gebhart/patrepeval huggingface dataset:
Abnormalities of cAMP signaling are present in adrenocortical lesions associated with ACTH-independent Cushing syndrome despite the absence of mutations in known genes (2009)

Lesions of the adrenal associated with AICS, independently of their GNAS, PRKAR1A, PDE11A, and PDE8B mutation status, have functional abnormalities of cAMP signaling. It is probable that epigenetic events or additional defects of genes involved in this pathway are responsible for this phenomenon.
Correction: Corrigendum: Leukocyte integrin Mac-1 regulates thrombosis via interaction with platelet GPIbα (2017)

This corrects the article DOI: 10.1038/ncomms15559.
Temperature dependence of the transverse lasing mode in vertical-cavity lasers (1995)

Experimental data are presented along with calculations which describe the near-threshold transverse modes in AlAs/GaAs/InGaAs vertical-cavity surface-emitting lasers with two different Bragg reflector systems. The Bragg reflector systems are composed of either AlAs/GaAs quarter-wave stacks or a combination of AlAs/GaAs and ZnSe/CaF. The temperature dependence of the lasing mode is studied for three different structures, and it is shown that higher-order lasing modes are favored with strong cavity detuning when the cavity resonance exists at a wavelength greater than the bulk emission peak. Important aspects of the lasing behavior are described by calculating the spontaneous mode which occurs at the lasing wavelength.
Regulation of Secondary Metabolism in Filamentous Fungi (2005)

Fungal secondary metabolites are of intense interest to humankind due to their pharmaceutical (antibiotics) and/or toxic (mycotoxins) properties. In the past decade, tremendous progress has been made in understanding the genes that are associated with production of various fungal secondary metabolites. Moreover, the regulatory mechanisms controlling biosynthesis of diverse groups of secondary metabolites have been unveiled. In this review, we present the current understanding of the genetic regulation of secondary metabolism from clustering of biosynthetic genes to global regulators balancing growth, sporulation, and secondary metabolite production in selected fungi with emphasis on regulation of metabolites of agricultural concern. Particularly, the roles of G protein signaling components and developmental regulators in the mycotoxin sterigmatocystin biosynthesis in the model fungus Aspergillus nidulans are discussed in depth.
Discovery and characterization of INCB028060, a novel, potent and selective Met RTK inhibitor for cancer treatment (2008)

2577 The Met receptor tyrosine kinase (RTK) is the only high-affinity receptor for the hepatocyte growth factor (HGF). Met kinase activation can be achieved via HGF stimulation, Met overexpression, or a variety of activating mutations. Met activation subsequently results in pleiotropic responses that, in a cell-context dependent manner, may include cell proliferation, motility, migration, invasion, survival and angiogenesis. While these effects are important for developmental processes, when dysregulated, Met has been shown to promote tumor growth, survival and metastasis. We have identified a series of novel, potent and selective small molecule inhibitors of Met kinase activity exemplified by INCB028060. INCB028060 exhibits pM potency against Met kinase in vitro. The compound is highly specific for Met kinase with > 10,000-fold selectivity over a panel of > 50 human kinases. Using human cancer cell lines derived from tumor types where Met is frequently overexpressed, we find that INCB028060 possesses nM or sub-nM potency in blocking Met phosphorylation as well as phosphorylation of downstream effectors such as ERK, AKT, STAT3, GAB-1 and FAK. As a result, INCB028060 has demonstrated potent inhibition of Met-dependent cell migration, proliferation, and effective induction of apoptosis in tumor cells, while the compound does not inhibit the growth of tumor cells (e.g. SNU-1 gastric cancer) that do not overexpress Met. While INCB028060 does not inhibit EGFR1, EGFR3 and IGF1R directly, treatment with INCB028060 causes a dramatic reduction in phosphorylated EGFR1, EGFR3 and IGF1R in the human Met-dependent SNU5 gastric cancer and H1993 lung cancer cell lines. The data indicate that in cancer cells where the met gene is amplified, the activated Met kinase may have pleiotropic effects on multiple RTK signaling pathways and therefore could play an important role in driving tumor cell growth and survival. INCB028060 has favorable in vitro ADME characteristics and excellent in vivo PK properties. Using Met/HGF-driven xenograft mouse tumor models, we find that oral dosing of INCB028060 results in dose-dependent inhibition of tumor growth and the compound is well tolerated in mice at doses that achieve complete inhibition of tumor growth. Together, the data suggest that INCB028060 is a potent, selective and orally available Met kinase inhibitor that may have therapeutic potential.
2.3 Wood pulp manufacturing and quality characteristics (2004)

