gebhart/patrepeval huggingface dataset:
Species Specificity of Amidine-Based Urokinase Inhibitors (2001)

Inhibition of the proteolytic activity of urokinase has been shown to inhibit the progression of tumors in rodent models and is being investigated for use in human disease. Understanding the rodent/human species-specificity of urokinase inhibitors is therefore critical for interpretation of rodent cancer progression models that use these inhibitors. We report here studies with a panel of 11 diverse urokinase inhibitors in both human and mouse enzymatic assays. Inhibitors such as amiloride, B428, and naphthamidine, that occupy only the S1 subsite pocket were found to be nearly equipotent between the human and the murine enzymes. Inhibitors that access additional, more distal, pockets were significantly more potent against the human enzyme but there was no corresponding potency increase against the murine enzyme. X-ray crystallographic structures of these compounds bound to the serine protease domain of human urokinase were solved and examined in order to explain the human/mouse potency differences. The differences in inhibitor potency could be attributed to four amino acid residues that differ between murine and human urokinases: 60, 99, 146, and 192. These residues are Asp, His, Ser, and Gln in human and Gln, Tyr, Glu, and Lys in mouse, respectively. Compounds bearing a cationic group that interacts with residue 60 will preferentially bind to the human enzyme because of favorable electrostatic interactions. The hydrogen bonding to residue 192 and steric considerations with residues 99 and 146 also contribute to the species specificity. The nonparallel human/mouse enzyme inhibition observations were extended to a cell-culture assay of urokinase-activated plasminogen-mediated fibronectin degradation with analogous results. These studies will aid the interpretation of in vivo evaluation of urokinase inhibitors.
Fault Detection and Isolation of a Real PEM Fuel Cell Using Interval LPV Observers (2012)

Chronic stress generally inhibits the activity of the reproductive system. Acute stress also is often inhibitory, but the mechanism involved and its persistence of action once animals are no longer exposed to the stressor are poorly understood. We investigated the effect of capture and restraint stress on plasma testosterone (T), luteinizing hormone (LH), and corticosterone (CORT) in free-ranging male rufous-winged sparrows, Peucaea carpalis. Stress decreased plasma T between 10 and 30 min after capture and restraint but did not influence plasma LH, the main hormone that controls T secretion, suggesting that stress did not decrease plasma T by inhibiting LH secretion. The stress-induced decrease in plasma T was associated with elevated plasma CORT, but there was no evidence that these effects were functionally related. Plasma stress-induced T was positively related to plasma initial T measured within 2 min of capture. This relationship was, however, complex as plasma T decreased proportionally more in response to stress in sparrows with high than low plasma initial T. The relative sensitivity to the same stressor was, therefore, individually variable and this variation was related to initial plasma T. Birds caught and restrained for 30 min, and then released on their breeding territory before recapture up to 6 h later, maintained depressed plasma T, indicating that the effect of acute stress on this hormone persists after the stressor removal. These studies provide new information on the effects of acute stress on plasma T in free-ranging birds. In particular, they are among the first to characterize the time course and to describe the persistence of these effects. The findings also contribute to identifying factors that are associated with individual differences in plasma hormone levels.
Modeling delayed feedback in display advertising (2014)

In performance display advertising a key metric of a campaign effectiveness is its conversion rate -- the proportion of users who take a predefined action on the advertiser website, such as a purchase. Predicting this conversion rate is thus essential for estimating the value of an impression and can be achieved via machine learning. One difficulty however is that the conversions can take place long after the impression -- up to a month -- and this delayed feedback hinders the conversion modeling. We tackle this issue by introducing an additional model that captures the conversion delay. Intuitively, this probabilistic model helps determining whether a user that has not converted should be treated as a negative sample -- when the elapsed time is larger than the predicted delay -- or should be discarded from the training set -- when it is too early to tell. We provide experimental results on real traffic logs that demonstrate the effectiveness of the proposed model.
Image clustering through community detection on hybrid image similarity graphs (2010)

