gebhart/patrepeval huggingface dataset:
An ion trap-ion mobility-time of flight mass spectrometer with three ion sources for ion/ion reactions (2009)

This instrument combines the capabilities of ion/ion reactions with ion mobility (IM) and time-of-flight (TOF) measurements for conformation studies and top-down analysis of large biomolecules. Ubiquitin ions from either of two electrospray ionization (ESI) sources are stored in a three dimensional (3D) ion trap (IT) and reacted with negative ions from atmospheric sampling glow discharge ionization (ASGDI). The proton transfer reaction products are then separated by IM and analyzed via a TOF mass analyzer. In this way, ubiquitin +7 ions are converted to lower charge states down to +1; the ions in lower charge states tend to be in compact conformations with cross sections down to approximately 880 A(2). The duration and magnitude of the ion ejection pulse on the IT exit and the entrance voltage on the IM drift tube can affect the measured distribution of conformers for ubiquitin +7 and +6. Alternatively, protein ions are fragmented by collision-induced dissociation (CID) in the IT, followed by ion/ion reactions to reduce the charge states of the CID product ions, thus simplifying assignment of charge states and fragments using the mobility-resolved tandem mass spectrum. Instrument characteristics and the use of a new ion trap controller and software modifications to control the entire instrument are described.
State of the Art and Future Trends of Electric Drives and Power Electronics for Automotive Engineering (2014)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Discussions about the optimal technology of propulsion systems for future ground vehicles have been raising over the last few years. Several options include different types of technologies. However, those who are advocating conventional internal combustion engines are faced with the fact that fossil fuels are limited. Others favor hydrogen fuel as the solution for the future, either in combination with combustion engines or as an energy carrier for fuel cells. In any case, the production and storage of hydrogen is an ongoing challenge of numerous research works. Finally, there are battery-electric or hybrid propulsion systems in use, gaining more and more popularity worldwide.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Ongoing advances in power electronics help to improve control systems within automotive applications. New developed or designed components enable more efficient system architectures and control. This paper includes a detailed comparison of different electric drive technologies, e.g. a DC motor, an asynchronous and synchronous motor in battery-electric or hybrid drivetrain configurations. Parameters for future drive architectures, such as high torque and power output, high system efficiency, low mass, low energy consumption, very low exhaust gas emissions, and low costs are introduced and discussed. Advantages and disadvantages of different drivetrain configurations are specified, evaluated, and discussed. Additionally, a selection of advances in power electronics is listed and described in detail. Practical examples of electric drive systems are given explicitly and conclusions for future development are made. The publication closes with an overview of current components in use and presents an outlook to future trends.&lt;/div&gt;&lt;/div&gt;
18-02: Fibrosis explains increased epicardial breakthrough in AF (2016)

Introduction: Recent work has shown that the transition from persistent to permanent AF in goats coincides with an increase in fibrosis in the outer millimeter of the atrial wall. Macroscopically this leads to reduced electrical conductivity orthogonal to the dominant fiber orientation. A causal relation has not been established yet. Our purpose was to test if subepicardial fibrosis can explain the increased incidence of epicardial breakthroughs, which is also observed in permanent AF. Methods: We constructed a detailed geometry of the human atria including all major bundle structures and two layers of fiber orientation. Computer simulations were run with a mesh of 0.2 mm resolution and an ionic current formulation specific for the human atrial myocyte. Subepicardial fibrosis was modeled by assigning zero transverse conductivity to a random selection of model elements. Simulations were performed with 0, 50, and 70% affected elements. Fibrillation was induced with incremental rapid pacing. Simulations were repeated with 10 different pacing locations, for a total of 30 simulations of 5 seconds each. We tested in the first place whether AF was induced by this protocol. In those simulations where fibrillation occurred, we computed the number of waves, number of phase singularities, percentage dyssynchrony, and number of breakthroughs in the 3 seconds after pacing. Conclusion: Subepicardial fibrosis can account for an increased susceptibility for AF as well as for the remarkable increase in epicardial breakthrough observed in experimental studies.
Comparison of the Faran Cylinder Model and the Weak Scattering Model for predicting the frequency dependence of backscatter from human cancellous femur in vitro (2008)

