gebhart/patrepeval huggingface dataset:
Protein–protein interaction network of the marine microalga Tetraselmis subcordiformis: prediction and application for starch metabolism analysis (2014)

Under stressful conditions, the non-model marine microalga Tetraselmis subcordiformis can accumulate a substantial amount of starch, making it a potential feedstock for the production of fuel ethanol. Investigating the interactions of the enzymes and the regulatory factors involved in starch metabolism will provide potential genetic manipulation targets for optimising the starch productivity of T. subcordiformis. For this reason, the proteome of T. subcordiformis was utilised to predict the first protein-protein interaction (PPI) network for this marine alga based on orthologous interactions, mainly from the general PPI repositories. Different methods were introduced to evaluate the credibility of the predicted interactome, including the confidence value of each PPI pair and Pfam-based and subcellular location-based enrichment analysis. Functional subnetworks analysis suggested that the two enzymes involved in starch metabolism, starch phosphorylase and trehalose-phosphate synthase may be the potential ideal genetic engineering targets.
Sustainable Oxygen: A low power approach for providing emergency medical oxygen for spacecraft and hospitals in developing countries (2011)

An oxygen concentrator targeting an 80% reduction in power demand over commercial systems is being developed using a pressure swing adsorption process. This system is targeted for a service interval five times longer than commercial systems, and is tolerant to high humidity environments- the leading cause of device failure in developing countries. This system could provide emergency medical oxygen in a spacecraft without increasing oxygen concentration in the vehicle. Flight surgeons seek this capability, but presently, there is no system that meets power, size, and delivery rate requirements. This type of system is also well suited for medical oxygen in hospitals in developing countries. Pneumonia accounts for 5% of all childhood deaths in Africa, and a lack of medical oxygen contributes to mortality rates. This new approach involves a high flow - low power - low purity device. The process proposes a regenerative blower instead of a piston compressor, a humidity tolerant sorbent, and a non-traditional separation cycle.
Antinociceptive properties of chalcones. Structure-activity relationships (2001)

Eleven chalcones were prepared and tested as antinociceptive agents using the writhing test in mice. Some compounds, given intraperitoneally, caused potent and dose-related antinociception, being several times more active than some reference drugs. The results evidenced that some physico-chemical parameters are involved in the pharmacological activity. 3,4-Dichlorochalcone (2) was the most effective compound, and was also studied in another model of pain in mice, the formalin test. Here it inhibited only the inflammatory pain (second phase), being equipotent to the reference drugs.
TCAD investigation of zero-cost high voltage transistor architectures for logic memory circuits (2019)

In this paper, a new device architecture has been studied by TCAD process simulations in order to provide the improvements on the electrical characteristics. We focus mainly on the drain-bulk junction breakdown voltage, of a double 130 nm poly gate transistor for Non-Volatile Memory technology. It is used as a word line select transistor, handling the drain voltage up to 13 V. The proposed structure has been implemented on silicon and the electrical measurements demonstrate the good predictability given by simulations. Finally, a new zero-cost added process asymmetric architecture is also studied to propose further improvements in terms of footprint or electrical characteristics.
Design of a palette of SNAP-tag mimics of fluorescent proteins and their use as cell reporters (2023)

Naturally occurring fluorescent proteins (FPs) are the most widely used tools for tracking cellular proteins and sensing cellular events. Here, we chemically evolved the self-labeling SNAP-tag into a palette of SNAP-tag mimics of fluorescent proteins (SmFPs) that possess bright, rapidly inducible fluorescence ranging from cyan to infrared. SmFPs are integral chemical-genetic entities based on the same fluorogenic principle as FPs, i.e., induction of fluorescence of non-emitting molecular rotors by conformational locking. We demonstrate the usefulness of these SmFPs in real-time tracking of protein expression, degradation, binding interactions, trafficking, and assembly, and show that these optimally designed SmFPs outperform FPs like GFP in many important ways. We further show that the fluorescence of circularly permuted SmFPs is sensitive to the conformational changes of their fusion partners, and that these fusion partners can be used for the development of single SmFP-based genetically encoded calcium sensors for live cell imaging.
Analysis and Design of Submilliwatt Interference-Tolerant Receivers Leveraging N-Path Filter-Based Translational Positive Feedback (2021)

