gebhart/patrepeval huggingface dataset:
ChemInform Abstract: Synthesis of Dimer Phosphoramidite Synthons for Oligodeoxyribonucleotide Phosphorothioates Using Diethyldithiocarbonate Disulfide as an Efficient Sulfurizing Reagent. (1999)

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.
Design and performance evaluation of a coarse/fine precision motion control system (2005)

This abstract presents current collaborative work on the development of a stage system for accurate nanometer level positioning for scanning specimens spanning an area of 50 mm x 50 mm. The completed system employs a coarse/fine approach which comprises a short-range, six degree-of-freedom fine-motion platform (5 microns 200 micro-radians) carried by a long-range, two-axis X-Y coarse positioning system. Relative motion of the stage to a fixed metrology frame will be measured using a heterodyne laser in an eight-pass interferometer configuration. The final stage system will be housed in a vacuum environment and operated in a temperature-controlled laboratory. Results from a simple single coarse/fine axis system will be the design basis for the final multi-axis system. It is expected that initial stage performance evaluation will be presented at the conference.
Data from Adiponectin Receptor Signaling on Dendritic Cells Blunts Antitumor Immunity (2023)

&lt;div&gt;Abstract&lt;p&gt;Immune escape is a fundamental trait of cancer. Dendritic cells (DC) that interact with T cells represent a crucial site for the development of tolerance to tumor antigens, but there remains incomplete knowledge about how DC-tolerizing signals evolve during tumorigenesis. In this study, we show that DCs isolated from patients with metastatic or locally advanced breast cancer express high levels of the adiponectin receptors AdipoR1 and AdipoR2, which are sufficient to blunt antitumor immunity. Mechanistic investigations of ligand–receptor interactions on DCs revealed novel signaling pathways for each receptor. AdipoR1 stimulated IL10 production by activating the AMPK and MAPKp38 pathways, whereas AdipoR2 modified inflammatory processes by activating the COX-2 and PPARγ pathways. Stimulation of these pathways was sufficient to block activation of NF-κB in DC, thereby attenuating their ability to stimulate antigen-specific T-cell responses. Together, our findings reveal novel insights into how DC-tolerizing signals evolve in cancer to promote immune escape. Furthermore, by defining a critical role for adiponectin signaling in this process, our work suggests new and broadly applicable strategies for immunometabolic therapy in patients with cancer. &lt;i&gt;Cancer Res; 74(20); 5711–22. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Nucleic Acid-Modified Nanostructures as Programmable Atom Equivalents: Forging a New “Table of Elements”* (2020)

Despite the rapid progress in the area of nucleic acid functionalized nanoparticle assembly, especially since 2008, several challenges remain as the focus of ongoing efforts. An additional challenge beyond simply synthesizing the nanoparticle building blocks is to functionalize them with nucleic acids without altering their structure or desired physical properties. The first type of nucleic acid functionalized nanostructure that was developed by our group utilized a spherical gold nanoparticle core as a scaffold for the covalent attachment of single-stranded oligonucleotides in a densely functionalized and highly oriented manner. Initial assemblies made from spherical nucleic acid–gold nanoparticle programmable atom equivalents were synthesized by combining sets of complementary conjugates in solution the melting temperature of the nucleic acid duplexes. By using nucleic acid functionalized nanostructures however, one can recreate the diversity observed in atomic lattices, but also surpass the limitations in programmability and predictability inherent in atomic systems.
Segmental Dynamics and Dielectric Constant of Polysiloxane Polar Copolymers as Plasticizers for Polymer Electrolytes (2016)