This letter presents the first side-by-side comparison of the Faran Cylinder Model and the Weak Scattering Model for predicting backscatter from human femur. Both models are applied to the same dataset of frequency-dependent backscatter coefficients from 26 human femur cancellous bone samples in vitro. The Faran Cylinder Model predicts a slightly slower rate of increase of backscatter with frequency than the Weak Scattering Model, but both models are in reasonable agreement with the data and with each other, given the uncertainty in the measurements.
Automatic target identification and multi-sensor data fusion in air defense command and control systems (1996)

Automatic target identification and multi-sensor data fusion in air defense command and control systems
Synthesis of α-iminoimidates by palladium catalysed double isonitrile insertion (2004)

Palladium catalysed selective double insertion of isonitriles into aryl bromides with trapping by sodium alkoxides provides an efficient 4-component synthesis of unusual alpha-iminoimidates.
FDK-type reconstruction algorithms for the reverse helical trajectory (2011)

For emergency cases in the interventional room, 3D long-object cone-beam(CB) imaging using a C-arm system could save valuable time and reduce risks to the patient by avoiding the traditionally-used CT scan, and thus could potentially be a crucial tool for patient health. To accomplish such a task, the reverse helix is an attractive trajectory, however theoretically-exact and stable (TES) reconstruction with a reverse helix is challenging. Two TES solutions are available, but both of them come with a heavy computational load and some issues in terms of image quality. This work proposes three new approximate reconstruction algorithms for the reverse helix that are stable and efficient, and thus practical. Though not exact, reconstruction results obtained from all three methods appear acceptable.
Nonlocal competition and the speciation transition on random networks (2008)

A simple model for competition-induced speciation is presented and analyzed. Logistic growth with nonlocal interaction is studied on regular and random networks, and the large scale structure of the emerging genomic frequencies is examined. The neutrality assumption is violated if the network is random and the competition is nonlocal. Instead, "hubs" in the sequence space are suppressed by the competition more than nodes of a lower degree. Thus speciation is unavoidable for large-scale free networks. The emerging genetic mixture depends strongly on the initial conditions. The frequency of hubs is much greater in a population that evolved from a single nucleation event than in a population that recovered from a catastrophe.
A New Aluminosilicate Molecular Sieve with a System of Pores between Those of ZSM-5 and Beta Zeolite (2011)

A new aluminosilicate zeolite (ITQ-39) has been synthesized. This is an extensively faulted structure with very small domains that makes the structure elucidation very difficult. However, a combination of adsorption spectroscopy and reactivity studies with selected probe molecules suggests that the pore structure of ITQ-39 is related to that of Beta zeolite, with a three-directional channel system with large pores (12-MR), but with an effective pore diameter between those of Beta and ZSM-5, or a three-directional channel system with interconnected large (12-MR) and medium pores (10-MR). The pore topology of ITQ-39 is very attractive for catalysis and shows excellent results for the preparation of cumene by alkylation of benzene, while it can be a promising additive for FCC.
Multiscale Gradient Computation for Multiphase Flow in Porous Media (2017)

Abstract A multiscale gradient computation method for multiphase flow in heterogeneous porous media is developed. The method constructs multiscale primal and dual coarse grids, imposed on the given fine-scale computational grid. Local multiscale basis functions are computed on (dual-) coarse blocks, constructing an accurate map (prolongation operator) between coarse- and fine-scale systems. While the expensive operations involved in computing the gradients are performed at the coarse scale, sensitivities with respect to uncertain parameters (e.g., grid block permeabilities) are expressed in the fine scale via the partial derivatives of the prolongation operator. Hence, the method allows for updating of the geological model, rather than the dynamic model only, avoiding upscaling and the inevitable loss of information. The formulation and implementation are based on automatic differentiation (AD), allowing for convenient extensions to complex physics. An IMPES coupling strategy for flow and transport is followed, in the forward simulation. The flow equation is computed using a multiscale finite volume (MSFV) formulation and the transport equation is computed at the fine scale, after reconstruction of mass conservative velocity field. To assess the performance of the method, a synthetic multiphase flow test case is considered. The multiscale gradients are compared against those obtained from a fine-scale reference strategy. Apart from its computational efficiency, the benefits of the method include flexibility to accommodate variables expressed at different scales, specially in multiscale data assimilation and reservoir management studies.
RouterFarm (2006)

