gebhart/patrepeval huggingface dataset:
Influence of chemical ordering on the thermal conductivity and electronic relaxation in FePt thin films in heat assisted magnetic recording applications (2016)

We report on the out-of-plane thermal conductivities of tetragonal L10 FePt (001) easy-axis and cubic A1 FePt thin films via time-domain thermoreflectance over a temperature range from 133 K to 500 K. The out-of-plane thermal conductivity of the chemically ordered L10 phase with alternating Fe and Pt layers is ~23% greater than the thermal conductivity of the disordered A1 phase at room temperature and below. However, as temperature is increased above room temperature, the thermal conductivities of the two phases begin to converge. Molecular dynamics simulations on model FePt structures support our experimental findings and help shed more light into the relative vibrational thermal transport properties of the L10 and A1 phases. Furthermore, unlike the varying temperature trends in the thermal conductivities of the two phases, the electronic scattering rates in the out-of-plane direction of the two phases are similar for the temperature range studied in this work.
Reduction-Responsive Disassemblable Core-Cross-Linked Micelles Based on Poly(ethylene glycol)-b-poly(N-2-hydroxypropyl methacrylamide)–Lipoic Acid Conjugates for Triggered Intracellular Anticancer Drug Release (2012)

Reduction-sensitive reversibly core-cross-linked micelles were developed based on poly(ethylene glycol)-b-poly(N-2-hydroxypropyl methacrylamide)-lipoic acid (PEG-b-PHPMA-LA) conjugates and investigated for triggered doxorubicin (DOX) release. Water-soluble PEG-b-PHPMA block copolymers were obtained with M(n,PEG) of 5.0 kg/mol and M(n,HPMA) varying from 1.7 and 4.1 to 7.0 kg/mol by reversible addition-fragmentation chain transfer (RAFT) polymerization. The esterification of the hydroxyl groups in the PEG-b-PHPMA copolymers with lipoic acid (LA) gave amphiphilic PEG-b-PHPMA-LA conjugates with degrees of substitution (DS) of 71-86%, which formed monodispersed micelles with average sizes ranging from 85.3 to 142.5 nm, depending on PHPMA molecular weights, in phosphate buffer (PB, 10 mM, pH 7.4). These micelles were readily cross-linked with a catalytic amount of dithiothreitol (DTT). Notably, PEG-b-PHPMA(7.0k)-LA micelles displayed superior DOX loading content (21.3 wt %) and loading efficiency (90%). The in vitro release studies showed that only about 23.0% of DOX was released in 12 h from cross-linked micelles at 37 °C at a low micelle concentration of 40 μg/mL, whereas about 87.0% of DOX was released in the presence of 10 mM DTT under otherwise the same conditions. MTT assays showed that DOX-loaded core-cross-linked PEG-b-PHPMA-LA micelles exhibited high antitumor activity in HeLa and HepG2 cells with low IC(50) (half inhibitory concentration) of 6.7 and 12.8 μg DOX equiv/mL, respectively, following 48 h incubation, while blank micelles were practically nontoxic up to a tested concentration of 1.0 mg/mL. Confocal laser scanning microscope (CLSM) studies showed that DOX-loaded core-cross-linked micelles released DOX into the cell nuclei of HeLa cells in 12 h. These reduction-sensitive disassemblable core-cross-linked micelles with excellent biocompatibility, superior drug loading, high extracellular stability, and triggered intracellular drug release are promising for tumor-targeted anticancer drug delivery.
New Perspectives on Silver Nanowire Formation from Dynamic Silver Ion Concentration Monitoring and Nitric Oxide Production in the Polyol Process (2016)

For the first time, previously unknown multiple reaction stages have been identified during the reduction of silver ions in the high-temperature polyol process of synthesizing silver nanowires. New in situ potentiometric silver ion measurements clearly show different phases of the crystal growth process along the reaction path as silver ions are reduced to metallic silver. Incorporation of nitric oxide monitoring of the reaction headspace gases provides additional insight into the reactions affecting the silver ion reduction process. The combination of monitoring the Ag+ ion concentration with evolved nitric oxide demonstrates that the reduction of silver ions to form crystalline silver of various morphologies in the polyol process is far more complicated than previously realized. These new approaches also provide powerful new tools to study other elevated temperature metal reduction reactions.
Influenza virus: The biology of a changing virus (2008)

