gebhart/patrepeval huggingface dataset:
Identification of Cellular Genes Affecting the Infectivity of Foot-and-Mouth Disease Virus (2009)

Foot-and-mouth disease virus (FMDV) produces one of the most infectious of all livestock diseases, causing extensive economic loss in areas of breakout. Like other viral pathogens, FMDV recruits proteins encoded by host cell genes to accomplish the entry, replication, and release of infectious viral particles. To identify such host-encoded proteins, we employed an antisense RNA strategy and a lentivirus-based library containing approximately 40,000 human expressed sequence tags (ESTs) to randomly inactivate chromosomal genes in a bovine kidney cell line (LF-BK) that is highly susceptible to FMDV infection and then isolated clones that survived multiple rounds of exposure to the virus. Here, we report the identification of ESTs whose expression in antisense orientation limited host cell killing by FMDV and restricted viral propagation. The role of one such EST, that of ectonucleoside triphosphate diphosphohydrolase 6 (NTPDase6; also known as CD39L2), a membrane-associated ectonucleoside triphosphate diphosphohydrolase that previously was not suspected of involvement in the propagation of viral pathogens and which we now show is required for normal synthesis of FMDV RNA and proteins, is described in this report.
Evaluation of seismic action in Sweden using the European Seismic Hazard Model (2017)

In 2013 the European Seismic Hazard Model 2013 (ESHM13) was released as a result of the EU-funded project Seismic Harmonization in Europe (SHARE). This hazard model provides seismic data applicable for structural engineering for every location in Europe and Turkey that directly correlates to the seismic regulations provided by Eurocode 8. Currently, earthquake engineering according to Eurocode is not standard procedure for structures in Sweden due to the low regional seismicity. The objective of this thesis is to employ the data from ESHM13 and evaluate if there is reason to consider earthquakes in relation to building construction in Sweden. Specifically, the response from seismic loads for buildings of normal importance (e.g. apartment buildings) and building of vital importance (e.g. hospitals) were examined. Eurocode 8 states that buildings of normal importance should be designed for an earthquake with a return period of 475 years. The way to differentiate building in terms of reliabilities in Eurocode 8 is to scale the reference seismic action for buildings of ordinary importance with a factor depending on importance class. This factor is a nationally determined parameter, and since these are absent in the Swedish annex it was shown that the recommended factor approximately correlates to an implicit return period of 1300 years for buildings of vital importance. With the use of hazard data for Lund, modal response spectrum analyses were carried out on simple 2D models and a more complex 3D FE-model. The results were compared to static analyses on the same models using the wind load as comparative action. From parametric studies, that varies a range of levels and stiffnesses, the resulting base response was compared between wind load and seismic load. Spectra with return periods correlating to 475- and 1300-year were used. An additional case study was carried out on a five story building, comparing sectional forces in a shear wall due to seismic loads and wind loads. The parametric studies clearly showed that the base response when using a 1300-year spectrum envelopes the base response from the wind load for almost every single parameter. In some cases, even a 475-year spectrum gives a higher response compared to the wind. Since the seismic response is mass-dependent and the wind response is surfacedependent, it was shown that the 475-year spectrum could easily envelope the wind for elongated building when analyzed in the long direction. The comparison of the sectional forces in the case study suggests that the base response is a relevant measure when the overall response is compared for seismic load and wind load. However, it was shown that the seismic response is not necessarily largest at its base which suggests that the critical findings in the parametric study are potentially on the non-conservative side.
3-D Electromagnetic Modeling of Parasitics and Mutual Coupling in EMI Filters (2013)