The wide adoption of photo sharing applications such as Flickr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">©</sup> and the massive amounts of user-generated content uploaded to them raises an information overload issue for users. An established technique to overcome such an overload is to cluster images into groups based on their similarity and then use the derived clusters to assist navigation and browsing of the collection. In this paper, we present a community detection (i.e. graph-based clustering) approach that makes use of both visual and tagging features of images in order to efficiently extract groups of related images within large image collections. Based on experiments we conducted on a dataset comprising publicly available images from Flickr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">©</sup> , we demonstrate the efficiency of our method, the added value of combining visual and tag features and the utility of the derived clusters for exploring an image collection.
Superdirective dielectric spherical multilayer antennae (2019)

Dielectric electrically small antennae are attracting high interest due to their promising applications both in optical and microwave bands. Efficiency of such antennas is usually bounded by low directivity. The stochastic optimization procedure is used to demonstrate superdirective designs of small all-dielectric antennas being spherical multilayer structure. The procedure is based on an efficient and accurate rigorous electromagnetic model which allows for performing large scale optimization on personal computers with limited resources. For optimization we compared different stochastic algorithms, and the JADE demonstrated the best performance. The found designs possess the directivity that go beyond the conventional theoretical bounds for antennas smaller than the wavelength and outperform previously attained results.
Efficient production of ethylene by Pseudomonas syringae pv. glycinea which causes halo blight in soybeans. (1987)

Ethylene is a plant hormone produced by various plants and microorganisms including some plant pathogens.1 ~3) It is also an important starting material in petrochemical industries, and it is mainly produced through the cracking of petroleum at present. Due to the global shortage of crude oil deposits, the unique idea of developing a process for microbial ethylene production was proposed.40 Accordingly a search for excellent ethylene producing organisms is thought to be very worthwhile.
Design, Construction and Measurement of a Laminated Transverse Flux Machine (2022)

This paper presents the design, construction and measurements on a transverse flux machine. The lamination concept is designed for easy fabrication and low iron losses. For a good flux guidance and a high magnetic field, electrical sheet is used for the soft magnetic circuit. The design of the machine is performed with a fast semi-analytical calculation and validated by 3D finite element analysis. The calculated quantities are compared with measurements on a prototype. Despite certain deviations, the measurements show good agreement with the calculations for the induced voltage and torque. In terms of efficiency, however, the measurement deviates significantly from the simulation. This is due to the iron losses being calculated much too small, which is evident from the separation of the measured losses.
Route towards Dirac and Weyl antiferromagnetic spintronics (2017)

Topological quantum matter and spintronics research have been developed to a large extent independently. In this review, we discuss a new role that the antiferromagnetic order has taken in combining topological matter and spintronics. This occurs due to the complex microscopic symmetries present in antiferromagnets that allow for, e.g., topological relativistic quasiparticles and the newly discovered Néel spin–orbit torques to coexist. We first introduce the concepts of topological semimetals and spin‐orbitronics. Secondly, we explain the antiferromagnetic symmetries on a minimal Dirac semimetal model and the guiding role of ab initio calculations in predictions of examples of Dirac and Weyl antiferromagnets: SrMnBi 2 , CuMnAs, and Mn 3 Ge. Lastly, we illustrate the interplay of Dirac quasiparticles, topology and antiferromagnetism on: (i) the experimentally observed quantum Hall effect in EuMnBi 2 ; (ii) the large anomalous Hall effect in Mn 3 Ge; and (iii) the theoretically predicted topological metal–insulator transition in CuMnAs. Dirac fermions at the Fermi level of the Dirac semimetal antiferromagnet calculated from the fist‐principles. Reorientation of the Néel vector drives the topological metal–insulator transition.
Data from Inhibiting WEE1 and IKK-RELA Crosstalk Overcomes TNFα Resistance in Head and Neck Cancers (2023)

