gebhart/patrepeval huggingface dataset:
DNER, an Epigenetically Modulated Gene, Regulates Glioblastoma-Derived Neurosphere Cell Differentiation and Tumor Propagation (2009)

Neurospheres derived from glioblastoma (GBM) and other solid malignancies contain neoplastic stem-like cells that efficiently propagate tumor growth and resist cytotoxic therapeutics. The primary objective of this study was to use histone-modifying agents to elucidate mechanisms by which the phenotype and tumor-promoting capacity of GBM-derived neoplastic stem-like cells are regulated. Using established GBM-derived neurosphere lines and low passage primary GBM-derived neurospheres, we show that histone deacetylase (HDAC) inhibitors inhibit growth, induce differentiation, and induce apoptosis of neoplastic neurosphere cells. A specific gene product induced by HDAC inhibition, Delta/Notch-like epidermal growth factor-related receptor (DNER), inhibited the growth of GBM-derived neurospheres, induced their differentiation in vivo and in vitro, and inhibited their engraftment and growth as tumor xenografts. The differentiating and tumor suppressive effects of DNER, a noncanonical Notch ligand, contrast with the previously established tumor-promoting effects of canonical Notch signaling in brain cancer stem-like cells. Our findings are the first to implicate noncanonical Notch signaling in the regulation of neoplastic stem-like cells and suggest novel neoplastic stem cell targeting treatment strategies for GBM and potentially other solid malignancies.
MOSFET-Embedded Microcantilevers: An All-Electronic Label- and Optics-Free Signal Transduction Paradigm for Bio-Chem Sensing (2006)

We recently introduced all-electronic label- and optics-free detection paradigm for biochemical binding events on metal-oxide semiconductor field-effect transistor (MOSFET)-embedded microcantilevers. Microcantilever bending as small as ~5 nm, leads to a measurable and reproducible change in the MOSFET drain current, which forms the basis for the microelectronics-based detection of molecular binding events. MOSFET-embedded microcantilevers are able to detect diverse probe-target binding events, ranging from DNA hybridization to protein-protein binding, at high sensitivity. Such label- and optics-free all-electronic MOSFET detection approach will bridge the current gap between integration of nano-bio nanostructures with microelectronics, and promises a universal and widely deployable bio-chem diagnosis platform, compatible with all the advantages of established CMOS technology for wide variety of biomolecular and chemical detection and diagnosis.
The subcellular localization of PBX1 and EXD proteins depends on nuclear import and export signals and is modulated by association with PREP1 and HTH (1999)

Nuclear localization of the Extradenticle (EXD) and PBX1 proteins is regionally restricted during Drosophila and mammalian development. We studied the subcellular localization of EXD, PBX, and their partners Homothorax (HTH) and PREP1, in different cell contexts. HTH and PREP1 are cytoplasmic and require association with EXD/PBX for nuclear localization. EXD and PBX1 are nuclear in murine fibroblasts but not in Drosophila Schneider cells, in which they are actively exported to the cytoplasm. Coexpression of EXD/PBX with HTH/PREP1 causes nuclear localization of their heterodimers in both cell contexts. We propose that heterodimerization with HTH/PREP induces nuclear translocation of EXD and PBX1 in specific cell contexts by blocking their nuclear export.
Hydrogen Sulfide Facilitated Transport in Perfluorosulfonic Acid Membranes (1987)

Hydrogen sulfide and methane fluxes were measured at ambient conditions for 200 µm perfluorosulfonic acid cation exchange membranes containing monopositive EDA counterions as carriers. Facilitation factors up to 26.4 and separation factors for H2S/CH4 up to 1200 were observed. The H2S transport is diffusion limited. The data are well represented by a simplified reaction equilibrium model. Model predictions indicate that H2S facilitated transport would be diffusion limited even at a membrane thickness of 1 µm.
Cognitive computing (2011)

Unite neuroscience, supercomputing, and nanotechnology to discover, demonstrate, and deliver the brain's core algorithms.
Development of a tripartite solvent blend for sustainable chromatography (2014)

Favorable solvents supplant dichloromethane in routine silica gel chromatography and eliminate halogenated waste, thereby improving safety, economics, and environmental impact.
Grafted septal neurons form cholinergic synaptic connections in the dentate gyrus of behaviorally impaired aged rats (1986)

