gebhart/patrepeval huggingface dataset:
Monofunctional and Higher-Valent Platinum Anticancer Agents (2013)

Platinum compounds represent one of the great success stories of metals in medicine. Following the serendipitous discovery of the anticancer activity of cisplatin by Rosenberg, a large number of cisplatin variants have been prepared and tested for their ability to kill cancer cells and inhibit tumor growth. These efforts continue today with increased realization that new strategies are needed to overcome issues of toxicity and resistance inherent to treatment by the approved platinum anticancer agents. One approach has been the use of so-called “non-traditional” platinum(II) and platinum(IV) compounds that violate the structure–activity relationships that governed platinum drug-development research for many years. Another is the use of specialized drug-delivery strategies. Here we describe recent developments from our laboratory involving monofunctional platinum(II) complexes together with a historical account of the manner by which we came to investigate these compounds and their relationship to previous...
Improvement of Thermal Stability via Outer-Loop Ion Pair Interaction of Mutated T1 Lipase from Geobacillus zalihae Strain T1 (2012)

Mutant D311E and K344R were constructed using site-directed mutagenesis to introduce an additional ion pair at the inter-loop and the intra-loop, respectively, to determine the effect of ion pairs on the stability of T1 lipase isolated from Geobacillus zalihae. A series of purification steps was applied, and the pure lipases of T1, D311E and K344R were obtained. The wild-type and mutant lipases were analyzed using circular dichroism. The T(m) for T1 lipase, D311E lipase and K344R lipase were approximately 68.52 °C, 70.59 °C and 68.54 °C, respectively. Mutation at D311 increases the stability of T1 lipase and exhibited higher T(m) as compared to the wild-type and K344R. Based on the above, D311E lipase was chosen for further study. D311E lipase was successfully crystallized using the sitting drop vapor diffusion method. The crystal was diffracted at 2.1 Å using an in-house X-ray beam and belonged to the monoclinic space group C2 with the unit cell parameters a = 117.32 Å, b = 81.16 Å and c = 100.14 Å. Structural analysis showed the existence of an additional ion pair around E311 in the structure of D311E. The additional ion pair in D311E may regulate the stability of this mutant lipase at high temperatures as predicted in silico and spectroscopically.
Regenerative Hydride Heat Pump (1992)

Hydride heat pump features regenerative heating and single circulation loop. Counterflow heat exchangers accommodate different temperatures of FeTi and LaNi4.7Al0.3 subloops. Heating scheme increases efficiency.
Denoising of electron beam Monte Carlo dose distributions using digital filtering techniques (2000)

The Monte Carlo (MC) method has long been viewed as the ultimate dose distribution computational technique. The inherent stochastic dose fluctuations (i.e. noise), however, have several important disadvantages: noise will affect estimates of all the relevant dosimetric and radiobiological indices, and noise will degrade the resulting dose contour visualizations. We suggest the use of a post-processing denoising step to reduce statistical fluctuations and also improve dose contour visualization. We report the results of applying four different two-dimensional digital smoothing filters to two-dimensional dose images. The Integrated Tiger Series MC code was used to generate 10 MeV electron beam dose distributions at various depths in two different phantoms. The observed qualitative effects of filtering include: (a) the suppression of voxel-to voxel (high-frequency) noise and (b) the resulting contour plots are visually more comprehensible. Drawbacks include, in some cases, slight blurring of penumbra near the surface and slight blurring of other very sharp real dosimetric features. Of the four digital filters considered here, one, a filter based on a local least-squares principle, appears to suppress noise with negligible degradation of real dosimetric features. We conclude that denoising of electron beam MC dose distributions is feasible and will yield improved dosimetric reliability and improved visualization of dose distributions.
A Model-Driven Framework for Process-Centric Business Continuity Management (2010)

