gebhart/patrepeval huggingface dataset:
Surface Stress and Surface Tension in Polymeric Networks (2018)

Understanding of how surface properties could change upon deformation is of paramount importance for controlling adhesion, friction, and lubrication of soft polymeric materials (i.e., networks and gels). Here, we use a combination of the theoretical calculations and coarse-grained molecular dynamics simulations to study surface stress dependence on deformation in films made of soft and rigid polymeric networks. Simulations have shown that films of polymeric networks could demonstrate surface properties of both polymer melts and elastic solids depending on their deformation. In particular, at small film deformations the film surface stress ϒ is equal to the surface tension obtained at zero film strains, γ<sub>0</sub>, and surface properties of networks are similar to those of polymer melts. The surface stress begins to show a strain dependence when the film deformation ratio λ approaches its maximum possible value λ<sub>max</sub> corresponding to fully stretched network strands without bond deformations. In the entire film deformation range the normalized surface stress ϒ(λ)/γ<sub>0</sub> is a universal function of the ratio λ/λ<sub>max</sub>. Analysis of the simulation data at large film deformations points out that the significant increase in the surface stress can be ascribed to the onset of the bond deformation. In this deformation regime network films behave as elastic solids.
Pedicle Screw Surface Coatings Improve Fixation in Nonfusion Spinal Constructs (2009)

Pedicle screw coatings that promote mechanical interlocking, TPS, or direct osteoblast bonding(HA) increased screw fixation in this nonfusion model. More non-HA coated screws, however, were thought to be "loose" with a nearly zero peak extraction torque and fibrous encapsulation. Increased osseointegration with HA may result in a decreased incidence of screw loosening and improved outcomes of transpedicular spinal instrumentation in nonfusion procedures.
In situ observation of the effect of the twin boundary orientation on the mechanical properties of single crystalline Ni (2022)

The construction of twin boundaries (TBs) in materials is a remarkable way of promoting their strength and ductility. However, the effects of TB orientation on the mechanical properties have not been reported experimentally so far. Using a state-of-the-art in situ tensile stage equipped in a transmission electron microscope, uniaxial tensile tests were performed on three single-crystalline Ni samples with TB parallel and perpendicular to the tensile direction and no TB. The results showed that the uniform tensile elongation strongly depends on TB, 120% for the perpendicular TB sample, 99% for the parallel TB sample, and only 55% for the no TB sample. In addition, dislocation interaction before reaching the perpendicular CTB contribute to cross-slip and dynamic formation of dislocation jogs, thereby improving strain hardening and resulting in a large uniform tensile elongation.
Automated Trace and Copper Plane Extraction of X-ray Tomography Imaged PCBs (2021)

Reverse engineering (RE) of Printed circuit boards (PCBs) can be achieved through X-ray Computed Tomography (CT) in a non-destructive manner. For practical applications such as obsolescence replacement and hardware assurance, it is important to perform RE as automated and fast as possible. While our past work has focused on automated via detection, this paper introduces a framework for automated and unsupervised extraction of traces and copper conducting planes in an X-ray CT imaged PCB. We employ a series of algorithms from image processing, computer vision, and graph theory for a robust solution that produces a high fidelity result. We compare our results against off-the-shelf methodologies utilizing ridge detection and Canny edge detection in combination with connected components and show the necessity of utilizing a graph-theoretic approach. Our results are demonstrated on an in-house designed PCB for qualitative and quantitative analysis. On average across all layers, our proposed framework outperforms the relevant methods with IoU, SSIM, Correlation, and Dice image quality scores of 0.9166, 0.9954, 0.8952, and 0.9453, respectively.
Suboptimal extracellular pH values alter DNA damage response to induced double‐strand breaks (2018)

Conditions leading to unrepaired DNA double-stranded breaks are potent inducers of genetic instability. Systemic conditions may lead to fluctuation of hydrogen ions in the cellular microenvironment, and we show that small variations in extracellular pH, termed suboptimal pHe, can decrease the efficiency of DNA repair in the absence of intracellular pH variation. Recovery from bleomycin-induced DNA double-stranded breaks in fibroblasts proceeded less efficiently at suboptimal pHe values ranging from 7.2 to 6.9, as shown by the persistence of repair foci, reduction of H4K16 acetylation, and chromosomal instability, while senescence or apoptosis remained undetected. By allowing escape from these protective mechanisms, suboptimal pHe may therefore enhance the genotoxicity of double-stranded breaks, leading to genetic instability.
Suppression of endotoxin-inducible cytokines in whole blood from human subjects following single dose of recombinant human interleukin-11 (1999)

