gebhart/patrepeval huggingface dataset:
Effects of in vivo Treatment with an LHRH Antagonist Analog (D-PHE2-D-TRP3-D-PHE6) in the Immature Male Rat1 (1978)

The effect of an antagonist analog (D-Phe2-D-Trp3-D-Phe6) of luteinizing hormone releasing hormone (LHRH) on the reproductive system of immature male rats was investigated in vivo. Subcutaneous administration of the analog twice daily for 2 weeks led to a severe depletion of pituitary gonadotropins without modifying the serum gonadotropin levels or the plasma or testicular testosterone levels. The weights of the body, anterior pituitary, testes or sex accessory organs were not affected by the analog. Progression of spermatogenesis in the analog treated animals was also comparable to that observed in control animals which received injections of diluent alone. The reduced pituitary gonadotropin levels may have been due to a direct effect of the analog on the pituitary gland, the hypothalamus or both.
Dissection of cell cycle–dependent dynamics of Dnmt1 by FRAP and diffusion-coupled modeling (2013)

DNA methyltransferase 1 (Dnmt1) reestablishes methylation of hemimethylated CpG sites generated during DNA replication in mammalian cells. Two subdomains, the proliferating cell nuclear antigen (PCNA)-binding domain (PBD) and the targeting sequence (TS) domain, target Dnmt1 to the replication sites in S phase. We aimed to dissect the details of the cell cycle-dependent coordinated activity of both domains. To that end, we combined super-resolution 3D-structured illumination microscopy and fluorescence recovery after photobleaching (FRAP) experiments of GFP-Dnmt1 wild type and mutant constructs in somatic mouse cells. To interpret the differences in FRAP kinetics, we refined existing data analysis and modeling approaches to (i) account for the heterogeneous and variable distribution of Dnmt1-binding sites in different cell cycle stages; (ii) allow diffusion-coupled dynamics; (iii) accommodate multiple binding classes. We find that transient PBD-dependent interaction directly at replication sites is the predominant specific interaction in early S phase (residence time Tres ≤ 10 s). In late S phase, this binding class is taken over by a substantially stronger (Tres ∼22 s) TS domain-dependent interaction at PCNA-enriched replication sites and at nearby pericentromeric heterochromatin subregions. We propose a two-loading-platform-model of additional PCNA-independent loading at postreplicative, heterochromatic Dnmt1 target sites to ensure faithful maintenance of densely methylated genomic regions.
To GEE or Not to GEE (2010)

Two modeling approaches are commonly used to estimate the associations between neighborhood characteristics and individual-level health outcomes in multilevel studies (subjects within neighborhoods). Random effects models (or mixed models) use maximum likelihood estimation. Population average models typically use a generalized estimating equation (GEE) approach. These methods are used in place of basic regression approaches because the health of residents in the same neighborhood may be correlated, thus violating independence assumptions made by traditional regression procedures. This violation is particularly relevant to estimates of the variability of estimates. Though the literature appears to favor the mixed-model approach, little theoretical guidance has been offered to justify this choice. In this paper, we review the assumptions behind the estimates and inference provided by these 2 approaches. We propose a perspective that treats regression models for what they are in most circumstances: reasonable approximations of some true underlying relationship. We argue in general that mixed models involve unverifiable assumptions on the data-generating distribution, which lead to potentially misleading estimates and biased inference. We conclude that the estimation-equation approach of population average models provides a more useful approximation of the truth.
Strong spin–orbit quenching via the product Jahn–Teller effect in neutral group IV qubits in diamond (2020)

Abstract Artificial atom qubits in diamond have emerged as leading candidates for a range of solid-state quantum systems, from quantum sensors to repeater nodes in memory-enhanced quantum communication. Inversion-symmetric group IV vacancy centers, comprised of Si, Ge, Sn, and Pb dopants, hold particular promise as their neutrally charged electronic configuration results in a ground-state spin triplet, enabling long spin coherence above cryogenic temperatures. However, despite the tremendous interest in these defects, a theoretical understanding of the electronic and spin structure of these centers remains elusive. In this context, we predict the ground-state and excited-state properties of the neutral group IV color centers from first principles. We capture the product Jahn–Teller effect found in the excited state manifold to second order in electron–phonon coupling, and present a nonperturbative treatment of the effect of spin–orbit coupling. Importantly, we find that spin–orbit splitting is strongly quenched due to the dominant Jahn–Teller effect, with the lowest optically-active 3 E u state weakly split into m s -resolved states. The predicted complex vibronic spectra of the neutral group IV color centers are essential for their experimental identification and have key implications for use of these systems in quantum information science.
Molecular recognition of ketamine by a subset of olfactory G protein–coupled receptors (2015)

