gebhart/patrepeval huggingface dataset:
Functional delineation of the Ca(2+)-deficient EF-hand in cardiac muscle, with genetically engineered cardiac-skeletal chimeric troponin C. (1992)

Cardiac and fast skeletal isoforms of TnC each comprise four putative EF-hand (helix-loop-helix) motifs as potential Ca(2+)-binding sites (sites 1-4), except that site 1 in cardiac TnC is deficient in Ca2+ coordination. In skeletal TnC, the N-terminal sites 1 and 2 are both essential for the trigger mechanism of the contraction switch. However, the mechanism in cardiac muscle is unsettled; it is obscure whether the cardiac site 1 is functionally inert due to calcium deficiency and consequently site 2 is the lone trigger site, or whether sites 1 and 2 perform interactively despite the impairment. These possibilities were addressed by mutagenizing site 1 in skeletal TnC to mimic the cardiac response. In one mutant (STnC-1), two selected Ca(2+)-ligands were abolished. In another (C1/S chimera), 41 N-terminal residues from cardiac TnC were spliced to STnC. The Ca(2+)-binding capacities as well as skinned fiber responses were measured. The STnC-1 derivative failed to switch on contraction. In contrast, the chimeric construct expressed close to full contractile potential in myocardium (74 +/- 3% Po; Po = maximal tension) and also the manifest cardiac phenotype. By devising supplemental chimeric constructs, cardiac-type N-terminal overhang together with cardiac-type EF-hand for site 1 both were found essential for the phenotype. We conclude that cardiac TnC site 1 is actively engaged in the trigger mechanism and in fact dominates the phenotype despite the inability to chelate Ca2+. The N-terminal overhang also participates in this mechanism, which is a novel finding. The conclusion that a non-chelating site functions interactively with a proximal site in cardiac TnC may have wider significance, inasmuch as similar pairings of disparate EF-hands are of common occurrence.
IRMPD spectroscopy of anionic group II metal nitrate cluster ions (2009)

Anionic group II metal nitrate clusters of the formula [M(2)(NO(3))(5)](-), where M(2) = Mg(2), MgCa, Ca(2), and Sr(2), are investigated by infrared multiple photon dissociation (IRMPD) spectroscopy to obtain vibrational spectra in the mid-IR region. The IR spectra are dominated by the symmetric and the antisymmetric nitrate stretches, with the latter split into high and low-frequency components due to the distortion of nitrate anion symmetry by interactions with the cation. Density functional theory (DFT) is used to predict geometries and vibrational spectra for comparison to the experimental spectra. Calculations yield two stable isomers: the first one contains two terminal nitrate anions on each cation and a single bridging nitrate ("mono-bridging"), while the second structure features a single terminal nitrate on each cation with three bridging nitrate ligands ("tri-bridging"). The tri-bridging isomer is calculated to be lower in energy than the mono-bridging one for all species. Theoretical spectra of the tri-bridging structure provide a better qualitative match to the experimental infrared spectra of [Mg(2)(NO(3))(5)](-) and [MgCa(NO(3))(5)](-). However, the profile of the low-frequency nu(3) band for the Mg(2) complex suggests a third possible isomer not predicted by theory. The IRMPD spectra of the Ca(2) and Sr(2) complexes are better reconciled by a weighted summation of the spectra of both isomers suggesting that a mixture of structures is present.
P-type conductivity and suppression of green luminescence in Mg/N co-implanted GaN by gyrotron microwave annealing (2021)

Co-implantation of Mg with N has been shown to improve p-type conductivity in Mg-implanted GaN. Achievement of p-type material still requires temperatures beyond the thermodynamic stability of GaN, however. In this study, we present results of implantation and anneal activation of GaN, co-implanted with Mg and N or Mg only by repeated, short thermal cycles of 1350 °C using a high-power gyrotron microwave source with a quasi-gaussian intensity profile. Spatial variations in optical and electrical properties of the resulting films are characterized by photoluminescence and diode I–V and C–V measurements. Resistive Mg/N co-implanted and annealed material shows dominant luminescence of the VN-related green luminescence (GL2) band at 2.37 eV and relatively lower intensity acceptor-related ultraviolet luminescence (UVL) at 3.27 eV. However, a material showing p–n diode behavior shows higher-intensity UVL luminescence and suppression of the GL2 band, permitting observation of the yellow luminescence (YL) present in the as-grown GaN. The YL is attributed to unintentionally introduced CN–ON complexes and is commonly observed in GaN grown by metalorganic chemical vapor deposition but is typically absent in implanted/annealed GaN. Co-implanted material is compared to material implanted only with Mg and annealed under the same conditions, which shows p-type activation, but contains persistent GL2 luminescence post-anneal and lowers maximum hole concentration.
Self‐Assembling Peptide‐Based Nanostructures for Regenerative Medicine (2010)