To determine whether a single injection of recombinant human interleukin-11 (rhIL-11) to human subjects would affect endotoxin-inducible cytokine production, 6 dialysis-dependent patients with renal failure and 4 healthy volunteers were subcutaneously injected with rhIL-11 (50 µg/kg). The circulating concentrations of rhIL-11 remained at a constant level of approximately 12 ng/ml for 0.25—6 h in healthy volunteers but were 2-fold higher in dialysis-dependent patients. Venous blood obtained before and after rhIL-11 was stimulated with 10 ng/ml of LPS for 24 h at 37°C and production of TNFα, IL-1β, and IL-8 determined. The maximum suppression of IL-1β, TNFα and IL-8 production (66%, 24% and 58%, respectively) was observed 1 h after rhIL-11 administration. After 24 h, when circulating concentration of rhIL-11 had decreased to near pre-injection levels, LPS-induced TNFα and IL-1β production remained suppressed (56 ± 17%, P &lt; 0.05; 46 ± 4.7, P&lt;0.01, respectively) but returned to baseline at 48 h. These findings suggest that there is a therapeutic benefit of single doses of rhIL-11 in reducing LPS-induced IL-1β and TNFα production.
Degradable Silyl Ether–Containing Networks from Trifunctional Thiols and Acrylates (2020)

The purpose of this study was the synthesis of novel degradable polymer-based devices capable of releasing an encapsulated agent in a controlled manner with specific interest for use as drug delivery materials. Base-catalyzed thiol Michael additions between trithiols and triacrylates containing silyl ether groups were exploited to prepare a series of degradable cross-linked networks. Disodium fluorescein was loaded as a hydrophilic drug surrogate inside the networks, and the degradation of the networks and the release of dye were monitored. The networks were characterized by Fourier transform infrared spectroscopy, and their thermal and mechanical properties were investigated through thermogravimetric analysis and dynamic mechanical analysis. The effects of the monomer structure on degradation, release behavior, and thermal properties were investigated. The networks prepared from more sterically hindered silyl ether monomers exhibited decreased rates of degradation and correspondingly slower release of encapsulated disodium fluorescein dye. The results suggest that the characteristics of the networks can be fine-tuned by manipulation of the group attached to the Si atom in the silyl ether monomers.
Membrane Interaction of Botulinum Neurotoxin A Translocation (T) Domain (2008)

The translocation of the catalytic domain through the membrane of the endosome to the cell cytoplasm is a key step of intoxication by botulinum neurotoxin (BoNT). This step is mediated by the translocation (T) domain upon endosome acidification, although the mechanism of interaction of the T domain with the membrane is still poorly understood. Using physicochemical approaches and spectroscopic methods, we studied the interaction of the BoNT/A T domain with the membrane as a function of pH. We found that the interaction with membranes does not involve major secondary or tertiary structural changes, as reported for other toxins like diphtheria toxin. The T domain becomes insoluble around its pI value and then penetrates into the membrane. At that stage, the T domain becomes able to permeabilize lipid vesicles. This occurs for pH values lower than 5.5, in agreement with the pH encountered by the toxin within endosomes. Electrostatic interactions are also important for the process. The role of the so-called belt region was investigated with four variant proteins presenting different lengths of the N-extremity of the T domain. We observed that this part of the T domain, which contains numerous negatively charged residues, limits the protein-membrane interaction. Indeed, interaction with the membrane of the protein deleted of this extremity takes place for higher pH values than for the entire T domain. Overall, the data suggest that acidification eliminates repulsive electrostatic interactions between the T domain and the membrane, allowing its penetration into the membrane without triggering detectable structural changes.
Stochastic Simulation for Characterizing Ecological Spatial Patterns and Appraising Risk (1993)

