gebhart/patrepeval huggingface dataset:
Parallel Conductive-AFM Lithography on LaAlO$_{3}$ /SrTiO$_{3}$ Interfaces (2013)

Nanoscale devices can be created at the LaAlO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> /SrTiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> interface by metastable charging of the top LaAlO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> surface with a voltage-biased conductive-atomic force microscope (c-AFM) tip. In order to create scalable nanoelectronic circuits, it will be important to develop procedures that allow multiple tips to “write” nanostructures in parallel. Here, we demonstrate parallel writing of conductive nanostructures at the LaAlO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> /SrTiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> interface using an array of c-AFM tips. Independent control over the writing process for each tip is achieved by holding the tip array at a fixed potential and varying the voltage applied to individual electrodes. The approach developed here should be applicable to 2-D tip arrays with millions of probes.
A Unified Strategy to Integrate Information and Methods Across Multiple Training Environments for Assembly Simulations (2014)

Training for assembly simulations can be provided using a wide range of technologies from a simple computer-based training (CBT) approach to a complex virtual reality (VR)-based immersive training (IMT) approach. The CBT approach allows user interactions through traditional keyboard and mouse applications, while the IMT approach immerses the user in a virtual environment for a more realistic experience. Typically, for a particular scenario, tools and applications for each of these approaches are developed independently. Consequently, there is much duplication of data and effort, and a lack of synchronization between them. This paper focuses on an integrated approach with support from ontologies to address this problem. Ontologies provide an opportunity to capture and manage common data and map concepts from one application to another in a logical and measured manner. Methods are developed to enable knowledge in these ontologies to be used and shared in a comprehensive and effective manner between CBT and IMT tools. The key contribution of this work is that the ontologies instantiating concepts and properties for the training domain are used effectively among different training tools to deal with common and disparate characteristics between them.
Dextran and poly(butyl methacrylate) graft copolymers as non-adherent materials for vascular applications (2016)

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THE OUTCOME OF OPERATIVELY TREATED ANTERIOR CRUCIATE LIGAMENT DISRUPTIONS IN THE SKELETALLY IMMATURE CHILD (1996)

Abstract The purpose of this study was to evaluate the outcome of transphyseal ligament reconstruction in skeletally immature children with midsubstance anterior cruciate ligament (ACL) disruption. Five consecutive patients (mean age, 12.9 years; range, 8 to 14 years) with radiographically documented wide open growth plates and a minimum of 5 cm of expected remaining growth, underwent intraarticular reconstruction of the ACL. Operative treatment included three ACL reconstructions using hamstring tendons and two with quadriceps patellar tendon. All involved a centrally placed 6-mm or smaller tibial drill hole through an open physis and graft placement in an over-the-top position on the femur. At an average follow-up of 7.4 years (range, 4.5 to 9.9 years), no patient had a positive anterior drawer, Lachman, or pivot shift test. On KT- 1000 arthrometer testing, all patients had 3 mm or less of increased anterior-posterior displacement (mean ± SD=1.0 ± 1.6 mm). Magnetic resonance imaging showed that four tibial physes had fused in a symmetric fashion and one was still open. Orthoroentgenograms showed that no patient had a significant leg length discrepancy (−0.8 mm ± 3.4 mm). The mean increase in height postoperatively was 17.7 cm (range, 7.6 to 31.0 cm). Overall, using the International Knee Documentation Committee (IKDC) evaluation form, there were four patients with grade A and one with grade C. The one patient with a poor IKDC grade had sustained a subsequent patellar dislocation with osteochondral fracture. In conclusion, ACL reconstruction using small drill holes placed through open tibial physes does not seem to adversely affect outcome or future growth.
Sensitivity and resolution improvement for in-vivo magnetic resonance current density imaging (MRCDI) of the human brain (2021)