Abstract Biomaterials designed at the molecular and supramolecular levels to interact with cells, biomolecules such as growth factors and biopolymers, and pharmaceuticals will all have a profound impact on technologies targeted towards the regeneration of damaged tissues as a result of trauma, disease or genetic defects. Advances in materials science, chemistry, genomics and stem cell biology will all contribute towards the development of therapies leading to the successful regeneration of specific tissues. Regenerative medicine therapies should be minimally invasive, and thus the notion of cell scaffolds that self‐assemble from injected liquids is highly attractive for clinical translation. In this regard, self‐assembling materials will play a key role in future regenerative medicine technologies. In this chapter we focus on the current development of injectable, self‐assembling scaffolds that can be designed to provide a biomimetic and bioactive environment to stimulate cell‐signaling pathways that are critical in the regenerative process. We also describe the use of self‐assembling coatings to render traditional inert materials more bioactive and biocompatible, especially in orthopedic applications.
NDP (2019)

The key goals of datacenter networks are to simultaneously provide wire-level latency for RPC-style applications and high-throughput for network-bound applications such as storage. Folded Clos networks [1, 11] are used in datacenters worldwide; such networks use many cheap commodity switches to provide the illusion of a big non-blocking switch to all hosts in a datacenter, offering many paths between any two pairs of hosts.
Supplementary Data from The Single-Cell Immunogenomic Landscape of B and Plasma Cells in Early-Stage Lung Adenocarcinoma (2023)

Supplementary Data from The Single-Cell Immunogenomic Landscape of B and Plasma Cells in Early-Stage Lung Adenocarcinoma
Kinetics of the reaction of OH radicals with a series of ethers under simulated atmospheric conditions at 295 K (1989)

Abstract Ethers are being increasingly used as motor fuel additives to increase the octane number and to reduce CO emissions. Since their reaction with hydroxyl radicals (OH) is a major loss process for these oxygenated species in the atmoshpere, we have conducted a relative rate study of the kinetics of the reactions of OH radicals with a series of ethers and report the results of these measurements here. Experiments were performed under simulated atmospheric conditions; atmospheric pressure (≃ 740 torr) in synthetic air at 295 K. Using rate constants of 2.53 × 10 −12 , and 1.35 × 10 −11 cm 3 molecule −1 s −1 for the reaction of OH radicals with n ‐butane and diethyl ether, the following rate constants were derived, in units of 10 −11 cm 3 molecule −1 s −1 : dimethylether, (0.232 ± 0.023); di‐ n ‐propylether, (1.97 ± 0.08); di‐ n ‐butylether, (2.74 ± 0.32); di‐ n ‐pentylether, (3.09 ± 0.26); methyl‐ t ‐butylether, (0.324 ± 0.008); methyl‐ n ‐butylether, (1.29 ± 0.03); ethyl‐ n ‐butylether, (2.27 ± 0.09); and ethyl‐ t ‐butylether, (0.883 ± 0.026). Quoted errors represent 2σ from the least squares analysis and do not include any systematic errors associated with uncertainties in the reference rate constants used to place our relative measurements on an absolute basis. The implications of these results for the atmospheric chemistry of ethers are discussed.
miR-432 Induces NRF2 Stabilization by Directly Targeting KEAP1 (2017)

