gebhart/patrepeval huggingface dataset:
Charge Transfer Interactions in Biology: A New View of the Protein-Water Interface (1999)

In this paper we employ linear-scaling quantum mechanical methodologies to carry out the first fully quantum mechanical calculation on a protein/water system (∼5,000 atoms total). These calculations demonstrate for the first time that the superposition of a number of small charge transfer interactions at the protein/water interface results in a substantial transfer of charge from the protein surface to the surrounding solvent. Furthermore, we show that the charge transfer interaction is a significant contributor to the overall interaction energy in hydrogen bonding complexes - even more so than the closely related polarization interaction. Finally, we discuss the theoretical and experimental ramifications of the charge transfer interaction for biomolecules in aqueous solution.
Polymorphonuclear leucocyte activation after trauma: evidence for increased generation of oxygen free radicals in response to in vitro endotoxin stimulation. (1989)

The effects of moderate bone trauma on the functional status of circulating polymorphonuclear neutrophil (PMN) leucocytes were studied over a 3-day period in a porcine model. Nine pigs were submitted to femur marrow nailings and six acted as controls. The PMNs were studied in regard to production of oxygen free radicals and locomotion. The trauma was followed by leucocytosis, dominated by granulocytosis. Oxygen free radical production by PMNs, measured by chemiluminescence, was significantly greater in the traumatized animals than in the controls. Stimulation of the PMNs with low concentrations of endotoxin disclosed intergroup differences until 48 hours post-trauma. No intergroup difference in PMN locomotion were demonstrated. The results indicated post-traumatic functional changes in the circulating PMNs, suggesting increased reactivity and sensitivity for gram-negative bacteria and their endotoxins during septicaemia.
ChemInform Abstract: A STUDY OF THE BASICITY OF THE METAL‐METAL BOND IN (μ‐SCH3FE(CO)2L)2 COMPLEXES. IV. INTERACTION WITH SULFUR DIOXIDE AND REACTIVITY OF THE COORDINATED SULFUR DIOXIDE TOWARD OXYGEN (1979)

Abstract SO 2 verhält sich gegenüber den dimeren Fe‐Komplexen (I) als Lewissäure und schiebt sich in die Fe‐Fe‐Bindung unter Bildung der Produkte (II) ein.
Target engagement and drug residence time can be observed in living cells with BRET (2015)

The therapeutic action of drugs is predicated on their physical engagement with cellular targets. Here we describe a broadly applicable method using bioluminescence resonance energy transfer (BRET) to reveal the binding characteristics of a drug with selected targets within intact cells. Cell-permeable fluorescent tracers are used in a competitive binding format to quantify drug engagement with the target proteins fused to Nanoluc luciferase. The approach enabled us to profile isozyme-specific engagement and binding kinetics for a panel of histone deacetylase (HDAC) inhibitors. Our analysis was directed particularly to the clinically approved prodrug FK228 (Istodax/Romidepsin) because of its unique and largely unexplained mechanism of sustained intracellular action. Analysis of the binding kinetics by BRET revealed remarkably long intracellular residence times for FK228 at HDAC1, explaining the protracted intracellular behaviour of this prodrug. Our results demonstrate a novel application of BRET for assessing target engagement within the complex milieu of the intracellular environment.
When does a suspension droplet splash (2013)

We investigate the impact of droplets of dense suspensions onto a solid substrate. We show that a global hydrodynamic balance is unable to predict the splash onset and propose to replace it by an energy balance at the level of the particles in the suspension. We experimentally verify that the resulting, particle-based Weber number gives a reliable, particle size and density dependent splash onset criterion. We further show that the same argument also explains why in bimodal systems smaller particles are more likely to escape than larger ones.
Characterization of CAX4, an Arabidopsis H+/Cation Antiporter (2002)