A group of aged, behaviorally impaired rats received suspension grafts of fetal septal-diagonal band tissue into the otherwise intact hippocampal formation. Three months after grafting, behaviorally recovered rats were studied by immunocytochemistry by using monoclonal antibodies to choline acetyltransferase (ChAT) and electron microscopy. The innervation of the host dentate gyrus by graft-derived ChAT-positive fibres was unmasked by acute removal of the intrinsic septal cholinergic innervation by fimbria-fornix transection 5-7 days before perfusion. The pattern of termination and ultrastructural connectivity were compared with previous results obtained from both young nonoperated control animals and a group of young rats with intrahippocampal septal grafts that had been subjected to denervation of the intrinsic cholinergic input at the time of transplantation. Graft-derived, ChAT-immunoreactive terminals formed abundant synaptic specializations with neuronal elements in the host dentate gyrus. The predominant postsynaptic target (about 65% of all boutons) was dendritic shafts, whereas about 20% of the boutons contacted dendritic spines. Very few synapses onto neuronal perikarya were found in the grafted aged rats. In some of these cases, however, it was possible to identify the target as dentate granule cells. This situation is very similar to that seen in young control rats but significantly different than the distribution observed in the denervated young grafted group, where axosomatic contacts predominated. The results indicate that the graft-induced behavioral improvement seen in the aged rats may depend on the formation of functional cholinergic graft connections with neuronal elements in the host hippocampal formation.
The Rotator Cuff Organ: Integrating Developmental Biology, Tissue Engineering, and Surgical Considerations to Treat Chronic Massive Rotator Cuff Tears (2017)

The torn rotator cuff remains a persistent orthopedic challenge, with poor outcomes disproportionately associated with chronic, massive tears. Degenerative changes in the tissues that comprise the rotator cuff organ, including muscle, tendon, and bone, contribute to the poor healing capacity of chronic tears, resulting in poor function and an increased risk for repair failure. Tissue engineering strategies to augment rotator cuff repair have been developed in an effort to improve rotator cuff healing and have focused on three principal aims: (1) immediate mechanical augmentation of the surgical repair, (2) restoration of muscle quality and contractility, and (3) regeneration of native enthesis structure. Work in these areas will be reviewed in sequence, highlighting the relevant pathophysiology, developmental biology, and biomechanics, which must be considered when designing therapeutic applications. While the independent use of these strategies has shown promise, synergistic benefits may emerge from their combined application given the interdependence of the tissues that constitute the rotator cuff organ. Furthermore, controlled mobilization of augmented rotator cuff repairs during postoperative rehabilitation may provide mechanotransductive cues capable of guiding tissue regeneration and restoration of rotator cuff function. Present challenges and future possibilities will be identified, which if realized, may provide solutions to the vexing condition of chronic massive rotator cuff tears.
Decay of a Quantum Knot (2019)

We experimentally study the dynamics of quantum knots in a uniform magnetic field in spin-1 Bose-Einstein condensates. The knot is created in the polar magnetic phase, which rapidly undergoes a transition toward the ferromagnetic phase in the presence of the knot. The magnetic order becomes scrambled as the system evolves, and the knot disappears. Strikingly, over long evolution times, the knot decays into a polar-core spin vortex, which is a member of a class of singular SO(3) vortices. The polar-core spin vortex is stable with an observed lifetime comparable to that of the condensate itself. The structure is similar to that predicted to appear in the evolution of an isolated monopole defect, suggesting a possible universality in the observed topological transition.
Possible relationship between changes in islet neogenesis and islet neogenesis-associated protein-positive cell mass induced by sucrose administration to normal hamsters (2000)