Planned maintenance is a fact of life in IP networks. Examples of maintenance activities include updating router software as well as processor upgrades, memory upgrades, installation of additional line cards, and other hardware upgrades. While planned maintenance is clearly necessary, it is also costly. Software upgrades, for example, require rebooting the router. Due to the time required to reboot the router, and then synchronize state (such as BGP routing information) with network neighbors, the upgrade process can yield outages of 10--15 minutes.
Phase I/II Clinical Trial of Encapsulated, Cytochrome P450 Expressing Cells as Local Activators of Cyclophosphamide to Treat Spontaneous Canine Tumours (2014)

Based upon promising preclinical studies, a clinical trial was performed in which encapsulated cells overexpressing cytochrome P450 enzyme isoform 2B1 were implanted around malignant mammary tumours arising spontaneously in dogs. The dogs were then given cyclophosphamide, one of the standard chemotherapeutic agents used for the treatment of mammary tumours. The dogs were assessed for a number of clinical parameters as well as for reduction in tumour size. The treatment was well tolerated with no evidence of adverse reactions or side effects being associated with the administration of the encapsulated cells. Reductions in tumour size of more than 50% were observed for 6 out of the 11 tumours analysed while 5 tumours showing minor responses, i.e. stable disease. In contrast, the tumours that received cyclophosphamide alone showed only stable disease. Taken together, this data suggests that encapsulated cytochrome P450 expressing cells combined with chemotherapy may be useful in the local treatment of a number of dog mammary tumours and support the performance of further clinical studies to evaluate this new treatment.
Identifying Patterns and Anomalies within Spatiotemporal Water Sampling Data (2018)

This paper presents our solution to the Mini Challenge 2 (MC2) of the VAST Challenge 2018. We will analyze the provided data set and introduce our visualization tool, which was implemented and tailored to the tasks given by MC2. The tool combines the power of stream graphs, innovative glyph visualizations, box plots, sparklines, heat maps and cross-filter strategies. It allows identifying patterns and anomalies within the provided data set.
Localized Mode DFT-S-OFDMA Implementation Using Frequency and Time Domain Interpolation (2009)

This paper presents a novel method to generate a localized mode single-carrier frequency division multiple access (SC-FDMA) waveform. Instead of using DFT-spread OFDMA (DFT-S-OFDMA) processing, the new structure called SCiFI-FDMA relies on frequency and time domain interpolation followed by a user-specific frequency shift. SCiFI-FDMA can provide signal waveforms that are compatible to DFT-S-OFDMA. In addition, it provides any resolution of user bandwidth allocation for the uplink multiple access with comparable computational complexity, because the DFT is avoided. Therefore, SCiFI-FDMA allows a flexible choice of parameters appreciated in broadband mobile communications in the future.
Growth conditions and environmental factors impact aerosolization but not virulence of Francisella tularensis infection in mice (2012)

In refining methodology to develop a mouse model for inhalation of Francisella tularensis, it was noted that both relative humidity and growth media impacted the aerosol concentration of the live vaccine strain (LVS) of F. tularensis. A relative humidity of less than 55% had a negative impact on the spray factor, the ratio between the concentration of LVS in the aerosol and the nebulizer. The spray factor was significantly higher for LVS grown in brain heart infusion (BHI) broth than LVS grown in Mueller-Hinton broth (MHb) or Chamberlain's chemically defined medium (CCDM). The variability between aerosol exposures was also considerably less with BHI. LVS grown in BHI survived desiccation far longer than MHb-grown or CCDM-grown LVS (~70% at 20 min for BHI compared to <50% for MHb and CCDM). Removal of the capsule by hypertonic treatment impacted the spray factor for CCDM-grown LVS or MHb-grown LVS but not BHI-grown LVS, suggesting the choice of culture media altered the adherence of the capsule to the cell membrane. The choice of growth media did not impact the LD(50) of LVS but the LD(99) of BHI-grown LVS was 1 log lower than that for MHb-grown LVS or CCDM-grown LVS. Splenomegaly was prominent in mice that succumbed to MHb- and BHI-grown LVS but not CCDM-grown LVS. Environmental factors and growth conditions should be evaluated when developing new animal models for aerosol infection, particularly for vegetative bacterial pathogens.
Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers (2021)