Ion compartmentalization is essential for plant growth and development. The Arabidopsis open reading frames for CAX1, CAX2, and CAX3 (cation exchangers 1, 2, and 3) were previously identified as transporters that may modulate ion fluxes across the vacuolar membrane. To understand the diversity and role of H(+)/cation transporters in controlling plant ion levels, another homolog of the CAX genes, CAX4, was cloned from an Arabidopsis cDNA library. CAX4 is 53% identical to CAX1 at the amino acid level, 42% identical to CAX2, and 54% identical to CAX3. CAX4 transcripts appeared to be expressed at low levels in all tissues and levels of CAX4 RNA increased after Mn(2+), Na(+), and Ni(2+) treatment. An N-terminal CAX4-hemagglutinin fusion appeared to localize to both yeast and plant vacuolar membranes. When expressed in yeast, CAX4, like CAX3, failed to suppress the Ca(2+) sensitivity of yeast strains deficient in vacuolar Ca(2+) transport. Several modifications to CAX4 allowed the protein to transport Ca(2+). Addition of amino acids to the N terminus of CAX4 and CAX3 caused both transporters to suppress the sensitivity of yeast strains deficient in vacuolar Ca(2+) transport. These findings suggest that CAX transporters may modulate their ion transport properties through alterations at the N terminus.
A phase 1 study to evaluate the safety and pharmacokinetics of PQ912, a glutaminyl cyclase inhibitor, in healthy subjects (2015)

This first-in-man study of a compound-targeting QC inhibition justifies further development of PQ912 for the treatment of AD.
Interaction of Hepatitis B Viral X Protein and CCAAT/ Enhancer-binding Protein α Synergistically Activates the Hepatitis B Viral Enhancer II/Pregenomic Promoter (1999)

The hepatitis B viral X protein (HBx) is known to exert its transactivation activity by the interaction with several cellular transcription factors. Here we report the interaction of HBx and CCAAT/enhancer-binding protein alpha (C/EBPalpha) and their effects on the enhancer/promoters of hepatitis B virus (HBV). A chloramphenicol acetyltransferase assay showed that the cotransfection of HBx and C/EBPalpha strongly activated the enhancer II/pregenomic promoter of HBV in a synergistic manner. This effect was also observed in the heterologous expression system with promoters of SV40 and herpes simplex virus thymidine kinase genes. Serial deletion analysis of the enhancer II/pregenomic promoter identified the responsible region (nucleotides 1639-1679), in which two C/EBP-binding sites are located. An in vitro interaction assay and electrophoretic mobility shift assay showed that HBx augmented the DNA binding activity of C/EBPalpha by direct interaction with it, and its basic leucine zipper domain was responsible for the interaction with HBx. Domain analysis of HBx showed that the central region (amino acids 78-103) was necessary for direct interaction with C/EBPalpha. However, the complete form of HBx was necessary for the synergistic activation of the HBV pregenomic promoter. These results suggest that the interaction of HBx and C/EBPalpha enhances the transcription of the HBV pregenomic promoter for the effective life cycle of HBV in hepatocytes.
Efficiency, Efficacy, and Safety of EZ-Blocker Compared with Left-sided Double-lumen Tube for One-lung Ventilation (2013)

The EZB is an efficient and effective device for one-lung ventilation and causes less injury and sore throat than a DLT.
Chemiluminescence of carbon disulfide(1+) (CS2+) initiated by a thermal energy charge-transfer reaction with argon(1+) (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemiluminescence of carbon disulfide(1+) (CS2+) initiated by a thermal energy charge-transfer reaction with argon(1+)B. L. Upschulte, R. J. Shul, R. Passarella, R. E. Leuchtner, R. G. Keesee, and A. W. Castleman Jr.Cite this: J. Phys. Chem. 1986, 90, 1, 100–104Publication Date (Print):January 1, 1986Publication History Published online1 May 2002Published inissue 1 January 1986https://pubs.acs.org/doi/10.1021/j100273a023https://doi.org/10.1021/j100273a023research-articleACS PublicationsRequest reuse permissionsArticle Views41Altmetric-Citations6LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Estimation des HRTFs Individuelles sur la base d'enregistrements binauraux en conditions non supervisées (2016)

