of beta-catenin. hADA2a and hADA3 physically interact with beta-catenin, and the interaction is mediated through Armadillo repeats 6 through 12 and the C-terminal transactivation domain of beta-catenin. Both hADA2a and hADA3 reside with beta-catenin at the enhancer for the Wnt target gene c-Myc. RNA interference-mediated reduction of hADA2a and hADA3 results in reduced beta-catenin acetylation, reduced activity in reporter gene assays and reduced activation of endogenous beta-catenin target genes. Overall, loss of hADA2a and hADA3 negatively impacts beta-catenin-mediated proliferation. Our studies identify hADA2a and hADA3 as crucial cofactors of beta-catenin that are likely involved in the assembly of transactivation-competent beta-catenin complexes at Wnt target genes.
On the development of a novel high VSWR programmable impedance tuner (2016)

Impedance tuners are key instruments used for load- and source–pull measurements. They are crucial for any active microwave components, circuits, and systems characterization and optimization. This paper reports theoretical, simulated, and experimental results related to the development of a novel programmable impedance tuner offering high-voltage standing wave ratio (VSWR). After presenting the proposed tuner principle, a fabricated prototype operating at microwave frequencies and based on a 3.5 mm coaxial line is introduced with experimental results. Depending on the targeted frequency band, different pairs of slugs, with optimized length and characteristic impedance, can be used to obtain an optimal VSWR. This first prototype allowed us to demonstrate the interest of the proposed impedance synthesis principle and to identify ways forward to further improve its performances and push forward this promising technology.
Versatility of Boron-Mediated Coupling Reaction of Oxetanes and Epoxides with CO2: Selective Synthesis of Cyclic Carbonates or Linear Polycarbonates (2020)

Achieving simultaneously high selectivity and high rate in the coupling reaction of CO2 with poorly reacting oxetanes remains a major challenge. Here, the selective and nearly quantitative conversion of the coupling reaction of oxetanes with CO2 into six-membered cyclic organic carbonates (COCs) is described, when a binary metal-free system composed of commercially available alkyl borane and onium iodide salts is used under 10 bar CO2 pressure between 90 and 110 °C. Kinetic investigations provide quantitatively the enthalpy and entropy of activation [ΔH⧧ = 6.7 ± 1.2 kcal/mol and ΔS⧧ = −57 ± 4 cal/(mol·K)] of the back-biting, cyclic formation reaction. In addition to forming borate complexes with the anions responsible for the CO2/oxetane coupling reaction, these alkyl boranes activate the cyclic ethers as unambiguously confirmed by density functional theory studies. Upon selecting onium salts other than iodide-based ones, in particular those with poor leaving ability, the process is driven toward chain growth and the formation of linear polycarbonates. This metal-free system also exhibits both versatility and an activity comparable to that of metal catalysts (turnover frequency values of 14–124 h–1) for the synthesis of various five-membered COCs from epoxides and CO2.
A half‐mode substrate integrated waveguide filtering power divider with Fourier‐varying via holes (2021)

Abstract In this article, a novel design methodology of a half‐mode substrate integrated waveguide (HM‐SIW) filtering Wilkinson power divider is proposed. The width between the two metallic rows of vias in the conventional HM‐SIW divider is governed by a truncated Fourier series expansion to obtain specific passband/stopband performance. The optimized varying width is obtained using the even‐mode analysis, whereas the odd‐mode analysis is used to find the optimum values of three isolation resistors that achieve acceptable isolation and output ports matching over specific frequency range. For validation, a HM‐SIW divider with a center frequency of 12.3 GHz and 3.7% 10‐dB fractional bandwidth is designed, simulated, and measured. Simulated and measured results show a good agreement with passband return loss and transmission losses better than −15 and −3.0 dB, respectively.
Identification of two core types in lipopolysaccharides ofActinobacillus pleuropneumoniaerepresenting serotypes 1 to 12 (1996)

Lipopolysaccharides (LPS) of Actinobacillus pleuropneumoniae were separated by Tricine-SDS-polyacrylamide gel electrophoresis, which has been shown to improve resolution of low-molecular-mass fast migrating bands. Strains representing the 12 serotypes of A. pleuropneumoniae can be divided in two groups according to the gel mobility of the core - lipid A region of their LPS. The first electromorphic core type (core type I), found in serotypes 1, 6, 9, and 11, had a migration slower than Salmonella typhimurium Ra LPS. The second electromorphic core type (core type II), found in the remaining serotypes (i.e., 2, 3, 4, 5, 7, 8, 10, and 12) had a migration similar to S. typhimurium Ra LPS. Furthermore, we observed that these two core types were antigenically different. Western blot analyses indicated that core - lipid A region of LPS from electromorphic core type I strains reacted when probed with serum from a pig experimentally infected with a core type I strain but not when probed with serum from a pig experimentally infected with a core type II strain. Conversely, core - lipid A region of LPS from electromorphic core type II strains reacted only when probed with serum from a pig experimentally infected with a core type II strain. Our results, based on both electrophoretic mobility and antigenicity, suggest the presence of two LPS core types in A. pleuropneumoniae.