The electromagnetic compatibility (EMC) analysis of electromagnetic interference (EMI) filter circuits using 3-D numerical modeling by the partial element equivalent circuit (PEEC) method represents the central topic of this paper. The PEEC-based modeling method is introduced as a useful tool for the prediction of the high frequency performance of EMI input filters, which is affected by PCB component placement and self- and mutual-parasitic effects. Since the measuring of all these effects is rather difficult and time consuming, the modeling and simulation approach represents a valuable design aid before building the final hardware prototypes. The parasitic cancellation techniques proposed in the literature are modeled by the developed PEEC-boundary integral method (PEEC-BIM) and then verified by the transfer function and impedance measurements of the L-C and C-L-C filter circuits. Good agreement between the PEEC-BIM simulation and the measurements is achieved in a wide frequency range. The PEEC-BIM method is implemented in an EMC simulation tool GeckoEMC. The main task of the presented research is the exploration of building an EMC modeling environment for virtual prototyping of EMI input filters and power converter systems.
More protection in collisions with vehicles: Pedestrian protection with engine hoods (2006)

New requirements under the law in the European Union are expected to better protect pedestrians in their collisions with vehicles. The putting into effect of these requirements presents a challenge to the development of the entire forward part of the vehicle. ThyssenKrupp Steel develops concepts that fulfill the regulations for engine hoods. Steel as material of construction has effective energy absorption and an outstanding price/performance ratio. Limits on forces and accelerations must be maintained. A special challenge is the required impact for the engine hood. The regulations are divided into two phases. Phase 1 relates to vehicles that are new on the market since October 2005. The head impact test is made with a 3.5 kg impactor which with a speed of 35 km/hr impacts the engine hood. From the acceleration and the time of acceleration the head injury criteria (HIC) value is calculated that is a measure for the loading on the head. On 67% of the prescribed surface the HIC may be 1,000 at most, on 33% of the surface at most 2,000. With Phase 2 the regulation starting in 2010 is considerably sharpened. The collision with the engine hood will be 40 km/hr and the HIC limiting value of 1,000 must be maintained on the total defined surface. The discussion covers the engine hood for improved pedestrian protection. Materials of construction used in the engine hood have a large influence on pedestrian protection. Therefore, the Auto division of ThyssenKrupp Steel has constructed an engine hood of modern steel for optimized pedestrian protection. The developments have related to Phases 1 and 2. They include computer aided design (CAD) data and finite element (FE) network. Diagrams.
A Survey on Visual Analytics of Social Media Data (2016)

The unprecedented availability of social media data offers substantial opportunities for data owners, system operators, solution providers, and end users to explore and understand social dynamics. However, the exponential growth in the volume, velocity, and variability of social media data prevents people from fully utilizing such data. Visual analytics, which is an emerging research direction, has received considerable attention in recent years. Many visual analytics methods have been proposed across disciplines to understand large-scale structured and unstructured social media data. This objective, however, also poses significant challenges for researchers to obtain a comprehensive picture of the area, understand research challenges, and develop new techniques. In this paper, we present a comprehensive survey to characterize this fast-growing area and summarize the state-of-the-art techniques for analyzing social media data. In particular, we classify existing techniques into two categories: gathering information and understanding user behaviors. We aim to provide a clear overview of the research area through the established taxonomy. We then explore the design space and identify the research trends. Finally, we discuss challenges and open questions for future studies.
Supplementary Table 5 from A Diverse Array of Cancer-Associated <i>MTOR</i> Mutations Are Hyperactivating and Can Predict Rapamycin Sensitivity (2023)

&lt;p&gt;XLSX file 17K, All site-directed mutagenesis primers to generate mutant mTOR and Rheb1 are listed&lt;/p&gt;
Cartoon rendering of smoke animations (2004)

We describe a technique for generating cartoon style animations of smoke. Our method takes the output of a physically-based simulator and uses it to drive particles that are rendered using a variant of the depth differences technique (originally used for rendering trees). Specific issues we address include the placement and evolution of primitives in the flow and the maintenance of temporal coherence. The results are visually simple, flicker-free animations that convey the turbulent, dynamic nature of the gas with simple outlines.
An MMI-based Polarization Splitter Using Patterned Metal and Tilted Joint (2012)

A novel polarization splitter on an InP substrate utilizing an MMI coupler with a patterned gold layer and a tilted joint is proposed. The MMI section is less than 540 µm. Simulations show that the device has a polarization extinction ratio over 23 dB and an insertion loss below 0.7 dB over the entire C-band for both TE and TM polarizations.
Ontology-Grounded Topic Modeling for Climate Science Research (2018)