International audience
Planar MIMO antenna system with polarization diversity for 2.5–2.7 GHz LTE indoor FemtoCells (2015)

This paper presents a planar MIMO antenna system designed for the 2.5–2.7 GHz LTE indoor femtocell application. The proposed antenna system consists of two orthogonally polarized arrays; each array is realized on a single PCB and is comprised by two microstrip patch antenna elements. These patch antenna elements have increased bandwidth that is achieved by using parasitic radiating patches disposed coplanar with the main patch. The proposed patch arrays use the technique of sharing one of the parasitic patches by both elements in each array. That provides a narrow radiation pattern of the antenna system in the vertical plane with more compact size of the arrays. The designed MIMO antenna system was optimized for integration with commercial LTE femtocell base station produced by Telum LLC. The measurement results confirmed the bandwidth of 2.37 – 2.79 GHz (420 MHz) for the −10 dB level of the reflection coefficient and the isolation between two MIMO input ports of > 38 dB. The gain of the designed system at the central frequency of 2.6 GHz is 8 dBi. The half-power beamwidth in the horizontal plane is 71° whereas in the vertical plane is 46°. Such antenna pattern characteristics are desirable and allow femtocell base stations located at neighboring floors of a building improving coverage area at each floor while decrease interference level between the cells.
Mask-/reticle-making control system (1995)

The mask making is the first step in the semiconductor device manufacturing. It depends entirely upon mask delivery time whether it will take a short time or not to develop and produce the new devices. It is required to construct the system which can manage mask making and delivery quickly. It is very important to control the much various information on the many kinds of the mask for ASIC use quickly. It is also important to control the many various masks processing parameters, that is, to memorize the parameters and to use the appropriate parameters when the masks for general purpose device like a memory use are revised. The data base system to control the various information and parameters is requested from many mask makers and device ones. We have made a unitary data base including a large amount of information on the various ASIC devices and the various processing parameters of the memory devices, and information on the mask making progress, whereabouts of the masks. And we have constructed the new mask/reticle making control system using with the database.
Towards NIC-based intrusion detection (2003)

We present and evaluate a NIC-based network intrusion detection system. Intrusion detection at the NIC makes the system potentially tamper-proof and is naturally extensible to work in a distributed setting. Simple anomaly detection and signature detection based models have been implemented on the NIC firmware, which has its own processor and memory. We empirically evaluate such systems from the perspective of quality and performance (bandwidth of acceptable messages) under varying conditions of host load. The preliminary results we obtain are very encouraging and lead us to believe that such NIC-based security schemes could very well be a crucial part of next generation network security systems.
In vitro activity profile of the novel hypoxia-activated cytotoxic prodrug TH-302 (2008)

