gebhart/patrepeval huggingface dataset:
Fully Reversible Homogeneous and Heterogeneous Li Storage in RuO2 with High Capacity (2003)

Abstract In this paper, we report that Li can be stored in RuO 2 with an unusually high coulombic efficiency. The process involves three electrochemical steps: i) formation of a Ru/Li 2 O nanocomposite, ii) formation of a Li‐containing surface film, and iii) interfacial deposition of Li within the Ru/Li 2 O matrix. Corresponding to the storage of 5.6 mole of Li ions per mole of RuO 2 , a high capacity of 1130 mAh g –1 is achieved. Furthermore, virtually all inserted Li ions can be extracted, corresponding to a nearly 100 % coulombic efficiency at the first cycle. Achieving a complete reversibility for such a Li storage system through complex heterogeneous solid‐state electrochemical reactions is possible because of the formation of nanoscale Ru/Li 2 O during Li insertion and nano‐RuO 2 during Li extraction, in addition to the favorable transport properties of RuO 2 itself.
Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal coronaviruses (2021)

Several genome-wide CRISPR knockout screens have been conducted to identify host factors regulating SARS-CoV-2 replication, but the models used have often relied on overexpression of ACE2 receptor. Additionally, such screens have yet to identify the protease TMPRSS2, known to be important for viral entry at the plasma membrane. Here, we conducted a meta-analysis of these screens and showed a high level of cell-type specificity of the identified hits, arguing for the necessity of additional models to uncover the full landscape of SARS-CoV-2 host factors. We performed genome-wide knockout and activation CRISPR screens in Calu-3 lung epithelial cells, as well as knockout screens in Caco-2 intestinal cells. In addition to identifying ACE2 and TMPRSS2 as top hits, our study reveals a series of so far unidentified and critical host-dependency factors, including the Adaptins AP1G1 and AP1B1 and the flippase ATP8B1. Moreover, new anti-SARS-CoV-2 proteins with potent activity, including several membrane-associated Mucins, IL6R, and CD44 were identified. We further observed that these genes mostly acted at the critical step of viral entry, with the notable exception of ATP8B1, the knockout of which prevented late stages of viral replication. Exploring the pro- and anti-viral breadth of these genes using highly pathogenic MERS-CoV, seasonal HCoV-NL63 and -229E and influenza A orthomyxovirus, we reveal that some genes such as AP1G1 and ATP8B1 are general coronavirus cofactors. In contrast, Mucins recapitulated their known role as a general antiviral defense mechanism. These results demonstrate the value of considering multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential new targets for therapeutic interventions.
Endothelin Receptor Antagonists: A New Therapeutic Option for Improving the Outcome after Solid Organ Transplantation? (2003)

Initially described as the most potent vasoconstrictor peptide, endothelin (ET) has also been shown to possess extraordinary immunomodulatory and proinflammatory properties. Because of this broad spectrum of biological activities, a possible role of the ET-system in solid organ transplantation has soon become a focus of research. Several studies demonstrated a pathogenetic involvement of ET in ischemia/reperfusion injury of heart, liver, kidney, and lung grafts. ET accumulates during cold storage of organs and can be detected in the effluent preservation solution. In addition ET is very, likely to play a pivotal role in the development of chronic rejection, which represents the major cause of late allograft loss. Increased expression of components of the ET-system has been described in areas of neointimal proliferation, a hallmark of chronic graft rejection. Both selective ET-A as well as non-selective ET-A/B receptor antagonists improved histomorphological and functional sequelae of chronic rejection. However these data have largely been derived from experimental animal transplantation, and ET receptor blockers have only recently been introduced in clinical medicine. A significant number of investigational drugs are now being tested in humans, with a main focus on cardiovascular diseases, such as congestive heart failure and pulmonary hypertension. First results have markedly dampened the initial enthusiastic vision of ET receptor blockers being organoprotective super-weapons. Thus the clinical potential of ET antagonists in general, and especially in solid-organ transplantation, is still to be defined.
Ligand Enabled ortho-Arylation of (hetero)Aromatic Acids with 2,6-Disubstituted Aryl Halides (2023)