Nowadays businesses and business processes depend on Information Technology (IT) more than ever. Disruptions in an organisations' IT infrastructure causes disruptions in business processes which lead to financial losses, legal consequences, losses in reputation and may cause bankruptcies. Business Continuity Management (BCM) addresses these problems. In order to conduct a sound Business Impact Analysis BCM manager require an integrated and coherent view of all involved business processes and IT related resources. However, this integrated and coherent view is hard to establish using conventional analysis methods, such as questionnaires and Visio diagrams. Hence, BCM managers struggle to create current and thorough BCM analyses. In this paper we present a novel model-driven framework for BCM which integrates business process modelling and IT management. Our approach permits automatic consolidation of information from various stakeholders and multiple data sources. Furthermore, different kinds of analysis tools, such as simulation tools and analytical tools, can be utilised in an automatic fashion.
U-43,120; a new antitumor antibiotic. I. Production, biological activity, microbiological assay and taxonomy of the producing microorganism. (1976)

A new antitumor antibiotic, U-43,120 was discovered. It is produced by fermentation of a new species of Streptomyces, designated Streptomyces paulus DIETZ sp. n. Its antimicrobial activity is limited to bacteria. A microbiological assay with Bacillus subtilis was developed that can be detect concentrations of 1 approximately 2 mug/ml of the drug in fermentation liquors. U-43,120 was active in vivo against P-388 leukemia in mice.
A method of mechanical emulsification in a bulk tissue using shock wave heating and millisecond boiling. (2011)

Recent studies in high intensity focused ultrasound (HIFU) have shown significant interest in generating purely mechanical damage of tissue without thermal coagulation. Here, an approach using millisecond bursts of ultrasound shock waves and repeated localized boiling is presented. In HIFU fields, nonlinear propagation effects lead to formation of shocks only in a small focal region. Significant enhancement of heating due to absorption at the shocks leads to boiling temperatures in tissue in milliseconds as calculated based on weak shock theory. The heated and potentially necrotized region of tissue is small compared to the volume occupied by the mm-sized boiling bubble it creates. If the HIFU pulse is only slightly longer than the time-to-boil, thermal injury is negligible compared to the mechanical injury caused by the exploding boiling bubble and its further interaction with shocks. Experiments performed in transparent gels and various ex vivo and in vivo tissues have confirmed the effectiveness of this emulsification method. In addition, since mm-sized boiling bubbles are highly echogenic, tissue emulsification can be easily monitored in real-time using B-mode ultrasound imaging. [Work supported by NIH EB007643, RFBR 09-02-01530, and NSBRI through NASA NCC 9-58].
Rolling Upgrade with Dynamic Batch Size for IaaS Cloud (2016)

Cloud systems are upgraded regularly to improve their performance, fix bugs, deploy new software versions, etc. Their hosted services, for example, telecommunication services, may have stringent non-functional requirements such that they do not tolerate more than five minutes of downtime in a year regardless whether they are provided by a cloud system or the outage is due to an upgrade. Such services must remain highly available under any circumstance, which imposes availability requirements on the provider cloud system. The dynamicity of the environment is one of the main challenges for maintaining High Availability (HA) in cloud deployments during upgrades. To maintain availability during upgrades, most cloud providers use rolling upgrade, and to avoid any unexpected interference between the upgrade process and the cloud's scaling mechanism, scaling is disabled for the time of the upgrade. In this paper, we propose a novel approach for rolling upgrades applicable to - among others - IaaS cloud systems to address HA. This approach mitigates the interference between the upgrade process, any failure handling and scaling by dynamically adjusting the upgrade process to the changes in the cloud environment. Accordingly, the upgrade process can start/resume only when the system has sufficient resources to perform an upgrade iteration and suspends the process when this is not the case. As a result, scaling does not need to be disabled during upgrades, rather the scaling operations regulate the pace of the upgrade.
A kinetics scheme for the XeF laser (1978)

A kinetics scheme is described for electron-beam excitation of the XeF laser in a neon diluent. Both Ne+ and Ne* channels contribute significantly to the formation of the upper laser level. In each chain an important Penning ionization process leads to the formation of Xe+, which is the major intermediary in forming the upper laser level. Xe+2 is found to be the dominant absorber of laser radiation. The effect of the weakly bound XeF ground state is discussed.
Bis-benzylidine Piperidone RA190 Treatment of Hepatocellular Carcinoma via Binding RPN13 and Inhibiting NF-κB Signaling (2019)