1441 TH-302 is a hypoxia-activated cytotoxic prodrug comprised of a 2-nitroimidazole hypoxia trigger linked to a dibromo isophosphoramide mustard toxin. TH-302 exhibits potent in vitro cytotoxicity under hypoxia, is efficacious in both ectopic and orthotopic xenograft cancer models, and demonstrates a favorable PK and tox profile. TH-302 is currently in a Phase 1 clinical trial for the treatment of cancer. Here we present details of TH-302’s in vitro activity profile.  Examination of TH-302’s cytotoxic potency and hypoxia selectivity in different cancer cell lines (PC-3, MIA PaCa-2, ACHN, HCT 116) yielded results comparable to those observed in H460 cells (in a 2h exposure 3d proliferation assay 300). The cytoxicity of TH-302 under normoxia across the entire panel of 60 human cancer cell lines comprising the NCI-60 showed none to be more sensitive than H460 under normoxia (2d proliferation assay). This latter result indicates that, at least within this panel of cell lines, none are able to significantly activate TH-302 in a hypoxia-independent manner. When TH-302 was tested in pairs of cell lines that allow the profiling of susceptibility to efflux by the major drug resistance pumps (i.e. MDR1, MRP1, and BCRP), TH-302 showed no difference in potency or selectivity in lines over-expressing the specific pump, versus matched control lines (MESSA vs. MESSA-DX5; H69 vs. H69AR; HEK293-PCDNA vs. HEK293-BCRP, respectively). This result indicates that TH-302 is not a substrate for these clinically relevant drug resistance pumps.  The oxygen concentration dependence of TH-302 activation cytotoxicity was examined employing a set of defined gas mixtures (0%, 0.1%, 0.3%, 0.6%, 1%, 10%, 21% O2) in the 2h exposure 3d proliferation assay with H460 cells. Results demonstrated an O2 concentration dependence of prodrug activation (IC 50’s were 0.1, 1, 3, 5, 7, 30, and 30µM, respectively).  Examining downstream effects of TH-302 activity, we demonstrate both γH2AX phosphorylation and G2/M phase cell cycle arrest in a TH-302 concentration- and time-dependent manner in H460 cells. These activities mirrored the cytotoxicity profile in terms of potency and hypoxia-selectivity. Utilization of CHO cell-based DNA repair mutant cell lines showed that lines deficient in homologous recombination (irs1SF and UV41) exhibited greater sensitivity to TH-302 under hypoxia than the parental control line (AA8) or in lines deficient in base or nucleotide excision repair (EM9, UV35). These findings are consistent with a DNA cross-linking mechanism of action underlying TH-302’s cytotoxicity in vitro.  Taken together, these results demonstrate that TH-302 exhibits a favorable in vitro activity profile for a hypoxia-activated prodrug in clinical development.
Integrated Silicon-Polymer Laterally Stacked Bender for Sensing Microgrippers (2006)

This paper presents a novel electro-thermal microgripper based on integrated silicon-polymer laterally stacked microactuators. The device consists of a serpentine-shape deep silicon structure with a thin film aluminum heater on the top and filling polymer in the trenches among the vertical silicon parts. The fabrication is based on deep reactive ion etching of silicon, aluminum sputtering and SU8 filling. The actuator is 500 mum long, 65 mum wide and 50 mum high. The microgripper generates a large motion up to 52 mum at a driving voltage of only 2 V and with a power consumption of 50 mW. The maximum working temperature is 164degC at 2 V.
Whole-body transcriptome of selectively bred, resistant-, control-, and susceptible-line rainbow trout following experimental challenge with Flavobacterium psychrophilum (2015)

Genetic improvement for enhanced disease resistance in fish is an increasingly utilized approach to mitigate endemic infectious disease in aquaculture. In domesticated salmonid populations, large phenotypic variation in disease resistance has been identified but the genetic basis for altered responsiveness remains unclear. We previously reported three generations of selection and phenotypic validation of a bacterial cold water disease (BCWD) resistant line of rainbow trout, designated ARS-Fp-R. This line has higher survival after infection by either standardized laboratory challenge or natural challenge as compared to two reference lines, designated ARS-Fp-C (control) and ARS-Fp-S (susceptible). In this study, we utilized 1.1 g fry from the three genetic lines and performed RNA-seq to measure transcript abundance from the whole body of naive and Flavobacterium psychrophilum infected fish at day 1 (early time-point) and at day 5 post-challenge (onset of mortality). Sequences from 24 libraries were mapped onto the rainbow trout genome reference transcriptome of 46,585 predicted protein coding mRNAs that included 2633 putative immune-relevant gene transcripts. A total of 1884 genes (4.0% genome) exhibited differential transcript abundance between infected and mock-challenged fish (FDR < 0.05) that included chemokines, complement components, tnf receptor superfamily members, interleukins, nod-like receptor family members, and genes involved in metabolism and wound healing. The largest number of differentially expressed genes occurred on day 5 post-infection between naive and challenged ARS-Fp-S line fish correlating with high bacterial load. After excluding the effect of infection, we identified 21 differentially expressed genes between the three genetic lines. In summary, these data indicate global transcriptome differences between genetic lines of naive animals as well as differentially regulated transcriptional responses to infection.
Fabrication and near-room temperature transport of patterned gold cluster structures (1997)