Ketamine elicits various neuropharmacological effects, including sedation, analgesia, general anesthesia, and antidepressant activity. Through an in vitro screen, we identified four mouse olfactory receptors (ORs) that responded to ketamine. In addition to their presence in the olfactory epithelium, these G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors (GPCRs) are distributed throughout the central nervous system. To better understand the molecular basis of the interactions between ketamine and ORs, we used sequence comparison and molecular modeling to design mutations that (i) increased, reduced, or abolished ketamine responsiveness in responding receptors, and (ii) rendered nonresponding receptors responsive to ketamine. We showed that olfactory sensory neurons (OSNs) that expressed distinct ORs responded to ketamine in vivo, suggesting that ORs may serve as functional targets for ketamine. The ability to both abolish and introduce responsiveness to ketamine in GPCRs enabled us to identify and confirm distinct interaction loci in the binding site, which suggested a signature ketamine-binding pocket that may guide exploration of additional receptors for this general anesthetic drug.
Blockade of Nogo-66, Myelin-Associated Glycoprotein, and Oligodendrocyte Myelin Glycoprotein by Soluble Nogo-66 Receptor Promotes Axonal Sprouting and Recovery after Spinal Injury (2004)

The growth of injured axons in the adult mammalian CNS is limited after injury. Three myelin proteins, Nogo, MAG (myelin-associated glycoprotein), and OMgp (oligodendrocyte myelin glycoprotein), bind to the Nogo-66 receptor (NgR) and inhibit axonal growth in vitro. Transgenic or viral blockade of NgR function allows axonal sprouting in vivo. Here, we administered the soluble function-blocking NgR ectodomain [aa 27-310; NgR(310)ecto] to spinal-injured rats. Purified NgR(310)ecto-Fc protein was delivered intrathecally after midthoracic dorsal over-hemisection. Axonal sprouting of corticospinal and raphespinal fibers in NgR(310)ecto-Fc-treated animals correlates with improved spinal cord electrical conduction and improved locomotion. The ability of soluble NgR(310)ecto to promote axon growth and locomotor recovery demonstrates a therapeutic potential for NgR antagonism in traumatic spinal cord injury.
Human airway surface epithelial regeneration is delayed and abnormal in cystic fibrosis (2006)

Cystic fibrosis (CF) at an advanced stage of the disease is characterized by airway epithelial injury and remodelling. Whether CF remodelling is related to infection and inflammation or due to an abnormal regenerative process is still undecided. We have recently established the expression and secretion profiles of interleukin (IL)-8, matrix metalloproteinase (MMP)-7, MMP-9, and tissue inhibitor of metalloproteinase (TIMP)-1 during non-CF airway epithelial regeneration in a humanized nude mouse xenograft model. To enhance our understanding of CF remodelling, we compared the regeneration process of non-infected human CF and non-CF nasal epithelia. In both CF and non-CF situations, epithelial regeneration was characterized by successive steps of cell adhesion and migration, proliferation, pseudostratification, and terminal differentiation. However, histological examination of the grafts showed a delay in differentiation of the CF airway epithelium. Cell proliferation was higher in the regenerating CF epithelium, and the differentiated CF epithelium exhibited a pronounced height increase and basal cell hyperplasia in comparison with non-CF epithelium. In addition, while the number of goblet cells expressing MUC5AC was similar in CF and non-CF regenerated epithelia, the number of MUC5B-immunopositive goblet cells was lower in CF grafts. The expression of human IL-8, MMP-7, MMP-9, and TIMP-1 was enhanced in CF epithelium, especially early in the regenerative process. Together, our data strongly suggest that the regeneration of human CF airway surface epithelium is characterized by remodelling, delayed differentiation, and altered pro-inflammatory and MMP responses.
22.1 A 25Gb/s burst-mode receiver for rapidly reconfigurable optical networks (2015)