Abstract Background Hepatocellular carcinoma (HCC) is the fifth most common malignancy and the third leading cause of cancer mortality worldwide. The development of new anticancer agents targeting different pathways is imperative to improve the advanced HCC. The aberrant metabolism and aggressive growth of cancer cells can render them particularly susceptible to proteasome inhibition, as first demonstrated by the success of bortezomib treatment for multiple myeloma. However, resistance does emerge and this 20S proteasome inhibitor has not proven active against HCC. The bis-benzylidine piperidone RA190 represents a novel class of proteasome inhibitor that covalently binds to cysteine 88 of RPN13, a ubiquitin receptor subunit of the proteasome’s 19S regulatory particle. RA190 treatment inhibits proteasome function, causing rapid accumulation of polyubiquitinated proteins. Methods Human HCC cell lines were treated by RA190 in vitro in different concentration and time frame. We checked the killing effect and the possible mechanisms that lead the tumor apoptosis. We also performed the orthotopic HCC animal model to show the RA190 had significant killing effect in vivo. Results We showed RA190 is also toxic to HCC cells by triggering the rapid build-up of polyubiquitinated proteins, resulting in endoplasmic reticulum stress and the induction of cell death via apoptosis. Considerable evidence suggests that nuclear factor κB (NF-κB) signal is essential for promoting inflammation-associated cancer. Here, we showed that RA190 inhibited the NF-κB pathway in HCC by preventing the degradation of IκBα via the proteasome. Treatment of mice bearing an orthotopic HCC model with RA190 significantly reduced tumor growth. We therefore explored combining RA190 with a tyrosine kinase inhibitor currently used to the treat HCC, Sorafenib. Conclusions RA190 and Sorafenib exhibited synergetic killing of HCC cells in vitro, suggesting further exploration of such a combination treatment of HCC is warranted.
Porous bioactive glass scaffold with high compression strength (2006)

INTRODUCTION: Tissue engineering poses new challenges in the area of biomaterials. For bone and cartilage tissue engineering applications, in particular, there is a need for the development of better scaffold materials. Porous bioactive glass scaffolds have been manufactured by sintering bioactive glass fibres. The relative porosity of the scaffolds, size of the pores and compression strength can be controlled by altering the manufacturing parameters like fibre dimensions and sintering temperature and time . The aim of this study was to manufacture porous structures with high compression strength by sintering bioactive glass fibres. METHODS: The composition of the bioactive glass used in this study was as follows; 12% Na2O; 15% K2O; 3% MgO; 13% CaO; 1% B2O3; 2% P2O5 and 54% SiO2 (all in weight %). Glass fibres, with mean diameter of 100 μm, were manufactured from the glass by melt spinning. The fibres were further chopped either to a length of 1.3 mm or 2.0 mm. Porous scaffolds (height = 6 mm) were manufactured by sintering the fibre segments in a mould (with inside diameter of 15 mm) at 630 °C for time periods of 15, 20 or 30 minutes. Porosity and compression strength and compressive shear strength (as a maximum load) of the manufactured specimen were analyzed. The cross head speed of 5 mm/min was used in both testing methods.
Detection of Stress Induced by Soybean Aphid (Hemiptera: Aphididae) Using Multispectral Imagery from Unmanned Aerial Vehicles (2019)

Soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae), is a common pest of soybean, Glycine max (L.) Merrill (Fabales: Fabaceae), in North America requiring frequent scouting as part of an integrated pest management plan. Current scouting methods are time consuming and provide incomplete coverage of soybean. Unmanned aerial vehicles (UAVs) are capable of collecting high-resolution imagery that offer more detailed coverage in agricultural fields than traditional scouting methods. Recently, it was documented that changes to the spectral reflectance of soybean canopies caused by aphid-induced stress could be detected from ground-based sensors; however, it remained unknown whether these changes could also be detected from UAV-based sensors. Small-plot trials were conducted in 2017 and 2018 where cages were used to manipulate aphid populations. Additional open-field trials were conducted in 2018 where insecticides were used to create a gradient of aphid pressure. Whole-plant soybean aphid densities were recorded along with UAV-based multispectral imagery. Simple linear regressions were used to determine whether UAV-based multispectral reflectance was associated with aphid populations. Our findings indicate that near-infrared reflectance decreased with increasing soybean aphid populations in caged trials when cumulative aphid days surpassed the economic injury level, and in open-field trials when soybean aphid populations were above the economic threshold. These findings provide the first documentation of soybean aphid-induced stress being detected from UAV-based multispectral imagery and advance the use of UAVs for remote scouting of soybean aphid and other field crop pests.
Self-Assembly of Recombinant Prion Protein of 106 Residues (2000)

The central event in the pathogenesis of prion diseases is a profound conformational change of the prion protein (PrP) from an alpha-helical (PrP(C)) to a beta-sheet-rich isoform (PrP(Sc)). The elucidation of the mechanism of conformational transition has been complicated by the challenge of collecting high-resolution biophysical data on the relatively insoluble aggregation-prone PrP(Sc) isoform. In an attempt to facilitate the structural analysis of PrP(Sc), a redacted chimeric mouse-hamster PrP of 106 amino acids (MHM2 PrP106) with two deletions (Delta23-88 and Delta141-176) was expressed and purified from Escherichia coli. PrP106 retains the ability to support PrP(Sc) formation in transgenic mice, implying that it contains all regions of PrP that are necessary for the conformational transition into the pathogenic isoform [Supattapone, S., et al. (1999) Cell 96, 869-878]. Unstructured at low concentrations, recombinant unglycosylated PrP106 (rPrP106) undergoes a concentration-dependent conformational transition to a beta-sheet-rich form. Following the conformational transition, rPrP106 possesses properties similar to those of PrP(Sc)106, such as high beta-sheet content, defined tertiary structure, resistance to limited digestion by proteinase K, and high thermodynamic stability. In GdnHCl-induced denaturation studies, a single cooperative conformational transition between the unstructured monomer and the assembled beta-oligomer was observed. After proteinase K digestion, the oligomers retain an intact core with unusually high beta-sheet content (>80%). Using mass spectrometry, we discovered that the region of residues 134-215 of rPrP106 is protected from proteinase K digestion and possesses a solvent-independent propensity to adopt a beta-sheet-rich conformation. In contrast to the PrP(Sc)106 purified from the brains of neurologically impaired animals, multimeric beta-rPrP106 remains soluble, providing opportunities for detailed structural studies.
Micro/Nano-scale Strain Distribution Measurement from Sampling Moir&#233; Fringes (2017)

This work describes the measurement procedure and principles of a sampling moiré technique for full-field micro/nano-scale deformation measurements. The developed technique can be performed in two ways: using the reconstructed multiplication moiré method or the spatial phase-shifting sampling moiré method. When the specimen grid pitch is around 2 pixels, 2-pixel sampling moiré fringes are generated to reconstruct a multiplication moiré pattern for a deformation measurement. Both the displacement and strain sensitivities are twice as high as in the traditional scanning moiré method in the same wide field of view. When the specimen grid pitch is around or greater than 3 pixels, multi-pixel sampling moiré fringes are generated, and a spatial phase-shifting technique is combined for a full-field deformation measurement. The strain measurement accuracy is significantly improved, and automatic batch measurement is easily achievable. Both methods can measure the two-dimensional (2D) strain distributions from a single-shot grid image without rotating the specimen or scanning lines, as in traditional moiré techniques. As examples, the 2D displacement and strain distributions, including the shear strains of two carbon fiber-reinforced plastic specimens, were measured in three-point bending tests. The proposed technique is expected to play an important role in the non-destructive quantitative evaluations of mechanical properties, crack occurrences, and residual stresses of a variety of materials.
Synthesis of biobased epoxy and curing agents using rosin and the study of cure reactions (2008)

