gebhart/patrepeval huggingface dataset:
Identifying Fundamental Limitations in Halide Perovskite Solar Cells (2016)

The temperature dependence of the principal photovoltaic parameters of perovskite photovoltaics is studied. The recombination activation energy is in good agreement with the perovskite's bandgap energy, thereby placing an upper bound on the open-circuit voltage. The photocurrent increases moderately with temperature and remains high at low temperature, reinforcing that the cells are not hindered by insufficient thermally activated mobility or carrier trapping by deep defects.
Fluoroalcohol-Methacrylate Resists for 193nm Lithography (2005)

We have designed and developed a variety of hexafluoroalcohol (HFA) pendant methacrylate monomers and the corresponding imaging polymers for ArF lithography. It was found that HFA side chains are critical for "swelling free" dissolution properties for the polymers and resists. Through the incorporation of HFA functionalities, ArF resists can obtain linear dissolution properties commonly seen in 248nm ESCAP resists. These improved dissolution properties in turn significantly reduce PEB sensitivity of higher activation protecting group (e.g., methyladamantanyl) based ArF resists. We have also showed that the fluorine impact on etch rates can be modulated through the insertion of cyclic and aliphatic spacers between the main chain and the HFA functionalities. The key application space for HFA-methacrylate resists appears to be trench level lithography. It was also demonstrated that these HFA materials are compatible with immersion lithography and result in dramatically improved process windows for iso trench features, in addition to other lines/space features.
Discovery of application workloads from network file traces (2010)

An understanding of application I/O access patterns is useful in several situations. First, gaining insight into what applications are doing with their data at a semantic level helps in designing efficient storage systems. Second, it helps create benchmarks that mimic realistic application behavior closely. Third, it enables autonomic systems as the information obtained can be used to adapt the system in a closed loop.All these use cases require the ability to extract the application-level semantics of I/O operations. Methods such as modifying application code to associate I/O operations with semantic tags are intrusive. It is well known that network file system traces are an important source of information that can be obtained non-intrusively and analyzed either online or offline. These traces are a sequence of primitive file system operations and their parameters. Simple counting, statistical analysis or deterministic search techniques are inadequate for discovering application-level semantics in the general case, because of the inherent variation and noise in realistic traces.In this paper, we describe a trace analysis methodology based on Profile Hidden Markov Models. We show that the methodology has powerful discriminatory capabilities that enable it to recognize applications based on the patterns in the traces, and to mark out regions in a long trace that encapsulate sets of primitive operations that represent higher-level application actions. It is robust enough that it can work around discrepancies between training and target traces such as in length and interleaving with other operations. We demonstrate the feasibility of recognizing patterns based on a small sampling of the trace, enabling faster trace analysis. Preliminary experiments show that the method is capable of learning accurate profile models on live traces in an online setting. We present a detailed evaluation of this methodology in a UNIX environment using NFS traces of selected commonly used applications such as compilations as well as on industrial strength benchmarks such as TPC-C and Postmark, and discuss its capabilities and limitations in the context of the use cases mentioned above.
l-Fucose Synthesis Using a Halo- and Thermophilic l-Fucose Isomerase from Polyextremophilic Halothermothrix orenii (2022)

l-Fucose isomerase (l-FucI)-mediated isomerization is a promising biotechnological approach for synthesizing various rare sugars of industrial significance, including l-fucose. Extremozymes that can retain their functional conformation under extreme conditions, such as high temperature and salinity, offer favorable applications in bioprocesses that accompany harsh conditions. To date, only one thermophilic l-FucI has been characterized for l-fucose synthesis. Here, we report l-FucI from Halothermothrix orenii (HoFucI) which exhibits both halophilic and thermophilic properties. When evaluated under various biochemical conditions, HoFucI exhibited optimal activities at 50–60 °C and pH 7 with 0.5–1 M NaCl in the presence of 1 mM Mn2+ as a cofactor. The results obtained here show a unique feature of HoFucI as a polyextremozyme, which facilitates the biotechnological production of l-fucose using this enzyme.
Expanding the Repertoire of Amyloid Polymorphs by Co-polymerization of Related Protein Precursors (2013)