Abstract Directed C–H arylations have proven to be some of the most advantageous strategies for the synthesis of biaryls. However, their sensitivity towards steric hindrance is a key limitation. Couplings of 2,6-disubstituted aryl halides with arenes have so far been elusive. This weakness is overcome by a ruthenium 3,4,7,8-tetramethyl-1,10-phenanthroline catalyst. It allows the selective ortho -C–H arylation of widely available (hetero)aromatic acids with bulky aryl halides in up to 95% isolated yield. 46 Examples of tri-substituted (hetero)biaryls, all outside the scope of established catalyst systems, demonstrate the efficiency of the protocol. Computational and experimental studies illustrate how this unique combination of carboxylate directing group and chelating N-ligand facilitate selectivity determining C–H activation step. The preference for oxidative addition of the aryl halide over competing benzoic acid coordination is decisive to suppress unwanted dehydrogenative homo-coupling.
Intercellular Adhesion Molecule-1 Expression on the Alveolar Epithelium and Its Modification by Hyperoxia (1993)

The distribution of intercellular adhesion molecule-1 (ICAM-1) on alveolar epithelial cells and the effects of exposure to 100% O2 on ICAM-1 expression in mouse lungs were studied by EM immunocytochemistry and immunoblot analysis. Cryoultrathin sections from mouse lungs exposed to air or 100% O2 for 84 h were labeled with a monoclonal rat anti-mouse ICAM-1 antibody. In the normal lung, abundant ICAM-1 expression was found on the alveolar surface of type I epithelial cells. Furthermore, ICAM-1 is highly concentrated on the surfaces near cell junctions. ICAM-1 was also found on the capillary surface of endothelial cells and alveolar surface of type II cells at densities considerably lower than that found on type I epithelial cells. After exposure to O2, the labeling density of ICAM-1 on the central surface of type I epithelial cells was not changed significantly. However, the gradient of ICAM-1 on the surfaces near cell junctions was nearly abolished. ICAM-1 labeling on the capillary surface of endothelial cells remained low. ICAM-1 was also markedly induced on the alveolar surface of type II epithelial cells after hyperoxic exposure. These results show that ICAM-1 is expressed primarily on type I epithelial cell surfaces near cell junctions. Exposure to hyperoxia causes a dramatic change in the distribution pattern of ICAM-1 on alveolar type I epithelial cells and induces expression of ICAM-1 on alveolar type II epithelial cells. These hyperoxia-induced changes may influence the associated neutrophil invasion/retention in the alveolar air spaces or alveolar walls.
Molecular biology, endocrinology, and pharmacology of the cardiac renin-angiotensin system. (1991)

Recent evidence for the existence of extrarenal tissue renin-angiotensin systems has raised the question whether such a system also exists in the heart. In this communication, we present evidence for a cardiac renin-angiotensin system based on molecular biological and biochemical data. In addition, we address the question whether the components of this system interact as a locally integrated, biologically functioning unit. Using radiolabeled cRNA probes prepared from specific cDNA fragments, we were able to document renin and angiotensinogen gene expression in atria and ventricles of the rat heart by Northern blot and liquid hybridization analysis. Relative signal strength for both mRNAs was highest in the atria, followed by the right and left ventricle. Using specific, HPLC-controlled RIAs for angiotensin peptides, we demonstrated the presence of both angiotensin I and angiotensin II in all anatomical regions of the monkey and rat heart. Similarly, the presence of converting enzyme activity was ascertained by direct in vitro determinations. Additional experiments evaluating the spontaneous release of angiotensinogen from isolated, perfused rat hearts revealed a bimodal pattern of high, but rapidly declining rates during the first hour (perhaps representing the washout of a pool sequestered from plasma), followed by a prolonged period of steady, low level release, consistent with the secretion of locally synthesized protein. In separate experiments aimed at examining the possible local integration of the components of the cardiac renin-angiotensin system, we measured angiotensin II concentrations in the coronary sinus effluent of isolated, perfused rat hearts. Infusion of angiotensin I resulted in the prompt appearance of angiotensin II, amounting to a single pass fractional conversion of 6.42 +/- 0.33%.(ABSTRACT TRUNCATED AT 250 WORDS)
Stress tuning of the fundamental absorption edge of pure germanium waveguides (2015)