A low-power 2.2-2.4-GHz receiver front end for Internet-of-Things (IoT) applications is presented. The front end consists of a capacitively cross-coupled common-gate low-noise amplifier (CC-CGLNA), with translational positive feedback from baseband to RF through a four-phase switching mixer, providing RF filtering and matching, in conjunction with a 1:4 transformer. A detailed analysis of the architecture is presented, highlighting the design tradeoffs between noise, out-of-band filtering, and power. A prototype integrated circuit, fabricated in 28-nm CMOS, consumes 580 μW of power for the entire receiver front end. With this submilliwatt power consumption, it achieves a noise figure (NF) of 11.9 dB, an in-band IIP3 of -6.5 dBm, and an out-of-band IIP3 of +3.3 dBm.
Flame resistance of geopolymer foam coatings for the fire protection of steel (2021)

This research investigates the fire resistance of novel geopolymer (GP) foams, based on alkali-activated metakaolin and silica fume (SF). Fresh GP foams are applied as coatings on steel plates. After one week curing, the foams are subjected to a flame burn-through test. Changes in their physico-chemical properties are characterized before and after fire test, mainly with XRD , quantitative MAS NMR, electron probe micro-analysis, quantitative X ray micro-computed tomography and heat conductivity . Results show that GP foams are excellent thermal barriers, providing up to 251 °C less than for uncoated steel plate. Their porosity ranges between 25 and 81%, for typical pore sizes d 50 from 0.5 to 3.0 mm 29 Si MAS NMR shows that the proportion of GP cement only decreases from 60-68% to 53–58% after fire. SF expands and creates small pores in the coating, which is favorable to decrease heat conductivity by a factor of 2 whatever the foam. • Novel GP foams based on MK + SF are formulated and characterized for fire resistance. • H 2 O 2 and CTABr foam stabilizing agent provide a controlled porosity of 81%. • GP foams provide superior fire protection to steel in a burn-through scenario. • The amount of GP cement only decreases from 60-68% to 53–58% after fire test. • Due to SF expansion, heat conductivity of foams is reduced by a factor of 2.
First Measurements of Ionisation Clusters on the DNA Scale in a Wall-less Sensitive Volume (1999)

Journal Article First Measurements of Ionisation Clusters on the DNA Scale in a Wall-less Sensitive Volume Get access S. Shchemelinin, S. Shchemelinin Search for other works by this author on: Oxford Academic PubMed Google Scholar A. Breskin, A. Breskin Search for other works by this author on: Oxford Academic PubMed Google Scholar R. Chechik, R. Chechik Search for other works by this author on: Oxford Academic PubMed Google Scholar P. Colautti, P. Colautti Search for other works by this author on: Oxford Academic PubMed Google Scholar R.W.M. Schulte R.W.M. Schulte Search for other works by this author on: Oxford Academic PubMed Google Scholar Radiation Protection Dosimetry, Volume 82, Issue 1, 1 March 1999, Pages 43–50, https://doi.org/10.1093/oxfordjournals.rpd.a032605 Published: 01 March 1999
ChemInform Abstract: Chiral Diamines in Asymmetric Synthesis (1995)

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.
Phenyl‐Glutarimides: Alternative Cereblon Binders for the Design of PROTACs (2021)

Targeting cereblon (CRBN) is currently one of the most frequently reported proteolysis-targeting chimera (PROTAC) approaches, owing to favorable drug-like properties of CRBN ligands, immunomodulatory imide drugs (IMiDs). However, IMiDs are known to be inherently unstable, readily undergoing hydrolysis in body fluids. Here we show that IMiDs and IMiD-based PROTACs rapidly hydrolyze in commonly utilized cell media, which significantly affects their cell efficacy. We designed novel CRBN binders, phenyl glutarimide (PG) analogues, and showed that they retained affinity for CRBN with high ligand efficiency (LE >0.48) and displayed improved chemical stability. Our efforts led to the discovery of PG PROTAC 4 c (SJ995973), a uniquely potent degrader of bromodomain and extra-terminal (BET) proteins that inhibited the viability of human acute myeloid leukemia MV4-11 cells at low picomolar concentrations (IC<sub>50</sub> =3 pM; BRD4 DC<sub>50</sub> =0.87 nM). These findings strongly support the utility of PG derivatives in the design of CRBN-directed PROTACs.
Ki-67 Expression in a Cervical Cancer Organotypic Model Correlates with Growth and EGF-R Expression (1999)