Abstract Cellulose acetate being important in the fiber and textile industries is usually prepared from high quality cellulose such as cotton linters and wood pulps with an alpha cellulose content of more than 95%. In this section, therefore, wood pulps and cotton linters appropriate for cellulose acetate production were discussed in their chemical and physical properties so as to use them judiciously as natural raw materials for cellulose acetate production.
High-speed bolometry based on Johnson noise detection of hot electrons in cavity-coupled graphene (Conference Presentation) (2019)

High sensitivity and fast response are the most important metrics for infrared sensing and imaging and together form the primary tradeoff space in bolometry. To simultaneously improve both characteristics requires a paradigm shift on the thermal properties of bolometric materials. Due to a vanishingly small density of states at the charge neutrality point, graphene has a record-low electronic heat capacity which can reach values approaching one Boltzmann constant Ce ~ kb. In addition, its small Fermi surface and the high energy of its phonons result in an extremely weak electron-phonon heat exchange. The combination will allow a strong thermal isolation of the electrons in graphene for higher sensitivity without sacrificing the detector response time. These unique thermal properties and its broadband photon absorption, make graphene a promising platform for ultrasensitive and ultra-fast hot electron bolometers, calorimeters and single photon detectors for low energy light. Here, we introduce a hot-electron bolometer based on a novel Johnson noise readout of the electron gas in graphene [1,2,3], which is critically coupled to incident radiation through a photonic nanocavity. This proof-of-concept operates in the telecom spectrum, achieves an enhanced bolometric response at charge neutrality with a noise equivalent power NEP < 5pW/√Hz, a thermal relaxation time of τ < 34ps, an improved light absorption by a factor ~3, and an operation temperature up to T=300K [3]. Altogether this shows that our proof-of-concept device can be a promising bolometer with efficient light absorption and a superior sensitivity-bandwidth product. Since the detector also has no limitations on its operation temperature, it provides engineering flexibility, which overall opens a new route for practical applications in the fields of thermal imaging, observational astronomy, quantum information and quantum sensing. In particular, since it is more than 5 times faster than the bandwidth of the intermediate frequency in the hot electron bolometer mixer, it can be employed as a cutting edge bolometric mixer material. [1] K. C. Fong, PRX, 2 (2012); [2] J. Crossno et.al., Science, 351 (2016); [3] D. K. Efetov et. al., Nature Nano. (2018));
Native-like Conformations Are Sampled by Partially Folded and Disordered Variants of Bovine Pancreatic Trypsin Inhibitor (2004)

Partially folded conformational ensembles of bovine pancreatic trypsin inhibitor (BPTI) are accessed by replacing Cys 5, 30, 51, and 55 by alpha-amino-n-butyric acid (Abu) while retaining the disulfide between Cys 14 and 38; the resultant variant is termed [14-38](Abu). Two new analogues with modifications in the beta-turn, P26D27[14-38](Abu) and N26G27K28[14-38](Abu), are compared to partially folded [14-38](Abu), as well as to [R](Abu), the unfolded protein with all six Cys residues replaced by Abu. Structural features of the new analogues of [14-38](Abu) have been determined by circular dichroism (CD), one-dimensional (1)H NMR, and 8-anilino-1-naphthalenesulfonic acid (ANS) fluorescence experiments. Both analogues are more disordered than the parent [14-38](Abu), but while P26D27[14-38](Abu) has a small population of native-like conformations observed by NMR, no ordered structure is detected for N26G27K28[14-38](Abu). Trypsin inhibition assays were carried out using a modified rat trypsin, C191A/C220A, that minimizes cleavage of unfolded peptides. Both [14-38](Abu) and P26D27[14-38](Abu) significantly inhibit modified trypsin. N26G27K28[14-38](Abu) has low but measurable inhibitor activity, while [R](Abu) has no activity even when in very high molar excess relative to trypsin. ANS fluorescence is enhanced by [14-38](Abu) and by both variants but not by [R](Abu). We conclude that partially folded ensembles of BPTI, even those with little or no CD- or NMR-detectable structure, contain minor populations of native-like conformations. Partially folded [14-38](Abu) and both variants, as well as [R](Abu), have enhanced negative ellipticity in CD spectra acquired in the presence of the osmolyte trimethylamine N-oxide (TMAO). TMAO-induced structure is formed cooperatively, as indicated by thermal unfolding curves. Inhibitor activity as a function of TMAO concentration implies that the osmolyte-induced structure is native-like for [14-38](Abu) and P26D27[14-38](Abu) and is probably native-like for N26G27K28[14-38](Abu). [R](Abu) also shows increased CD-detected structure in the presence of TMAO, but such structure is likely to be collapsed and non-native.
Organocatalytic chain scission of poly(lactides): a general route to controlled molecular weight, functionality and macromolecular architecture. (2001)