One-dimensional stress dependence on the fundamental absorption edge of pure germanium (Ge) waveguide has theoretically and experimentally been studied, considering built-in two-dimensional stress-tensile Ge grown on Si. Based on the results, we have designed Ge Franz-Keldysh (FK) electroabsorption (EA) modulators to work at 1550 nm. Application of one-dimensional [110] compressive stress above -350 MPa on a pure Ge [-110] waveguide should allow 1550 nm light transmission, unless otherwise a pure Ge modulator can only operate at 1600 nm or longer due to the built-in two-dimensional tensile stress in Ge. The prediction has experimentally been verified using a SiNx stressor film. This concludes that the presented stress-tuning approach of the pure Ge waveguides should expand the operation wavelength of Ge FK-EA modulators to C band. Since stress tuning can be locally done in the back-end-of-line of complementary metal oxide semiconductor (CMOS) process, the presented stress-tuning method should enable "field-programable" control of the operation wavelengths of the monolithically integrated Ge modulators in Si photonics platform.
Recent developments in neutron dosimetry and radiation damage calculations for fusion-materials studies (1983)

This paper is intended as an overview of activities designed to characterize neutron irradiation facilities in terms of neutron flux and energy spectrum and to use these data to calculate atomic displacements, gas production, and transmutation during fusion materials irradiations. A new computerized data file, called DOSFILE, has recently been developed to record dosimetry and damage data from a wide variety of materials test facilities. At present data are included from 20 different irradiations at fast and mixed-spectrum reactors, T(d,n) 14 MeV neutron sources, Be(d,n) broad-spectrum sources, and spallation neutron sources. Each file entry includes activation data, adjusted neutron flux and spectral data, and calculated atomic displacements and gas production. Such data will be used by materials experimenters to determine the exposure of their samples during specific irradiations. This data base will play an important role in correlating property changes between different facilities and, eventually, in predicting materials performance in fusion reactors. All known uncertainties and covariances are listed for each data record and explicit references are given to nuclear decay data and cross sections.
FvVE1 Regulates Biosynthesis of the Mycotoxins Fumonisins and Fusarins in Fusarium verticillioides (2009)

The veA gene positively regulates sterigmatocystin production in Aspergillus nidulans and aflatoxin production in Aspergillus parasiticus and Aspergillus flavus . Whether veA homologues have a role in regulating secondary metabolism in other fungal genera is unknown. In this study, we examined the role of the veA homologue, FvVE1, on the production of two mycotoxin families, fumonisins and fusarins, in the important corn pathogen Fusarium verticillioides . We found that FvVE1 deletion completely suppressed fumonisin production on two natural substrates, corn and rice. Furthermore, our results revealed that FvVE1 is necessary for the expression of the pathway-specific regulatory gene FUM21 and structural genes in the fumonisin biosynthetic gene (FUM) cluster. FvVE1 deletion also blocked production of fusarins. The effects of FvVE1 deletion on the production of these toxins were found to be the same in two separate mating types. Our results strongly suggest that FvVE1 plays an important role in regulating mycotoxin production in F. verticillioides .
A New lncRNA, APTR, Associates with and Represses the CDKN1A/p21 Promoter by Recruiting Polycomb Proteins (2014)

Long noncoding RNAs (lncRNAs) have emerged as a major regulator of cell physiology, but many of which have no known function. CDKN1A/p21 is an important inhibitor of the cell-cycle, regulator of the DNA damage response and effector of the tumor suppressor p53, playing a crucial role in tumor development and prevention. In order to identify a regulator for tumor progression, we performed an siRNA screen of human lncRNAs required for cell proliferation, and identified a novel lncRNA, APTR, that acts in trans to repress the CDKN1A/p21 promoter independent of p53 to promote cell proliferation. APTR associates with the promoter of CDKN1A/p21 and this association requires a complementary-Alu sequence encoded in APTR. A different module of APTR associates with and recruits the Polycomb repressive complex 2 (PRC2) to epigenetically repress the p21 promoter. A decrease in APTR is necessary for the induction of p21 after heat stress and DNA damage by doxorubicin, and the levels of APTR and p21 are anti-correlated in human glioblastomas. Our data identify a new regulator of the cell-cycle inhibitor CDKN1A/p21 that acts as a proliferative factor in cancer cell lines and in glioblastomas and demonstrate that Alu elements present in lncRNAs can contribute to targeting regulatory lncRNAs to promoters.
Exact calculations of discrete-time process noise statistics for hybrid continuous/discrete time applications (2002)