In scientific disciplines where research findings have a strong impact on society, reducing the amount of time it takes to understand, synthesize and exploit the research is invaluable. Topic modeling is an effective technique for summarizing a collection of documents to find the main themes among them and to classify other documents that have a similar mixture of co-occurring words. We show how grounding a topic model with an ontology, extracted from a glossary of important domain phrases, improves the topics generated and makes them easier to understand. We apply and evaluate this method to the climate science domain. The result improves the topics generated and supports faster research understanding, discovery of social networks among researchers, and automatic ontology generation.
PST‐24: A Zeolite with Varying Intracrystalline Channel Dimensionality (2020)

Abstract Herein we report the synthesis, structure solution, and catalytic properties of PST‐24, a novel channel‐based medium‐pore zeolite. This zeolite was synthesized via the excess fluoride approach. Electron diffraction shows that its structure is built by composite cas‐zigzag (cas‐zz) building chains, which are connected by double 5‐ring (d5r) columns. While the cas‐zz building chains are ordered in the PST‐24 framework, the d5r columns adopt one of two possible arrangements; the two adjacent d5r columns are either at the same height or at different heights, denoted arrangements S and D, which can be regarded as open and closed valves that connect the channels, respectively. A framework with arrangement D only has a 2D 10‐ring channel system, whereas that with arrangement S only contains 3D channels. In actual PST‐24 crystals, the open and closed valves are almost randomly dispersed to yield a zeolite framework where the channel dimensionality varies locally from 2D to 3D.
Novel WLAN hotspot authentication (2004)

The following paper describes the challenges of providing consistent authentication procedures across WLAN hotspots owned by different operators, where the set of credentials that the user should present to the network can be quite large depending on user subscription and inter-operator roaming agreements. This paper provides a description of the set of features that are needed to support secure, authenticated access to the network, and highlights how current authentication solutions provide at least some of these features. Finally the paper introduces two new techniques for enhancing the operation of these authentication solutions to provide a consistent look and feel and level of security across different hotspots.
Induction of Multiepitopic and Long‐Lasting Immune Responses Against Tumour Antigens by Immunization with Peptides, DNA and Recombinant Adenoviruses Expressing Minigenes (2008)

The development of immunization strategies to induce strong and multiepitopic T-cell responses against tumour antigens is needed for anti-tumour immunotherapy. However, a common finding after immunization with complex antigens is the preferential induction of immune responses against immunodominant epitopes. In this study, with the aim of inducing multiepitopic responses against several common tumour antigens, we have designed a minigene construct encoding four human leucocyte antigen (HLA)-A2-restricted epitopes belonging to tumour antigens CEA (CEA-691 and CEA-571), MAGE2 (MAGE2-157) and MAGE3 (MAGE3-112), as well as the universal PADRE epitope recognized by T helper lymphocytes. To optimize the activation of immune responses against these epitopes, we have used different antigen formats (short peptides encompassing individual epitopes and DNA plasmids or adenoviral constructs expressing the minigene) in single or combined immunization schedules. A single immunization with either DNA plasmid or recombinant adenovirus induced a monospecific immune response against the immunodominant epitope CEA-571, whereas immunization with the peptide pool induced responses against all epitopes. Combination of peptide priming followed by a boost with the plasmid and the recombinant adenovirus expressing the minigene induced stronger, multi-specific and long-lasting immune responses, overcoming the immunodominance imposed by the main T-cell epitope. Moreover, these combined immunization strategies were able to induce responses that were able to recognize Mel624 HLA-A2+ tumour cells expressing MAGE2. These results suggest that heterologous immunization strategies combining peptides and DNA or recombinant adenoviruses can be useful to broaden the specificity and enhance the efficacy of subunit vaccines.
PB2111: SUBGROUP ANALYSIS IN RE-MIND2, AN OBSERVATIONAL, RETROSPECTIVE COHORT STUDY OF TAFASITAMAB + LENALIDOMIDE VERSUS SYSTEMIC THERAPIES IN PATIENTS WITH RELAPSED/REFRACTORY DIFFUSE LARGE B-CELL LYMPHOMA (2022)

