gebhart/patrepeval huggingface dataset:
Challenges in Precisely Aligning Models of Human Anatomy Using Generic Schema Matching (2004)

This paper describes how we used generic schema matching algorithms to align the Foundational Model of Anatomy (FMA) and the GALEN Common Reference Model (CRM), two large models of human anatomy. We summarize the generic schema matching algorithms we used to identify correspondences. We present sample results that highlight the similarities and differences between the FMA and the CRM. We also identify uses of aggregation, transitivity, and reification, for which generic schema matching fails to produce an accurate mapping and present manually constructed solutions for them.
EditAR: A Digital Twin Authoring Environment for Creation of AR/VR and Video Instructions from a Single Demonstration (2022)

Augmented/Virtual reality and video-based media play a vital role in the digital learning revolution to train novices in spatial tasks. However, creating content for these different media requires expertise in several fields. We present EditAR, a unified authoring, and editing environment to create content for AR, VR, and video based on a single demonstration. EditAR captures the user’s interaction within an environment and creates a digital twin, enabling users without programming backgrounds to develop content. We conducted formative interviews with both subject and media experts to design the system. The prototype was developed and reviewed by experts. We also performed a user study comparing traditional video creation with 2D video creation from 3D recordings, via a 3D editor, which uses freehand interaction for in-headset editing. Users took 5 times less time to record instructions and preferred EditAR, along with giving significantly higher usability scores.
Proteomic analysis of Aspergillus niger type strain (MUM 03.01) after accelerated freeze-drying preservation (2013)

Industrial processes based on biotechnology require a reliable source of microbial cultures, raising a need for the microbial safe long-term storage. The expanding biotechnological applications of Aspergillus niger requires effective long-term preservation that maintains their viability and also their physiological and genetic features [I]. From the best of our knowledge, proteomic analysis for monitoring the effect of preservation techniques on fungai intra- and extracellular protein expression by filamentous fungi has not been studied. Proteomic analysis is a powerful methodology for evaluation of proteins in complex mixtures and for the study of alteration of protein expression in an organism under varying environmental conditions. Proteomics can also be used as an important monitoring tool on the fungai cellular structure and enzymatic expression before and after filamentous fungi long-term preservation. ln this study, a comparative proteomic analysis of intra- and extracellular protein secretion expressed by A. niger type strain (MUM 03.01) preserved on freeze-drying ampoules and then subjected to accelerated shelf-life aging through the temperature increasing was assessed. Proteomic analysis based on 2D gel electrophoresis of A. niger (MUM 03.01) was assessed in 5 different liquid media. According to the results obtained the intracellular fungai proteomic profile was not modified by the accelerated shelf-life aging. It was also observed that the extracellular fungai proteomic profile was negligible which makes this A. niger type strain a weak fungallineage for biotechnological applications.
Design of Biotin-Functionalized Luminescent Quantum Dots (2007)

We report the design and synthesis of a tetraethylene glycol- (TEG-) based bidentate ligand functionalized with dihydrolipoic acid (DHLA) and biotin (DHLA-TEG-biotin) to promote biocompatibility of luminescent quantum dots (QD's). This new ligand readily binds to CdSe-ZnS core-shell QDs via surface ligand exchange. QDs capped with a mixture of DHLA and DHLA-TEG-biotin or polyethylene glycol- (PEG-) (molecular weight average approximately 600) modified DHLA (DHLA-PEG600) and DHLA-TEG-biotin are easily dispersed in aqueous buffer solutions. In particular, homogeneous buffer solutions of QDs capped with a mixture of DHLA-PEG600 and DHLA-TEG-biotin that are stable over broad pH range have been prepared. QDs coated with mixtures of DHLA/DHLA-TEG-biotin and with DHLA-PEG600/DHLA-TEG-biotin were tested in surface binding assays and the results indicate that biotin groups on the QD surface interact specifically with NeutrAvidin-functionalized microtiter well plates.
Safety of AFM11 in the treatment of patients with B-cell malignancies: Findings from two phase 1 studies (2022)