Objective The study objective was to measure the effects of retinoid treatment on Ki-67 expression in a cervical carcinoma organotypic culture model and to determine whether a correlation exists between retinoid effects on Ki-67 expression and effects on growth and epidermal growth factor receptor (EGF-R) expression. Methods Organotypic cultures of the cervical carcinoma cell line were treated for 7 days with all-trans retinoic acid, 9-cis retinoic acid, or control solvent. Cultures were fixed and embedded in paraffin, and sections were stained with Ki-67 antibodies. Ki-67 expression was determined by light microscopy. Results Ki-67 expression was inhibited 25% in the organotypic culture treated with 9-cis retinoic acid and 32% in the culture treated with all-frans retinoic acid. Previous data demonstrated a 45% and 44% inhibition of EGF-R expression and a 49% and 63% inhibition of growth, respectively. Discussion The inhibition of Ki-67 expression by retinoids correlates with inhibition of EGF-R expression and growth as determined by a Pearson correlation (R = 0.88). Inhibition of Ki-67 and EGF-R demonstrates quantifiable effects of retinoids at both the membrane receptor and nuclear protein levels in our organotypic culture model.
QUASI-OPTICAL MILLIMETER WAVE SOLID-STATE OSCILLATORS. PART 2: HIGH-STABLE OSCILLATORS AND APPLICATION (2019)

The results of the study and development of quasi-optical solid-state oscillators are: the level of frequency noise is not more than 115...120 dB/Hz; power of generation at the first harmonic is up to 130...150 mW at a frequency of 40-50 GHz; at the second harmonic – up to 10 mW at a frequency of 60...90 GHz; generation power is not less than 3 mW at a frequency of 150 GHz; long-term frequency instability is 3·10–8 at active temperature control ΔT ~ 0.1 °C. The paper analyzes the areas of application of solid-state quasi-optical oscillators: heterodynes in receiving devices, refractometry, dielectrometry and other fields where high stability and low level of frequency noise are needed. The perspective directions of the search for new physical phenomena to create nonlinear elements in the terahertz frequency range are determined.
Frequent emergence and limited geographic dispersal of methicillin-resistant Staphylococcus aureus (2008)

A small number of clonal lineages dominates the global population structure of methicillin-resistant Staphylococcus aureus (MRSA), resulting in the concept that MRSA has emerged on a few occasions after penicillinase-stable beta-lactam antibiotics were introduced to clinical practice, followed by intercontinental spread of individual clones. We investigated the evolutionary history of an MRSA clone (ST5) by mutation discovery at 108 loci (46 kb) within a global collection of 135 isolates. The SNPs that were ascertained define a radial phylogenetic structure within ST5 consisting of at least 5 chains of mutational steps that define geographically associated clades. These clades are not concordant with previously described groupings based on staphylococcal protein A gene (spa) typing. By mapping the number of independent imports of the staphylococcal cassette chromosome methicillin-resistance island, we also show that import has occurred on at least 23 occasions within this single sequence type and that the progeny of such recombinant strains usually are distributed locally rather than globally. These results provide strong evidence that geographical spread of MRSA over long distances and across cultural borders is a rare event compared with the frequency with which the staphylococcal cassette chromosome island has been imported.
Oligomérisation fonctionnelle du norbornène : application à la synthèse de réseaux (1990)