Recent discoveries in the field of influenza virology are the focus of this chapter. Influenza viruses are members of the family Orthomyxoviridae and include influenza virus types A, B, and C. This introduction provides a detailed overview of influenza virus classification, structure, and life cycle. We also include a brief review of the clinical manifestations of influenza and the molecular determinants for virulence. The genetic diversity of influenza A viruses and their capability to successfully infect an array of hosts, including avian and mammalian species, is highlighted in a discussion about host range and evolution. The importance of viral receptor-binding hemagglutinins and host sialic acid distribution in species-restricted binding of viruses is underscored. Finally, recent advances in our understanding of the seasonality and transmission of influenza viruses are described and their importance for the control of the spread of these viruses discussed.
Omi/HtrA2 protease mediates cisplatin-induced cell death in renal cells (2004)

Omi/HtrA2 is a mitochondrial proapoptotic serine protease that is able to induce both caspase-dependent and caspase-independent cell death. After apoptotic stimuli, Omi is released to the cytoplasm where it binds and cleaves inhibitor of apoptosis proteins. In this report, we investigated the role of Omi in renal cell death following cisplatin treatment. Using primary mouse proximal tubule cells, as well as established renal cell lines, we show that the level of Omi protein is upregulated after treatment with cisplatin. This upregulation is followed by the release of Omi from mitochondria to the cytoplasm and degradation of XIAP. Reducing the endogenous level of Omi protein using RNA interference renders renal cells resistant to cisplatin-induced cell death. Furthermore, we show that the proteolytic activity of Omi is necessary and essential for cisplatin-induced cell death in this system. When renal cells are treated with Omi's specific inhibitor, ucf-101, they become significantly resistant to cisplatin-induced cell death. Ucf-101 was also able to minimize cisplatin-induced nephrotoxic injury in animals. Our results demonstrate that Omi is a major mediator of cisplatin-induced cell death in renal cells and suggest a way to limit renal injury by specifically inhibiting its proteolytic activity.
Polybrominated Phenolics from Lendenfeldia dendyi with Antibacterial, Antifungal and Anti-HIV Activities (2010)

Bioassay guided fractionation of the marine sponge Ledenfeldia denyi resulted in the isolation of four polybrominated diphenyl ethers (1–4). The structures of the isolated compounds were determined using spectroscopic methods (1D and 2D NMR). The structure of compounds 1 and 2 were confirmed by X-ray analysis. Antimicrobial testing [1] of the isolated compounds indicated that they displayed significant antibacterial activity against methicillin-resistant Staphylococcus aureus with IC50S of 0.1–0.6µg/mL., and potent antifungal activity against Cryptococcus neoformans (IC50S of 0.15–1.5µg/mL). Compounds 1 and 2 displayed mild anti-HIV activity in Human PBM cells [2] with EC50 of 35.9 and 10.9µM, respectively.
Chemistry and Molecular Biology of Transmissible Spongiform Encephalopathies (1997)

Abstract Prion diseases are currently in the spotlight. Among them, the Creutzfeldt–Jakob disease in humans, scrapie in sheep, and bovine spongiform encephalopathy, or mad cow disease, are most commonly known. The term “spongiform” refers to the characteristic appearance of the lesions found in affected brains. It is likely that prion diseases originate from a causative agent that replicates independently of nucleic acids. Current research assumes that a structural isoform of prion protein, the scrapie form PrP Sc , is the responsible pathogen. The three‐dimensional structure, but not the amino acid sequence of the isoform differs from that of the normal cellular isoform, PrP c . According to a widely accepted hypothesis, the normal isoform of the protein is converted by an autocatalytic process into the scrapie form upon contact with the latter. This hypothesis has not yet been proven. However, considerable progress has been made in the last few years, which might provide answers to many open questions about prion diseases, the subject of this review.
Tensile and Fatigue Behaviour of AA6022-T4 to IF Steel Resistance Spot Welds (2017)