Abstract BackgroundThe prognosis for patients with relapsed and/or refractory (R/R) non-Hodgkin’s lymphoma (NHL) or acute lymphoblastic leukaemia (ALL) remains poor, with existing treatments having significant side effects. Developed for the treatment of these cancers, AFM11 is a tetravalent, bispecific humanised recombinant antibody construct (TandAb®) designed to bind to human CD19 and CD3 and lead to the activation of T cells inducing apoptosis and killing of malignant B cells.MethodsTwo open-label, multicentre, dose-escalation phase 1 studies evaluated the safety, pharmacokinetics and activity of AFM11 in patients with R/R CD19-positive B cell NHL (AFM11-101) and in patients with CD19+ B-precursor Philadelphia-chromosome negative ALL (AFM11-102). Adverse events (AEs) were assessed and recorded, imaging (NHL) or bone marrow assessment (ALL) were used to evaluate response. Additional pharmacodynamic assays undertaken included cytokine release analysis, B-cell and T-cell depletion.ResultsIn AFM11-101, 16 patients with R/R NHL received AFM11 in five different dose cohorts. Of which, 14 experienced drug-related treatment-emergent AEs (TEAEs) [including five serious AEs (SAEs)], five patients experienced dose-limiting toxicity (DLT) and ten patients discontinued the study. The high number of neurological events led to a decrease in infusion frequency during the study. No objective response to treatment was observed. In AFM11-102, 17 patients with R/R ALL received AFM11 in six different dose cohorts. Thirteen patients experienced drug-related TEAEs (including four SAEs), DLTs occurred in two patients and five patients discontinued the study. An objective response was recorded in three patients. The maximum tolerated dose could not be determined in either study due to early termination.ConclusionsAFM11 treatment was associated with frequent neurological adverse reactions that were severe in some patients. In ALL some signs of activity, albeit short lived, were observed whereas no activity was observed in patients with NHL; therefore, further clinical development was terminated.Trial IdentifiersNCT02106091, NCT02848911
Developmental Biology Protocols: Overview I (2003)

As the next millennium dawns, developmental biology, the study of the processes that give rise to cellular diversity and order within an organism and to the continuation from one generation to the next, has reached a most exciting stage as an experimental science. In particular, in the last two decades, the application of analytical and technical know-hows generated from the “molecular biology revolution” have critically advanced our understanding of development in a mechanistic way. There is every reason to believe that the study of development will be one of the most promising areas of the life sciences in the next millennium.
Insights into rooted and non-rooted Android mobile devices with behavior analytics (2016)

In the Android community, a commonly held belief is that rooted devices are more at-risk than their standard counterparts. Many applications include "protections" that disable certain functionality in the presence of a "rooted" device. In this paper, we carry out a detailed quantitative analysis on 6.14 million Android devices comparing rooted and non-rooted devices across a broad range of characteristics. Specifically our study focuses on measuring and analyzing various behavioral differences between rooted and non-rooted devices, and how such differences impact the security of rooted devices, e.g. making them more susceptible to malware or at higher risk. We further leverage our insights and implement a machine learning system to determine whether a device is rooted based on a comprehensive set of features with an accuracy of approximately 90%.
Spatio-temporal clustering of probabilistic region trajectories (2011)

We propose a novel model for the spatio-temporal clustering of trajectories based on motion, which applies to challenging street-view video sequences of pedestrians captured by a mobile camera. A key contribution of our work is the introduction of novel probabilistic region trajectories, motivated by the non-repeatability of segmentation of frames in a video sequence. Hierarchical image segments are obtained by using a state-of-the-art hierarchical segmentation algorithm, and connected from adjacent frames in a directed acyclic graph. The region trajectories and measures of confidence are extracted from this graph using a dynamic programming-based optimisation. Our second main contribution is a Bayesian framework with a twofold goal: to learn the optimal, in a maximum likelihood sense, Random Forests classifier of motion patterns based on video features, and construct a unique graph from region trajectories of different frames, lengths and hierarchical levels. Finally, we demonstrate the use of Isomap for effective spatio-temporal clustering of the region trajectories of pedestrians. We support our claims with experimental results on new and existing challenging video sequences.
In Vivo Genome Editing in Neonatal Mouse Liver Preferentially Utilizes Homology Directed Repair (2015)