Background: Tafasitamab (tafa) + lenalidomide (LEN) demonstrated efficacy in adult patients with relapsed/refractory diffuse large B-cell lymphoma (R/R DLBCL) ineligible for autologous stem-cell transplant in the pivotal Phase II study L-MIND (NCT02399085). The combination received accelerated approval in the United States in 2020 and conditional marketing authorization in Europe and Canada in 2021 in this setting. RE-MIND2 (NCT04697160), an observational, retrospective cohort study compared patient outcomes from L-MIND with matched patient cohorts treated with other NCCN/ESMO recommended therapies. Prolonged overall survival (OS) with tafa + LEN was detected compared to a cohort of systemic therapies for DLBCL pooled (STP), bendamustine + rituximab (BR), rituximab + gemcitabine + oxaliplatin (R-GemOx), polatuzumab vedotin + BR (pola-BR), and rituximab + LEN (R2). Comparable OS was detected versus CD19 CAR-T therapies (CAR-T). However, limited information is available on the comparative effectiveness of tafa + LEN in specific subpopulations. Aims: To inform on the relative effectiveness of tafa + LEN versus other treatment regimens for R/R DLBCL in clinically relevant patient subgroups in the absence of head-to-head trials. Methods: Data were collected from health records of eligible patients aged ≥18 years with histologically confirmed DLBCL, who had received ≥2 systemic therapies for DLBCL (including ≥1 anti-CD20 therapy). Patients from L-MIND were matched with patients from the RE-MIND2 observational cohort using estimated propensity score-based 1:1 nearest neighbor matching, balanced for nine or six covariates. Hypothesis-generating analyses were conducted for patient subgroups of number of extranodal sites (ENS) (0–1 vs ≥2) and elevated lactate dehydrogenase (LDH) (yes vs no) in matched cohorts of patients receiving tafa + LEN vs STP, pola-BR, R2, and CAR-T. The primary endpoint was OS. Results: Of 3,454 patients enrolled, 961, 106, 106, and 149 were treated with STP, pola-BR, R2, and CAR-T, resulting in 76, 24, 33, and 37 matched pairs for patients receiving tafa + LEN, respectively. Hazard ratios (HR) for OS show a trend toward favoring tafa + LEN in most patient subgroups (Table). Image:Summary/Conclusion: These analyses suggest that tafa + LEN may be associated with improved OS vs selected systemic therapies for certain patients with high-risk disease and may further inform physicians’ treatment choices for patients with R/R DLBCL. These analyses are not powered for statistical comparison; small sample sizes in some subgroups result in wide confidence intervals and, although supported by several sensitivity analyses, the observed trends must be interpreted with caution. Additional analyses including other patient subgroups, endpoints, and cohort balancing approaches will be presented.
Coherence control of illumination optics in mask inspection systems (2008)

One annoying problem that degrades high-fidelity pattern images in mask-defect inspection systems is the generation of ghost images in the imaging process. Ghost images arise from spatial coherence periodicity on the mask plane, which is due to periodic and discrete arrangements of fly-eye elements in mask inspection optics. By considering the contrast of ghost images under partial coherence illumination, we can derive the condition that represents the necessary number of fly-eye elements to substantially suppress ghost images in the image field. In addition, we confirm this theoretically derived condition of suppressing ghost images by numerical calculations. As a result, we prove that this suppresing condition is effective, and that the nonuniformity in distribution of image intensity can also be reduced in this way.
High quality Nb/Al-AlOx/Nb Josephson junction (1985)

We have improved the quality of Nb/Al-AlOx/Nb Josephson junctions and obtained the most excellent junction characteristics ever obtained for all refractory Josephson junctions. The Vm values (the product of the critical current and the subgap resistance measured at 2 mV) are 88 mV at the critical current density Ij =500 A/cm2 and 72 mV at Ij =1000 A/cm2. The Vm values are larger than 40 mV up to Ij of 2400 A/cm2. The high Vm values are important to obtain the low subgap leakage current and not to reduce the transfer current to the load in Josephson circuit. These characteristics have been achieved by improving the quality of the Nb film and optimizing the Al thickness. We have also confirmed that Ij can be controlled by both the oxidation pressure and time in the range of 40–4600 A/cm2.
Nonlinear absorption in a series of Donor–π–Acceptor cyanines with different conjugation lengths (2009)