The theory and a case study are presented for a class of techniques known as stochastic simulation. Stochastic simulations can characterize the certainty of estimates of spatially and/or temporally correlated ecological variables. Rather than merely providing a unique estimate, a conditional probability distribution is built for the unsampled location. This distribution provides the researcher with any summary statistic or confidence limit desired. Moreover, the techniques are flexible enough to incorporate expected economic losses into the analysis. A simple analogy of a jigsaw puzzle is used first to introduce key concepts. Then, the mathematical highlights of two leading stochastic simulation procedures are presented. Finally, one simulation method, known as sequential Gaussian conditional simulation, is used to generate multiple, equally probable images of adult corn rootworm densities over a large (225 x 150 km) area in northwestern Iowa during the summer of 1989. The results show the simulated density of rootworms to be influenced strongly by the choice of summary statistic and density threshold. Economic risk is appraised from the point of view of the farmer by incorporating the expected economic losses due to the use of a soil insecticide. Since the cost to the farmer of not using an insecticide when in fact it is needed is over three times greater than the cost of using one when it is not needed, the area identified as potentially requiring treatment is much larger than when a summary statistic like the mean or median is used. Stochastic simulation allows the environmental researcher, policy-maker, or manager the opportunity to characterize uncertainty and economic or other losses, and to determine areas requiring treatment and additional samples.
The formation of inflammatory demyelinated lesions in cerebral white matter (2014)

This study provides compelling evidence that in marmoset EAE, which forms lesions strongly resembling those of MS, early changes in vascular permeability are associated with perivascular inflammatory cuffing and parenchymal microglial activation but precede the arrival of blood-derived monocytes that accompany demyelination. Prospective detection of transient permeability changes could afford an opportunity for early intervention to forestall tissue damage in newly forming lesions.
Abstract 3366: Imaging of Peroxidase Activity in Injured Myocardium (2007)

Ischemic myocardial injury causes timed recruitment of neutrophils and monocyte/macrophages, which produce significant amounts of myeloperoxidase (MPO). MPO leads to the formation of reactive chlorinating species capable of oxidizing proteins. We developed a small molecule based MPO substrate for MRI, Gd-bis-5-HT-DPTA, which is first radicalized, and then oligomerized and covalently bound to matrix proteins, all leading to enhanced R1-relaxivity and delayed wash out kinetics. Mice were subjected to coronary artery ligation and injected with 0.3mmol/kg Gd-bis-5-HT-DPTA (or Gd-DTPA as control). We performed T1-weighted cardio-respiratory gated MRI 10–120min later, followed by immunoreactive staining for MPO. 3 mice each were studied at day 1, 2, 4, 8, and &gt;1 month after MI. Subsequently, MPO tissue activity was determined with the guaiacol method. MPO activity peaked 2 days after MI (contrast-to-noise-ratio (CNR) day 1, 26+/−4; day 2, 39+/−10; day 4, 29+/−3), and tissue levels of MPO over time correlated well with probe activity in vivo (r2=0.65, p&lt;0.01). CNR following Gd-DTPA peaked ten minutes after injection (10.5+/−0.2), and returned to pre-injection values at 60min. In contradistinction, following injection Gd-bis-5-HT-DPTA, CNR was higher and peaked later (p&lt;0.05 vs. Gd-DTPA, arrows depict MI in figure ). Immunoreactive staining for MPO correlated well with enhancement (r2=0.92, p&lt;0.05). Gd-bis-5-HT-DPTA facilitates in-vivo assessment of MPO activity in injured myocardium. This approach allows non-invasive probing of the inflammatory response to ischemia and has the potential to guide the development and application of novel cardioprotective therapies.
Plasminogen Activators Contribute to Impairment of Hypercapnic and Hypotensive Cerebrovasodilation After Cerebral Hypoxia/Ischemia in the Newborn Pig (2005)

These data show that exogenous PA administration potentiates the impairment of hypercapnic and hypotensive PAD that occurs after H/I. Inhibition of endogenous PA may ameliorate the impairment of PAD induced by hypercapnia and hypotension PAD that develops after hypoxic central nervous system injury of diverse etiologies.
Interactions of Microbicide Nanoparticles with a Simulated Vaginal Fluid (2012)