A facile, single-step transesterification approach to poly(lactides) with controlled molecular weights and end-group functionality, as well as block and star-shaped architectures is described using nucleophilic amine catalysts.
Additional file 1: Supplement methods and Table S1. of Development of TASP0410457 (TASP457), a novel dihydroquinolinone derivative as a PET radioligand for central histamine H3 receptors (2016)

Receptor binding selectivity of radioligand candidate compounds. (PDF 172 kb)
Acoustic Actuation of Integrin‐Bound Microbubbles for Mechanical Phenotyping during Differentiation and Morphogenesis of Human Embryonic Stem Cells (2018)

Early human embryogenesis is a dynamic developmental process, involving continuous and concomitant changes in gene expression, structural reorganization, and cellular mechanics. However, the lack of investigation methods has limited the understanding of how cellular mechanical properties change during early human embryogenesis. In this study, ultrasound actuation of functionalized microbubbles targeted to integrin (acoustic tweezing cytometry, ATC) is employed for in situ measurement of cell stiffness during human embryonic stem cell (hESC) differentiation and morphogenesis. Cell stiffness, which is regulated by cytoskeleton structure, remains unchanged in undifferentiated hESCs, but significantly increases during neural differentiation. Further, using the recently established in vitro 3D embryogenesis models, ATC measurements reveal that cells continue to stiffen while maintaining pluripotency during epiblast cyst formation. In contrast, during amniotic cyst formation, cells first become stiffer during luminal cavity formation, but softens significantly when cells differentiate to form amniotic cysts. These results suggest that cell stiffness changes not only due to 3D spatial organization, but also with cell fate change. ATC therefore provides a versatile platform for in situ measurement of cellular mechanical property, and cell stiffness may be used as a mechanical biomarker for cell lineage diversification and cell fate specification during embryogenesis.
Nanoscale Observation of Enhanced Electromagnetic Field (1999)

The surface of nanosized discontinuous or rough metal thin films is able to induce Raman scattering enhanced by several orders of magnitude. This effect has been theoretically attributed to the local field distribution at the surface of the films. As for the relevant parameter in phase transitions, the fields experience here huge fluctuations, leading to localized giant peaks so called “hot spots”. Using a Scanning Near-Field Optical Microscope (SNOM) of extremely high lateral resolution (10 nm), we have been able to record the field distribution close to the surface of gold films. We report here the first direct observation of the hot spots with such lateral resolution. Their intensities and spatial distribution are found in good agreement with the theoretical predictions. We also have performed local spectroscopy, which shows up sharp variations at nanometric scale (much smaller than the wavelength).
Supplementary Figure 4 from Development of an Fc-Enhanced Anti–B7-H3 Monoclonal Antibody with Potent Antitumor Activity (2023)

&lt;p&gt;PDF file, 78KB, Measurement of the absolute level of circulating B cells (CD20+; Panel A), T cells (CD3+; Panel B) and NK cells (CD159a+)Panel C) in blood samples collected from cynomolgus monkeys at the indicated days prior to administration (Day -2), or following intravenous administration of PBS vehicle on Day 1 (all animals received PBS vehicle on Day 1) or MGA271 on Day 8 at the indicated dose. The panels on the left for each group represent all animals (N=6) in each dosing group, while the panels on the right represent only the recovery group animals (N=2) in each dosing group.&lt;/p&gt;
Branch retinal vein occlusion and optic nerve head topographic parameters: the Singapore Indian eye study (2013)