Chromosomal translocations are important drivers of haematological malignancies whereby proto-oncogenes are activated by juxtaposition with enhancers, often called <i>enhancer hijacking</i> We analyzed the epigenomic consequences of rearrangements between the super-enhancers of the immunoglobulin heavy locus (<i>IGH</i>) and proto-oncogene <i>CCND1</i> that are common in B cell malignancies. By integrating BLUEPRINT epigenomic data with DNA breakpoint detection, we characterized the normal chromatin landscape of the human <i>IGH</i> locus and its dynamics after pathological genomic rearrangement. We detected an H3K4me3 broad domain (BD) within the <i>IGH</i> locus of healthy B cells that was absent in samples with <i>IGH-CCND1</i> translocations. The appearance of H3K4me3-BD over <i>CCND1</i> in the latter was associated with overexpression and extensive chromatin accessibility of its gene body. We observed similar cancer-specific H3K4me3-BDs associated with hijacking of super-enhancers of other common oncogenes in B cell (<i>MAF</i>, <i>MYC</i>, and <i>FGFR3/NSD2</i>) and T cell malignancies (<i>LMO2</i>, <i>TLX3</i>, and <i>TAL1</i>). Our analysis suggests that H3K4me3-BDs can be created by super-enhancers and supports the new concept of <i>epigenomic translocation</i>, in which the relocation of H3K4me3-BDs from cell identity genes to oncogenes accompanies the translocation of super-enhancers.
Genetic risk score based on the prevalence of vertebral fracture in Japanese women with osteoporosis (2016)

A genetic risk score (GRS) was developed for predicting fracture risk based on the prevalence of vertebral fractures in 441 Japanese females with osteoporosis. A total of 979 (858 nonsynonymous and 121 silent) single-nucleotide polymorphisms (SNPs) located in 74 osteoporosis-susceptibility genes were genotyped and evaluated for their association with fracture prevalence. Four SNPs (protein kinase domain containing, cytoplasmic [<i>PKDCC</i>; rs4952590], CDK5-regulatory subunit-associated protein 1-like 1 [<i>CDKAL1</i>; rs4712556], wingless-type MMTV-integration site family member 16 [<i>WNT16</i>; rs2707466], and G-patch domain-containing gene 1 [<i>GPATCH1</i>; rs10416265]) showed a significant association (<i>p</i> < 0.05) with the fracture, in which the minor allele of the former two SNPs was the protective allele and that of the latter two SNPs was the risk allele. Applying a dominant-genetic model, we allotted - 1 point each to the protective-allele carriers and 1 point each to the risk-allele carriers, and GRS values were calculated as the sum of the points. The receiver-operating characteristic curves showed that GRS adequately predicted vertebral fracture. For the model predicted by the GRS with and without the effect of age, areas under the curves were 0.788 (95% confidence interval [CI]: 0.736-0.840) and 0.667 (95% CI: 0.599-0.735), respectively. Multiple logistic regression analysis revealed that the odds ratio for the association between fracture prevalence and GRS was 3.27 (95% CI: 1.36-7.87, <i>p</i> = 0.008) for scores of - 1 to 0 (<i>n</i> = 303) and 12.12 (95% CI: 4.19-35.07, <i>p</i> < 0.001) for scores of 1 to 2 (<i>n</i> = 35) relative to a score of - 2 (<i>n</i> = 103). The GRS based on the four SNPs could help identify at-risk individuals and enable implementation of preventive measures for vertebral fracture.
Improvement of nano-imprint lithography performance for device fabrication (2018)