NF-E2-related factor 2 (NRF2) is a master transcriptional regulator that integrates cellular stress responses and is negatively regulated by Kelch-like ECH-associated protein 1 (KEAP1) at the post-translational level. In human cancers, aberrantly stabilized NRF2, by the mutation of either NRF2 or KEAP1 or by the potential inhibition of autophagy, plays a vital role in tumor growth and chemoresistance through the activation of target genes. MicroRNAs (miRNA) are endogenous small noncoding RNAs that can negatively regulate gene expression by interfering with translation and/or stability of target transcripts. However, miRNA-mediated regulation of the NRF2-KEAP1 pathway under physiological conditions is poorly understood. Here, <i>miR-432-3p</i> positively regulates NRF2 activity through the downregulation of KEAP1 by a direct-binding mechanism to the coding region of KEAP1. Overexpression of <i>miR-432-3p</i> resulted in a decreased sensitivity of esophageal squamous cell carcinoma (ESCC) cells to chemotherapy drugs including cisplatin (CDDP). Conversely, the inhibition of <i>miR-432-3p</i> expression by the CRISPR/Cas9 system resulted in an increased sensitivity of ESCC cells to CDDP. Furthermore, <i>miR-432-3p</i> was overexpressed in primary ESCC tumors (55 of 84, 65.5%) and a negative correlation between the expression level of KEAP1 and <i>miR-432-3p</i> in primary ESCC tumors was observed.<b>Implications:</b> These findings provide novel insights into the mechanism of NRF2 stabilization in human cancers. <i>Mol Cancer Res; 15(11); 1570-8. ©2017 AACR</i>.
Modern and Last Glacial Maximum eolian sedimentation patterns in the Atlantic Ocean interpreted from sediment iron oxide content (1995)

Eolian dust derived from the desert regions of North Africa is blown far into the tropical Atlantic Ocean by persistent easterly and northeasterly winds. In this paper, we demonstrate that the iron oxides, hematite and goethite, are a worthwhile addition to proxy monitors of eolian sedimentation in the tropical Atlantic. Iron oxides are identified by diffuse reflectance spectrophotometry, a technique capable of identifying these minerals in concentrations as low as 0.01% by weight. We analyze samples from both the modern and last glacial maximum (LGM) synoptic levels from 178 sample locations yielding a total of 356 samples distributed throughout the Atlantic Ocean. To determine the relative contribution of the iron oxides, we factor analyzed the modern and LGM levels as a single data set. The iron oxide factor explains about 25% of the variance in the combined core top and LGM data set. Mapped factor scores for the LGM and modern ocean indicate high iron oxide values are present in just two regions, one off eastern North America and the other off northwest Africa. In the region off eastern North America, iron oxide occurs primarily during the LGM as the previously noted “brick red lutite,” a unique sediment type derived from the erosion of Permo‐Carboniferous red beds in Atlantic Canada. A larger, lobe‐shaped area of iron oxide rich sediment is present off northwest Africa in both the modern and LGM levels. The modern iron oxide lobe is coincident with the distribution of eolian dust as determined by observations from ships, satellites, and analysis of air samples. During the LGM, iron oxides exhibit a similar distribution except the southern margin of the region shifts equatorward and iron oxide concentration increases.
Pharmacology and Antitumor Effect of Novel Paclitaxel Formulations (1994)

Taxol (paclitaxel) is a highly-promising but poorly water-soluble anticancer agent for which the development of safe and effective formulations has been a challenge. Clinical experience with the drug has shown vehicle-dependent toxicity, and experiments in animal models have shown a relationship between formulation and antitumor effect. Therefore, formulation of taxol in better-tolerated vehicles was undertaken. Taxol was encapsulated in liposomes (phospholipid vesicles) composed of phosphatidylglycerol and phosphatidylcholine and tested for activity and toxicity against (a) subcutaneous C-26, a taxol-resistant murine model for colon carcinoma, and (b) intraperitoneal P388 leukemia. Antitumor potency of taxol was retained or slightly enhanced in liposome-based formulations, while adverse effects were reduced considerably. Physical studies were initiated to identify aspects of taxol-taxol and taxol-lipid interaction that determine stability and efficacy of these liposome-based formulations.
From Wood to Textiles: Top‐Down Assembly of Aligned Cellulose Nanofibers (2018)