Discrete-time models of continuous-time plants are commonly required due to the popular use of computers to implement control and estimation algorithms. When stochastic design techniques are utilized, it is necessary to determine the equivalent discrete-time process noise statistics from the continuous-time process noise statistics. Several references on the object of discrete-time control and estimation present approximate solutions for the necessary transformation; in this paper exact solutions are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Solid-State Light-Emitting Devices Based on the Tris-Chelated Ruthenium(II) Complex:  3. High Efficiency Devices via a Layer-by-Layer Molecular-Level Blending Approach (1999)

High efficiency, solid-state light-emitting devices have been fabricated from a water soluble, polymeric ruthenium (II) complex, Ru(bpy)32+ polyester, via the use of a layer-by-layer processing scheme. Spin-coated devices of this material were found to produce maximum luminance levels of 250−300 cd/m2 with an external quantum efficiency of 0.2% photons/electron. Devices based on sequentially adsorbed layers of the Ru(bpy)32+ polyester and poly(acrylic acid), on the other hand, exhibit external quantum efficiencies in the 1−3% range with a maximum light output of 40−50 cd/m2. These high device efficiencies were obtained by optimizing the relative amounts of Ru(bpy)32+ polyester and poly(acrylic acid) incorporated into the film via a layer-by-layer molecular-level blending approach. Through this type of control, it was also possible to create compositionally graded heterostructures and to produce devices that emit light only in the forward or reverse bias or that were completely symmetrical (similar light output, current flow, and efficiency in both forward and reverse bias).
An Evaluation of the Spontaneous Proliferation of Peripheral Blood Mononuclear Cells in HTLV-1-Infected Individuals Using Flow Cytometry (2011)

The spontaneous proliferation of peripheral blood mononuclear cells (PBMCs) is a hallmark of the human T-lymphotropic virus (HTLV) type-1. Cell proliferation is usually measured using a [(3)H]thymidine incorporation assay. This study aims to quantify the spontaneous proliferation of PBMCs using flow cytometry. PBMCs were cultured for 24 to 120 hours in the presence of 5,6-carboxyfluorescein diacetate succinimidyl ester (CFSE). For comparison, PBMCs were also cultured with [(3)H]thymidine. The cutoff values for spontaneous proliferation were >0.06 for the division index and >5.8% for the percentage of divided cells. Sixty-two percent of HTLV-1-infected individuals presented spontaneous proliferation of PBMCs, which was detected in the first 24 hours. Moreover, proliferation was detected in CD4(+) and CD8(+) T-lymphocyte subsets. A positive correlation was found between the division index and [(3)H]thymidine incorporation. This method may prove useful to better understand the phenomenon of spontaneous proliferation of PBMC of patients infected with HTLV-1.
Rapid demonstration of diversity of sulfatide molecular species from biological materials by MALDI-TOF MS (2006)

By combining the partition method for enrichment of sulfatides without any chromatographic procedures and the preparation method of lysosulfatides, we succeeded in analyzing these sulfated glycosphingolipids from biological materials by matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) to reduce the complexity of mass fragmentation patterns within a day. We found that sulfated GalCer (HSO3-3Gal beta 1Cer) (SM4s [galactosylsulfatide]) was composed of different species. While composition of SM4s specifically depended on source materials, it always contained hydroxy fatty acids of various degrees. In addition to the common sphingoid 4-sphingenine (d18:1), uncommon/unusual sphingoids phytosphingosine (4-hydroxysphinganine) (t18:0), eicosasphinganine (d20:0), 4-eicosasphingenine (d20:1), and sphingadienine (d18:2) were easily detected. Finally, in addition to SM4s, sulfatide sulfated LacCer (HSO3-3Gal beta 4Glc beta 1Cer) (SM3 [sulfated lactosylceramide]) and sulfated Gg3Cer (GalNAc beta 4(HSO3-3)Gal beta 4Glc beta 1Cer) (SM2 [sulfated gangliotriaosylceramide]) were clearly detected in renal tubule cells. The major SM4s was composed of ceramides possessing d18:1 with C22 hydroxy fatty acids (C22:0 h), C23:0 h, and C24:0 h, whereas the major SM3/SM2 were composed of ceramides possessing t18:0 with C22 normal fatty acids (C22:0), C23:0, C24:0. Namely, in these two series of sulfatides, either fatty acids or sphingoids were hydroxylated, and chain lengths of these components were exactly the same, consequently resulting in a similar polarity of ceramide moieties in these sulfatide species. These results demonstrated diversities of sulfatide molecular species, not only with respect to sugar moieties but also to ceramide moieties, which are probably important for specific effective functions in particular microenvironments such as lipid membrane microdomains.
Growth and Characterization of Conducting ZnO Thin Films by Atomic Layer Deposition (2010)