A low cost alternative lithographic technology is desired to cope with the challenges in decreasing feature size of semiconductor devices. Nano-imprint lithography (NIL) is one of the viable candidates.<sup>[1][2][3]</sup> NIL has been a promising solution to overcome the cost issue associated with expensive process and tool of multi patterning and EUVL. NIL is a simple technology and is capable of forming critical patterns easily. On the other hand, the critical issues of NIL are defectivity, overlay, and throughput. In order to introduce NIL into the High Volume Manufacturing (HVM), it is necessary to overcome these three challenges simultaneously.<sup>[4]-[10]</sup> In our previous study, we have reported improvement in NIL overlay, defectivity and throughput by the optimization of resist process on a pilot line tool, FPA-1200 NZ2C. In this study, we report recent evaluation of the NIL performance to judge its applicability in semiconductor device HVM. We have described that the NIL is getting closer to the target of HVM for 2x nm half pitch.<sup>[8]</sup>Defectivity level below 1pcs/cm2 has been achieved for the 2x nm half pitch L/S. The overlay accuracy of the test device is being improved down to 6nm or lower by introducing high order distortion correction.
Navigating in the Cayley graph of $SL_2(F_p)$ and applications to hashing (2014)

Cayley hash functions are based on a simple idea of using a pair of (semi)group elements, $A$ and $B$, to hash the 0 and 1 bit, respectively, and then to hash an arbitrary bit string in the natural way, by using multiplication of elements in the (semi)group. In this paper, we focus on hashing with $2 \times 2$ matrices over $F_p$. Since there are many known pairs of $2 \times 2$ matrices over $Z$ that generate a free monoid, this yields numerous pairs of matrices over $F_p$, for a sufficiently large prime $p$, that are candidates for collision-resistant hashing. However, this trick can "backfire", and lifting matrix entries to $Z$ may facilitate finding a collision. This "lifting attack" was successfully used by Tillich and Zémor in the special case where two matrices $A$ and $B$ generate (as a monoid) the whole monoid $SL_2(Z_+)$. However, in this paper we show that the situation with other, "similar", pairs of matrices from $SL_2(Z)$ is different, and the "lifting attack" can (in some cases) produce collisions in the group generated by $A$ and $B$, but not in the positive monoid. Therefore, we argue that for these pairs of matrices, there are no known attacks at this time that would affect security of the corresponding hash functions. We also give explicit lower bounds on the length of collisions for hash functions corresponding to some particular pairs of matrices from $SL_2(F_p)$.
Windowed PWM: A Configurable Modulation Scheme for Modular Multilevel Converter-Based Traction Drives (2020)

This article introduces a modulation technique for modular multilevel converter (MMC) in variable speed traction drives for electrical transportation referred as windowed pulsewidth modulation (W-PWM). The windowed PWM (W-PWM) is derived by blending the principles of operation of conventional modulation schemes for MMC based on the nearest level control (NLC) and on PWM with the aim of combining their inherent strengths and offering a higher degree of flexibility. This can reduce switching losses compared to classical PWM schemes and lower the current harmonic distortion compared to NLC schemes. The window in which the PWM is applied can be seen as an additional degree of freedom that allows a dynamic optimization of the performance of the traction drive depending on its operating characteristics. The performance of the W-PWM technique is assessed in this article for several operating conditions and compared with conventional schemes based on NLC and on the phase opposition disposition PWM with both numerical simulation and experimental verification on a small-scale prototype. Results demonstrate the flexibility of the W-PWM and its potential for applications in electrical traction drives.
Small Signal Frequency-Domain Model of a LCC-HVDC Converter Based on an Infinite Series-Converter Approach (2020)

In this paper, an improved analytical small signal model of the line commutated converter (LCC) is developed in direct-quadrature-zero coordinates based on the assumption of infinite six-pulse converters. The dynamics of the commutation inductance and transportation delays during commutation are included in the model, and the sampling of the measurement of firing and extinction angles is added to accommodate actual converters with a finite pulse number (e.g., 12-pulse). The model is validated by comparing the frequency response with one obtained by frequency scanning in an electromagnetic transients (EMT) simulation. The model is shown to be effective in investigating system stability when the LCC is connected to an arbitrary external network. To do this, the frequency response of the combined system is plotted, and the generalized Nyquist stability criterion is applied. This stability result is validated by a time domain simulation on an EMT program using the first CIGRE HVDC benchmark system and the IEEE 14-bus system. Compared to the traditional LCC model, the proposed model is shown to have significantly better accuracy in system stability determination.