Abstract Genome editing has the potential to provide long-term therapeutic gene expression in vivo. We have previously demonstrated efficient editing in a mouse model of hemophilia B through liver-directed adeno-associated viral vector (AAV) delivery of a zinc finger nuclease (ZFN) pair and a corrective donor. We determined that homology is not necessary to achieve efficient levels of genome editing in adult mice, consistent with the fact that quiescent cells, including adult hepatocytes, are not thought to be amenable to homology directed repair (HDR). As a consequence of the donor containing a splice acceptor, both HDR and homology independent vector integration are capable of driving human factor 9 (hF.IX) expression. In this study we sought to determine whether hF.IX expression in mice treated as neonates, undergoing substantial hepatocyte proliferation, is predominantly the result of HDR or homology independent genome editing. Provided the efficacy is not substantially reduced, an HDR dependent approach would impose additional constraints on targeting. Treatment of neonatal hF9mut mice (harboring the ZFN target site) with 1x1011 vg AAV8-ZFN and 5x1011 vg AAV8-Donor via retro-orbital injection resulted in a drastic difference in hF.IX expression between donors with and without homology 10 weeks post injection (Homology: 1531 ± 174.5 ng/mL vs. No-homology: 146.1 ± 5.8 ng/mL; n=12 and 7, respectively). We next asked whether HDR could be stimulated even more specifically through the induction of DNA single strand breaks at the target site. We treated neonatal mice with homologous or non-homologous donors, as well as ZFNs or ZFNickases (in which one FokI nuclease domain was inactivated with the D450A mutation). ZFNickases were indeed active, resulting in ~250 ng/mL hF.IX 4 weeks post injection (Figure 1). Interestingly, we could not detect hF.IX in mice treated with ZFNickase and no-homology donor (LOD: 15ng/mL). To rule out the possibility that this was simply due to the lower efficacy of ZFNickases compared to ZFNs, we increased the ZFNickase dose 4 fold. Four weeks post treatment, we observed substantial levels of hF.IX in mice treated with homologous donor (2041 ± 269 ng/mL) and were again unable to detect hF.IX in mice treated with the non-homologous donor (n=10 and 7, respectively). These data point to homology directed repair as the primary mechanism of protein production for genome editing in neonatal mouse liver, and suggest improvements in both efficacy and specificity can be made through deeper understanding of the molecular requirements of this approach. Figure 1. Figure 1. Disclosures Anguela: Spark Therapeutics, Inc.: Employment, Equity Ownership, Patents &amp; Royalties. Doyon:Sangamo BioSciences: Employment. Wechsler:Sangamo BioSciences: Employment. Paschon:Sangamo BioSciences: Employment. Davidson:Spark Therapeutics: Consultancy. Gregory:Sangamo BioSciences: Employment. Holmes:Sangamo BioSciences: Employment. High:Spark Therapeutics: Employment, Equity Ownership, Patents &amp; Royalties.
Direct Effects of Gonadotropin Releasing Hormone and Its Antagonist upon Ovarian Functions Stimulated by FSH, Prolactin, and LH1 (1981)

The role of gonadotropin releasing hormone (GnRH) and its antagonist, [D-pGlu1, D-Phe2-DTrp3,6] GnRH, in the direct regulation of ovarian functions was studied in vivo and in vitro. Immature hypophysectomized rats were treated twice daily with FSH in the presence or absence of 30 μg GnRH or 500 μg antagonist or both. GnRH inhibited FSH stimulation of ovarian weight as well as LH receptor content and aromatase activity in the ovarian granulosa cells. In contrast, concomitant treatment with the antagonist blocked the inhibitory effect of GnRH. In cultured granulosa cells, GnRH treatment resulted in time-dependent inhibition of FSH-induced increase in estrogen and progesterone production, whereas addition of the antagonist to these cells reversed the inhibitory effect of GnRH in a time-related manner. Priming with FSH for 2 days in vitro induced functional PRL and LH receptors. Subsequent treatment with PRL for 2 days stimulated progesterone production and LH receptor content of these cells in vitro. PRL stimulation of LH receptor and progesterone production was inhibited by GnRH, whereas concomitant treatment with the antagonist blocked the GnRH inhibition. The GnRH inhibition of PRL-stimulated progesterone production was time-dependent and the addition of the antagonist to cells treated with PRL and GnRH reversed the GnRH inhibition in a time-related manner. LH treatment of FSH-primed granulosa cells stimulated both estrogen and progesterone production, whereas GnRH inhibited the LH-stimulated steroidogenesis. In contrast, concomitant treatment with the antagonist blocked the GnRH inhibition of the LH effect. Furthermore, the antagonist blocked the GnRH inhibition of cholera toxin-induced estrogen and progesterone production in cultured granulosa cells. These results demonstrate the direct inhibitory effect of GnRH upon ovarian functions maintained by FSH, LH, PRL, and cholera toxin and the ability of a GnRH antagonist to block the GnRH inhibition in a time- and dose-related manner.
Computationally-Sound Proofs (2017)