Amyloid fibrils can be generated from proteins with diverse sequences and folds. Although amyloid fibrils assembled in vitro commonly involve a single protein precursor, fibrils formed in vivo can contain more than one protein sequence. How fibril structure and stability differ in fibrils composed of single proteins (homopolymeric fibrils) from those generated by co-polymerization of more than one protein sequence (heteropolymeric fibrils) is poorly understood. Here we compare the structure and stability of homo and heteropolymeric fibrils formed from human β2-microglobulin and its truncated variant ΔN6. We use an array of approaches (limited proteolysis, magic angle spinning NMR, Fourier transform infrared spectroscopy, and fluorescence) combined with measurements of thermodynamic stability to characterize the different fibril types. The results reveal fibrils with different structural properties, different side-chain packing, and strikingly different stabilities. These findings demonstrate how co-polymerization of related precursor sequences can expand the repertoire of structural and thermodynamic polymorphism in amyloid fibrils to an extent that is greater than that obtained by polymerization of a single precursor alone.
Guiding bone formation using semi‐onlay calcium phosphate implants in an ovine calvarial model (2022)

The restoration of cranio-maxillofacial deformities often requires complex reconstructive surgery in a challenging anatomical region, with abnormal soft tissue structures and bony deficits. In this proof-of-concept, the possibility of vertical bone augmentation was explored by suspending hemispherically shaped titanium-reinforced porous calcium phosphate (CaP) implants (n = 12) over the frontal bone in a sheep model (n = 6). The animals were euthanized after week 13 and the specimens were subject to micro-computed tomography (μCT) and comprehensive histological analysis. Histology showed that the space between implant and the recipient bone was filled with a higher percentage of newly formed bone (NFB) versus soft tissue with a median of 53% and 47%, respectively. Similar results were obtained from the μ-CT analysis, with a median of 56% NFB and 44% soft tissue filling the void. Noteworthy, significantly higher bone-implant contact was found for the CaP (78%, range 14%-94%) versus the Titanium (29%, range 0%-75%) portion of the implant exposed to the surrounding bone. The histological analysis indicates that the CaP replacement by bone is driven by macrophages over time, emphasized by material-filled macrophages found in close vicinity to the CaP with only a small number of single osteoclasts found actively remodeling the NFB. This study shows that CaP based implants can be assembled with the help of additive manufacturing to guide vertical bone formation without decortification or administration of growth factors. Furthermore, it highlights the potential disadvantage of a seamless fit between the implant and the recipient's bone.
Data from Adoptive Transfer of Autologous Natural Killer Cells Leads to High Levels of Circulating Natural Killer Cells but Does Not Mediate Tumor Regression (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Adoptive transfer of tumor-infiltrating lymphocytes (TIL) can mediate regression of metastatic melanoma. However, many patients with cancer are ineligible for such treatment because their TIL do not expand sufficiently or because their tumors have lost expression of antigens and/or MHC molecules. Natural killer (NK) cells are large granular lymphocytes that lyse tumor cells in a non–MHC-restricted manner. Therefore, we initiated in a clinical trial to evaluate the efficacy of adoptively transferred autologous NK cells to treat patients with cancers who were ineligible for treatment with TIL.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Patients with metastatic melanoma or renal cell carcinoma were treated with adoptively transferred &lt;i&gt;in vitro&lt;/i&gt; activated autologous NK cells after the patients received a lymphodepleting but nonmyeloablative chemotherapy regimen. Clinical responses and persistence of the adoptively transferred cells were evaluated.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Eight patients were treated with an average of 4.7 × 10&lt;sup&gt;10&lt;/sup&gt; (± 2.1 × 10&lt;sup&gt;10&lt;/sup&gt;) NK cells. The infused cells exhibited high levels of lytic activity &lt;i&gt;in vitro&lt;/i&gt;. Although no clinical responses were observed, the adoptively transferred NK cells seemed to persist in the peripheral circulation of patients for at least one week posttransfer and, in some patients, for several months. However, the persistent NK cells in the circulation expressed significantly lower levels of the key activating receptor NKG2D and could not lyse tumor cell targets &lt;i&gt;in vitro&lt;/i&gt; unless reactivated with IL-2.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; The persistent NK cells could mediate antibody-dependent cell-mediated cytotoxicity without cytokine reactivation &lt;i&gt;in vitro&lt;/i&gt;, which suggests that coupling adoptive NK cell transfer with monoclonal antibody administration deserves evaluation. &lt;i&gt;Clin Cancer Res; 17(19); 6287–97. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Fatigue Behavior in Monocrystalline Ni-Based Superalloys for Blade Applications (2008)