Vehicle light weighting plays an integral role in achieving the mandatory fuel efficiency requirements as established in the Corporate Average Fuel Economy Standards (CAFE), USA. To optimize vehicle structures for both performance and mass savings, materials such as aluminum alloys may be used in combination with steels, especially advanced high strength steels. Although joining dissimilar materials is a challenge, General Motors (GM) has recently succeeded in developing a proprietary resistance spot welding process using a multi-ring, domed (MRD) electrode geometry that is capable of producing welds between aluminum alloys and steel materials with acceptable joint strength. In this work, tensile and fatigue properties are presented of welds produced between dissimilar materials in lap-shear configuration. The dissimilar metal resistance spot welds (RSWs) were composed of wrought aluminum 1.2-mm thick AA6022-T4 sheet and 2.0-mm thick IF steel. For comparison, similar metal lap-shear RSWs were made and tested of 1.2-mm and 2.0-mm thick AA6022-T4. Average lap-shear strengths of 4400 N and 3200 N were observed for AA6022-T4 to IF steel welds and AA6022-T4 to AA6022-T4 welds, respectively. In load-controlled fatigue testing, limited scatter in fatigue life was observed for both stack-ups tested at maximum fatigue loads below 1500 N. The overall fatigue life was lower for the AA6022-T4 to AA6022-T4 welds compared to AA6022-T4 to IF steel welds. Failure modes for both stack-ups, particularly at long lives, were primarily a result of crack growth through the thickness direction in the AA6022-T4 sheet around the outer edge of the weld nugget. The superior performance of the AA6022-T4 to IF steel welds was most likely primarily due to the larger size of the weld nuggets created in that joint. Also contributing to the superior performance of the Al-steel welds was a more favourable notch root opening geometry that reduced stress concentration as well as a microstructure in the region of the crack path that contained fine, columnar grains alloyed with iron that SEM analyses indicated slowed fatigue crack growth. Using the structural stress concept, it was found that the fatigue life of lap-shear AA60222-T4 to AA6022-T4 and AA6022-T4 to IF steel welds falls onto a master curve indicating that the nugget size dominates the fatigue life.
Nonequilibrium Sorption of Water in Polylactide (2012)

The sorption of water in polylactide (PLA) was measured at various vapor activities (0–0.85) and temperatures using a number of experimental techniques, including quartz spring microbalance (QSM), quartz crystal microbalance (QCM), and in situ time-resolved Fourier transform infrared-attenuated total reflectance (FTIR-ATR) spectroscopy. Additionally, a prediction of the water sorption isotherm in PLA was obtained with the use of the nonequilibrium lattice fluid (NELF) model, where an excellent agreement between the model prediction and experimental sorption data was observed at different experimental temperatures (all below the glass transition temperature of PLA) for water vapor activities less than 0.65. Results from in situ time-resolved FTIR-ATR spectroscopy revealed that water is present predominately as dimers in PLA at water vapor activities less than 0.65, and the presence of larger hydrogen-bound water clusters was observed at water vapor activities >0.65. This provides a rationale for the deviation between the NELF model prediction and water sorption data at high vapor activities, where the NELF model does not account for the strong self-association interactions present in large hydrogen-bound water clusters. Furthermore, non-Fickian sorption kinetic behavior was observed with all the experimental techniques, and this highlights the nonequilibrium nature of the water–glassy polymer system and provides insight into the variability in the sorption isotherms reported in the literature.
Enabling mobile microinteractions (2010)

While much attention has been paid to the usability of desktop computers, mobile computers are quickly becoming the dominant platform. Because mobile computers may be used in nearly any situation—including while the user is actually in motion, or performing other tasks—interfaces designed for stationary use may be inappropriate, and alternative interfaces should be considered. 
In this dissertation I consider the idea of microinteractions —interactions with a device that take less than four seconds to initiate and complete. Microinteractions are desirable because they may minimize interruption; that is, they allow for a tiny burst of interaction with a device so that the user can quickly return to the task at hand. 
My research concentrates on methods for applying microinteractions through wrist-based interaction. I consider two modalities for this interaction: touchscreens and motion-based gestures. In the case of touchscreens, I consider the interface implications of making touchscreen watches usable with the finger, instead of the usual stylus, and investigate users' performance with a round touchscreen. For gesture-based interaction, I present a tool, MAGIC, for designing gesture-based interactive system, and detail the evaluation of the tool.
Benchmark of sensor options (2023)

In this deliverable, a prioritized list of sensors to enhance cell performance, safe operation, etc. will be<br> established. The sensor requirements will be re-evaluated and updated after initial sensor test results are<br> available.
Expression and characterization of the type III polyketide synthase 1,3,6,8-tetrahydroxynaphthalene synthase from Streptomyces coelicolor A3(2) (2003)