Advanced textiles made of macroscopic fibers are usually prepared from synthetic fibers, which have changed lives over the past century. The shortage of petrochemical resources, however, greatly limits the development of the textile industry. Here, a facile top-down approach for fabricating macroscopic wood fibers for textile applications (wood-textile fibers) comprising aligned cellulose nanofibers directly from natural wood via delignification and subsequent twisting is demonstrated. Inherently aligned cellulose nanofibers are well retained, while the microchannels in the delignified wood are squeezed and totally removed by twisting, resulting in a dense structure with approximately two times higher mechanical strength (106.5 vs 54.9 MPa) and ≈20 times higher toughness (7.70 vs 0.36 MJ m<sup>-3</sup> ) than natural wood. Dramatically different from natural wood, which is brittle in nature, the resultant wood-textile fibers are highly flexible and bendable, likely due to the twisted structures. The wood-textile fibers also exhibit excellent knitting properties and dyeability, which are critical for textile applications. Furthermore, functional wood-textile fibers can be achieved by preinfiltrating functional materials in the delignified wood film before twisting. This top-down approach of fabricating aligned macrofibers is simple, scalable, and cost-effective, representing a promising direction for the development of smart textiles and wearable electronics.
Unsaturated Nitriles:  Precursors for a Domino Ozonolysis−Aldol Synthesis of Oxonitriles (1999)

Cyclic five-, six-, and seven-membered oxonitriles are prepared by a tandem ozonolysis-aldol sequence. Cyclopentenylacetonitrile (4) and cyclohexenylacetonitrile (12) afford the ring-expanded oxonitriles 3 (98%) and 17 (58%), respectively, in highly efficient one-pot syntheses. Homologous five-membered oxonitriles 22a-c are prepared by analogous ozonolysis-aldol cyclizations employing omega-alkenyl beta-ketonitriles. The method tolerates various substitution patterns and allows for the synthesis of beta,beta-disubstituted oxonitriles (22c). The reaction conditions are essentially neutral providing the beta-hydroxyoxonitriles 22d and 22e with only trace amounts of the aromatic dehydration product.
Optimization Strategies for Real-Time Rendering of Virtual Scenes on Heterogeneous Mobile Devices (2019)

Increasing numbers of VR applications are being developed for mobile devices. Due to the various hardware limitations of different mobile devices, the amounts of data for virtual scenes need to be restricted if one seeks to still obtain fast rendering and a real-time interaction experience. To alleviate this problem, this paper proposes novel optimization strategies for real-time rendering of virtual scenes on heterogeneous kinds of mobile devices with diverging processing abilities. In particular, we deploy a virtual scene around an editable roaming path so as to reduce the arrangement of invisible virtual objects, and optimize the scene layout in the design stage. The virtual objects are bounded with respect to the roaming path, such that the system can render the virtual scenes in the roaming stage in real-time. Our experiments show that these strategies can be adaptively applied for different smartphone devices, operating in larger-scale virtual scenes constructed in advance.
205 Surgical Management of Adult Intrinsic Brainstem Tumors (2012)

INTRODUCTION: Much of the nihilism associated with primary brainstem tumors in children has been reduced in the last decade through the promising results of a few pediatric series. The same cannot be said for the attitudes of adult neurosurgeons faced with a primary, intrinsic brainstem tumor. The literature is sparse and pessimism is prevalent. This large series of adult brainstem tumors underscores the importance of distinguishing focal from diffuse and the encouraging surgical results seen with an aggressive treatment algorithm. METHODS: A retrospective study was conducted of all adult patients who presented with an intrinsic brainstem tumor and who underwent surgery between January 2000 and December 2010. Patient records were used and data was updated after telephone interviews. Any patient who was subsequently proven to have an extra-axial tumor was excluded from this study. RESULTS: In the 10-year period 136 patients underwent surgery for a presumed intrinsic brainstem tumor. All patients younger than 18 years of age at time of presentation (n = 104) were excluded and only one patient was found to have a secondary neoplasm. Of the 31 patients, 16 have died of their disease and four were significantly worse after surgery. The overall survival (OS) rate is 61% and progression free survival (PFS) is 45% at 5 years. CONCLUSION: An aggressive surgical approach to patients with presumed intrinsic brainstem tumors significantly improves OS and PFS compared to adult non-surgical series. Although complications may be incapacitating, they are relatively uncommon and certainly acceptable.
Photonic ternary quantum random number generators (2023)