Ni-based superalloys are used for turbine airfoil applications due to their excellent high temperature properties. Alloy design has historically focused on creep resistance as the critical design limiting parameter. Recently, the focus has shifted to include fatigue resistance, resulting in the need to better understand the effects of alloy microstructure on fatigue crack initiation and propagation.
Molecular Imaging-Derived Biomarker of Cardiac Nerve Integrity — Introducing High NET Affinity PET Probe 18F-AF78 (2022)

<b>Background:</b> Radiolabeled agents that are substrates for the norepinephrine transporter (NET) can be used to quantify cardiac sympathetic nervous conditions and have been demonstrated to identify high-risk congestive heart failure (HF) patients prone to arrhythmic events. We aimed to fully characterize the kinetic profile of the novel <sup>18</sup>F-labeled NET probe AF78 for PET imaging of the cardiac sympathetic nervous system (SNS) among various species. <b>Methods:</b><sup>18</sup>F-AF78 was compared to norepinephrine (NE) and established SNS radiotracers by employing <i>in vitro</i> cell assays, followed by an <i>in vivo PET imaging</i> approach with healthy rats, rabbits and nonhuman primates (NHPs). Additionally, chase protocols were performed in NHPs with NET inhibitor desipramine (DMI) and the NE releasing stimulator tyramine (TYR) to investigate retention kinetics in cardiac SNS. <b>Results:</b> Relative to other SNS radiotracers, <sup>18</sup>F-AF78 showed higher transport affinity via NET in a cell-based competitive uptake assay (IC<sub>50</sub> 0.42 ± 0.14 µM), almost identical to that of NE (IC<sub>50</sub>, 0.50 ± 0.16 µM, n.s.). In rabbits and NHPs, initial cardiac uptake was significantly reduced by NET inhibition. Furthermore, cardiac tracer retention was not affected by a DMI chase protocol but was markedly reduced by intermittent TYR chase, thereby suggesting that <sup>18</sup>F-AF78 is stored and can be released via the synaptic vesicular turnover process. Computational modeling hypothesized the formation of a T-shaped π-π stacking at the binding site, suggesting a rationale for the high affinity of <sup>18</sup>F-AF78. <b>Conclusion:</b><sup>18</sup>F-AF78 demonstrated high <i>in vitro</i> NET affinity and advantageous <i>in vivo</i> radiotracer kinetics across various species, indicating that <sup>18</sup>F-AF78 is an SNS imaging agent with strong potential to guide specific interventions in cardiovascular medicine.
Readability Research: An Interdisciplinary Approach (2021)

Readability is on the cusp of a revolution. Fixed text is becoming fluid as a proliferation of digital reading devices rewrite what a document can do. As past constraints make way for more flexible opportunities, there is great need to understand how reading formats can be tuned to the situation and the individual. We aim to provide a firm foundation for readability research, a comprehensive framework for modern, multi-disciplinary readability research. Readability refers to aspects of visual information design which impact information flow from the page to the reader. Readability can be enhanced by changes to the set of typographical characteristics of a text. These aspects can be modified on-demand, instantly improving the ease with which a reader can process and derive meaning from text. We call on a multi-disciplinary research community to take up these challenges to elevate reading outcomes and provide the tools to do so effectively.
A cold atom interferometry sensor platform based on diffractive optics and integrated photonics (2021)

We report the current progress in the development of a compact, deployable cold-atom interferometry sensor platform towards atomic sensors for position, navigation, and time (PNT) applications. A simplified atomic sensor head with diffractive optics, an alignment-free optical package, and photonic-integrated-circuit (PIC) compatible laser architecture [1] are essential for its compactness and deployability. This cold-atom sensor platform can be generally applied to gravimeters, accelerometers, gyroscopes, and clocks, and the sensor platform includes significant engineering efforts in the development of grating-mirror magneto-optical traps (G-MOTs), custom titanium vacuum package with passive pumping, and silicon photonics multi-channel on-chip single sideband modulators.
Combined plasmonic Au-nanoparticle and conducting metal oxide high-temperature optical sensing with LSTO (2020)

