gebhart/patrepeval huggingface dataset:
Direct determination of the silicon donor ionization energy in homoepitaxial AlN from photoluminescence two-electron transitions (2013)

We report on the identification of a two-electron transition for the shallow donor silicon in homoepitaxial aluminum nitride (AlN). One c-oriented sample was analyzed by low temperature photoluminescence spectroscopy on multiple excitation spots. We find a unique correlation of one single emission band, 76.6 meV below the free excitonic emission, with the luminescence of excitons bound to neutral silicon proving the identity as a two-electron transition. The assignment is confirmed by temperature dependent photoluminescence investigations. We find a donor ionization energy of (63.5 ± 1.5) meV for silicon in AlN.
Association Between Type-specific HPV Infections and hTERT DNA Methylation in Patients with Invasive Cervical Cancer (2016)

Differences in patterns of methylation of the hTERT core promoter [region 1 (nt -208 to -1) and region 2 (nt +1 to +104) relative to first ATG] are related to the HPV species present.
Total cellular glycomics allows characterizing cells and streamlining the discovery process for cellular biomarkers (2013)

Although many of the frequently used pluripotency biomarkers are glycoconjugates, a glycoconjugate-based exploration of novel cellular biomarkers has proven difficult due to technical difficulties. This study reports a unique approach for the systematic overview of all major classes of oligosaccharides in the cellular glycome. The proposed method enabled mass spectrometry-based structurally intensive analyses, both qualitatively and quantitatively, of cellular N- and O-linked glycans derived from glycoproteins, glycosaminoglycans, and glycosphingolipids, as well as free oligosaccharides of human embryonic stem cells (hESCs), induced pluripotent stem cells (hiPSCs), and various human cells derived from normal and carcinoma cells. Cellular total glycomes were found to be highly cell specific, demonstrating their utility as unique cellular descriptors. Structures of glycans of all classes specifically observed in hESCs and hiPSCs tended to be immature in general, suggesting the presence of stem cell-specific glycosylation spectra. The current analysis revealed the high similarity of the total cellular glycome between hESCs and hiPSCs, although it was suggested that hESCs are more homogeneous than hiPSCs from a glycomic standpoint. Notably, this study enabled a priori identification of known pluripotency biomarkers such as SSEA-3, -4, and -5 and Tra-1-60/81, as well as a panel of glycans specifically expressed by hESCs and hiPSCs.
Antibody‐induced dimerization of HARPTPα–EGFR chimera suggests a ligand dependent mechanism of regulation for RPTPα (2000)

We developed a system to study the function of the ectodomain of RPTPalpha, a transmembrane protein-tyrosine phosphatase, by fusing the HA-epitope tagged ectodomain of RPTPalpha to the transmembrane and intracellular domain of the epidermal growth factor receptor, EGFR, a receptor protein-tyrosine kinase that is activated by dimerization. Although the use of chemical crosslinkers shows that preformed HARPTPalpha-EGFR dimers exist, bivalent anti-HA-tag antibody activated HARPTPalpha-EGFR chimeras, suggesting this system may be used to study regulation of dimerization. We used this system to show that newborn calf serum may contain (a) potential ligand(s) for RPTPalpha. Our results suggest that RPTPalpha dimerization and thus activity may be affected by ligand binding.
Efficient Production of Mannan-Degrading Enzymes by the Basidiomycete Sclerotium rolfsii (1998)

Sclerotium rolfsii CBS 191.62 was cultivated on a number of carbon (C) sources, including mono- and disaccharides, as well as on polysaccharides, to study the formation of different mannan-degrading enzyme activities. Highest levels of mannanase activity were obtained when α-cellulose-based media were used for growth, but formation of mannanase could not be enhanced by employing galactomannan as the only carbon source. Although both xylanase and cellulase formation was almost completely repressed when S. rolfsii was grown on more readily metabolizable carbohydrates, including glucose or mannose, considerable amounts of mannanase activity were secreted under these growth conditions. Enhanced mannanase production only commenced when glucose was depleted in the medium. The maximal mannanase activity of 240 IU/mL obtained in a laboratory fermentation is remarkable. Mannanase activity formed under these derepressed conditions could be mainly attributed to one major, acidic mannanase isoenzyme with a pI value of 2.75.
Force-based weld quality monitoring algorithm (2011)