The possible relationship between changes in islet cell mass and in islet neogenesis-associated protein (INGAP)-cell mass induced by sucrose administration to normal hamsters was investigated. Normal hamsters were given sucrose (10% in drinking water) for 5 (S8) or 21 (S24) weeks and compared with control (C) fed hamsters. Serum glucose and insulin levels were measured and quantitative immunocytochemistry of the endocrine pancreas was performed. Serum glucose levels were comparable among the groups, while insulin levels were higher in S hamsters. There was a significant increase in beta-cell mass (P<0.02) and in beta-cell 5-bromo-2'-deoxyuridine index (P<0.01), and a significant decrease in islet volume (P<0.01) only in S8 vs C8 hamsters. Cytokeratin (CK)-labelled cells were detected only in S8 hamsters. INGAP-positive cell mass was significantly larger only in S8 vs C8 hamsters. Endocrine INGAP-positive cells were located at the islet periphery ( approximately 96%), spread within the exocrine pancreas ( approximately 3%), and in ductal cells (<1%) in all groups. INGAP positivity and glucagon co-localization varied according to topographic location and type of treatment. In C8 hamsters, 49.1+/-6. 9% cells were INGAP- and glucagon-positive in the islets, while this percentage decreased by almost half in endocrine extra-insular and ductal cells. In S8 animals, co-expression increased in endocrine extra-insular cells to 36.3+/-9.5%, with similar figures in the islets, decreasing to 19.7+/-6.9% in ductal cells. INGAP-positive cells located at the islet periphery also co-expressed CK. In conclusion, a significant increase of INGAP-positive cell mass was only observed at 8 weeks when neogenesis was present, suggesting that this peptide might participate in the control of islet neogenesis. Thus, INGAP could be a potentially useful tool to treat conditions in which there is a decrease in beta-cell mass.
Application of crystallographic and modeling methods in the design of purine nucleoside phosphorylase inhibitors. (1991)

Competitive inhibitors of the salvage pathway enzyme purine-nucleoside phosphorylase (purine-nucleoside:orthophosphate ribosyltransferase, EC 2.4.2.1) have been designed by using the three-dimensional structure of the enzyme as determined by x-ray crystallography. The process was an iterative one that utilized interactive computer graphics, Monte Carlo-based conformational searching, energy minimization, and x-ray crystallography. The proposed compounds were synthesized and tested by an in vitro assay. Among the compounds designed and synthesized are the most potent competitive inhibitors of purine nucleoside phosphorylase thus far reported.
Improvement of near-field mastering with a 266-nm laser (2003)

Near-field mastering process with a 266 nm laser was improved in the stability for long time exposure and in the performance for ROM exposure. The exposure stability was achieved by using a chemically amplified type photoresist and by setting the air gap large. The exposure performance was achieved by reducing the aberration of the objective lens and by adjusting the focal position precisely. As a result, 100 nm narrow width was obtained in the groove structure, and good signal quality was obtained from a 25 gigabyte (GB) read only memory (ROM) disc. A full area exposure for a 25 GB ROM disc was also achieved.
A Zone‐Casting Technique for Device Fabrication of Field‐Effect Transistors Based on Discotic Hexa‐peri‐hexabenzocoronene (2005)

Field-effect transistors with highly ordered active layers are fabricated by zone-casting discotic dodecyl-substituted hexa-peri-hexabenzocoronene molecules onto hydrophobic substrates to form semiconducting columnar structures (see Figure). The discs form columns that possess long-range order on the scale of square centimeters, and the devices show order-of-magnitude improvements in charge-carrier mobilities over previously reported devices.
Stability of Buffer Solutions for SSC Tests of Stainless Steel OCTG Material by Experimental Approach (2018)

Abstract As an extended report on buffer stability following the previous paper from a theoretical approach in 2016, this paper focuses on the buffering capability of various test buffer solutions from an experimental viewpoint, and presents experimental data supporting the theoretical results, based on the scratch repassivation behavior in electrochemical measurements. In this paper, the stability of buffer solutions for martensitic stainless steel OCTG material, which corresponds to the ability of the solution to maintain the targeted pH throughout the test duration, was experimentally evaluated by the scratch repassivation technique in electrochemical measurements. The measurements were carried out by using a specially-designed electrochemical apparatus with a sharp-pointed crooked dental scaler to make scratches on the surface of stainless steel OCTG material samples in 1 bar CO2-saturated buffer solutions. While rest potential is being measured, a short linear scratch corresponding to artificial pitting corrosion is intentionally applied. The potential drops at the moment of scratching, and then returns to the original rest potential. The stability of the buffer solution is evaluated by the time required for the potential to return to the original level, that is, the time required to repassivate the scratched area. A series of scratch-based electrochemical tests were carried out at pH 3.0, pH 3.5 and pH 4.0 to determine the stability of four kinds of NACE-TM0177-based buffer solutions. The experimental results support the phenomena of buffer stability from the theoretical viewpoint. A buffer solution with a shorter time for repassivation is consistent with the one with a more stable buffering effect from the theoretical approach. Precisely, a rich-rich-pair-based buffer solution, which is composed of a highly-concentrated weak acid and highly-concentrated conjugated base, has greater buffering stability than a lean-lean-pair-based one, which is composed of a dilute weak acid and a dilute conjugated base.
Do reduced insulin sensitivity and dyslipidemia exist in borderline hypertensive patients? (1996)