La polymerisation metalla-carbenique (par reaction de metathese) du norbornene en presence de diesters insatures a permis d'obtenir des oligomeres du norbornene porteurs de fonctions ester aux extremites des chaines. Les diesters derives d'acides ethyleniques se sont averes les meilleurs agents de transfert et conduisent a des oligomeres de fonctionnalite proche de deux. Une etude cinetique du processus a ete realisee et a permis de proposer un mecanisme de la reaction. Ces oligomeres ont ete ensuite transformes en prepolymeres hydroxy-telecheliques lesquels peuvent etre utilises comme precurseurs de reseaux polyurethane. Les proprietes physico-chimiques et thermo-mecaniques de ces resequx ont ete evaluees
Platelet phospholipase D is activated by protein kinase C via an integrin αIIbβ3-independent mechanism (1995)

Blood platelets contain phospholipase D (PLD) that is rapidly activated following platelet stimulation. It is currently unclear, however, where PLD fits into the signalling cascade that leads to aggregation and secretion. Therefore we investigated the mechanism of activation of PLD in human platelets, using the formation of the PLD-specific product phosphatidylethanol as a measure of PLD activity. PLD was activated by a number of platelet agonists that also cause the activation of protein kinase C, including thrombin, collagen, the Ca2+ ionophore A23187 and the thromboxane A2-mimetic U46619. Phorbol 12-myristate 13-acetate (PMA), a direct activator of protein kinase C, also increased PLD activity. A selective inhibitor of protein kinase C, Ro-31-8220, totally blocked the stimulation of PLD by thrombin or PMA under conditions in which it also inhibited phosphorylation of pleckstrin, the major protein kinase C substrate in platelets. Ro-31-8220 additionally inhibited A23187-stimulated PLD activity, indicating that Ca2+ activation of PLD also occurs via a protein kinase C-dependent pathway. In the presence of the fibrinogen antagonist peptide RGDS, which inhibits fibrinogen binding to integrin alpha IIb beta 3 and allows little or no aggregation to occur, thrombin- and PMA-stimulated PLD activity was still observed, indicating that PLD activation is not simply a consequence of platelet aggregation. Furthermore, these agonists were able to stimulate PLD in platelets from a Glanzmann's thrombasthenia type I patient lacking the integrin alpha IIb beta 3 complex, which indicates that activation of PLD is also independent of the recruitment of integrin alpha IIb beta 3. Taken together, our results show that PLD is activated by a pathway involving protein kinase C, and suggest that PLD might be involved in signal transduction events occurring upstream of integrin alpha IIb beta 3 activation and fibrinogen binding, which are prerequisites for full platelet aggregation.
Scalable pipeline insertion in floating-point division and square root units (2004)

Division and square root are important operations in a number of data processing algorithms. They are inherently time consuming operations and can require a significant amount of resources when implemented in hardware. This work reports the development of scalable, floating-point (FP) division and square root operators with adjustable precision, range, and pipeline granularity. An algorithm for pipeline insertion was used for both operators, enabling speeds up to 204MFLOPS when implemented on a Xilinx Virtex II FPGA.
Nanoscience meets geochemistry: Size-dependent reactivity of hematite (2005)

Recent studies have demonstrated that nanoscale crystalline iron oxide minerals are common in natural systems. The discipline of nanoscience suggests that these particles in the size range of approximately 1-50 nm will have properties that deviate from the bulk properties of the same material and that these properties will change as a function of particle size. This study begins to fill the void of corresponding experimental investigations that apply the principles of nanoscience to the geochemical reactivity of nanominerals. The rate of Mn²⁺(aq) oxidation on hematite with average diameters of 7.3 nm and 37 nm was measured in the presence of O₂(aq). In the pH range of 7-8, the surface area normalized rate was one to two orders of magnitude greater on the 7.3 nm average diameter particles. Based on the application of electron transfer theory, it is hypothesized that the particles with diameters less than approximately 10 nm have surface crystal chemical environments which distort the symmetry of the MnMn²⁺ surface complex, reducing the energy required to reorganize the coordinated ligands after oxidation to Mn³⁺. Cu²⁺, an analog for Mn³⁺, was used to probe for the presence and nature of the proposed changes in surface structure. Cu²⁺ and Mn³⁺ show similar electronic structure changes in response to the surrounding crystal field due to their d-electron configurations and Jahn-Teller coordinative distortions. Batch sorption experiments on hematite nanoparticles revealed a shift in the pH-dependent adsorption of Cu²⁺(aq). Specifically, an affinity sequence of 7 nm > 25 nm = 88 nm was determined based on the shift of the 7 nm sorption edge to approximately 0.8 pH units lower than that for the 25 nm and 88 nm samples. These data support the hypothesis that unique binding sites exist on the 7 nm nanoparticles that are not significantly present on the larger particles. The National Nanotechnology Initiative stresses the need to address the broader societal impacts of nanoscale research. This dissertation embraces this viewpoint through the development and inclusion of "Nano2Earth: Introducing Nanotechnology Through Investigations of Groundwater," a curriculum which combines nanoscience with the Earth sciences for high school students.
Effect of Low-Dose Paclitaxel and Docetaxel on Endothelial Progenitor Cells (2009)