Traditionally, to check weld quality, destructive (the dominant method at industry until now) and non-destructive tests are used on randomly sampled work pieces at the production site. These processes tend to be predominantly off-line or end-of-line processes. The objective of the force-based weld monitoring algorithm is to classify the weld status, i.e. cold, normal and expulsion, by using non-intrusive force sensor. It is composed mainly from two sub-algorithms: expulsion and normal welds detection. This algorithm has been tested on medium frequency direct current (MFDC) constant current (CC) control. The results were as follows: the percentage of the false alarm (I) type-1 error is the lowest for cold welds case at 3.6%, 11.0% for normal welds and 21.7% for expulsion welds. As for the failed alarm (β) type-2 error, the lowest percentage is for expulsion welds 1.9%, 3.4% for cold welds and 16.5% for normal welds.
Transnitrilation from Dimethylmalononitrile to Aryl Grignard and Lithium Reagents: A Practical Method for Aryl Nitrile Synthesis (2015)

An electrophilic cyanation of aryl Grignard or lithium reagents, generated in situ from the corresponding aryl bromides or iodides, by a transnitrilation with dimethylmalononitrile (DMMN) was developed. DMMN is a commercially available, bench-stable solid. The transnitrilation with DMMN avoids the use of toxic reagents and transition metals and occurs under mild reaction conditions, even for extremely sterically hindered substrates. The transnitrilation of aryllithium species generated by directed ortho-lithiation enabled a net C-H cyanation. The intermediacy of a Thorpe-type imine adduct in the reaction was supported by isolation of the corresponding ketone from the quenched reaction. Computational studies supported the energetic favorability of retro-Thorpe fragmentation of the imine adduct.
Adoptive Cellular Therapy with Autologous Tumor-Infiltrating Lymphocytes and T-cell Receptor–Engineered T Cells Targeting Common p53 Neoantigens in Human Solid Tumors (2022)

Adoptive cellular therapy (ACT) targeting neoantigens can achieve durable clinical responses in patients with cancer. Most neoantigens arise from patient-specific mutations, requiring highly individualized treatments. To broaden the applicability of ACT targeting neoantigens, we focused on TP53 mutations commonly shared across different cancer types. We performed whole-exome sequencing on 163 patients with metastatic solid cancers, identified 78 who had TP53 missense mutations, and through immunologic screening, identified 21 unique T-cell reactivities. Here, we report a library of 39 T-cell receptors (TCR) targeting TP53 mutations shared among 7.3% of patients with solid tumors. These TCRs recognized tumor cells in a TP53 mutation- and human leucocyte antigen (HLA)-specific manner in vitro and in vivo. Twelve patients with chemorefractory epithelial cancers were treated with ex vivo-expanded autologous tumor-infiltrating lymphocytes (TIL) that were naturally reactive against TP53 mutations. However, limited clinical responses (2 partial responses among 12 patients) were seen. These infusions contained low frequencies of mutant p53-reactive TILs that had exhausted phenotypes and showed poor persistence. We also treated one patient who had chemorefractory breast cancer with ACT comprising autologous peripheral blood lymphocytes transduced with an allogeneic HLA-A*02-restricted TCR specific for p53R175H. The infused cells exhibited an improved immunophenotype and prolonged persistence compared with TIL ACT and the patient experienced an objective tumor regression (-55%) that lasted 6 months. Collectively, these proof-of-concept data suggest that the library of TCRs targeting shared p53 neoantigens should be further evaluated for the treatment of patients with advanced human cancers. See related Spotlight by Klebanoff, p. 919.
Antimicrobial efficacy against Pseudomonas aeruginosa biofilm formation in a three-dimensional lung epithelial model and the influence of fetal bovine serum (2017)