To evaluate the relationship between insulin resistance, dyslipidemia, and blood pressure (BP), we measured BP, blood glucose, plasma insulin (INS) levels, total cholesterol (T-ch), and triglyceride after an overnight fast in 454 Japanese young, nonobese, nondiabetic factory workers, including 226 normotensive (NT), 120 borderline hypertensive (BHT), and 108 essential hypertensive (EHT) subjects. Age and body mass index were strictly matched among the three groups. Fasting INS and T-ch were greater in BHT > EHT > NT (BHT ν NT, P < .05; EHT ν NT, P < .05). We also recognized significantly positive correlations between T-ch and mean BP (R = 0.39, P = .021), and between fasting INS and mean BP (r = 0.56, P = .013). These results suggests that insulin resistance and dyslipidemia are associated with hypertension in its early stage.
Toward Replacing Ethylene Oxide in a Sustainable World: Glycolaldehyde as a Bio‐Based C2 Platform Molecule (2020)

Fossil-based platform molecules such as ethylene and ethylene oxide currently serve as the primary feedstock for the C<sub>2</sub> -based chemical industry. However, in the search for a more sustainable chemical industry, fossil-based resources may preferentially be replaced by renewable alternatives, provided there is realistic economic feasibility. This Review compares and critically discusses several production routes toward bio-based structural analogues of ethylene oxide and the required adaptations for their implementation in state-of-the-art C<sub>2</sub> -based chemical processes. For example, glycolaldehyde, a structural analogue obtainable from carbohydrates by atom-economic retro-aldol reactions, may replace ethylene oxide's leading role. This alternative chemical route may not only allow the carbon footprint of conventional chemicals production to be lowered, but the introduction of a bio-based pathway may also contribute to safer production processes. Where possible, challenges, drawbacks, and prospects are highlighted.
Highly efficient gene transfer into hepatocyte‐like HepaRG cells: New means for drug metabolism and toxicity studies (2010)

HepaRG progenitor cells are capable of differentiating into hepatocyte-like cells that express a large set of liver-specific functions. These cells, however, only express small amounts of an important cytochrome P450, the CYP2E1, which limits their use for toxicological studies of drugs metabolized by this pathway. Our aim was to establish an efficient transfection protocol to increase CYP2E1 expression in HepaRG cells. Transfection protocols of the green fluorescent protein (GFP) reporter gene were evaluated using electroporation and cationic lipids belonging to the lipophosphonates, lipophosphoramidates and lipids derived from glycine betaine. Following optimization of the charge ratios, plasmid DNA and formulations with neutral co-lipids, the lipophosphoramidate compounds KLN47 and BSV10, allowed expression of the GFP in approximately 50% of adherent progenitor HepaRG cells, while electroporation targeted GFP expression in approximately 85% of both progenitor and differentiated cells in suspension. Transient enforced expression of active CYP2E1 was also achieved in progenitors and/or differentiated HepaRG cells using the electroporation and the lipophosphoramidate compound BSV10. Importantly, in electroporated cells, CYP2E1 expression level was correlated with a significant increase in CYP2E1-specific enzymatic activity, which opens new perspectives for this CYP-dependent drug metabolism and toxicity studies using HepaRG cells.
Blue Perovskite Light‐Emitting Devices: Blue Perovskite Nanocrystal Light‐Emitting Devices via the Ligand Exchange with Adamantane Diamine (Advanced Optical Materials 13/2020) (2020)