ABSTRACT Purpose Magnetic resonance current density imaging (MRCDI) combines MR brain imaging with the injection of time-varying weak currents (1-2 mA) to assess the current flow pattern in the brain. However, the utility of MRCDI is still hampered by low measurement sensitivity and poor image quality. Methods We recently introduced a multi-gradient-echo-based MRCDI approach that has the hitherto best documented efficiency. We now advanced our MRCDI approach in three directions and performed phantom and in-vivo human brain experiments for validation: First, we verified the importance of enhanced spoiling and optimize it for imaging of the human brain. Second, we improved the sensitivity and spatial resolution by using acquisition weighting. Third, we added navigators as a quality control measure for tracking physiological noise. Combining these advancements, we tested our optimized MRCDI method by using 1 mA transcranial electrical stimulation (TES) currents injected via two different electrode montages in five subjects. Results For a session duration of 4:20 min, the new MRCDI method was able to detect magnetic field changes caused by the TES current flow at a sensitivity level of 84 pT, representing in a twofold increase relative to our original method. Comparing both methods to current flow simulations based on personalized head models demonstrated a consistent increase in the coefficient of determination of Δ R 2 =0.12 for the current-induced magnetic fields and Δ R 2 =0.22 for the current flow reconstructions. Interestingly, some of the simulations still clearly deviated from the measurements despite of the strongly improved measurement quality. This suggests that MRCDI can reveal useful information for the improvement of head models used for current flow simulations. Conclusion The advanced method strongly improves the sensitivity and robustness of MRCDI and is an important step from proof-of-concept studies towards a broader application of MRCDI in clinical and basic neuroscience research.
Degradation of Nuclear Factor Kappa B during Foot-and-Mouth Disease Virus Infection (2007)

We have previously shown that the leader proteinase (L(pro)) of foot-and-mouth disease virus (FMDV) interferes with the innate immune response by blocking the translation of interferon (IFN) protein and by reducing the immediate-early induction of beta IFN mRNA and IFN-stimulated genes. Here, we report that L(pro) regulates the activity of nuclear factor kappaB (NF-kappaB). Analysis of NF-kappaB-dependent reporter gene expression in BHK-21 cells demonstrated that infection with wild-type (WT) virus has an inhibitory effect compared to infection with a genetically engineered mutant lacking the leader coding region. The expression of endogenous NF-kappaB-dependent genes tumor necrosis factor alpha and RANTES is also reduced in WT virus-infected primary porcine cells. This inhibitory effect is neither the result of a decrease in the level of the mRNA of p65/RelA, a subunit of NF-kappaB, nor a block on the nuclear translocation of p65/RelA, but instead appears to be a consequence of the degradation of accumulated p65/RelA. Viral L(pro) is localized to the nucleus of infected cells, and there is a correlation between the translocation of L(pro) and the decrease in the amount of nuclear p65/RelA. By using a recombinant cardiovirus expressing L(pro), we demonstrate that the disappearance of p65/RelA takes place in the absence of any other FMDV product. The observation that L(pro) disrupts the integrity of NF-kappaB suggests a global mechanism by which FMDV antagonizes the cellular innate immune and inflammatory responses to viral infection.
Inhibitors of Deacetylases Suppress Oncogenic KIT Signaling, Acetylate HSP90, and Induce Apoptosis in Gastrointestinal Stromal Tumors (2009)

Gastrointestinal stromal tumors (GIST) are characterized by activating mutations of KIT or platelet-derived growth factor receptor A (PDGFRA), and treatment with the tyrosine kinase inhibitor imatinib yields responses in the majority of patients. However, most patients develop secondary resistance, which is associated with a dismal prognosis. Histone deacetylase inhibitors (HDACI) have been shown to enhance imatinib activity in imatinib-resistant chronic myelogenous leukemia. Against this background, we explored whether HDACI might provide an alternative therapeutic strategy to KIT/PDGFRA kinase inhibitors in GIST. Inhibition of cell proliferation by HDACI was seen in KIT-positive but not in KIT-negative GIST cell lines, suggesting that HDACI activity is mainly conferred by targeting oncogenic KIT. KIT activity, expression, and activation of downstream pathways were strongly inhibited by several HDACI (SAHA, LBH589, VPA, trichostatin A, and NaButyrate). SAHA and LBH589 induced apoptosis in KIT-positive GIST, and strong synergism with imatinib was observed at low concentrations of SAHA and LBH589. Mechanistically, treatment with HDACI reduced KIT mRNA transcript levels and led to strong acetylation of HSP90, interfering with its activity as KIT chaperone. These results provide preclinical evidence for a disease-specific effect of HDACI in KIT-positive GIST, which could translate into therapeutic activity.
Match What Matters: Generative Implicit Feature Replay for Continual Learning. (2021)