In vitro models that mimic in vivo host-pathogen interactions are needed to evaluate candidate drugs that inhibit bacterial virulence traits. We established a new approach to study Pseudomonas aeruginosa biofilm susceptibility on biotic surfaces, using a three-dimensional (3-D) lung epithelial cell model. P. aeruginosa formed antibiotic resistant biofilms on 3-D cells without affecting cell viability. The biofilm-inhibitory activity of antibiotics and/or the anti-biofilm peptide DJK-5 were evaluated on 3-D cells compared to a plastic surface, in medium with and without fetal bovine serum (FBS). In both media, aminoglycosides were more efficacious in the 3-D cell model. In serum-free medium, most antibiotics (except polymyxins) showed enhanced efficacy when 3-D cells were present. In medium with FBS, colistin was less efficacious in the 3-D cell model. DJK-5 exerted potent inhibition of P. aeruginosa association with both substrates, only in serum-free medium. DJK-5 showed stronger inhibitory activity against P. aeruginosa associated with plastic compared to 3-D cells. The combined addition of tobramycin and DJK-5 exhibited more potent ability to inhibit P. aeruginosa association with both substrates. In conclusion, lung epithelial cells influence the efficacy of most antimicrobials against P. aeruginosa biofilm formation, which in turn depends on the presence or absence of FBS.
Early protective effect of hypothermia in newborn pigs after hyperoxic, but not after normoxic, reoxygenation (2010)

Abstract Mild hypothermia can attenuate the development of brain damage after asphyxia. Supplemental oxygen during resuscitation increases generation of reactive oxygen species, compared to room air. It is unknown if supplemental oxygen affects hypothermic neuroprotection. We studied the early effects of hyperoxic reoxygenation and subsequent hypothermia on tissue oxygenation, microcirculation, inflammation and brain damage after global hypoxia. Anesthetized newborn pigs were randomized to control (n=6), or severe global hypoxia (n=46). Three pigs died during hypoxia or reoxygenation. After 20-min reoxygenation with room air (n=22) or 100% oxygen (n=21), pigs were randomized to normothermia (deep rectal temperature 39 degrees C, n=22) or total body cooling (35 degrees C, n=21) for 6.5 h before the experiment was terminated. We demonstrated a differential effect of post-hypoxic hypothermia between animals reoxygenated with 100% oxygen and with room air, with reduced damage only in hypothermic animals reoxygenated with 100% oxygen (P=0.001). Hyperoxic reoxygenation resulted in a significant overshoot in striatal oxygen tension, without affecting microcirculation. Inflammatory response after the insult did not differ between groups. The results indicate an early protective effect of hypothermia which may vary with oxygen level used during reoxygenation.
Thermal amplitudes of surface atoms on Si(111) 2×1 and Si(001) 2×1 (1989)

Atomic displacement-displacement correlation functions for the surface atoms of the Si(111) 2\ifmmode\times\else\texttimes\fi{}1 and Si(001) 2\ifmmode\times\else\texttimes\fi{}1 surfaces are calculated using phonon energies and eigenvectors obtained from a tight-binding theory of the lattice dynamics of Si. The temperature dependence and the possible anisotropies of the amplitudes of vibration of the surface atoms are investigated. For the \ensuremath{\pi}-bonded chain model of Si(111) 2\ifmmode\times\else\texttimes\fi{}1 it is found that the surface atoms have larger vibrational amplitudes perpendicular to the surface than parallel to it, and this anisotropy (1.8 in the mean-squared amplitudes at 270 K) increases rapidly with increasing temperature. This is attributed to the existence of a small-wavelength acoustic phonon with an unusually low energy. For the surface atoms on Si(001) 2\ifmmode\times\else\texttimes\fi{}1 the anisotropy between perpendicular and parallel vibrations is not as marked. The interatomic vibrational correlations between surface atoms reveal the strength of the new bonds that are formed in the reconstruction of these surfaces.
Allogeneic Bone Marrow Transplantation, Zidovudine, and Human Immunodeficiency Virus Type 1 (HIV-I) Infection (2020)

Abstract Human immunodeficiency virus type 1 (HIV-1)-infected patients with non-Hodgkin lymphoma are classified as having the acquired immunodeficiency syndrome (AIDS). Allogeneic bone marrow trans...
Tin-Free Radical Cyclizations for the Synthesis of 7-Azaoxindoles, 7-Azaindolines, Tetrahydro[1,8]naphthyridines, and Tetrahydro-5H-pyrido[2,3-b]azepin-8-ones (2004)

[reaction: see text] Compounds containing a pyridine nucleus fused to a saturated nitrogen-containing ring, including 7-azaoxindoles, 7-azaindolines, tetrahydro[1,8]naphthyridines, and tetrahydro-5H-pyrido[2,3-b]azepin-8-ones, were prepared in good yield starting from various 2,6-dichloropyridines. The method hinges on a free-radical xanthate-mediated cyclization or intermolecular addition/cyclization sequence for the construction of the new fused rings.
Power-Spectrum Centroid Detection for Doppler Systems Applications (1980)