Ligand stabilized metal clusters are becoming of considerable interest for possible nanoscale electronics applications. In this article, we report the fabrication and near-room temperature electrical transport properties of structures made from the gold-cluster material Au55[P(C6H5)3]12Cl6. While other strategies to produce cluster arrays have been reported, this work is the first to use electron-beam lithography to laterally define the structures. We compare the current–voltage characteristics of nonpatterned and patterned structures, and show that in both cases the nonlinear behavior observed is consistent with Coulomb blockade dominated transport. We argue that charging of individual Au55 cores is responsible for the effects observed.
The Mechanism of Sertoli‐Germ Cell Interactiona (1987)

Peer Reviewed
High Performance Liquid Chromatography of Plant Pigments – A Review (1982)

Abstract High performance liquid chromatography (HPLC) has found wide application for qualitative and quantitative analysis of plant pigments. HPLC methods developed for the analysis of carotenoids, chlorophylls, flavonoids and betalaines are summarized. Compared to other chromatographic techniques the methods are precise, sensitive and less time consuming. Sample preparation prior to chromatography is generally minimal and often a simple extraction step is sufficient. The high resolution capability of HPLC has made the separation of closely related pigments possible and has provided a means for major advances into the study of plant pigments.
Fresnel transform as a projection onto a Nijboer–Zernike basis set (2015)

The Fresnel transform is widely used in optics to calculate the free-space propagation of paraxial fields. Generally, there is no analytical solution for the Fresnel transform; therefore, the numerical methods are used often. In this Letter, we propose a new semi-analytical method to calculate the Fresnel transform, which is based on an extended Nijboer-Zernike theory. We calculate two examples to investigate how the sampling rate and maximal number of Zernike polynomials affect the accuracy of our results, and then use this method to calculate the reconstruction of two different kinds of holograms. At the end, we discuss the advantages and disadvantages of our method.
[Stereotactic brain biopsy in AIDS patients: a necessary patient-oriented and cost-effective diagnostic measure?]. (1998)

Neurological complications occur in 40% of "human immunodeficiency virus type 1" (HIV-1)-infected patients. Aim of the study was to evaluate the diagnostic yield of stereotactic brain biopsy and non invasive diagnostic procedures (CT, antitoxoplasma antibodies) and to calculate the benefit of the brain biopsy for the patient and the costs of both methods. From October 1989 through September 1995 we biopsied 44 of 2749 (2%) HIV-1-infected patients after non invasive diagnostic procedures had been performed. In 93% of the patients an unambiguous diagnosis was possible based on the biopsy and lead in 73% of the patients to a change of therapy. No complications occurred after biopsy. 40 CTs and 15 MRIs were done. The radiological appearance of toxoplasmosis and non Hodgkin lymphoma (NHL) differed from that of progressive multifocal leucencephalopathy (PML) in respect to enhancement (PML). CT showed a sensitivity of 55% (toxoplasmosis, NHL) and 78% (PML) and a specificity of 83% (PML), 84% (NHL) and 96% (toxoplasmosis), respectively. Antitoxoplasma antibodies showed a sensitivity of 45%, only. The stereotactic brain biopsy was more expensive (20.166,- ATS) than CT, MRI and antitoxoplasma antibodies (4109,- ATS up to 6959,- ATS). We conclude that stereotactic brain biopsy is an efficient and safe and for the patients important diagnostic procedure. In selected patients even expensive investigations should be undertaken considering specific therapy and cost effective homecare.
Notes (1956)

J. A. Ballantine, W. B. Whalley, L. Mester, Á. Major, E. Móczár, C. C. Addison, C. G. L. Furmidge, K. B. L. Mathur, R. S. Thakur, D. G. Saunders, C. F. Garbers, G. M. Badger, R. G. Buttery, E. A. Braude, E. A. Evans, C. A. Bunton, V. A. Welch, D. Buckley, M. S. Gibson, F. Bell, J. Castells, G. A. Fletcher, J. Chatt, A. A. Williams, S. E. S. El Wakkad and H. A. M. Rizk, J. Chem. Soc., 1956, 3224 DOI: 10.1039/JR9560003224