gebhart/patrepeval huggingface dataset:
Herpes simplex virus type 1 origin-specific binding protein: oriS-binding properties and effects of cellular proteins (1991)

The herpes simplex virus type 1 (HSV-1) origin of replication, oriS, contains three highly homologous sequences, sites I, II, and III. The HSV-1 origin-binding protein (OBP), the product of the UL9 gene, has been shown to bind specifically to sites I and II. In this study, gel shift analysis was used to characterize interactions between site I DNA and proteins in infected and uninfected cell extracts. The formation of two protein-DNA complexes, bands A and B, was demonstrated with infected cell extracts, and one predominant protein-DNA complex, band M, was identified with mock-infected extracts. Protein interactions with the highly homologous site II and III DNAs were also characterized. Incubation of infected cell extracts with the lower-affinity site II DNA as a probe resulted in the appearance of two protein-DNA complexes with mobilities identical to those of the A and B complexes, while incubation with site III DNA resulted in the formation of a single complex with the mobility of band B; no A-like band was observed. Incubation of high concentrations of partially purified OBP with site I DNA resulted in the formation of two novel complexes, bands 9-1 and 9-2. Addition of uninfected or HSV-1-infected cell extracts to the purified OBP-site I DNA mix significantly enhanced the formation of complex 9-1. The enhanced formation of complex 9-1 by uninfected cell extracts implicates a cellular factor or factors in the formation or stabilization of the OBP-site I DNA complex.
Retrieval analyses of total hip replacements (1996)

Metal ion release was assessed in 31 patients with loosening of total hip replacements (THR). Three types of alloys were used for these prostheses: stainless steel (9/31), Ni-Cr-Mo (5/31) and Co-Cr (17/31). The exposure periods were from 2 to 15 years.Intracellular deposits were observed in macrophages, fibroblasts, histiocytes and numerous multinucleated giant cells. X-ray microprobe analyses by energy dispersive spectrometry (EDS) on ultrathin sections revealed the presence of elements contained in the alloys (Ni, Cr, Fe, Mo) and of additional elements, in particular P, CI, Ca and S. Co was only detected in wear particles. Metal distribution in tissues and body fluids was related to the alloys used. Stainless steel THR induced the lowest metal concentrations, Ni-Cr-Mo alloys showed high increases of Ni and Cr. Co-Cr alloys induced very high Co levels: 100- to 400-fold concentrations in body fluids and 600- to 1000-fold concentrations in tissues with respect to normal upper levels. The metal clearing was studied in three patients with Co-Cr-THR. Two years after removal, only Ni reached normal values. The sometimes alarming high concentrations should lead to a systematic follow up and surveillance of patients.
Radical‐Pair Formation in Hydrocarbon (Aut)Oxidation (2019)

The reaction profiles for the uni- and bimolecular decomposition of benzyl hydroperoxide have been studied in the context of initiation reactions for the (aut)oxidation of hydrocarbons. The unimolecular dissociation of benzyl hydroperoxide was found to proceed through the formation of a hydrogen-bonded radical-pair minimum located +181 kJ mol<sup>-1</sup> above the hydroperoxide substrate and around 15 kJ mol<sup>-1</sup> below the separated radical products. The reaction of toluene with benzyl hydroperoxide proceeds such that O-O bond homolysis is coupled with a C-H bond abstraction event in a single kinetic step. The enthalpic barrier of this molecule-induced radical formation (MIRF) process is significantly lower than that of the unimolecular O-O bond cleavage. The same type of reaction is also possible in the self-reaction between two benzyl hydroperoxide molecules forming benzyloxyl and hydroxyl radical pairs along with benzaldehyde and water as co-products. In the product complexes formed in these MIRF reactions, both radicals connect to a centrally placed water molecule through hydrogen-bonding interactions.
ChemInform Abstract: Electrochemical Fluorination of Di‐ and Tri‐(2‐hydroxyethyl)‐substituted Alkylamines. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Enhanced intracellular delivery of small molecules and drugs via non-covalent ternary dispersions of single-wall carbon nanotubes (2016)