The interaction with cervicovaginal mucus presents the potential to impact the performance of drug nanocarriers. These systems must migrate through this biological fluid in order to deliver their drug payload to the underlying mucosal surface. We studied the ability of dapivirine-loaded polycaprolactone (PCL)-based nanoparticles (NPs) to interact with a simulated vaginal fluid (SVF) incorporating mucin. Different surface modifiers were used to produce NPs with either negative (poloxamer 338 NF and sodium lauryl sulfate) or positive (cetyltrimethylammonium bromide) surface charge. Studies were performed using the mucin particle method, rheological measurements, and real-time multiple particle tracking. Results showed that SVF presented rheological properties similar to those of human cervicovaginal mucus. Analysis of NP transport indicated mild interactions with mucin and low adhesive potential. In general, negatively charged NPs underwent subdiffusive transport in SVF, i.e., hindered as compared to their diffusion in water, but faster than for positively charged NPs. These differences were increased when the pH of SVF was changed from 4.2 to 7.0. Diffusivity was 50- and 172-fold lower in SVF at pH 4.2 than in water for negatively charged and positively charged NPs, respectively. At pH 7.0, this decrease was around 20- and 385-fold, respectively. The estimated times required to cross a layer of SVF were equal to or lower than 1.7 h for negatively charged NPs, while for positively charged NPs these values were equal to or higher than 7 h. Overall, our results suggest that negatively charged PCL NPs may be suitable to be used as carriers in order to deliver dapivirine and potentially other antiretroviral drugs to the cervicovaginal mucosal lining. Also, they further reinforce the importance in characterizing the interactions of nanosystems with mucus fluids or surrogates when considering mucosal drug delivery.
Synthesis and in vitro evaluation of iodine labelled pyrazolo[1,5‐a]pyridines as highly selective dopamine D4 receptor ligands (2001)

Abstract Two 131 I‐labelled radioligands, namely 3‐(4‐[ 131 I]iodophenylpiperazin‐1‐ylmethyl)‐pyrazolo[1,5‐ a ]pyridine and 3‐(4‐chlorophenylpiperazin‐1‐ylmethyl)‐7‐[ 131 I]iodopyrazolo[1,5‐ a ]pyridine, which are required for studies or binding of these ligands to the D4 receptor, have been synthesized in 80% and 32% radiochemical yields, respectively; the radiochemical purity in each case was &gt;97%. For the second radioligand a kit preparation, based on iododestannylation followed by solid‐phase extraction, was possible. In vitro characterization using CHO‐cells expressing different dopamine receptor subtypes gave K i values of 3.1 and 2.6 nM. Both radioligands are highly selective for the D4 subtype as compared to other dopamine subtypes. Copyright © 2001 John Wiley &amp; Sons, Ltd.
Digital backpropagation accounting for polarization-mode dispersion (2017)

Digital backpropagation (DBP) is a promising digital-domain technique to mitigate Kerr-induced nonlinear interference. While it successfully removes deterministic signal-signal interactions, the performance of ideal DBP is limited by stochastic effects, such as polarization-mode dispersion (PMD). In this paper, we consider an ideal full-field DBP implementation and modify it to additionally account for PMD; reversing the PMD effects in the backward propagation by passing the reverse propagated signal also through PMD sections, which concatenated equal the inverse of the PMD in the forward propagation. These PMD sections are calculated analytically at the receiver based on the total accumulated PMD of the link estimated from channel equalizers. Numerical simulations show that, accounting for nonlinear polarization-related interactions in the modified DBP algorithm, additional signal-to-noise ratio gains of 1.1 dB are obtained for transmission over 1000 km.
Effect of gelling agent on colony formation in solid cultivation of microbial community in lake sediment (2009)

Since Robert Koch and colleagues found agar to be an effective gelling agent over a century ago, the pure culture method using agar plates has long been a standard of microbiology. Agar is undoubtedly easy to handle and useful for culture of microorganisms, but recent discovery of the ubiquity of microorganisms that cannot be cultured on agar raises a question: is agar really the best agent? In this study, we investigated the effect of two gelling agents, agar and gellan gum, on colony formation of a diverse array of microorganisms (total 108 strains) newly isolated from freshwater sediments and a representative microorganism as a slow grower on agar medium, Gemmatimonas aurantiaca, to clarify (i) whether they can grow on both agar and gellan gum plates, and (ii) the difference in time required for colony formation between the two gelling agents. Interestingly, 22 of 108 isolates showed no ability to form any visible colonies on the agar medium but did so on the gellan gum medium, and showed low 16S rRNA gene sequence similarities to their closest species. The remaining 86 isolates grew on both agar and gellan gum, but 52 of them grew much faster on gellan gum than on agar. Moreover, gellan gum also significantly stimulated the colony formation of the representative slow-growing microorganism G. aurantiaca. Our results demonstrate that the gelling agent is a crucial factor for the growth of bacteria on plate media, and that alternatives to agar will be very important for increasing the culturability of yet-to-be cultured microorganisms.
Scapular Muscle Tests in Subjects With Shoulder Pain and Functional Loss: Reliability and Construct Validity (2005)