We construct a class of three-dimensional photonic quantum random number generators (QRNGs) and prove that each of them generates maximally unpredictable digits via measurements that are robust to errors. This shows that every sequence generated is strongly incomputable; hence its quality is provably better than that of every pseudo-random sequence. These results suggest that incomputability in physics is real and practically applicable. Finally, we present photonic implementations of three-dimensional QRNGs and discuss device independence.
Bufalin, a component in Chansu, inhibits proliferation and invasion of hepatocellular carcinoma cells (2013)

Bufalin is a potential anti-HCC therapeutic candidate through its inhibition of the AKT/GSK3β/β-catenin/E-cadherin signaling pathway. Further studies with bufalin are warranted in patients with HCC, especially those with the disease at advanced stages.
Contemporary limbal stem cell transplantation – a review (2010)

Conjunctivalization of the cornea is the hallmark of limbal stem cell deficiency (LSCD). This is often associated with persistent corneal epithelial defects and a fibrovascular pannus. LSCD can be unilateral or bilateral and partial or total. In partial LSCD involving the visual axis sequential sector conjunctival epitheliectomy (SSCE) is a useful option. In total LSCD, transplantation of limbal tissue or of ex vivo expanded sheets is the mainstay. In unilateral cases autolimbal transplant is the procedure of choice. In bilateral cases living (related) and cadaver donors are considered. The former has the advantage of being fresh and can be human leucocyte antigen matched. Procedures for harvesting limbal tissue from living donors are identical. Different strategies are required for harvesting tissue from cadaver whole globes or sclero-corneal rims. Recipient eye preparation requires removal of the fibrovascular tissue. Donor explants are generally sutured directly on the denuded recipient surface without the preparation of a 'bed' to fit the explant. It is imperative that inflammation is meticulously controlled before limbal transplantation especially if tissue from living donors is used. Limbal transplantation, with the exception of a corneal graft, should be the last surgical intervention planned. Meticulous postoperative care and treatment with antibiotics, steroids, artificial tears and autologous serum are required. With allografts long-term immunosuppression is necessary. Limbal transplantation is contraindicated in the presence of severe dry eye. Despite its complexities limbal transplantation does significantly improve vision related quality of life. Autografts give the best results and living related donor grafts are next best. Majority of cadaver grafts fail in 5 years.
Assessment of Appearance Match by Visual Observation and Clinical Colorimetry (1989)

Judgments of appearance matching by means of the visual criteria established by the United States Public Health Service (USPHS) and by means of an extended visual rating scale were determined for composite resin veneer restorations and their comparison teeth. Using a colorimeter of 45 degrees/0 degrees geometry and the CIELAB color order system we used the color of the restorations and comparison teeth to calculate a color difference for every visual rating. Statistically significant relationships were found between each of the two visual rating systems and the color differences. The average CIELAB color difference of those ratings judged a match by the USPHS criteria was found to be 3.7. However, the overlap in ranges of the color differences for those comparisons rated matches and mismatches indicates the importance of other factors in appearance matching, such as translucency and the effects of other surrounding visual stimuli. The extended visual rating scale offers no advantages to the more broadly defined criteria established by the USPHS.
Porosity of surgical mesh fabrics: New technology (1989)

A new method using an image processing system developed in our laboratories is used to measure the pore size in Mersilene, Marlex, and Teflon surgical meshes. All three meshes appear to have sufficiently large pores and should facilitate tissue growth/attachment. Results obtained in this study are compared to results of an earlier paper.
Severe Pancreatitis in an AIDS Patient in Association With Cytomegalovirus Infection (1989)

We have reported a case of pancreatitis caused by CMV in an AIDS patient. Although CMV has caused clinical disease of other gastrointestinal organs, pancreatic involvement has previously been demonstrated only in autopsy specimens. The etiology of "idiopathic" pancreatitis in AIDS patients should be investigated, as therapeutic intervention may be available for some of these persons.
Sensors and microsystems : proceedings of the 3rd Italian Conference, Genova, Italy, 11-13 February 1998 (1999)

Plenary talk biosensors and bioelectronics chemical sensors based on organic materials ad conducting polymers chemical sensors based on inorganic materials electronic nose and multisensor systems chemFET fibre optics sensors IR and optical sensors physical sensors micromechanics and technologies electronics for sensors.