Albumins are used biologically and pharmacologically as transport proteins to deliver molecules to cells. Albumins also efficiently coat single-wall carbon nanotubes (SWCNTs) and promote their entry into mammalian and immune cells by the millions. Here, we show SWCNTs dispersed with bovine serum albumin (BSA) that are pre-loaded with rhodamine B (RB), small hydrophobic dye molecules that we consider here as models for drugs, drastically increase delivery of RB to HeLa cells and macrophages in culture. We determine spatial and concentration distribution of RB by independently visualizing SWCNTs and RB within the cells using unique SWCNT NIR fluorescence and fluorescence lifetime imaging of RB. The SWCNTs-BSA-RB ternary complexes are stable in water for days, and RB is only released when BSA is thermally or enzymatically denatured. We demonstrate efficacy of this approach by delivering daunomycin, a fluorescent chemotherapeutic drug that reduces proliferation in HeLa cells. Furthermore, we use molecular dynamics simulations to identify separate regions in BSA for drug loading and binding to SWCNTs. Together, our results demonstrate a pathway to enhance the delivery of a wide variety of drugs to cells through SWCNTs coated with albumin pre-loaded with drug molecules.
Extraction sélective des actinides : application à l'analyse radiotoxicologique (1997)

Le rendement d'extraction de l'uranium a été étudié par extraction liquide-liquide, à l'aide d'une molécule macrocyclique, le calix[6]arène, 46, fonctionnalisé par des groupements acide carboxylique. La phase aqueuse comprenait l'uranium en présence d'ions sodium et la phase organique le calixarène dissous dans le benzène. L' étude des paramètres d'extraction a permis de proposer un mécanisme d'extraction. Le rendement d'extraction augmente avec le pH et atteint un maximum voisin de 100% pour un pH>3,7. Sur des solutions contenant en plus de l'uranium des ions sodium, marquées au 22-Na et/ou du plutonium 239, l'extraction de l'uranium reste optimale. Sur des échantillons d'urine, après minéralisation, environ 100% de l'uranium sont extraits par le calixarène. Ces premiers résultats montrent que le calixarène choisi présente une structure adéquate vis-à-vis de la structure de coordination de l'ion uranyle, permettant ainsi une extraction sélective de l'uranium.
Hydrophobic Treatment of Potassium Titanate Whisker by a Surface Modification System Using Spiral Flow (2002)

スパイラルフローを利用した新規表面改質装置を用いて, チタン酸カリウムウィスカーの表面改質を行った。コーティング剤には, シランカップリング剤であるγ-グリシドキシプロピルトリメトキシシランを用いた。メタノールを溶媒としてシランカップリング処理を行ったウィスカー表面の定性および観察FT-IR, XPS, SEMを用いて行ったところ, ウィスカーは形状変化や凝集を引き起こすことなく均一に表面改質されていることがわかった。さらに, 表面改質にともないウィスカーの水およびヘキサンに対する分散安定性に大きな変化が認められた。
Silencing Subdomains of v-ErbA Interact Cooperatively with Corepressors: Involvement of Helices 5/6 (2000)

Members of the thyroid hormone receptor (TR) family act on vertebrate development and homeostasis by activating or repressing transcription of specific target genes in a ligand-dependent way. Repression by TR in the absence of ligand is mediated by an active silencing mechanism. The oncogene v-ErbA is a variant form of TR unable to bind hormone and thus acts as a constitutive repressor. Functional studies and mutation analysis revealed that the TR/v-ErbA silencing domain is composed of three silencing subdomains (SSD1-3) which, although nonfunctional individually, synergize such that silencing activity is restored when they are combined in a heteromeric complex. Here we demonstrate, using protein interaction assays in vitro and in vivo, that the inactive v-ErbA point mutant L489R within helix 5/6 in SSD2 fails to interact with the two corepressors N-CoR (nuclear receptor corepressor) or SMRT (silencing mediator of retinoic acid and thyroid hormone receptor). Furthermore, mutants in SSD1 and SSD3 exhibit a reduced corepressor recruitment corresponding to their weak residual silencing activity. In mammalian two-hybrid assays, only the combination of all three silencing subdomains, SSD1-3, leads to a cooperative binding to the corepressors N-CoR or SMRT comparable to that of the full-length v-ErbA repression domain. In conclusion, full silencing activity requires corepressor interaction with all three silencing subdomains, SSD1-3. Among these, SSD2 is a new target for N-CoR and SMRT and is essential for corepressor binding and function.
Novel EUV mask black border suppressing EUV and DUV OoB light reflection (2016)