Neural networks are prone to catastrophic forgetting when trained incrementally on different tasks. In order to prevent forgetting, most existing methods retain a small subset of previously seen samples, which in turn can be used for joint training with new tasks. While this is indeed effective, it may not always be possible to store such samples, e.g., due to data protection regulations. In these cases, one can instead employ generative models to create artificial samples or features representing memories from previous tasks. Following a similar direction, we propose GenIFeR (Generative Implicit Feature Replay) for class-incremental learning. The main idea is to train a generative adversarial network (GAN) to generate images that contain realistic features. While the generator creates images at full resolution, the discriminator only sees the corresponding features extracted by the continually trained classifier. Since the classifier compresses raw images into features that are actually relevant for classification, the GAN can match this target distribution more accurately. On the other hand, allowing the generator to create full resolution images has several benefits: In contrast to previous approaches, the feature extractor of the classifier does not have to be frozen. In addition, we can employ augmentations on generated images, which not only boosts classification performance, but also mitigates discriminator overfitting during GAN training. We empirically show that GenIFeR is superior to both conventional generative image and feature replay. In particular, we significantly outperform the state-of-the-art in generative replay for various settings on the CIFAR-100 and CUB-200 datasets.
DNPLab/DNPLab: DNPLab 1.0.4 (2021)

Improved documentation Fixed issues with saving h5 files Improvements to Hydration GUI Improvements to importing data
Cubic or Orthorhombic? Revealing the Crystal Structure of Metastable Black-Phase CsPbI3 by Theory and Experiment (2018)

Room-temperature films of black-phase cesium lead iodide (CsPbI3) are widely thought to be trapped in a cubic perovskite polymorph. Here, we challenge this assumption. We present structural refinement of room-temperature black-phase CsPbI3 in an orthorhombic polymorph. We demonstrate that this polymorph is adopted by both powders and thin films of black-phase CsPbI3, fabricated either by high- or low-temperature processes. We perform electronic band structure calculations for the orthorhombic polymorph and find agreement with experimental data and close similarities with orthorhombic methylammonium lead iodide. We investigate the structural transitions and thermodynamic stability of the various polymorphs of CsPbI3 and show that the orthorhombic polymorph is the most stable among its other perovskite polymorphs, but it remains less stable than the yellow nonperovskite polymorph.
Study of the B$^+ \to $J$/\psi\overline{\Lambda}$p decay in proton-proton collisions at $\sqrt{s}=$ 8 TeV (2019)

A study of the B$^+\to $J$/\psi\overline{\Lambda}$p decay using proton-proton collision data collected at $\sqrt{s}=$ 8 TeV by the CMS experiment at the LHC, corresponding to an integrated luminosity of 19.6 fb$^{-1}$, is presented. The ratio of branching fractions $\mathcal{B}$(B$^+ \to $J$/\psi\overline{\Lambda}$p )$/\mathcal{B}$(B$^\to $J$/\psi$K$^*$(892)$^+$) is measured to be (1.054 $\pm$ 0.057 (stat) $\pm$ 0.035 (syst) $\pm$ 0.011 ($\mathcal{B}$))%, where the last uncertainty reflects the uncertainties in the world-average branching fractions of $\overline{\Lambda}$ and K$^*$(892)$^+$ decays to reconstructed final states. The invariant mass distributions of the J$/\psi\overline{\Lambda}$, J$/\psi$p, and $\overline{\Lambda}$p systems produced in the B$^+\to $J$/\psi\overline{\Lambda}$p decay are investigated and found to be inconsistent with the pure phase space hypothesis. The analysis is extended by using a model-independent angular amplitude analysis, which shows that the inclusion of contributions from excited kaons decaying to the $\overline{\Lambda}$p system improves the description of the observed invariant mass distributions.
Monoclonal antibodies that distinguish between human cellular and plasma fibronectin. (1984)