&lt;div&gt;Abstract&lt;p&gt;TNFα is a key mediator of immune and radiotherapy-induced cytotoxicity, but many cancers, including head and neck squamous cell carcinomas (HNSCC), display TNF resistance due to activation of the canonical IKK–NF-κB/RELA pro-survival pathway. However, toxicities associated with direct targeting of the canonical pathway point to the need to identify mechanism(s) contributing to TNFα resistance and synthetic lethal targets to overcome such resistance in cancer cells. Here, RNAi screening for modulators of TNFα–NF-κB reporter activity and cell survival unexpectedly implicated the WEE1 and CDC2 G&lt;sub&gt;2&lt;/sub&gt;–M checkpoint kinases. The IKKα/β-RELA and WEE1-CDC2 signaling pathways are activated by TNFα and form a complex in cell lines derived from both human papillomavirus (−) and (+) subtypes of HNSCC. WEE1 inhibitor AZD1775 reduced IKK/RELA phosphorylation and the expression of NF-κB–dependent pro-survival proteins Cyclin D1 and BCL2. Combination of TNFα and AZD1775 enhanced caspase-mediated apoptosis &lt;i&gt;in vitro&lt;/i&gt;, and combination treatment with radiotherapy and AZD1775 potentiated inhibition of HNSCC tumor xenograft growth &lt;i&gt;in vivo&lt;/i&gt;, which could be significantly attenuated by TNFα depletion. These data offer new insight into the interplay between NF-κB signaling and WEE1-mediated regulation of the G&lt;sub&gt;2&lt;/sub&gt;–M cell-cycle checkpoint in HNSCC.&lt;/p&gt;Implications:&lt;p&gt;Inhibiting WEE1 and IKK-RELA crosstalk could potentially enhance the effects of therapies mediated by TNFα with less systemic immune suppression and toxicity than observed with direct interruption of IKK-NF-κB/RELA signaling.&lt;/p&gt;&lt;/div&gt;
Fluid–metasedimentary rock interactions in subduction-zone mélange: Implications for the chemical composition of arc magmas (2004)

Elevated concentrations of certain large ion lithophile elements (LILE; e.g., Ba, K, Rb,&#13;\nCs, Ca, Sr), U, and Pb in arc magmas relative to high field strength elements (HFSE; e.g.,&#13;\nTi, Th, Hf, Nb, Zr) are considered key indicators of fluid addition to arc magma source&#13;\nregions worldwide, but the fluid sources and processes of mass transfer are controversial.&#13;\nDehydration of downgoing slabs releases fluids that can flow through and react with metamorphosed&#13;\nultramafic-mafic rock packages in me´lange zones near slab-mantle interfaces.&#13;\nNew geochemical data from Syros, Greece, reveal that these fluids preferentially leach&#13;\nLILEs, U, and Pb when they infiltrate and react with subducted metasedimentary rocks.&#13;\nTransfer of these LILE-, U-, and Pb-enriched fluids to the mantle wedge at subarc depths&#13;\ncould directly trigger partial melting and generate magmas with elevated Ba/Th, Sr/Th,&#13;\nPb/Th, and U/Th, as well as radiogenic Sr. Alternatively, if fluid transfer occurs at shallower&#13;\ndepths (e.g., Syros), the metasomatized mantle could be carried deeper by wedge&#13;\ncorner flow to ultimately undergo partial melting in subarc regions.
Evaluation of the prognostic role of a panel of biomarkers in stage IB-IIIA non-small cell lung cancer patients. (2008)

Even though the biomarkers tested are expressed in a significant proportion of lung tumors, none of them was found to be of prognostic significance in patients with NSCLC.
Ultra-high-speed optical serial-to-parallel data conversion by time-domain optical Fourier transformation in a silicon nanowire (2011)

We demonstrate conversion from 64 × 10 Gbit/s optical time-division multiplexed (OTDM) data to dense wavelength division multiplexed (DWDM) data with 25 GHz spacing. The conversion is achieved by time-domain optical Fourier transformation (OFT) based on four-wave mixing (FWM) in a 3.6 mm long silicon nanowire. A total of 40 out of 64 tributaries of a 64 × 10 Gbit/s OTDM-DPSK data signal are simultaneously converted with a bit-error rate (BER) performance below the 2 × 10(-3) FEC limit. Using a 50 m long highly nonlinear fiber (HNLF) for higher FWM conversion efficiency, 43 tributaries of a 64 × 10 Gbit/s OTDM-OOK data signal are converted with error-free performance (BER<10(-9)).
Mitigation of Current Distortion in a Three-Phase Microinverter With Phase Skipping Using a Synchronous Sampling DC-Link Voltage Control (2017)