Rapidly reconfigurable optical networks that keep the data in the optical domain potentially offer significant advantages in latency, bandwidth and power dissipation. Existing optical switch technologies (e.g., MEMS-based) are limited to millisecond-scale reconfiguration times, severely reducing their application space. The emerging field of silicon photonics enables optical switches operating on a nanosecond scale [1]. However, full utilization of the speed of these switches requires nanosecond-scale burst-mode transceivers, similar to those used in passive optical networks [2]. In this work, we reporta burst-mode receiver for optical links in a dynamically reconfigurable network. Through the introduction of interlocking search algorithms, a robust 25Gb/s burst-mode operation is achieved with 31ns lock time, −10.9dBm sensitivity, and 4.4pJ/b efficiency.
SQIF Antenna Measurement in Near Field (2015)

We have been developing superconducting microwave (8-15 GHz bandwidth) magnetic field receiving antennas based on a two-dimensional (2D) Superconducting Quantum Interference Filter (SQIF) composed of bi-SQUID arrays. The 2D arrays are designed and fabricated using standard HYPRES niobium 4.5 kA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> process. The designed non-uniformity in inductances of bi-SQUID cells produces a pronounced zero-field antipeak in the flux-voltage response curve. We select the active antenna operation point by applying an appropriate dc flux bias current to set it in the middle of the antipeak linear slope. We measured comparative responses of the antenna with the SQIF dc bias at ON and OFF states when irradiated by a microwave signal from four different conventional planar ring and patch antennas placed in the near field.
Polymer‐based Spherical Activated Carbons – From Adsorptive Properties to Filter Performance (2011)

Abstract Polymer‐based spherical activated carbon (PBSAC), produced by means of carbonization and subsequent activation of a polymeric precursor in a batch process represent adsorbents with adjustable pore size distribution and adsorption characteristics. This flexibility results from batch operation and from the possibility to combine different activation media, therefore controlling the mechanisms of pore generation. The geometry and the mechanical properties of PBSAC allow for structuring of filter media e.g., for adsorbent enlargement or fixation. Other intrinsic product properties such as roundness, high crush strength and high abrasion resistance of PBSAC offer advantages in various adsorption applications.
Supplementary Figure Legends 1-6 from Lin<sup>−</sup>Sca-1<sup>+</sup>CD49f<sup>high</sup> Stem/Progenitors Are Tumor-Initiating Cells in the <i>Pten</i>-Null Prostate Cancer Model (2023)

Supplementary Figure Legends 1-6 from Lin&lt;sup&gt;−&lt;/sup&gt;Sca-1&lt;sup&gt;+&lt;/sup&gt;CD49f&lt;sup&gt;high&lt;/sup&gt; Stem/Progenitors Are Tumor-Initiating Cells in the &lt;i&gt;Pten&lt;/i&gt;-Null Prostate Cancer Model
Distributed Adaptive Constrained Optimization for Smart Matter Systems (2002)

The remarkable increase in computing power together with a similar increase in sensor and actuator capabilities now under way is enabling a significant change in how systems can sense and manipulate their environment. These changes require control algorithms capable of operating a multitude of interconnected components. In particular, novel “smart matter” systems will eventually use thousands of embedded, microsize sensors, actuators and processors. In this paper, we propose a new framework for a on-line, adaptive constrained optimization for distributed embedded applications. In this approach, on-line optimization problems are decomposed and distributed across the network, and solvers are controlled by an adaptive feedback mechanism that guarantees timely solutions. We also present examples from our experience in implementing smart matter systems to motivate our ideas.
Experimental observation of photonic bandgaps in two dimensional hyperuniform disordered materials (2011)

We report the first experimental demonstration of photonic bandgaps (PBGs) in 2D hyperuniform disordered materials and show that is possible to obtain isotropic, disordered, photonic materials of arbitrary size with complete PBGs. There are only limited numbers of allowed rotational symmetries in periodic or quasiperiodic structures. Periodicity and Bragg scattering lead to different stop gap center frequencies in different directions, since periodicities change in different directions. Hyperuniformity together with short range geometric order and uniform local topology are enough to give raise to an isotropic PBG. Hyperuniform systems have a variance in mass or particle number which varies with distance, r, from an arbitrary point less rapidly than the d dimensional volume. We present a new class of photonic materials posessing PBGs that have a number of advantages, including: isotropy, robustness against disorder (they are already disordered), flexibility (can fit arbitrary regions of space in which one may have trouble putting a periodic system), and possibly lower minimum dielectric contrast.
Impact of Coronary Remodeling on Fractional Flow Reserve (2018)