EUV lithography is the most promising technology for semiconductor device manufacturing of the 10nm node and beyond. The image border is a pattern free dark area around the die on the photomask serving as transition area between the parts of the mask that is shielded from the exposure light by the Reticle Masking (REMA) blades and the die. When printing a die at dense spacing on an EUV scanner, the reflection from the image border overlaps edges of neighboring dies, affecting CD and contrast in this area. This is related to the fact that EUV absorber stack reflects 1-3% of actinic EUV light. To reduce this effect several types of image border with reduced EUV reflectance (<0.05%) have been proposed; such an image border is referred to as a black border. In particular, an etched multilayer type black border was developed; it was demonstrated that CD impact at the edge of a die is strongly reduced with this type of the black border (BB). However, wafer printing result still showed some CD change in the die influenced by the black border reflection. It was proven that the CD shift was caused by DUV Out of Band (OOB) light from the EUV light source. New types of a multilayer etched BB were evaluated and showed a good potential for DUV light suppression. In this study, a novel BB called ‘Hybrid Black Border’ (HBB) has been developed to eliminate EUV and DUV OOB light reflection by applying optical design technique and special micro-fabrication technique. A new test mask with HBB is fabricated without any degradation of mask quality according to the result of CD performance in the main pattern, defectivity and cleaning durability. The imaging performance for N10 imaging structures is demonstrated on NXE:3300B in collaboration with ASML. This result is compared to the imaging results obtained for a mask with the earlier developed BB, and HBB has achieved ~3x improvement; less than 0.2 nm CD changes are observed in the corners of the die. A CD uniformity budget including impact of OOB light in the die edge area is evaluated which shows that the OOB impact from HBB becomes comparable with other CDU contributors in this area. Finally, we state that HBB is a promising technology allowing for CD control at die edges.
Basic fibroblast growth factor is an extracellular matrix component required for supporting the proliferation of vascular endothelial cells and the differentiation of PC12 cells. (1989)

Vascular endothelial cells (ECs) seeded sparsely on extracellular matrix (ECM) will proliferate in the absence of exogenous basic fibroblast growth factor (bFGF). This ECM will also stimulate neurite outgrowth in PC12 cells in the absence of exogenous growth factors. We have previously shown that bFGF is found in subendothelial ECM (Vlodavsky, I., J. Folkman, R. Sullivan, R. Fridman, R. Ishai-Michaeli, J. Sasse, and M. Klagsburn. 1987. Proc. Natl. Acad. Sci. USA. 84:2292-2296) and in basement membranes (Folkman, J., M. Klagsburn, J. Sasse, M. Wadzinski, D. Ingber, and I. Vlodavsky. 1988. Am. J. Pathol. 130:393-400). The actual requirement of ECM-associated bFGF for the growth of ECs and differentiation of PC12 cells was shown in two ways. First, polyclonal anti-bFGF antibodies added to subendothelial ECM inhibited both EC proliferation and PC12 neurite outgrowth. Secondly, PF-HR-9 cells, which do not synthesize bFGF and which produce an ECM not permissive for EC proliferation and PC12 neurite outgrowth, were transfected with bFGF cDNA. PF-HR-9 cells transfected with bFGF, but not with the dominant selectable marker SV2-neomycin, were found to express bFGF and to produce an ECM which did support both EC proliferation and PC12 differentiation. The ECM-mediated stimulatory effects were inhibited by anti-bFGF antibodies but not by anti-nerve growth factor antibodies or nonimmune rabbit IgG. These results indicate that bFGF associated with ECM is a required ECM component for ECM-mediated cell proliferation and differentiation.
Laser implemented depth profiling and surfacing cleaning of human hair using laser ablation inductively coupled plasma mass spectrometry (2009)