The theoretical basis for the development of a power-spectrum centroid detector is presented, and known and new applications to centroid detection are described. Based on these applications, the requirements are formulated for a versatile centroid detector which can be employed in various types of ultrasonic doppler systems. An analysis method for centroid estimation is developed and applied to the correlation- and √f-type detectors. Closed-form expressions for estimation errors are derived and used for detector evaluation with and without additive noise at the input. A noise-reduction technique is introduced that enables accurate centroid detection despite the presence of strong input noise. Based on the results of this analysis, theoretical comparisons of the detectors, and system requirements, the √f detector is selected for implementation and use.
Machine Learning-based Prediction for Dynamic Architectural Optimizations (2019)

Embedded system complexity is rapidly evolving, becoming more desktop-system-like, requiring more complex optimization methods to adhere to more stringent design constraints (e.g., area, thermal pressures, performance, battery lifetime, etc.) given restricted resources, widely varying applications, and environmental stimuli. Configurable architectural parameters (e.g., voltage, frequency, pipeline depth, cache specifics, etc.) can be specialized to meet these application-specific constraints and requirements (e.g., available parallelism, cache locality and access patterns, etc.) based on the available resources (e.g., heterogeneous cores with different architectural parameters). Unfortunately, due to this environmental-and application-dependent information, embedded system designers are challenged with meeting constraints and requirements with no a priori knowledge of this dynamic runtime information, which results in a very large dynamic design space. In this work, we propose a machine-learning-based method to meet these runtime optimization challenges using a fast and reactive methodology. Our methodology uses offline feature selection and neural network training to create a model that can be used online to predict the best configurable parameter values based on unknown runtime applications, environmental stimuli, resource availability, user expectations, etc. Without loss of generality, we propose a cache line size online/dynamic prediction module. Results show that our prediction module achieves 86% and 91% classification accuracies, comparable to prior work, for predicting the instruction and data cache line sizes, respectively, and achieves average energy consumption optimizations within 1% of the applications' optimal energy consumptions determined using exhaustive simulation.
Attitude control of quadruped robot by using combination of mono-and bi-articular muscles (2015)

Generally, animal robots have actuators that drive only a single joint. However, the limbs of animals not only have single joint muscles, but also bi-articular muscles. Bi-articular muscles are critical because they function across two joints. Three antagonistic muscle pairs are constructed of six muscles. A combination of one bi-articular and two single joint muscles is defined as providing functional effective muscular strength. Therefore, a quadruped robot with a mechanism that imitates a bi-articular muscle is developed in this research, and its attitude control is proposed.
Impact and mitigation of narrow-band radar interference in down-link LTE (2015)

This paper investigates the impact of radar interference on LTE by directly injecting narrow-band radar waveforms into a state of the art LTE down-link simulator. We show detailed results demonstrating the impact of interference on various parts of LTE signaling including reference symbols. Then we show how the presence of radar interference causes errors in the noise and interference estimates, impacts decoding in the LTE soft decoder, and ultimately leads to erroneously received Sub-frames. We propose a mechanism to combat such interference and improve LTE throughput in the presence of narrow-band radar using selective erasures. We simulate the proposed scheme and show that it is extremely effective in mitigating narrow-band interference and realizing the throughput expected from LTE.
Depression of Dioxin Concentrations in Flue Gas and Fly Ash by Injection of Iron Oxide Catalyst in Flue Gas of a Municipal Solid Waste Incinerator, and Prevention of Leaching of Heavy Metals by Ferrite Formation (2003)

稼働中の都市ごみ焼却炉の排ガス中にAH入ロでα-Fe2O3を，EP入口で（α-Fe2O3+Ca(OH)2）を噴射して燃焼を行い，排ガス中のDXNs濃度が1/2に，飛灰中のそれが1/10に低減することを確認した．さらに，飛灰を加熱処理することにより，FeとPbをフェライト化させ，Pbの溶出を防止することができた．
Hot on the Trail of Kinesin-1 with MINFLUX (2023)