Two monoclonal antibodies have been developed against human fibronectin expressed by simian virus 40 transformed human mammary epithelial cells. Monoclonal antibody ICRF-FN-3 recognizes a determinant on human cellular but not plasma fibronectin. The antigenic site recognized by FN-3 is lost after limited proteolysis of cellular fibronectin with alpha-chymotrypsin but not trypsin. Monoclonal antibody, ICRF-FN-4, against a determinant on both human plasma and cellular fibronectin reacts with an antigenic site on fibronectin which is not destroyed by trypsin or alpha-chymotrypsin. Although the epitopes recognized by FN-3 and FN-4 are expressed similarly by cells from the human breast they are expressed differently on rat mammary (RAMA) cell lines.
Analgesic Effects of GpTx-1, PF-04856264 and CNV1014802 in a Mouse Model of NaV1.7-Mediated Pain (2016)

Loss-of-function mutations of Na(V)1.7 lead to congenital insensitivity to pain, a rare condition resulting in individuals who are otherwise normal except for the inability to sense pain, making pharmacological inhibition of Na(V)1.7 a promising therapeutic strategy for the treatment of pain. We characterized a novel mouse model of Na(V)1.7-mediated pain based on intraplantar injection of the scorpion toxin OD1, which is suitable for rapid in vivo profiling of Na(V)1.7 inhibitors. Intraplantar injection of OD1 caused spontaneous pain behaviors, which were reversed by co-injection with Na(V)1.7 inhibitors and significantly reduced in Na(V)1.7(-/-) mice. To validate the use of the model for profiling Na(V)1.7 inhibitors, we determined the Na(V) selectivity and tested the efficacy of the reported Na(V)1.7 inhibitors GpTx-1, PF-04856264 and CNV1014802 (raxatrigine). GpTx-1 selectively inhibited Na(V)1.7 and was effective when co-administered with OD1, but lacked efficacy when delivered systemically. PF-04856264 state-dependently and selectively inhibited Na(V)1.7 and significantly reduced OD1-induced spontaneous pain when delivered locally and systemically. CNV1014802 state-dependently, but non-selectively, inhibited Na(V) channels and was only effective in the OD1 model when delivered systemically. Our novel model of Na(V)1.7-mediated pain based on intraplantar injection of OD1 is thus suitable for the rapid in vivo characterization of the analgesic efficacy of Na(V)1.7 inhibitors.
The subrenal capsule assay in mice. Prediction of rat tumor sensitivity to chemotherapy (1984)

The predictive value of the subrenal capsule (SRC) assay for cancer chemotherapy was tested in five rat tumors. Tumor-bearing rats were used as controls. In order to simulate clinical chemotherapy, different dose regimens and drug combinations were used. All five tumors were evaluable in in the SRC assay. Taking into account cytotoxic drugs, 86% compatibility was obtained between the SRC assay and the rat model. Antitumor effect of three antiestrogenic compounds could not be predicted by the SRC assay. It is concluded that the SRC assay can be expected to have predictive value in the assessment of tumor sensitivity to single and combination chemotherapy based on experimental animal models.
Efficient Calculation of Molecular Configurational Entropies Using an Information Theoretic Approximation (2012)

Accurate computation of free energy changes upon molecular binding remains a challenging problem, and changes in configurational entropy are especially difficult due to the potentially large numbers of local minima, anharmonicity, and high-order coupling among degrees of freedom. Here we propose a new method to compute molecular entropies based on the maximum information spanning tree (MIST) approximation that we have previously developed. Estimates of high-order couplings using only low-order terms provide excellent convergence properties, and the theory is also guaranteed to bound the entropy. The theory is presented together with applications to the calculation of the entropies of a variety of small molecules and the binding entropy change for a series of HIV protease inhibitors. The MIST framework developed here is demonstrated to compare favorably with results computed using the related mutual information expansion (MIE) approach, and an analysis of similarities between the methods is presented.
Efficient stereo video encoding for mobile applications using the 3D+F codec (2012)