Laser ablation ICP-MS appears to be capable of employing the laser to both depth profile human hair and to remove exogenous material, thereby minimizing sample preparation requirements.
Prediction of the H2 Response of an FBAR Resonator Using Finite Element Method (2018)

Finite element method (FEM) is used to simulate the H2 and H3 emissions of FBAR resonators resulting from piezoelectric material nonlinearities [5]. The method incorporates both the linear and higher-order terms in the free energy state variable. The variational principle is applied to the Lagrangian, which includes the free energy state variable to obtain the weak form of the materials continuum of the resonator. The COMSOL FEM solver uses this weak form expression to find the H2 and H3 emissions solutions. The method is validated by comparing an H2 emissions simulation of a 1-D resonator simulated with: (1) the COMSOL FEM solver, and (2) Keysight's harmonic balance nonlinear circuit solver [2]. The method is further validated by comparing measured H2 emissions of a circular resonator with a 2-D COMSOL simulation of the same. In addition, spurious modes which are a solution of 2-D COMSOL, are shown to give rise to H2 “spike”” emissions - emissions which correlate with the peaks of time averaged elastic energy. 2-D COMSOL is also used to simulate the H2 emissions of a pair of resonators that are connected in an anti-parallel configuration.
ChemInform Abstract: Electronic Effects in Migratory Groups. [1,4]‐ versus [1,2]‐Rearrangement in Rhodium Carbenoid Generated Bicyclic Oxonium Ylides. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Tackling probiotic and gut microbiota functionality through proteomics (2016)

Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host. Molecular basis underlying the functional properties of probiotic bacteria responsible for the health promoting effects have been in the background for many years. Breakthrough of omics technologies in the probiotic and microbiota fields has had a very relevant impact in the elucidation of probiotic mechanisms and in the procedures to select these microorganisms, based on solid scientific evidence. It is unquestionable that, in the near future, the evolution of proteomic techniques will play a pivotal role in the generation of knowledge about the functions of probiotics and gut commensals, still a pending issue in the field of intestinal microbiomics.
Prophylactic Antibiotics in Breast Surgery (2007)

Journal of the American College of Surgeons 204(3):p 519-520, March 2007. | DOI: 10.1016/j.jamcollsurg.2006.12.015
Novel method for fabricating high efficiency 10 &#x03BC;m thick c-Si solar cells (2013)

The most straightforward route to reducing the cost of c-Si photovoltaics is to make cells thinner. However, as cell thickness is reduced, light absorption is compromised. This necessitates the use of light trapping mechanisms to mitigate reduction in absorption. In this paper, we present a novel method to fabricate a high efficiency solar cell on a 10 μm thick silicon membrane. The method involves in-house fabrication of 10 μm thick membranes and integration of optically efficacious inverted pyramid texture with feature size and pitch on the order of the solar wavelength via a resist-free laser-writing method.
Site-directed alterations to the geometry of the aspartate transcarbamoylase zinc domain: Selective alteration to regulation by heterotropic ligands, isoelectric point, and stability in urea (1993)

Structural aspects requisite for allosteric function in the regulatory chain of aspartate transcarbamoylase were explored by site-specific amino acid insertion or substitution within the zinc domain in the region of contact between the catalytic and regulatory chains. Amino acid substitution at two positions yielded enzymes which retained a maximum velocity similar to that of the wild-type enzyme but responded differently from the native enzyme in the presence of regulatory nucleoside triphosphates. A change of zinc coordinate amino acid C109 to histidine and a change of E119 to aspartic acid resulted in enzymes which demonstrated synergistic inhibition by CTP and UTP but not inhibition by CTP in either phosphate buffer or a morpholino-based tri-partate (TP) buffer at pH 7. At pH 8.3, where there is a higher proportion of T-state conformers in the native enzyme, the mutants diverged from their similar kinetic behavior. C109H remained an enzyme which was not inhibited by CTP but was still inhibited by CTP+UTP. E119D was inhibited by both CTP and CTP+UTP. Activation of the mutants by ATP was found to vary either with pH or with phosphate as a buffer component. C109H was activated by ATP in phosphate, while in TP at either pH 7 or 8.3 its activation by ATP was diminished or absent. E119D was activated by ATP in phosphate at pH 7 or in TP at pH 8.3, but not in TP at pH 7. In TP at pH 7, where neither mutant was activated by ATP, the S values and Hill coefficients of the unliganded mutant enzymes resembled those of the ATP-liganded wild-type enzyme. While neither mutation would be predicted to alter the net charge of the holoenzyme, differences in the isoelectric point of the mutants were observed if phosphate was present. This result suggests that the isoelectric point of aspartate transcarbamoylase is conformationally dependent and that the mutants exist in an altered conformation. In addition, the stabilities of both mutant holoenzymes were reduced substantially from those of the wild-type enzyme in 4 M urea. C109H was more stable at pH 8.25 in a Tris buffer; E119D was more stable at pH 7 in the phosphate buffer. Potential effects of these mutations on the active site chemistry and geometry are discussed.
An artificial multi-channel model for generating abnormal electrocardiographic rhythms (2008)