Dielectric relaxation spectroscopy was used to investigate the segmental dynamics of a series of siloxane-based polar copolymers combining pendant cyclic carbonates and short poly(ethylene oxide) (PEO) chains. The homopolymer with cyclic carbonate as the only side chain exhibits higher glass transition temperature T(g) and dielectric constant ε(s) than the one with only PEO side chains. For their copolymers the observed T(g) (agreeing well with the predicted values from the Fox equation) and ε(s) decrease with increasing PEO side chain content. These polar polymers exhibit a glassy β relaxation with Arrhenius character, attributed to local chain motions of side groups attached to the main chain, and a segmental α relaxation, associated with the glass transition with a Vogel temperature dependence. As PEO side chain content increases, narrowing of the local glassy β relaxation was observed in the copolymers. The segmental α dynamics were observed to be faster, with an increase in breadth and decrease in strength with increasing PEO side chain content. Owing to the trade-off between T(g) and ε(s), copolymers of intermediate composition result in the highest ionic conductivity when these copolymers are used to plasticize Li single-ion conducting ionomers.
Radiation therapy induces the DNA damage response in peripheral blood (2013)

Stereotactic body radiation therapy (SBRT) is a radiotherapy modality that delivers highly conformal, ablative doses to a well-defined target. Here, using a semiquantitative multiplexed assay to analyze ATM and H2AX phosphorylation, we show that ATM kinase activity in peripheral blood mononuclear cells is induced following SBRT. This observation of a systemic ATM kinase-dependent DNA damage response in the peripheral blood is unprecedented and promotes the use of ATM serine-1981 phosphorylation as a predictive biomarker for DNA damaging modalities and ATM inhibitors.
Biotin dependency due to a defect in biotin transport (2002)

We describe a 3-year-old boy with biotin dependency not caused by biotinidase, holocarboxylase synthetase, or nutritional biotin deficiency. We sought to define the mechanism of his biotin dependency. The child became acutely encephalopathic at age 18 months. Urinary organic acids indicated deficiency of several biotin-dependent carboxylases. Symptoms improved rapidly following biotin supplementation. Serum biotinidase activity and Biotinidase gene sequence were normal. Activities of biotin-dependent carboxylases in PBMCs and cultured skin fibroblasts were normal, excluding biotin holocarboxylase synthetase deficiency. Despite extracellular biotin sufficiency, biotin withdrawal caused recurrent abnormal organic aciduria, indicating intracellular biotin deficiency. Biotin uptake rates into fresh PBMCs from the child and into his PBMCs transformed with Epstein Barr virus were about 10% of normal fresh and transformed control cells, respectively. For fresh and transformed PBMCs from his parents, biotin uptake rates were consistent with heterozygosity for an autosomal recessive genetic defect. Increased biotin breakdown was ruled out, as were artifacts of biotin supplementation and generalized defects in membrane permeability for biotin. These results provide evidence for a novel genetic defect in biotin transport. This child is the first known with this defect, which should now be included in the identified causes of biotin dependency.
A fast routability-driven router for FPGAs (1998)

Three factors are driving the demand for rapid FPGA compilation. First, as FPGAs have grown in logic capacity, the compile computation has grown more quickly than the compute power of the available computers. Second, there exists a subset of users who are willing to pay for very high speed compile with a decrease in quality of result, and accordingly being required to use a larger FPGA or use more real-estate on a given FPGA than is otherwise necessary. Third, very high speed compile has been a long-standing desire of those using FPGA-based custom computing machines, as they want compile times at least closer to those of regular computers.This paper focuses on the routing phase of the compile process, and in particular on routability-driven routing (as opposed to timing-driven routing). We present a routing algorithm and routing tool that has three unique capabilities relating to very high-speed compile: For a “low stress” routing problem (which we define as the case where the track supply is at least 10% greater than the minimun number of tracks per channel actually needed to route a circuit) the routing time is very fast. For example, the routing phase (after the netlist is parsed and the routing graph is constructed) for a 20,000 LUT/FF pair circuit with 30% extra tracks is only 23 seconds on a 300 MHz Sparcstation.For low-stress routing problems the routing time is near-linear in the size of the circuit, and the linearity constant is very small: 1.1 ms per LUT/FF pair, or roughly 55,000 LUT/FF pairs per minute.For more difficult routing problems (where the track supply is close to the minimum needed) we provide a method that quickly identifies and subdivides this class into two sub-classes: (i) those circuits which are difficult (but possible) to route and will take significantly more time than low-stress problems, and (ii) those circuits which are impossible to route. In the first case the user can choose to continue or reduce the amount of logic; in the second case the user is forced to reduce the amount of logic or obtain a larger FPGA.
Micromechanics of ultra-toughened electrospun PMMA/PEO fibres as revealed by in-situ tensile testing in an electron microscope (2014)