In article number 2000289, Takayuki Chiba, Junji Kido and co-workers demonstrate the development of mixed-halide CsPb(Cl/Br)3 nanocrystals (NCs) by ligand exchange with adamantane-1,3-diamine (ADDA) having a bidentate structure for the use in blue light-emitting devices (LEDs). The ligand exchange of CsPb(Cl/Br)3 NCs with ADDA improves photoluminescence quantum yield. Blue LEDs based on CsPb(Cl/Br)3 NCs with ADDA reached a maximum external quantum efficiency of 1.1% at electroluminescence wavelength of 456 nm.
Pharmacodynamic Activity and Antithrombotic Efficacy of RPR120844, a Novel Inhibitor of Coagulation Factor Xa (1999)

These studies were designed to examine the pharmacodynamic profile and antithrombotic efficacy of RPR120844, a competitive inhibitor of coagulation factor Xa, with a K(i) of 7 nM against human factor Xa. In vitro, RPR120844 doubled activated partial thromboplastin time (APTT) at concentrations of 1.54, 1.48, and 0.74 microM in plasma obtained from humans, dogs, and rats, respectively. Intravenous bolus administration of RPR 120844 at 0.3, 1, and 3 mg/kg to rats resulted in maximal increases in APTT of 1.8-, 2.6-, and 8.4-fold over baseline, respectively. The effect on prothrombin time (PT) was less pronounced, resulting in a 4.4-fold increase at 3 mg/kg. These effects were rapidly reversible; APTT and PT returned to control values by 30 min after dosing. Intragastric administration to rats at 50, 100, and 200 mg/kg resulted in modest increases in APTT and PT of 1.5- and 1.3-fold over baseline at the highest dose. Plasma levels were estimated by anti-Xa activity by using an amidolytic, chromogenic assay. Plasma levels were 0.65, 1.29, and 2.45 microM at 30 min after dosing at 50, 100, and 200 mg/kg, respectively. Intravenous administration to dogs at 0.1 and 0.3 mg/kg produced maximal increases in APTT of 1.7- and 2.4-fold over baseline, respectively. Intragastric administration to dogs at 50 mg/kg resulted in maximal increases in APTT and PT of 1.7- and 1.1-fold over baseline, with peak plasma levels of 3.9 microM observed at 15 min after dosing. In a rat model of FeCl2-induced carotid artery thrombosis, RPR120844 (3 mg/kg, i.v. bolus + 300 microg/kg/min constant infusion; n = 4) significantly increased time-to-occlusion from 18+/-1 min (vehicle, n = 4) to 60 min (maximal observation time) and reduced thrombus mass from 5.5 +/- 0.2 mg (vehicle) to 1.4 +/- 0.2 mg. These results indicate that RPR120844 is a potent, selective inhibitor of Xa that exhibits oral activity and is efficacious in a standard model of arterial thrombosis.
ChemInform Abstract: Spectroscopic Studies on Cyanocuprate‐Catalyzed 3‐Component Couplings: Understanding the Catalytic Cycle (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Asymptotics of Ridge Regression in Convolutional Models (2021)

Understanding generalization and estimation error of estimators for simple models such as linear and generalized linear models has attracted a lot of attention recently. This is in part due to an interesting observation made in machine learning community that highly over-parameterized neural networks achieve zero training error, and yet they are able to generalize well over the test samples. This phenomenon is captured by the so called double descent curve, where the generalization error starts decreasing again after the interpolation threshold. A series of recent works tried to explain such phenomenon for simple models. In this work, we analyze the asymptotics of estimation error in ridge estimators for convolutional linear models. These convolutional inverse problems, also known as deconvolution, naturally arise in different fields such as seismology, imaging, and acoustics among others. Our results hold for a large class of input distributions that include i.i.d. features as a special case. We derive exact formulae for estimation error of ridge estimators that hold in a certain high-dimensional regime. We show the double descent phenomenon in our experiments for convolutional models and show that our theoretical results match the experiments.
2D Electrides: MXene Phase with C3 Structure Unit: A Family of 2D Electrides (Adv. Funct. Mater. 24/2021) (2021)

In article number 2100009, Gustavo M. Dalpian, Hannes Raebiger, and co-workers report the discovery of a family of 2D electride materials with composition M2CO2, where M = Sc, Y, La, Lu, Tm, and Ho. The electride behavior emerges in a new structural phase for MXenes, where the hexagonal carbon layer is broken up into C3 trimers, and anionic electrons get trapped in the voids between the C3 units.