We present generalizations of our previously published artificial models for generating multi-channel ECG so that the simulation of abnormal rhythms is possible. Using a three-dimensional vectorcardiogram (VCG) formulation, we generate the normal cardiac dipole for a patient using a sum of Gaussian kernels, fitted to real VCG recordings. Abnormal beats are then specified either as new dipoles, or as perturbations of the existing dipole. Switching between normal and abnormal beat types is achieved using a hidden Markov model (HMM). Probability transitions can be learned from real data or modeled by coupling to heart rate and sympathovagal balance. Natural morphology changes form beat-to-beat are incorporated as before from varying the angular frequency of the dipole as a function of the inter-beat (RR) interval. The RR interval time series is generated using our previously described model whereby time-and frequency-domain heart rate (HR) and heart rate variability (HRV) characteristics can be specified. QT-HR hysteresis is simulated by coupling the Gaussian kernels associated with the T-wave in the model with a nonlinear factor related to the local HR (determined from the last n RR intervals). Morphology changes due to respiration are simulated by coupling the RR interval to the angular frequency of the dipole. We demonstrate an example of the use of this model by simulating T-Wave Alternans (TWA). The magnitude of the TWA effect is modeled as a disturbance on the T-loop of the dipole with a magnitude that differs in each of the three VCG planes. The effect is then turned on or off using a HMM. The values of the transition matrix are determined by the local heart rate, such that when the HR ramps up towards 100 BPM, the probability of observing a TWA effect rapidly but smoothly increases. In this way, no 'sudden' switching from non-TWA to TWA is observed, and the natural tendency for TWA to be associated with a critical HR-related activation level is simulated. Finally, to generate multi-lead signals, the VCG is mapped to any set of clinical leads using a Dower-like transform derived from a least-squares optimization between known VCGs and known lead morphologies. ECGs with calibrated amounts of TWA were generated by this model and included in the PhysioNet/CinC Challenge 2008 data set.
Architectures of archaeal GINS complexes, essential DNA replication initiation factors (2011)

The DNA metabolizing proteins from archaea are similar to those from eukaryotes, and the archaeal multi-subunit complexes are occasionally simplified versions of the eukaryotic ones. The overall similarity in the architectures between the archaeal and eukaryotic GINS complexes suggests that the GINS function, directed through interactions with other protein components, is basically conserved. On the other hand, the different subunit contacts, including the locations and contributions of the C-terminal domains to the tetramer formation, imply the possibility that the archaeal and eukaryotic GINS complexes contribute to DNA unwinding reactions by significantly different mechanisms in terms of the atomic details.
ChemInform Abstract: HOMOLYTIC SUBSTITUTION AND CARBENOIDIC REACTIONS IN THE PREPARATION OF BENZIMIDAZOLE DERIVATIVES OF PHARMACEUTICAL INTEREST: SYNTHESIS AND PROPERTIES OF (2‐CYCLOALKYL‐1‐BENZIMIDAZOLYL)‐N,N‐DIETHYLACETAMIDES (1985)

Abstract Benzimidazol (I) wird mit verschiedenen Cycloalkylcarbonsäuren (II) radikalisch zu (III) alkyliert.