Quantitative optic disc parameters (optic cup and disc area) are associated with BRVO, even in non-glaucomatous eyes. Optic nerve head morphology may play a role in BRVO pathogenesis.
Propofol General Anesthesia Decreases the Coupling Strength Between Mean Arterial Blood Pressure and Mean Cerebral Blood Flow Velocity in Patients Undergoing Coronary Artery Bypass Grafting (2019)

Cerebral autoregulation (CA) maintains mean cerebral blood flow velocity (MCBFV) stable in spite of variations in mean arterial pressure (MAP). Propofol anesthesia is known to preserve CA, although information on the anesthesia effect on MCBFV and MAP variability coupling at sedation levels typical of major cardiac surgery is limited. MAP and MCBFV time series were respectively recorded from radial artery and left middle cerebral artery via transcranial Doppler, before (PRE) and after (POST) general anesthesia induction with propofol and remifentanil in 10 male subjects (age 64.7±7.0 years) undergoing coronary artery bypass grafting. Squared coherence (K2) was computed in the typical bands of CA, namely very low (0.02-0.07 Hz), low (0.07-0.15 Hz) and high frequency (0.15-0.4 Hz). The null hypothesis of coupling was tested through a surrogate analysis associating MAP and MCBFV series taken from different patients in the same experimental condition. MAP and MCBFV original series were significantly more associated than surrogate ones during PRE. K2 was reduced in the three frequency bands during POST to a level comparable with surrogates. By decoupling MCBFV and MAP propofol general anesthesia favors situations of stable MCBFV in response to slow modifications of MAP but the full decoupling might hide the limited resources of the cerebrovascular control to actively regulate MCBFV.
Molecular determinants for a cardiovascular collapse in anthrax (2014)

Bacillus anthracis releases two bipartite proteins, lethal toxin and edema factor, that contribute significantly to the progression of anthrax-associated shock. As blocking the anthrax toxins prevents disease, the toxins are considered the main virulence factors of the bacterium. The anthrax bacterium and the anthrax toxins trigger multi-organ failure associated with enhanced vascular permeability, hemorrhage and cardiac dysfunction in animal challenge models. A recent study using mice that either lacked the anthrax toxin receptor in specific cells and corresponding mice expressing the receptor in specific cell types demonstrated that cardiovascular cells are critical for disease mediated by anthrax lethal toxin. These studies are consistent with involvement of the cardiovascular system, and with an increase of cardiac failure markers observed in human anthrax and in animal models using B. anthracis and anthrax toxins. This review discusses the current state of knowledge regarding the pathophysiology of anthrax and tries to provide a mechanistic model and molecular determinants for the circulatory shock in anthrax.
Plasma-Etching Technology With In Situ Etched-Surface Modification for Highly Reliable Low-&lt;tex&gt;$ k$&lt;/tex&gt;/Cu Dual Damascene Interconnects (2005)

The plasma-etching technology presented in this paper is for fabricating highly reliable Cu dual damascene interconnects (DDI) with organic low-k film through modification of the in situ etched surface during low-k etching. Nitrogen-based plasma with oxygen and high-molecular-weight fluorocarbon gas (C>2) chemically modifies the sidewall surface of the etched low-k film, changing it into the carbon nitride with fluorocarbon-polymer passivation from the etching gas. After wet cleaning, the fluorocarbon-polymer is removed selectively, leaving a carbon nitride modified layer (CNL) on the sidewall. The CNL has been found to suppress Cu diffusion into the low-k film. A stacked barrier structure of conventional barrier metal and CNL is expected to have high tolerance to Cu diffusion. Combining a dual-hard-mask etching sequence with the CNL modification, Cu DDIs with organic low-k film were fabricated with high yield.
Quasi-3D Light Confinement in Double Photonic Crystal Reflectors VCSELs for CMOS-Compatible Integration (2011)