ZnO thin films were grown on Si or <TEX>$SiO_2$</TEX>/Si substrates, at growth temperatures ranging from 150 to <TEX>$400^{\circ}C$</TEX>, by atomic layer deposition (ALD) using diethylzinc and water. Despite the large band gap of 3.3 eV, the ALD ZnO films show high n-type conductivity, i.e. low resistivity in the order of <TEX>$10^{-3}\;{\Omega}cm$</TEX>. In order to understand the high conductivity of ALD ZnO films, the films were characterized with X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy, elastic recoil detection, Rutherford backscattering, Photoluminescence, and Raman spectroscopy. In addition, the various analytical data of the ZnO films were compared with those of ZnO single crystal. According to our analytical data, metallic zinc plays an important role for the high conductivity in ALD ZnO films. Therefore when the metallic zinc was additionally oxidized with ozone by a modified ALD sequence, the resistivity of ZnO films could be adjusted in a range of <TEX>$3.8{\times}10^{-3}\;{\sim}\;19.0\;{\Omega}cm$</TEX> depending on the exposure time of ozone.
Non-viral gene transfer in hydrogel matrices with octacalcium phosphate microgranules in optimization of reparative osteogenesis (2021)

There is a strong unmet need for bone grafts and substitutes combining osteoinductive capacities and biophysical properties for using them in minimally invasive surgical interventions. We have developed three variants of injectable gene-activated bone substitutes containing three components: octacalcium phosphate microgranules (OCP), plasmid DNA delivering the gene of vascular endothelial growth factor, and one of the hydrogels based on sodium alginate, type I collagen, and hyaluronic acid. The molecules of the gene constructs were contained both in the hydrogel and on the surface of the OCP microgranules. In the model of a critical-sized bone defect in rabbit parietal bone, we found that all the gene-activated hydrogels contributed to bone tissue regeneration, however, the largest amount of newly formed bone, including those in the central part of the defect, was detected in the groups with gene-activated materials based on hyaluronic acid and collagen. Thus, the developed materials can be considered as candidates for medical devices, but additional studies are required to assess the dose-depended effect and optimize the materials composition.
Accurate in vivo tumor detection using plasmonic-enhanced shifted-excitation Raman difference spectroscopy (SERDS) (2021)

For the majority of cancer patients, surgery is the primary method of treatment. In these cases, accurately removing the entire tumor without harming surrounding tissue is critical; however, due to the lack of intraoperative imaging techniques, surgeons rely on visual and physical inspection to identify tumors. Surface-enhanced Raman scattering (SERS) is emerging as a non-invasive optical alternative for intraoperative tumor identification, with high accuracy and stability. However, Raman detection requires dark rooms to work, which is not consistent with surgical settings. <b>Methods:</b> Herein, we used SERS nanoprobes combined with shifted-excitation Raman difference spectroscopy (SERDS) detection, to accurately detect tumors in xenograft murine model. <b>Results:</b> We demonstrate for the first time the use of SERDS for <i>in vivo</i> tumor detection in a murine model under ambient light conditions. We compare traditional Raman detection with SERDS, showing that our method can improve sensitivity and accuracy for this task. <b>Conclusion:</b> Our results show that this method can be used to improve the accuracy and robustness of <i>in vivo</i> Raman/SERS biomedical application, aiding the process of clinical translation of these technologies.