Rosin is an abundantly available natural product. Rosin is a mixture of acidic (ca. 90%) and neutral (ca. 10%) compounds. The characteristic fused ring structure of rosin acids is analogous to that of some aromatic compounds in rigidity, and makes rosin and its derivatives potential substitutes for those aromatic compounds in polymers. In this study, the synthesis of biobased epoxy and curing agent using rosin and the cure reaction were investigated. Abietyl glycidyl ether and methyl maleopimarate were synthesized from one of the rosin acids. Abietyl glycidyl ether was used as a model compound representing rosin-based epoxies, while methyl maleopimarate was used as a model compound representing rosin-based anhydride curing agents. The synthesis methods of the model compounds were examined and the chemical structures were confirmed by 1H NMR, 13C NMR, FT-IR and ESI-MS. Curing of abietyl glycidyl ether with aniline and curing of methyl maleopimarate with phenyl glycidyl ether were investigated separately. Nonisothermal curing of the model systems was studied by DSC, and the cured products were characterized by 1H NMR.
Spider minor ampullate silk proteins contain new repetitive sequences and highly conserved non‐silk‐like “spacer regions” (1998)

Spider minor ampullate silk is a strong non-elastic deformably stretchable silk used in web formation. This silk from Nephila clavipes is composed of two proteins, MiSp 1 and 2, whose transcripts are 9.5 and 7.5 kb, respectively, as determined by Northern blots. Both MiSp proteins are organized into a predominantly repetitive region and a small nonrepetitive carboxy terminal region. These highly repetitive regions are composed mainly of glycine and alanine, but also contain tyrosine, glutamine, and arginine. The sequences are mainly GGX and GA repeats. The repetitive regions are interrupted by nonrepetitive serine-rich spacer regions. Although the sequences of the spacer regions differ from the repetitive regions, sequences of the spacers from different regions of the proteins are nearly identical. The sequence differences between major and minor ampullate silks may explain the differing mechanical properties of the fibers.
Remarn: A Reconfigurable Multi-threaded Multi-core Accelerator for Recurrent Neural Networks (2022)

This work introduces Remarn, a reconfigurable multi-threaded multi-core accelerator supporting both spatial and temporal co-execution of Recurrent Neural Network (RNN) inferences. It increases processing capabilities and quality of service of cloud-based neural processing units (NPUs) by improving their hardware utilization and by reducing design latency, with two innovations. First, a custom coarse-grained multi-threaded RNN/Long Short-Term Memory (LSTM) hardware architecture, switching tasks among threads when RNN computational engines meet data hazards. Second, the partitioning of this hardware architecture into multiple full-fledged sub-accelerator cores, enabling spatially co-execution of multiple RNN/LSTM inferences. These innovations improve the exploitation of the available parallelism to increase runtime hardware utilization and boost design throughput. Evaluation results show that a dual-threaded quad-core Remarn NPU achieves 2.91 times higher performance while only occupying 5.0% more area than a single-threaded one on a Stratix 10 FPGA. When compared with a Tesla V100 GPU implementation, our design achieves 6.5 times better performance and 15.6 times higher power efficiency, showing that our approach contributes to high performance and energy-efficient FPGA-based multi-RNN inference designs for datacenters.
Floating source multilevel inverter uses hybrid double switching frequencies (2017)

In most of the power electronics inverters it is desired to produce clean sinusoidal waves without the use for any filtration in the output. This topic gathered the attentions of many researchers because it helps reduce the cost of the inverters. This paper presents floating source multilevel inverters that utilize double switching frequency modulation technique. This modulation method consists of inverse sinusoidal wave with two frequencies as a carrier. The modulation scheme uses hybrid method where one pair of the switches operates at high frequency using this carrier while the other switches are operated at the line frequency. This technique generated more steps in the inverter output while maintain the same number of switching devices. Besides, it reduces the total harmonic distortion because of the double frequency modulation technique by increasing the fundamental component of the inverter output waveform. The proposed method was verified by simulation using PSCAD/EMTPS.
Modeling And Analysis Of Chaos-Modulated Dual Oscillator-Based Random Number Generators (2008)

Publication in the conference proceedings of EUSIPCO, Lausanne, Switzerland, 2008