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Quantum nature of adsorbed hydrogen on single-wall carbon nanohorns (2005)

We have measured N2 adsorption isotherms on single-wall carbon nanohorns (SWNHs) over the temperature range of 77–92 K, and isosteric heat of adsorption, q st, were determined. Adsorption measurements for SWNHs have been also done for for H2 at 20 K, and for H2 and D2 at 77 K, respectively. We have performed grand canonical Monte Carlo (GCMC) simulations of N2, H2, and D2 for single-wall carbon nanotube (SWNT) models to compare with the experimental data. Simulated N2 adsorption isotherm on a SWNT bundle model is in reasonably good agreement with the experimental isotherm on the SWNH assembly over a wide range of pressures at 77 K; however, simulated q st-values for the SWNT bundle suggest that the SWNH particles are incompletely arranged in the SWNH assembly. Simulated endohedral isotherm of classical H2 inside an isolated SWNT model at 20 K showed that a density of adsorbed H2 in the internal space of the SWNH particle is quite smaller than that of classical H2 because of large quantum effects. In simulating H2 and D2 adsorption isotherms on the model SWNT bundle at 77 K, GCMC simulations based on the Feynman-Hibbs (FH) effective potential were applied to introduce quantum effects to the statistical properties generated by the classical Lennard-Jones (LJ) potential. We found that an adsorption ratio of H2 to D2 on the SWNT bundle from the FH-GCMC simulations is less than 0.91 depending on adsorption pressure; this is because the potential field of the SWNT bundle for H2 is relatively weaker than that for D2 even at 77 K, due to the wide quantum spreading of a H2 molecule.
Virtual eXtensible Local Area Network (VXLAN): A Framework for Overlaying Virtualized Layer 2 Networks over Layer 3 Networks (2014)

This document describes Virtual eXtensible Local Area Network (VXLAN), which is used to address the need for overlay networks within virtualized data centers accommodating multiple tenants. The scheme and the related protocols can be used in networks for cloud service providers and enterprise data centers. This memo documents the deployed VXLAN protocol for the benefit of the Internet community.
A novel pulse compression scheme based on minimum mean-square error reiteration [radar signal processing] (2004)

This paper presents an alternative approach to pulse compression that is based upon iterative minimum mean-square error (MMSE) estimation. It is similar to the well known least squares (LS) approach but does not suffer from the adverse effects caused by scatterers closer than some nominal range. This results in a more robust estimate of the radar returns while maintaining nearly the same sidelobe level. Furthermore, the proposed pulse compression scheme is highly parallelizable in range and therefore can be computed efficiently.
100 MS/s 10-25 MHz Wireless Voltage Probe (2011)

For developing and testing of power electronic converters and circuits, voltages and currents have to be measured to verify the proper mode of operation. In cascaded converters or multi-level topologies, the voltages to be measured contain common mode components up to several kV with transients up to several tens of kV/µs. Conventional isolated voltage measurement systems do either not meet the high voltage isolation requirements or exhibit a rather large coupling capacitance to ground. In combination with the high voltage transients, this coupling capacitance on the one hand impacts the circuit under test and on the other hand influences the voltage measurement. To reduce these effects, the coupling capacitance of the measurement system must be minimized. In this paper, a wireless voltage probe (WVP) is introduced to measure accurately on a high and transient reference voltage with minimal impact on the circuit under test. The basic concept and practical realization of the WVP are discussed and finally verified with measurements on a high power medium voltage IGBT converter system.
Compressed sensing for body MRI (2016)