A missing cornerstone in the development of tough micro/nano fibre systems is an understanding of the fibre failure mechanisms, which stems from the limitation in observing the fracture of objects with dimensions one hundredth of the width of a hair strand. Tensile testing in the electron microscope is herein adopted to reveal the fracture behaviour of a novel type of toughened electrospun poly(methyl methacrylate)/poly(ethylene oxide) fibre mats for biomedical applications. These fibres showed a toughness more than two orders of magnitude greater than that of pristine PMMA fibres. The in-situ microscopy revealed that the toughness were not only dependent on the initial molecular alignment after spinning, but also on the polymer formulation that could promote further molecular orientation during the formation of micro/nano-necking. The true fibre strength was greater than 150 MPa, which was considerably higher than that of the unmodified PMMA (17 MPa). This necking phenomenon was prohibited by high aspect ratio cellulose nanocrystal fillers in the ultra-tough fibres, leading to a decrease in toughness by more than one order of magnitude. The reported necking mechanism may have broad implications also within more traditional melt-spinning research.
HEVC ALF decode complexity analysis and reduction (2011)

This paper analyzes the decoder implementation complexity of a new tool called Adaptive Loop Filtering (ALF) being considered for the ITU-T/ISO/IEC High Efficiency Video Coding (HEVC) standard, and proposes new luma filters (Nx7 and Nx5) for ALF that reduce memory bandwidth, memory size requirements, and number of computations. The luma filters in ALF of the initial version HEVC Test Model (HM-1.0) have a maximum vertical size of 9. The vertical size of the ALF filters determines the memory size (line buffers) and memory bandwidth requirements. Accordingly, this paper proposes reducing the vertical size of ALF filters to 7 and 5, which are referred to as Nx7 and Nx5 filter sets respectively. These filters reduce memory bandwidth and size requirements by 25% and 50% respectively with minimal impact on coding efficiency. In addition, the worst case computational complexity is reduced by -10% and -20% respectively. Reduced vertical size luma ALF filters are under consideration for inclusion in HEVC standard with Nx7 being been adopted into HM- 2.0 and Nx5 being under consideration for HM-4.0.
Interactive contribution of NK1 and kinin receptors to the acute inflammatory oedema observed in response to noxious heat stimulation: studies in NK1 receptor knockout mice (2001)

1. Scald injury in Sv129+C57BL/6 mice induced a temperature and time dependent oedema formation as calculated by the extravascular accumulation of [(125)I]-albumin. Oedema formation was suppressed in NK(1) knockout mice compared to wildtypes at 10 (P<0.01) and 30 min (P<0.001). However, at 60 min a similar degree of extravasation was observed in the two groups. 2. Kinin B(1) (des-Arg(10) Hoe 140; 1 micromol kg(-1)) and B(2) (Hoe 140; 100 nmol kg(-1)) antagonists caused an inhibition of oedema in wildtype mice at 10 and 30 min (P<0.001), but not at 60 min or at 30 min in NK(1) receptor knockout mice. 3. The inhibition of thermic oedema by des-Arg(10) Hoe 140 was reversed by des-Arg(9) bradykinin (0.1 micromol kg(-1); P<0.01) and also observed with a second B(1) receptor antagonist (des-Arg(9) Leu(8) bradykinin; 3 micromol kg(-1); P<0.01). Furthermore des-Arg(10) Hoe 140 had no effect on capsaicin (200 microg ear(-1)) ear oedema, but this was significantly reduced with Hoe 140 (P<0.05). 4. Scalding induced a large neutrophil accumulation at 4 h, as assessed by myeloperoxidase assay (P<0.001). This was not suppressed by NK(1) receptor deletion or kinin antagonists. 5. These results confirm an essential role for the NK(1) receptor in mediating the early, but not the delayed phase of oedema formation or neutrophil accumulation in response to scalding. The results also demonstrate a pivotal link between the kinins and sensory nerves in the microvascular response to burn injury, and for the first time show a rapid involvement of the B(1) receptor in murine skin.
Structural Determinants of Binding the Seven-transmembrane Domain of the Glucagon-like Peptide-1 Receptor (GLP-1R) (2016)