Contains fulltext : 190515.pdf (Publisher’s version ) (Open Access)
miRConnect 2.0: identification of oncogenic, antagonistic miRNA families in three human cancers (2013)

miRConnect 2.0 is useful for identifying activities of miRNAs that are relevant to primary cancers. The new correlation data on miRNAs and mRNAs deregulated in three primary cancers are available at miRConnect.org.
Dependence of proliferative vascular smooth muscle cells on CD98hc (4F2hc, SLC3A2) (2009)

Activation of vascular smooth muscle cells (VSMCs) to migrate and proliferate is essential for the formation of intimal hyperplasia. Hence, selectively targeting activated VSMCs is a potential strategy against vaso-occlusive disorders such as in-stent restenosis, vein-graft stenosis, and transplant vasculopathy. We show that CD98 heavy chain (CD98hc) is markedly up-regulated in neointimal and cultured VSMCs, and that activated but not quiescent VSMCs require CD98hc for survival. CD98hc mediates integrin signaling and localizes amino acid transporters to the plasma membrane. SMC-specific deletion of CD98hc did not affect normal vessel morphology, indicating that CD98hc was not required for the maintenance of resident quiescent VSMCs; however, CD98hc deletion reduced intimal hyperplasia after arterial injury. Ex vivo and in vitro, loss of CD98hc suppressed proliferation and induced apoptosis in VSMCs. Furthermore, reconstitution with CD98hc mutants showed that CD98hc interaction with integrins was necessary for the survival of VSMCs. These studies establish the importance of CD98hc in VSMC proliferation and survival. Furthermore, loss of CD98hc was selectively deleterious to activated VSMCs while sparing resident quiescent VSMCs, suggesting that activated VSMCs are physiologically dependent on CD98hc, and hence, CD98hc is a potential therapeutic target in vaso-occlusive disorders.
The assessment of fundus image quality labeling reliability among graders with different backgrounds (2022)

Image grading with a Python-based tool seems to be a simple yet possibly efficient solution for the labeling of fundus images according to image quality that does not necessarily require medical background. Such grading can be subject to variability but could still effectively serve the robust identification of images with insufficient quality. This emphasizes the opportunity for the democratization of ML-applications among persons with both medical and non-medical background. However, simplicity of the grading system is key to successful categorization.
Model-Based Design of Embedded Systems (2007)

Model-based design is presented as consisting of four elements: (i) executable specification, (ii) design with simulation, (iii) implementation through code generation, and (iv) continuous test and verification. This presentation concentrates on the combined design and implementation as model elaboration. It is shown how the design of an edge detection filter can be systematically brought to an implementation by comparing a reference algorithm to an increasingly detailed representation of the implementation. Automatic program synthesis allows the generation of C code or a representation in a hardware description language (HDL). The HDL emulation can then be co-simulated in the system context to study behavior of an implementation at a cycle accurate level. This reduces expensive hardware iteration, facilitates analysis of system characteristics with detailed component implementation models, and mitigates the need for extensive test bench design.
Spring-like behavior of cytoplasm holds the mitotic spindle in place (2022)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Rational Design of Highly Active “Hybrid” Phosphine–Phosphinite Pincer Iridium Catalysts for Alkane Metathesis (2013)

Both the bisphosphine and bisphosphinite pincer complexes (tBu4PCP)IrH2 and (tBu4POCOP)IrH2 can cocatalyze alkane metathesis in tandem with olefin metathesis catalysts, but the two complexes have different resting states during catalysis, suggesting that different steps are turnover-limiting in each case. This led to the hypothesis that a complex with intermediate properties would be catalytically more active than either of these two species. Accordingly, “hybrid” phosphine–phosphinite pincer ligands (PCOP) and the corresponding iridium complexes were synthesized (3c–e). In tandem with olefin-metathesis catalyst MoF12, (tBu4PCOP)IrH2 displays significantly higher activity for the metathesis of n-hexane than does (tBu4PCP)IrH2 or (tBu4POCOP)IrH2. (tBu2PCOPiPr2)IrH4 (3d) is even more active (>30-fold more active than (tBu4POCOP)IrH2) and affords nearly 4.6 M alkane products after 8 h at 125 °C.
Dynamic conformal arcs for lung stereotactic body radiation therapy: a\n comparison with volumetric modulated arc therapy (2019)