Fiber optic sensor technology offers several advantages for harsh-environment applications. However, the development of optical gas sensing layers that are stable under harsh environmental conditions is an ongoing research challenge. In this work, electronically conducting metal oxide lanthanum-doped strontium titanate (LSTO) films embedded with gold nanoparticles are examined as a sensing layer for application in reducing gas flows at high temperature (600-800 °C). A strong localized surface plasmon resonance (LSPR) based response to hydrogen is demonstrated in the visible region of the spectrum, while a Drude free electron-based response is observed in the near-IR. Characteristics of these responses are studied both on planar glass substrates and on silica fibers. Charge transfer between the oxide film and the gold nanoparticles is explored as a possible mechanism governing the Au LSPR response and is considered in terms of the corresponding properties of the conducting metal oxide-based matrix phase. Principal component analysis is applied to the combined plasmonic and free-carrier based response over a range of temperatures and hydrogen concentrations. It is demonstrated that the combined visible and near-IR response of these films provides improved versatility for multiwavelength interrogation, as well as improved discrimination of important process parameters (concentration and temperature) through application of multivariate analysis techniques.
A m-Terphenyl-Modifed Sulfone Derivative as a Host Material for High-Efficiency Blue and Green Phosphorescent OLEDs (2012)

A m-terphenyl-modified sulfone derivative, BTPS was designed and prepared as a host material for phosphorescent OLEDs. By using BTPS, high power efficiencies of over 46 lm W1− (EQE 22%) for blue and 105 lm W1− (EQE 28%) for green were obtained at 100 cd m−2.
Simplest Simulation Model for Three-Dimensional Xenon Oscillations in Large PWRs (2004)

Xenon oscillations in large PWRs are well understood and there have been no operational problems remained. However, in order to suppress the oscillations effectively, optimal control strategy is preferable. Generally speaking in such optimality search based on the modern control theory, a large volume of transient core analyses is required. For example, three dimensional core calculations are inevitable for the analyses of radial oscillations. From this point of view, a very simple 3-D model is proposed, which is based on a reactor model of only four points. As in the actual reactor operation, the magnitude of xenon oscillations should be limited from the view point of safety, the model further assumes that the neutron leakage can be also small or even constant. It can explicitly use reactor parameters such as reactivity coefficients and control rod worth directly. The model is so simplified as described above that it can predict oscillation behavior in a very short calculation time even on a PC. However the prediction result is good. The validity of the model in comparison with measured data and the applications are discussed.
Dynamic learning for cognitive radio sensing (2013)

Spectrum sensing algorithms for cognitive radios that can interpolate and predict the spatio-temporal interference power distribution are proposed using the dictionary learning framework. The algorithms jointly estimate the dictionaries to capture the spatial spectrum measurements as well as their temporal dynamics via parsimoniously chosen atoms. Both batch and efficient online implementations are developed. Numerical tests verify the effectiveness of the novel approach.
Effect of FGF-binding Protein 3 on Vascular Permeability (2008)

Fibroblast growth factor-binding protein 1 (FGF-BP1 is BP1) is involved in the regulation of embryonic development, tumor growth, and angiogenesis by mobilizing endogenous FGFs from their extracellular matrix storage. Here we describe a new member of the FGF-BP family, human BP3. We show that the hBP3 protein is secreted from cells, binds to FGF2 in vitro and in intact cells, and inhibits FGF2 binding to heparin. To determine the function of hBP3 in vivo, hBP3 was transiently expressed in chicken embryos and resulted in > 50% lethality within 24 h because of vascular leakage. The onset of vascular permeability was monitored by recording the extravasation kinetics of FITC-labeled 40-kDa dextran microperfused into the vitelline vein of 3-day-old embryos. Vascular permeability increased as early as 8 h after expression of hBP3. The increased vascular permeability caused by hBP3 was prevented by treatment of embryos with PD173074, a selective FGFR kinase inhibitor. Interestingly, a C-terminal 66-amino acid fragment (C66) of hBP3, which contains the predicted FGF binding domain, still inhibited binding of FGF2 to heparin similar to full-length hBP3. However, expression of the C66 fragment did not increase vascular permeability on its own, but required the administration of exogenous FGF2 protein. We conclude that the FGF binding domain and the heparin binding domain are necessary for the hBP3 interaction with endogenous FGF and the activation of FGFR signaling in vivo.
Matrix Macromolecules That Affect the Viscoelasticity of Calfskin (1994)