In people with shoulder pain and functional loss, the intrarater reliability and error over 1 to 3 days were established using an HHD for measurement of isometric force for the assessment of scapular muscle performance. Error values can be used to make decisions regarding individual patients. Construct validity was established for the lower and upper trapezius muscle tests; therefore, these tests are advocated for use. However, construct validity was not demonstrated for the serratus anterior and middle trapezius muscle tests as performed in this study. Further investigation of these muscle tests is warranted.
Efficient Ammonia Electrosynthesis from Nitrate on Strained Ruthenium Nanoclusters (2020)

The limitations of the Haber-Bosch reaction, particularly high-temperature operation, have ignited new interests in low-temperature ammonia-synthesis scenarios. Ambient N<sub>2</sub> electroreduction is a compelling alternative but is impeded by a low ammonia production rate (mostly <10 mmol g<sub>cat</sub><sup>-1</sup> h<sup>-1</sup>), a small partial current density (<1 mA cm<sup>-2</sup>), and a high-selectivity hydrogen-evolving side reaction. Herein, we report that room-temperature nitrate electroreduction catalyzed by strained ruthenium nanoclusters generates ammonia at a higher rate (5.56 mol g<sub>cat</sub><sup>-1</sup> h<sup>-1</sup>) than the Haber-Bosch process. The primary contributor to such performance is hydrogen radicals, which are generated by suppressing hydrogen-hydrogen dimerization during water splitting enabled by the tensile lattice strains. The radicals expedite nitrate-to-ammonia conversion by hydrogenating intermediates of the rate-limiting steps at lower kinetic barriers. The strained nanostructures can maintain nearly 100% ammonia-evolving selectivity at >120 mA cm<sup>-2</sup> current densities for 100 h due to the robust subsurface Ru-O coordination. These findings highlight the potential of nitrate electroreduction in real-world, low-temperature ammonia synthesis.
How I treat Waldenström macroglobulinemia (2009)

Waldenström macroglobulinemia (WM) is a distinct B-cell disorder resulting from the accumulation, predominantly in the bone marrow, of clonally related IgM-secreting lymphoplasmacytic cells. Genetic factors play an important role, with 20% of patients demonstrating a familial predisposition. Asymptomatic patients should be observed. Patients with a disease-related hemoglobin level less than 10 g/L, platelet count less than 100 x 10(9)/L, bulky adenopathy or organomegaly, symptomatic hyperviscosity, peripheral neuropathy, amyloidosis, cryoglobulinemia, cold-agglutinin disease, or evidence of disease transformation should be considered for therapy. Plasmapheresis should be considered for symptomatic hyperviscosity and for prophylaxis in patients in whom rituximab therapy is contemplated. The use of rituximab as monotherapy or in combination with cyclophosphamide, nucleoside analog, bortezomib, or thalidomide-based regimens can be considered for the first-line therapy of WM and should take into account specific treatment goals, future autologous stem cell transplantation eligibility, and long-term risks of secondary malignancies. In the salvage setting, the reuse or use of an alternative frontline regimen can be considered as well as bortezomib, alemtuzumab, and stem cell transplantation. Newer agents, such as bendamustine and everolimus, can also be considered in the treatment of WM.
Dibenzo[c,g]indolo[3,2,1-jk]carbazole as a new chromophore for blue organic light-emitting diodes (2019)

A novel sky blue emitter derived from a dibenzo[<italic>c</italic>,<italic>g</italic>]indolo[3,2,1-<italic>jk</italic>]carbazole chromophore was developed and realized high external quantum efficiency of 6.2% in the blue organic light-emitting diodes.