This paper presents a stereo video codec called 3D+F which has specifically been designed to meet the low complexity requirements imposed by mobile applications while trying to be competitive with the state-of-the-art coders, such as the multi view video coding (MVC) extension of the H.264/AVC standard, in terms of rate-distortion (RD). By exploiting the stereo geometry of stereoscopic image pairs it is possible to transcode a 3D movie into a 2D movie and a 2-bit labeling. The 2D movie can then be compressed using any video coder while the labeling needs to be compressed losslessly. Preliminary subjective testing shows that the resulting quality has potential to be very competitive.
Stability Test of a Pair of Conical Coils for Open-Bore MRI Magnet (2016)

To improve the openness of MRI scanners and reduce potential patient claustrophobia, a novel magnet concept with conical-shaped outermost main coils was investigated. This concept may also improve the coil stability because the Lorentz force acting on conical coils is mostly perpendicular to the coil/former interface, which may reduce friction-slip induced quench risk. A pair of conical superconducting coils has been tested to evaluate its stability. The test coil has 16° conical angle with a 50-cm diameter at the smaller diameter end. Both coils are supported by an aluminum former embracing coil OD surfaces. The pair of coils was ramped in a vertical Dewar with instrumentation measuring coil temperature, current, voltage, and strains. Two training quenches were observed at 74% and 81% Io/Ic before the coil current reached 100% of the short sample Ic value.
A103 (1998)

Melan-A is a previously defined, melanocyte differentiation antigen, and an anti-Melan-A murine monoclonal antibody, A103, was recently developed by our group. In this study, we evaluated A103 immunoreactivity on formalin-fixed, paraffin-embedded tissues, exploring the potential of A103 in the diagnosis of metastatic melanoma. Seventy-five metastatic melanomas, 10 primary melanomas, and 10 benign melanocytic nevi were tested. The reactivity of A103 was compared with HMB-4, an anti-gp100 antibody. Results showed that all nevi were A103 positive, and most primary melanomas were A103 and HMB45 positive. Of 75 metastatic melanomas, 61 (81%) were A103 positive, and 56 (75%) were HMB45 positive. Of 19 HMB45-negative lesions, 8 were A103 positive; of 14 A103-negative lesions, 3 were HMB45 positive. Eleven metastatic lesions, as well as 2 of 10 primary melanomas, were dual negative. These negative cases consisted mainly of the spindle cell and desmoplastic variants. Of the positive cases, A103 showed homogeneous staining in a significantly higher proportion of cases than HMB45 (72% versus 52%). In addition, focal staining with less than 5% reactive tumor cells was seen more frequently in HMB45 (12 of 56) than in A103 (5 of 61). These results indicated that A103 can be used as a first-line antibody in the diagnosis of metastatic melanoma. Our results also showed that A103 reacted with angiomyolipoma, which is known to be HMB45 positive. Of normal tissues, unexpected A103 reactivity was observed in the adrenal cortex, granulosa and theca cells of the ovary, and Leydig cells of the testis. This A103 immunoreactivity in benign and neoplastic tissues of nonmelanocytic origin, the basis of which is unclear, could also be of potential diagnostic value.
Clustering Techniques for Rule Extraction from Unstructured Text Fragments (2005)

This paper focuses on techniques for clustering unstructured text fragments which are generated from a rule extraction agent. The text fragments represent paragraphs of text containing potential rules. The latent semantic indexing method is applied to map the unstructured text into a linear vector space. Similar text fragments are identified based on the similarity between their vector representations. The problem of clustering based on general similarity measures that are different than the conventional distance based measures is discussed. A new version of the mountain clustering method is developed to address the problem of identifying groups of similar vectors that correspond to documents with analogous content. Several clustering algorithms are compared in their ability to satisfactorily cluster these text fragments into sets of related concepts. An intelligent agent algorithm for extraction of rules from text documents is proposed and demonstrated.