The glucagon-like peptide-1 receptor (GLP-1R) belongs to the secretin-like (class B) family of G protein-coupled receptors. Members of the class B family are distinguished by their large extracellular domain, which works cooperatively with the canonical seven-transmembrane (7TM) helical domain to signal in response to binding of various peptide hormones. We have combined structure-based site-specific mutational studies with molecular dynamics simulations of a full-length model of GLP-1R bound to multiple peptide ligand variants. Despite the high sequence similarity between GLP-1R and its closest structural homologue, the glucagon receptor (GCGR), nearly half of the 62 stably expressed mutants affected GLP-1R in a different manner than the corresponding mutants in GCGR. The molecular dynamics simulations of wild-type and mutant GLP-1R·ligand complexes provided molecular insights into GLP-1R-specific recognition mechanisms for the N terminus of GLP-1 by residues in the 7TM pocket and explained how glucagon-mimicking GLP-1 mutants restored binding affinity for (GCGR-mimicking) GLP-1R mutants. Structural analysis of the simulations suggested that peptide ligand binding mode variations in the 7TM binding pocket are facilitated by movement of the extracellular domain relative to the 7TM bundle. These differences in binding modes may account for the pharmacological differences between GLP-1 peptide variants.
The Syndrome of Dehydration, Coma and Severe Hyperglycemia without Ketosis in Patients Convalescing from Burns (1965)

IN 1951 Evans and Butterfield1 first reported a syndrome of glycosuria, dehydration, coma and severe hyperglycemia without ketosis occurring during the recovery phase of patients with major burns. Nine years later Arney, Pearson and Sutherland2 described 2 more burned patients in whom an almost identical syndrome occurred. Bailey3 presented an additional case in 1960. In only 1 of these patients was there a history of diabetes, and in all survivors carbohydrate metabolism reverted to normal after the episode. To our knowledge, these reports represent the only adequately documented cases of this syndrome in the literature.We have had an opportunity . . .
A robust capillary liquid chromatography/tandem mass spectrometry method for quantitation of neuromodulatory endocannabinoids (2015)

The microscale method is a sensitive, economical and robust alternative to the larger scale LC/MS methods currently implemented for quantitation of AEA and 2-AG.
Angle-Sensorless Zero- and Low-Speed Control of Bearingless Machines (2016)

Bearingless machines are successfully used for a variety of applications that demand for low mechanical losses, low wear, and low contamination. These machines require exact knowledge of the radial and angular rotor position in order to ensure stable levitation. This information is obtained with different position sensors. Alternatively, a sensorless approach can be used to determine the rotor position. The omission of the angular sensors leads to a reduction in costs and an improvement in reliability and allows to explore new areas of applications for bearingless machines. However, few zero and low-speed sensorless angle estimators are published to this date. Therefore, a novel model-based estimator to determine the rotor angle at zero and at low speeds and, thus, to allow sensorless operation over the whole speed range of the bearingless permanent magnet synchronous machine is proposed in this paper. The observer utilizes the radial position measurements and a model of the bearing force generation to determine the error of the angular position estimation. The method is implemented on a bearingless machine prototype, and the functionality is shown by measurements.
Coxiella burnetii fails to stimulate human neutrophil superoxide anion production. (1990)