The chemical basis of viscoelasticity of bovine skin was explored by mechanical relaxation spectroscopy after selective enzymatic degradation. Measurements covered a wide range of time scales because water was replaced in the tissue with aqueous mixtures of ethylene glycol, which maintained a water-like electrical environment for the charged macromolecules down to -50 degrees C. Macromolecular components that couple the fibrils to the interfibrillar matrix contribute about half the values of the resultant storage and loss moduli, while removal of components that are readily extractable, so perhaps free in the matrix, did not alter these mechanical quantities or their relaxations. The precision of the method reveals the effects of fibril-attached matrix, when conventional methods of mechanical testing fail.
(S)-2-Amino-3-(3-hydroxy-7,8-dihydro-6H-cyclohepta[d]isoxazol-4-yl)propionic Acid, a Potent and Selective Agonist at the GluR5 Subtype of Ionotropic Glutamate Receptors. Synthesis, Modeling, and Molecular Pharmacology (2003)

We have previously described (RS)-2-amino-3-(3-hydroxy-7,8-dihydro-6H-cyclohepta[d]isoxazol-4-yl)propionic acid (4-AHCP) as a highly effective agonist at non-N-methyl-d-aspartate (non-NMDA) glutamate (Glu) receptors in vivo, which is more potent than (RS)-2-amino-3-(3-hydroxy-5-methylisoxazol-4-yl)propionic acid (AMPA) but inactive at NMDA receptors. However, 4-AHCP was found to be much weaker than AMPA as an inhibitor of [(3)H]AMPA binding and to have limited effect in a [(3)H]kainic acid binding assay using rat cortical membranes. To shed light on the mechanism(s) underlying this quite enigmatic pharmacological profile of 4-AHCP, we have now developed a synthesis of (S)-4-AHCP (6) and (R)-4-AHCP (7). At cloned metabotropic Glu receptors mGluR1alpha (group I), mGluR2 (group II), and mGluR4a (group III), neither 6 nor 7 showed significant agonist or antagonist effects. The stereoisomer 6, but not 7, activated cloned AMPA receptor subunits GluR1o, GluR3o, and GluR4o with EC(50) values in the range 4.5-15 microM and the coexpressed kainate-preferring subunits GluR6 + KA2 (EC(50) = 6.4 microM). Compound 6, but not 7, proved to be a very potent agonist (EC(50) = 0.13 microM) at the kainate-preferring GluR5 subunit, equipotent with (S)-2-amino-3-(5-tert-butyl-3-hydroxyisothiazol-4-yl)propionic acid [(S)-Thio-ATPA, 4] and almost 4 times more potent than (S)-2-amino-3-(5-tert-butyl-3-hydroxyisoxazol-4-yl)propionic acid [(S)-ATPA, 3]. Compound 6 thus represents a new structural class of GluR5 agonists. Molecular modeling and docking to a crystal structure of the extracellular binding domain of the AMPA subunit GluR2 has enabled identification of the probable active conformation and binding mode of 6. We are able to rationalize the observed selectivities by comparing the docking of 4 and 6 to subtype constructs, i.e., a crystal structure of the extracellular binding domain of GluR2 and a homology model of GluR5.
Challenges in managing dependable data systems (2006)

Recent work shows how to automatically design storage systems that meet performance and dependability requirements by appropriately selecting and configuring storage devices, and creating snapshot, remote mirror, and traditional backup copies. Although this work represents a solid foundation, users demand an even higher level of functionality: the ability to cost-effectively manage data according to application-centric (or better, business process-centric) performance, dependability and manageability requirements, as these requirements evolve over the data's lifetime. In this paper, we outline several research challenges in managing dependable data systems, including capturing users' high-level goals; translating them into storage-level requirements; and designing, deploying, and analyzing the resulting data systems.