MINFLUX pioneers the dynamic measurement of protein movement with nanometer spatial and (sub)millisecond temporal resolution, while only requiring the detection of as little as ∼20 photons from an ∼1 nm-sized fluorophore [1,2].Harnessing this spatiotemporal resolution, we dissect the stepping of the motor protein kinesin-1 on microtubules at up to physiological ATP concentrations.By attaching the fluorophore to different kinesin-1 sites and resolving steps and substeps of these protein constructs, we uncover a re-orientation of the kinesin head during stepping, and we identify kinesin's one-head-bound state as the ATP-binding state and its two-head-bound state as the ATP-hydrolyzing state [3].Our results establish MINFLUX as a noninvasive tool for tracking (sub)millisecond conformational changes of proteins with nanometer resolution.
Synthesis of Highly Soluble and Oxidatively Stable Tetraceno[2,3-b]thiophenes and Pentacenes (2007)

A comparative study of suitably functionalized, highly soluble tetraceno[2,3-b]thiophenes (1-3) and pentacenes (4-6) that show higher photoxidative stability than that of unfunctionalized corresponding acenes is reported. The absorption and emission of 1-3 (Amax = 624-656 nm, lambda max = 634-672 nm, PhiF approximately 10%) and 4-6 (Amax = 672-704 nm, lambda max = 682-718 nm, PhiF approximately 10%) were found to be systematically red-shifted by the substitution in the order of the tert-butylethynyl < triisopropylsilylethynyl < phenylethynyl groups. The oxidation potentials of these compounds were similar (E1/2 approximately 0.70 V), except for 4, which showed lower oxidation potential (E1/2 approximately 0.63 V).
Novel electro-absorption modulator with germanium fins evanescently coupled to silicon waveguide (2016)

Electro-Absorption (EA) modulator is a promising candidate for the next generation devices in Si photonics with even lower power consumptions for short-reach optical interconnections. However, its relatively higher insertion loss must be addressed, and the efficient coupling from a Si waveguide to EA modulator is a challenging topic. Here, we propose, for the first time, to use novel Ge fin structures for EA modulators. An array of Ge fins evanescently coupled to a Si waveguide is used for the modulation by the Franz-Keldysh effect (FKE). We have designed this new EA modulator using Ge fins based on simulations.
Coffee consumption protects disease progression in liver cirrhosis and increases long-term survival after liver transplantation (2015)

Background: Therapeutic options to treat progression of end-stage liver disease (ESLD) or long-term survival after liver transplantation remain scarce. As coffee consumption has been shown to be hepatoprotective we evaluated its impact in these matters.
Heterogeneity of Brain GABA Transporters (1996)

Molecular cloning has revealed a surprising degree of heterogeneity in GABA transport systems. To investigate the potential of GABA transporters as therapeutic targets, we have applied a combined approach including cDNA cloning, pharmacological characterization, mRNA localization, and synthesis of novel GABA uptake inhibitors. Four high-affinity GABA transporters are present in brain and each has a unique pattern of mRNA distribution, with multiple transporters contributing to both neuronal and glial GABA uptake. We have designed and synthesized a novel GABA uptake inhibitor, (S)-SNAP-5114, with moderate affinity and selectivity for human GAT-3. The identification of selective inhibitors will help to elucidate the function and therapeutic potential of GABA transporters in the brain.
Dimethyl Acetylenedicarboxylate (2001)

[762-42-5] C6H6O4 (MW 142.11) InChI = 1S/C6H6O4/c1-9-5(7)3-4-6(8)10-2/h1-2H3 InChIKey = VHILMKFSCRWWIJ-UHFFFAOYSA-N (an electron deficient symmetrical alkynic diester useful as a dienophile and dipolarophile in cycloaddition reactions;1 can undergo [2 + 2] cycloaddition;2 Michael acceptor;3 synthesis of phthalic acid derivatives4 and heteroaromatics5) Alternate Name: DMAD. Physical Data: bp 195–198 °C; bp 98 °C/20 mmHg; d 1.1564 g cm−3. Solubility: sol common organic solvents, e.g. diethyl ether, ethyl alcohol, carbon tetrachloride. Form Supplied in: commercially available liquid. Handling, Storage, and Precautions: lachrymator and vesicant; avoid inhalation and contact with skin or eyes. Use in a fume hood.