A novel architecture of one-dimensional photonic crystal membrane (PCM) reflectors embodying a heterostructure is proposed as a robust design aimed at a 3-D efficient confinement of light in single-mode polarization-controlled 1.55-μm vertical-cavity surface-emitting laser (VCSEL) microsources for heterogeneous integration on complementary metal-oxide-semiconductor (CMOS). On the basis of a theoretical approach, the paper focuses on the deep interweaving between the kinetics of light transport in the mirrors and the physical nature of the exploited Fano resonances. An example of VCSEL design for optical pumping employing heterostructure-confined photonic crystal mirrors is presented. The predicted photons kinetics along with the considerable improvement in cavity modal features owing to the enhanced mirror architecture have been confirmed by performing rigorous three-dimensional finite-difference time-domain (3-D FDTD) calculations. Finally, experimental observations of photoluminescence (PL) emission performed on first-ever fabricated devices for optical pumping show striking agreement with theoretical considerations and ab initio modelling.
Electron Injection from Colloidal PbS Quantum Dots into Titanium Dioxide Nanoparticles (2008)

Injection of photoexcited electrons from colloidal PbS quantum dots into TiO(2) nanoparticles is investigated. The electron affinity and ionization potential of PbS quantum dots, inferred from cyclic voltammetry measurements, show strong size dependence due to quantum confinement. On the basis of the measured energy levels, photoexcited electrons should transfer efficiently from the quantum dots into TiO(2) only for quantum-dot diameter below approximately 4.3 nm. Continuous-wave fluorescence spectra and fluorescence transients of PbS quantum dots coupled to titanium dioxide nanoparticles are consistent with electron transfer for small quantum dots. The measured electron transfer time is surprisingly slow ( approximately 100 ns), and implications of this for future photovoltaics will be discussed. Initial results obtained from solar cells sensitized with PbS quantum dots are presented.
Bend insensitivity of large-mode-area CLING fibers (Conference Presentation) (2020)

Cladded linear index graded (CLING) fibers are designed to reduce the spatial overlap between the fundamental mode and higher-order modes in order to mitigate thermal mode instability. Numerical simulations were used to study the effects of bending on loss and mode deformation in CLING fibers. It was found that CLING fibers experience mode deformation at a >10x tighter bend radius than conventional large-mode-area (LMA) fiber. The CLING fiber therefore retains all the advantages of an LMA fiber but at small bend radii, enabling much larger mode areas than allowable in conventional LMA fibers (currently 25-µm core).
MCD spectroscopy and TD-DFT calculations of low-symmetry acenaphthoporphyrins with dual fluorescence (2013)

Magnetic circular dichroism (MCD) spectroscopy and TD-DFT calculations are used to analyze the electronic structure and optical properties of low-symmetry acenaphthoporphyrins with AAAB, ABAB and AABB structures. Evidence for dual fluorescence caused by tautomerism has been identified in the emission spectra of the AAAB and ABAB compounds. The sign sequences observed for the Q and B bands in the MCD spectra have been used to validate the results of the TD-DFT calculations. An anomalous +/- sign sequence is observed in the B band region with ascending energy similar to that reported previously for metal tetraphenyltetraacenaphthoporphyrin complexes.
Domain and range decomposition methods for coded aperture x-ray coherent scatter imaging (2016)

Coded aperture X-ray coherent scatter imaging is a novel modality for ascertaining the molecular structure of an object. Measurements from different spatial locations and spectral channels in the object are multiplexed through a radiopaque material (coded aperture) onto the detectors. Iterative algorithms such as penalized expectation maximization (EM) and fully separable spectrally-grouped edge-preserving reconstruction have been proposed to recover the spatially-dependent coherent scatter spectral image from the multiplexed measurements. Such image recovery methods fall into the category of domain decomposition methods since they recover independent pieces of the image at a time. Ordered subsets has also been utilized in conjunction with penalized EM to accelerate its convergence. Ordered subsets is a range decomposition method because it uses parts of the measurements at a time to recover the image. In this paper, we analyze domain and range decomposition methods as they apply to coded aperture X-ray coherent scatter imaging using a spectrally-grouped edge-preserving regularizer and discuss the implications of the increased availability of parallel computational architecture on the choice of decomposition methods. We present results of applying the decomposition methods on experimental coded aperture X-ray coherent scatter measurements. Based on the results, an underlying observation is that updating different parts of the image or using different parts of the measurements in parallel, decreases the rate of convergence, whereas using the parts sequentially can accelerate the rate of convergence.