Sequence analysis of the metabolically rich 8.7-Mbp genome of the model actinomycete Streptomyces coelicolor A3(2) revealed three genes encoding predicted type III polyketide synthases (PKSs). We report the inactivation, expression, and characterization of the type III PKS homologous SCO1206 gene product as 1,3,6,8-tetrahydroxynaphthalene synthase (THNS). Incubation of recombinant THNS with malonyl-CoA showed THN production, as demonstrated by UV and HPLC analyses. The K(m) value for malonyl-CoA and the k(cat) value for THN synthesis were determined spectrophotometrically to be 3.58+/-0.85 micro M and 0.48+/-0.03 min(-1), respectively. The C-terminal region of S. coelicolor THNS, which is longer than most other bacterial and plant type III PKSs, was shortened by 25 amino acid residues and the resulting mutant was shown to be slightly more active (K(m)=1.97+/-0.19 micro M, k(cat)=0.75+/-0.04 min(-1)) than the wild-type enzyme.
Aerial Energy Provisioning for Massive Energy-Constrained IoT by UAVs (2022)

Autonomy of devices is a major challenge in many Internet of Things (IoT) applications, in particular when the nodes are deployed remotely or difficult to assess places. In this paper we present an approach to provide energy to these devices by Unmanned Aerial Vehicles (UAVs). Therefore, the two major challenges, finding and charging the node are presented. We propose a model to give the energy constrained node an unlimited autonomy by taking the Wireless Power Transfer (WPT) link and battery capacity into account. Selecting the most suitable battery technology allows a reduction in battery capacity and waste. Moreover, an upgrade of existing IoT nodes is feasible with a limited impact on the design and form factor.
Vascular anomaly, lipoma, and polymicrogyria associated with schizencephaly: developmental and diagnostic insights. Illustrative case (2023)

BACKGROUND Schizencephaly is an uncommon central nervous system malformation. Intracranial lipomas are also rare, accounting for approximately 0.1% of brain “tumors.” They are believed to be derived from a persistent meninx primitiva, a neural crest–derived mesenchyme that develops into the dura and leptomeninges. OBSERVATIONS The authors present a case of heterotopic adipose tissue and a nonshunting arterial vascular malformation arising within a schizencephalic cleft in a 22-year-old male. Imaging showed right frontal gray matter abnormality and an associated suspected arteriovenous malformation with evidence of hemorrhage. Brain magnetic resonance imaging revealed right frontal polymicrogyria lining an open-lip schizencephaly, periventricular heterotopic gray matter, fat within the schizencephalic cleft, and gradient echo hypointensity concerning for prior hemorrhage. Histological assessment demonstrated mature adipose tissue with large-bore, thick-walled, irregular arteries. Mural calcifications and subendothelial cushions suggesting nonlaminar blood flow were observed. There were no arterialized veins or direct transitions from the arteries to veins. Hemosiderin deposition was scant, and hemorrhage was not present. The final diagnosis was consistent with ectopic mature adipose tissue and arteries with meningocerebral cicatrix. LESSONS This example of a complex maldevelopment of derivatives of the meninx primitiva in association with cortical maldevelopment highlights the unique challenges from both a radiological and histological perspective during diagnostic workup.
Developability Assessment of an Isolated CH2 Immunoglobulin Domain (2020)