To improve light load efficiency, a three-phase photovoltaic (PV)-based microinverter may operate in single-phase, two-phase or three-phase mode depending on the available input power. Therefore, its dc-link capacitor may be subjected to large peak-to-peak voltage ripple when operating in phase skipping mode. This paper determines the minimum value of the dc-link capacitor by allowing the maximum acceptable voltage ripple on the dc link. This allows for the use of film capacitors instead of electrolytic capacitors in order to improve the microinverter reliability. Unfortunately, higher dc-link voltage ripple introduces harmonic distortion on the inverter output current waveform if it is not compensated for by the dc-link voltage controller. This paper proposes a simple synchronous control method to regulate the dc-link voltage with the presence of large voltage ripple. The dc-link voltage controller is synchronized with the phase-locked loop and samples the average value of dc-link voltage without introducing unwanted harmonics into the voltage sense path. Experimental results were obtained from a 300-W three-phase half-bridge microinverter prototype to verify the proposed dc-link voltage control performance. Inverter output current total harmonic distortion of 1.6% was achieved even though the dc-link peak-to-peak voltage ripple reached as high as 87 V with 219-V split dc-link voltage. Dynamic response is fast enough to easily track the most extreme ramp change in input PV power.
An Investigation of Optimum NLC‐Sunscreen Formulation Using Taguchi Analysis (2013)

This study used three kinds of wax and three kinds of oil, with fixed mixture ratio including UV‐blocking materials of ethylhexyl methoxycinnamate, oxybenzone, and avobenzone, and applied hot high‐pressure homogenization process to prepare nanolipid sunscreen formulations. The measured particle size of the sunscreen formulations was 100~300 nm around PDI of 0.2 having a moderate polydisperse system. The distribution of zeta potential was −50 mV to −35 mV, showing a stable system. The UV light‐absorbing range of 9 groups of sunscreen formulations was 275 nm~380 nm ranging within UVA and UVB. The rheological analysis found that the viscosity change is shear, thinning exhibiting colloid behavior. Taguchi analysis found that the optimum combinations are the carnauba wax and the blackcurrant oil combination for crystallinity and the beeswax and CPG oil for UV absorption. In addition, UV‐blocking ability shows that the SPF was 51.5 and PFA was three stars for SU9 formulation. Finally, the effect of temperature on the properties of sunscreen formulations was also explored.
A case report of treatment with pegylated interferon alpha for lamivudine-resistant chronic hepatitis B virus infection (2008)

The wide use of lamivudine in chronic hepatitis B has produced a monotonic increase in patients with lamivudine resistance. Therefore, treating lamivudine resistance in chronic hepatitis B is a major concern in clinical practice for the treatment of hepatitis B virus (HBV). There is conflicting evidence on the outcome of pegylated interferon alpha (PEG-IFN alpha) therapy against lamivudine-resistant HBV, which is due to mutations in the YMDD motif. We experienced a patient with chronic hepatitis B who was successfully treated with PEG-IFN alpha-2a after the development of virologic and biochemical breakthrough during lamivudine therapy. Virologic breakthrough was associated with the emergence of YMDD mutants 48 months after starting lamivudine therapy. Treatment with PEG-IFN alpha-2a for 12 months resulted in an undetectable serum level of HBV DNA and the resolution of hepatitis, and the virologic response was maintained over 16 months after cessation of PEG-IFN alpha-2a.
Cataract Prevalence Varies Substantially with Assessment Systems: Comparison of Clinical and Photographic Grading in a Population-Based Study (2011)

The prevalence of cataract in a population varies substantially by measurement methods, with systematically different estimates found using the two most frequent cataract grading systems. This study re-emphasizes the need for global standards to assess and define cataract for epidemiologic and clinical studies.
Internal Coordinate Molecular Dynamics: A Foundation for Multiscale Dynamics (2014)

Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed with Cartesian MD simulations to enhance the conformational sampling. This makes the equations of motion in the Cartesian coordinates differential-algebraic, which adversely impacts the complexity and the robustness of the simulations. On the other hand, constraints can be easily placed in BAT coordinates by removing the degrees of freedom that need to be constrained. Thus, the internal coordinate MD (ICMD) offers an attractive alternative to Cartesian coordinate MD for developing multiscale MD method. The torsional MD method is a special adaptation of the ICMD method, where all the bond lengths and bond angles are kept rigid. The advantages of ICMD simulation methods are the longer time step size afforded by freezing high frequency degrees of freedom and performing a conformational search in the more important low frequency torsional degrees of freedom. However, the advancements in the ICMD simulations have been slow and stifled by long-standing mathematical bottlenecks. In this review, we summarize the recent mathematical advancements we have made based on spatial operator algebra, in developing a robust long time scale ICMD simulation toolkit useful for various applications. We also present the applications of ICMD simulations to study conformational changes in proteins and protein structure refinement. We review the advantages of the ICMD simulations over the Cartesian simulations when used with enhanced sampling methods and project the future use of ICMD simulations in protein dynamics.
Characterization of Regenerative Phenotype of Unrestricted Somatic Stem Cells (USSC) from Human Umbilical Cord Blood (hUCB) by Functional Secretome Analysis (2015)

Stem cell transplantation is a promising therapeutic strategy to enhance axonal regeneration after spinal cord injury. Unrestricted somatic stem cells (USSC) isolated from human umbilical cord blood is an attractive stem cell population available at GMP grade without any ethical concerns. It has been shown that USSC transplantation into acute injured rat spinal cords leads to axonal regrowth and significant locomotor recovery, yet lacking cell replacement. Instead, USSC secrete trophic factors enhancing neurite growth of primary cortical neurons in vitro. Here, we applied a functional secretome approach characterizing proteins secreted by USSC for the first time and validated candidate neurite growth promoting factors using primary cortical neurons in vitro. By mass spectrometric analysis and exhaustive bioinformatic interrogation we identified 1156 proteins representing the secretome of USSC. Using Gene Ontology we revealed that USSC secretome contains proteins involved in a number of relevant biological processes of nerve regeneration such as cell adhesion, cell motion, blood vessel formation, cytoskeleton organization and extracellular matrix organization. We found for instance that 31 well-known neurite growth promoting factors like, e.g. neuronal growth regulator 1, NDNF, SPARC, and PEDF span the whole abundance range of USSC secretome. By the means of primary cortical neurons in vitro assays we verified SPARC and PEDF as significantly involved in USSC mediated neurite growth and therewith underline their role in improved locomotor recovery after transplantation. From our data we are convinced that USSC are a valuable tool in regenerative medicine as USSC's secretome contains a comprehensive network of trophic factors supporting nerve regeneration not only by a single process but also maintained its regenerative phenotype by a multitude of relevant biological processes.
Phenotypic Suppression of ALS/FTD-Associated Neurodegeneration Highlights Mechanisms of Dysfunction (2019)

A fundamental question regarding the etiology of amyotrophic lateral sclerosis (ALS) is whether the various gene mutations associated with the disease converge on a single molecular pathway or act through multiple pathways to trigger neurodegeneration. Notably, several of the genes and cellular processes implicated in ALS have also been linked to frontotemporal dementia (FTD), suggesting these two diseases share common origins with varied clinical presentations. Scientists are rapidly identifying ALS/FTD suppressors that act on conserved pathways from invertebrates to vertebrates to alleviate degeneration. The elucidation of such genetic modifiers provides insight into the molecular pathways underlying this rapidly progressing neurodegenerative disease, while also revealing new targets for therapeutic development.
Functional Requirements-Based Automated Testing for Avionics (2017)

We propose and demonstrate a method for the reduction of testing effort in safety-critical software development using DO-178 guidance. We achieve this through the application of Bounded Model Checking (BMC) to formal low-level requirements, in order to generate tests automatically that are good enough to replace existing labor-intensive test writing procedures while maintaining independence from implementation artefacts. Given that existing manual processes are often empirical and subjective, we begin by formally defining a metric, which extends recognized best practice from code coverage analysis strategies to generate tests that adequately cover the requirements. We then formulate the automated test generation procedure and apply its prototype in case studies with industrial partners. In review, the method developed here is demonstrated to significantly reduce the human effort for the qualification of software products under DO-178 guidance.