Docetaxel and paclitaxel directly inhibited EPC-initiated vasculogenesis at low (non-cytotoxic) concentrations, causing suppression of tumor growth.
Surface patterning: Tool to modulate stem cell differentiation in an adipose system (2007)

There are several issues that need to be better understood before breast tissue-engineering becomes viable clinically. One of the key issues is the interaction between cells and the microtopography of the implant surface. The aim of this study was to evaluate the efficacy of D1 cells, multipotent mouse bone marrow stromal precursors, in differentiating to fat and to characterize their metabolic activity (lactic acid released and glucose consumed) and lipid production when cultured on patterned poly-L-lactide (PLLA) films. It was determined that, with appropriate stimulation, the D1 cells displayed morphological characteristics of adipocytes and produced lipid. The results show that the patterned surfaces did affect the rate of lipid production. Polynomial models were proposed to predict the metabolic activity of the cells over a period of time.
Rare event asymptotics for exploration processes for random graphs (2019)

Much work in the study of large deviations for random graph models is focused on the dense regime where the theory of graphons has emerged as a principal tool. These tools do not give a good approach to large deviation problems for random graph models in the sparse regime. The aim of this paper is to study an approach for large deviation problems in this regime by establishing Large Deviation Principles (LDP) on suitable path spaces for certain exploration processes of the associated random graph sequence. Our work focuses on the study of one particular class of random graph models, namely the configuration model; however the general approach of using exploration processes for studying large deviation properties of sparse random graph models has broader applicability. The goal is to study asymptotics of probabilities of non-typical behavior in the large network limit. The first key step for this is to establish a LDP for an exploration process associated with the configuration model. A suitable exploration process here turns out to be an infinite dimensional Markov process with transition probability rates that diminish to zero in certain parts of the state space. Large deviation properties of such Markovian models is challenging due to poor regularity behavior of the associated local rate functions. Next, using the rate function in the LDP for the exploration process we formulate a calculus of variations problem associated with the asymptotics of component degree distributions. The second key ingredient in our study is a careful analysis of the infinite dimensional Euler-Lagrange equations associated with this calculus of variations problem. Exact solutions are identified which then provide explicit formulas for decay rates of probabilities of non-typical component degree distributions and related quantities. Please see the paper for the complete abstract.
The buffer-gas cell and the extraction RFQ for SHIPTRAP (2004)

SHIPTRAP is a new ion trap system for high-precision mass measurements of transuranium recoil-ions from the SHIP facility at GSI. The system consists of a buffer-gas cell to thermalise the incoming ions, an extraction system to separate the ions from the buffer gas, an RFQ buncher to cool and accumulate the ions and a tandem Penning-trap system for isobaric purification and high-precision mass measurements. The buffer-gas cell and the extraction RFQ were developed, assembled and tested within this thesis at the MLL in Garching and at the GSI.
ChemInform Abstract: The Synthesis of 6‐Amino‐5‐oxo‐7‐phenyl‐1,4‐oxazepines as Conformationally Constrained Gauche (‐)‐Dipeptide Mimetics. (1993)

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.