A detailed experimental and theoretical study of the linear and nonlinear absorption of a series of asymmetrical D–π–A cyanine dyes with the same trimethylindolin donor (D) and diethylamino-coumarin-dioxaborine acceptor (A) terminal groups and different conjugation lengths, is presented. Strong solvatochromic behavior affecting the fluorescence quantum yields, lifetimes, and the linear and nonlinear absorption properties is observed due to the presence of permanent ground state dipole moments. Detailed experimental studies of lifetime dynamics are performed by direct time-correlated single photon counting and pump–probe techniques. We find that an increase in π-conjugation in the investigated series of dyes leads to an enhancement of the excited-state absorption and two-photon absorption (2PA) cross-sections (δ2PA). The 2PA spectra for all of the investigated dyes consist of two well-separated bands. The first band occurs at two-photon excitation into the vibrational levels and not into the absorption peak of the main transition, S0 → S1, which is more typical of that observed for symmetrical cyanines. The position of the second 2PA band for all the molecules remains unchanged in solvents of different polarity contrary to the large solvatochromic shift of the S0 → S1 band, resulting in a large intermediate state resonance enhancement and, therefore, a larger 2PA in acetronitrile (δ2PA ≈ 10000 GM) compared to toluene (δ2PA ≈ 4700 GM).
Suppression of skeletal muscle signal using a crusher coil: A human cardiac 31p‐MR spectroscopy study at 7 tesla (2015)

A crusher coil is an SAR-efficient alternative for selectively suppressing skeletal muscle during cardiac (31)P-MRS at 7T. A crusher coil allows the use of sequence modules that would have been SAR-prohibitive, without compromising skeletal muscle suppression.
The effect of protein adsorption on the anticoagulant activity of surface immobilized heparin (1996)

The anticoagulant activity of albumin-heparin conjugates covalently immobilized on carboxylated polystyrene beads was determined before and after exposure to different plasma/PBS dilutions using a thrombin inhibition assay, a FXa inhibition assay, and a modified aPTT assay. Exposure of albumin-heparin modified surfaces (alb-hep surfaces) to plasma dilutions resulted in surfaces with a lower anticoagulant activity than surfaces which were not exposed to plasma dilutions. The reduction of the activity increased up to +/- 80% when the surfaces were exposed to solutions containing more than 70% plasma. Alb-hep surfaces incubated in plasma which was preexposed to heparin-Sepharose retained 30% of their initial activity. These observations were attributed to non-specific adsorption of plasma proteins onto the surface and to interaction of heparin binding proteins with the immobilized heparin. Both processes result in a decreased accessibility of the immobilized heparin and thus in a reduced anticoagulant activity displayed by the heparinized surface. Identification of adsorbed proteins with SDS gel electrophoresis and immunoblotting revealed that many different proteins were present at the heparinized surface. Only small differences were observed between the gel electrophoresis pattern of adsorbed proteins obtained from heparinized surfaces and from a surface containing immobilized albumin.
Mobile robot simulation of clinical laboratory deliveries (2002)

Flexible automation in the form of mobile robots holds the potential for decreasing operating costs while improving delivery performance in mid-size hospital delivery systems. This paper discusses the use of simulation modeling to analyze the costs, benefits, and performance tradeoffs related to the installation and use of a fleet of mobile robots within mid-size hospital facilities. The results of this study enable a better understanding of the delivery and transportation requirements of mid-sized hospitals and how a fleet of mobile robots can meet those requirements. We show that for clinical laboratory deliveries a fleet of 6 mobile robots can achieve significant performance gains over the current system of 3 human couriers while still remaining cost effective. The 6-robot alternative reduces the annual cost by approximately 56% and improves turn-around time performance by 33%.