This study evaluates dynamic conformal arc (DCA) therapy as an alternative to\nvolumetric modulated arc therapy (VMAT) for stereotactic body radiation therapy\n(SBRT) of lung cancer. The rationale for DCA is lower geometric complexity and\nhence reduced risk for interplay errors induced by respiratory motion. Forward\nplanned DCA and inverse planned DCA based on segment-weight optimization were\ncompared to VMAT for single arc treatments of three lung patients. Analysis of\ndose-volume histograms and clinical goal fulfillment revealed that DCA can\ngenerate satisfactory and near equivalent dosimetric quality to VMAT, except\nfor complex tumor geometries. Segment-weight optimized DCA provided spatial\ndose distributions qualitatively similar to those for VMAT. Our results show\nthat DCA, and particularly segment-weight optimized DCA, is an attractive\nalternative to VMAT for lung SBRT treatments, where errors from intrafraction\nmotion cannot be expected to average out over the course of the treatment.\n
Microbial transformation of hydroxy metabolites of 1-oxohexyl derivatives of theobromine byCunninghamella echinulataNRRL 1384 (2008)

The conversion of (+/-)-OHPTX and (+/-)-OHPPT using Cunninghamella echinulata can be recognized as a process, which may be recommended as an alternative to the methods used to obtain (R)-OHPTX and (R)-OHPPT.
Titelbild: Selektive katalytische Synthesen mit Kohlendioxid und Wasserstoff: Katalyse‐Schach an der Nahtstelle zwischen Energie und Chemie (Angew. Chem. 26/2016) (2016)

Die kombinierte Nutzung von CO2 und H2 als Synthesebausteine eröffnet den Zugang zu großvolumigen Grundchemikalien ebenso wie zu komplexen, hoch funktionalisierten Molekülen. J. Klankermayer, W. Leitner et al. diskutieren in ihrem Aufsatz auf S. 7416 ff., wie sich mit effizienten Katalysatoren die notwendigen Transformationen wie strategische Züge auf einem molekularen Schachbrett planen lassen. Die kombinierte Nutzung von CO2 und H2 als Synthesebausteine eröffnet den Zugang zu großvolumigen Grundchemikalien ebenso wie zu komplexen, hoch funktionalisierten Molekülen. J. Klankermayer, W. Leitner et al. diskutieren in ihrem Aufsatz auf S. 7416 ff., wie sich mit effizienten Katalysatoren die notwendigen Transformationen wie strategische Züge auf einem molekularen Schachbrett planen lassen. Metalloborophene Hierarchische Nanomaterialien siRNA-Transport
The Faraday effect and magneto-optical figure of merit in the visible region for lithium borate glasses containing (1998)

Faraday-effect measurements have been carried out at room temperature for -containing lithium borate glasses to evaluate the magneto-optical figure of merit in the wavelength range of 350-850 nm. The magneto-optical figure of merit tends to increase with decreasing wavelength except for the range within which absorption bands due to the 4f-4f transitions are observed. Glasses with low content and high concentration of exhibit fairly large magneto-optical figures of merit at around 400 nm which corresponds to the emission wavelength of the (Ga, In)N laser diode; the magneto-optical figure of merit of glass is more than at 400 nm under an external magnetic field of 15 kOe. The analyses of the wavelength dependence of the Verdet constant indicate that the magnitude of the Verdet constant is large because the effective transition probability is high, coincident with the early suggestion by Shafer and Suits [ J. Am. Ceram. Soc. 49 (1966) 261]. This suggests that the magnitude of the Verdet constant remains large even in the wavelength range far from the position of the optical absorption peak due to the 4f-5d transition which causes the Faraday effect. Because the absorbance due to the 4f-5d transition is low in such a wavelength range, the -containing glasses show large magneto-optical figures of merit.