The IgG C<sub>H</sub>2 domain continues to hold promise for the development of new therapeutic entities because of its bifunctional role as a biomarker and effector protein. The need for further understanding of molecular stability and aggregation in therapeutic proteins has led to the development of a breakthrough quantum cascade laser microscope to allow for real-time comparability assessment of an array of related proteins in solution upon thermal perturbation. Our objective was to perform a comprehensive developability assessment of three similar monoclonal antibody (mAb) fragments: C<sub>H</sub>2, C<sub>H</sub>2s, and m01s. The C<sub>H</sub>2 construct consists of residues Pro238 to Lys340 of the IgG1 heavy chain sequence. C<sub>H</sub>2s has a 7-residue deletion at the N-terminus and a 16-residue C-terminal extension containing a histidine tag. The m01s construct is identical to C<sub>H</sub>2s, except for two cysteines introduced at positions 242 and 334. A series of hyperspectral images was acquired during thermal perturbation from 28 to 60 °C for all three proteins in an array. Co-distribution and two-dimensional infrared correlation spectroscopies yielded the mechanism of aggregation and stability for these three proteins. The level of detail is unprecedented, identifying the regions within C<sub>H</sub>2 and C<sub>H</sub>2s that are prone to self-association and establishing the differences in stability. Furthermore, C<sub>H</sub>2 helical segments, β-sheets, β-turns, and random coil regions were less stable than in C<sub>H</sub>2s and m01s because of the presence of the N-terminal 3<sub>10</sub>-helix and β-turn type III. The engineered disulfide bridge in m01s eliminated the self-association process and rendered this mAb fragment the most stable.
Cyclic Di-AMP Impairs Potassium Uptake Mediated by a Cyclic Di-AMP Binding Protein in Streptococcus pneumoniae (2013)

Cyclic di-AMP (c-di-AMP) has been shown to play important roles as a second messenger in bacterial physiology and infections. However, understanding of how the signal is transduced is still limited. Previously, we have characterized a diadenylate cyclase and two c-di-AMP phosphodiesterases in Streptococcus pneumoniae, a Gram-positive pathogen. In this study, we identified a c-di-AMP binding protein (CabP) in S. pneumoniae using c-di-AMP affinity chromatography. We demonstrated that CabP specifically bound c-di-AMP and that this interaction could not be interrupted by competition with other nucleotides, including ATP, cAMP, AMP, phosphoadenylyl adenosine (pApA), and cyclic di-GMP (c-di-GMP). By using a bacterial two-hybrid system and genetic mutagenesis, we showed that CabP directly interacted with a potassium transporter (SPD_0076) and that both proteins were required for pneumococcal growth in media with low concentrations of potassium. Interestingly, the interaction between CabP and SPD_0076 and the efficiency of potassium uptake were impaired by elevated c-di-AMP in pneumococci. These results establish a direct c-di-AMP-mediated signaling pathway that regulates pneumococcal potassium uptake.
Forced Vibrations of Slacked Carbon Nanotube Resonators (2010)

In this paper, we present an investigation of the dynamics of electrically actuated carbon nanotubes (CNTs) resonators including the effect of their initial curvature due to fabrication (slack). A nonlinear arch model is used to simulate the motion of the slacked CNT. A reduced-order model using a multimode Galerkin procedure based on the mode shapes of the straight un-actuated CNTs is derived. The reduced-order model equations are integrated numerically with time to reveal the steady-state response of the CNT when actuated by a DC load superimposed to an AC harmonic load. A perturbation method, the method of multiple scales, is used to obtain analytically the forced vibration response due to DC and small AC loads for various slacked CNT. Results of the perturbation method are verified with those obtained by numerically integrating the reduced-order model equations. The effective nonlinearity of the CNT is calculated as function of the slack and the DC load while using a beam model for the CNTs showing a softening dominant behavior.
Nearly diffraction limited FTIR mapping using an ultrastable broadband femtosecond laser tunable from 133 to 8 µm (2017)

Micro-Fourier-transform infrared (FTIR) spectroscopy is a widespread technique that enables broadband measurements of infrared active molecular vibrations at high sensitivity. SiC globars are often applied as light sources in tabletop systems, typically covering a spectral range from about 1 to 20 µm (10 000 - 500 cm−1) in FTIR spectrometers. However, measuring sample areas below 40x40 µm2 requires very long integration times due to their inherently low brilliance. This hampers the detection of ultrasmall samples, such as minute amounts of molecules or single nanoparticles. In this publication we extend the current limits of FTIR spectroscopy in terms of measurable sample areas, detection limit and speed by utilizing a broadband, tabletop laser system with MHz repetition rate and femtosecond pulse duration that covers the spectral region between 1250 - 7520 cm−1 (1.33 - 8 µm). We demonstrate mapping of a 150x150 µm2 sample of 100 nm thick molecule layers at 1430 cm−1 (7 µm) with 10x10 µm2 spatial resolution and a scan speed of 3.5 µm/sec. Compared to a similar globar measurement an order of magnitude lower noise is achieved, due to an excellent long-term wavelength and power stability, as well as an orders of magnitude higher brilliance.