5 J. Magn. Reson. Imaging 2017;45:966-987.
Residual malignant and normal plasma cells shortly after high dose melphalan and stem cell transplantation. Highlight of a putative therapeutic window in Multiple Myeloma? (2012)

Multiple Myeloma (MM) is an incurable malignant plasma cell disorder. We have evaluated the counts of Multiple Myeloma Cells (MMCs) and normal plasma cells (N-PCs), seven days after high-dose melphalan (HDM) and autologous stem transplantation (ASCT). Two third of patients had detectable minimal residual disease (MRD+) (71.7 MMCs/µL) after induction treatment with dexamethasone and proteasome inhibitor. MMC counts were reduced by 92% (P ≤ .05) but not eradicated 7 days after HDM+ASCT. Post-HDM+ASCT MMCs were viable and bathed in a burst of MMC growth factors, linked with post-HDM aplasia. In one third of patients (MRD- patients), MMCs were not detectable after induction treatment and remained undetectable after HDM+ASCT. Major difference between MRD- and MRD+ patients is that N-PC counts were increased 3 fold (P〈.05) by HDM+ASCT in MRD- patients, but were unaffected in MRD+ patients. Possible explanation could be that clearance of MMCs in MRD- patients makes more niches available for N-PCs. Thus, MMCs are not fully eradicated shortly after HDM, are bathed in high concentrations of MMC growth factors in an almost desert BM, are viable in short-term culture, which suggests providing additional therapies shortly after HDM to kill resistant MMCs before full repair of lesions.
Metal-insulator-vacuum type electron emission from N-containing chemical vapor deposited diamond (2001)

This letter presents a clear explanation of the electron emission mechanism of the high-resistivity N-doped diamond cathode. Due to the very low barrier to emission of electrons from the N-doped diamond conduction band into vacuum, electrons in the conduction band of diamond can establish an appreciable leakage current at very low anode voltage. When such a current starts to flow, there is a field which is developed across the diamond bulk. This field is observed as an increase in the electric field at the back contact, causing the injected tunneling current increases exponentially. This process leads to the low threshold emission from the high resistivity N-doped diamond cathode.
Antimalarial 1,2,4-Trioxanes Related to Artemisinin: Rules for Assignment of Relative Stereochemistry in Diversely Substituted Analogs (1997)

Abstract A series of rules has been developed, using mainly 1D and 2D NMR spectroscopy, for identification of relative stereochemistry in a variety of substituted antimalarial 1,2,4-trioxanes.
Conversion rate to the secondary conformation state in the binding mode of SARS-CoV-2 spike protein to human ACE2 may predict infectivity efficacy of the underlying virus mutant (2021)

ABSTRACT Since its outbreak in 2019 SARS-CoV-2 has spread with high transmission efficiency across the world, putting health care as well as economic systems under pressure [1, 2]. During the course of the pandemic, the originally identified SARS-CoV-2 variant has been widely replaced by various mutant versions, which showed enhanced fitness due to increased infection and transmission rates [3, 4]. In order to find an explanation, why SARS-CoV-2 and its emerging mutated versions showed enhanced transfection efficiency as compared to SARS-CoV 2002, an improved binding affinity of the spike protein to human ACE has been proposed by crystal structure analysis and was identified in cell culture models [5-7]. Kinetic analysis of the interaction of various spike protein constructs with the human ACE2 was considered to be best described by a Langmuir based 1:1 stoichiometric interaction. However, we demonstrate in this report that the SARS-CoV-2 spike protein interaction with ACE2 is best described by a two-step interaction, which is defined by an initial binding event followed by a slower secondary rate transition that enhances the stability of the complex by a factor of ∼190 with an overall KD of 0.20 nM. In addition, we show that the secondary rate transition is not only present in SARS-CoV-2 wt but is also found in B.1.1.7 where its transition rate is five-fold increased.