This study investigated the release of superoxide anion (O2-) as an indicator of the oxidative metabolism of human neutrophils during the phagocytosis of Phase I Coxiella burnetti. Human neutrophils were incubated for 1 hr at 37 degrees C with opsonized or unopsonized viable Phase I Coxiella burnetii (MOI was 100 : 1) and superoxide anion formation was measured by the reduction of ferricytochrome C. The data revealed that during its phagocytosis by human neutrophils, C. burnetii (opsonized or unopsonized) fails to stimulate superoxide anion production. In contrast, the uptake of Staphylococcus aureus or zymosan was accompanied by the release of measurable O2-. This release of O2- was abrogated by the addition of 100 micrograms/ml of superoxide dismutase (SOD). These results suggest that the establishment of C. burnetii within neutrophils, as occurs during persistent infection, may be due to the failure to stimulate the metabolic burst during phagocytosis.
A broad-band power spectrum analyzer based on twin-channel delayed sampling (1998)

This paper describes a power spectrum analyzer whose bandwidth is not limited by the mean sampling time. The procedure is based on the estimation of the spectral components of the autocorrelation function of the input signal through the simultaneous random sampling of the given input signal and its randomly "delayed copy". The samples are therefore randomly taken in a double-dimension space, time, and delay. By using a random process in the time domain with a recursive mean previously introduced by the authors in order to avoid any bandwidth limitation due to the sampling strategy, it is shown both theoretically and through simulation that the estimate of the power spectral components is asymptotically unbiased on the unique hypothesis of a synchronized random sampling in the delay domain, i.e., the sampling delays are uniformly distributed in an interval equal to the period of the input signal. The simulation results confirm the theoretical findings.
Abstract 1190: Multifactorial biological processes govern engraftment of patient-derived tumor tissue in immunodeficient mice (2014)

Abstract TumorGrafts (also known as patient-derived xenografts) are a valuable tool for the personalization of oncology treatment, as well as development of new cancer therapeutics. Tumor explants are engrafted into immunodeficient mice and allowed to develop prior to screening against a panel of drugs or drug combinations to assess which best inhibit tumor growth. These models capture the chaotic heterogeneity, histopathology, and biology of the original tumor, as well its 3-dimensional interaction with the surrounding stroma and other cells migrating into the tumor environment. TumorGrafts will serve basic and clinical research groups as an increasingly valuable preclinical model of cancer. One important variable governing the generation of these models is the take rate, or the percentage of patient tumors that successfully engraft and grow in the mice. This is a potentially critical limitation to applying these preclinical models for improving patient treatment and advancing novel drug regimens to the clinic. Hence, there is a need to understand and exploit the mechanisms that influence take rate in order to ensure that the majority of tumor explants readily engraft and expand. We describe here our experience in optimizing the engraftment of patient tumor tissue in immunodeficient mice. We found a number of factors contribute to take rate including tumor type, tissue quantity and quality, engraftment site, oxygenation state, neovascularization and the presence of extracellular stromal components and cells. We have also uncovered a correlation between the growth rate of tumors in the mice and the clinical aggressiveness of the original malignancy, information that may be useful in guiding clinical management. Moreover, we describe how we are now able to consistently use biopsy material rather than surgical explants to establish TumorGrafts, a crucial step forward that allows this technology to benefit patients diagnosed with early-stage cancers or where surgery is not indicated. Although engraftment of patient tumor tissue in immunodeficient mice is a complex process, with multiple factors impacting success, we have effectively optimized this process, improving our take rate and at the same time, reducing the time to obtaining drug screening results, all without compromising tumor integrity. Citation Format: David M. Vasquez-Dunddel, Gilson Baia, Amanda Katz, Daniel Ciznadija, David Sidransky, Keren Paz. Multifactorial biological processes govern engraftment of patient-derived tumor tissue in immunodeficient mice. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1190. doi:10.1158/1538-7445.AM2014-1190
Targeting Protein–Protein Interactions Perspective (2020)

Protein-protein interactions (PPIs) encompass a diverse range of molecular interfaces of high importance in biology. PPIs are classified as either obligate or transitory, although these perhaps represent two extremes of the spectrum. In 2005, the Wang group reported the structure-based design of spirooxindole-containing small molecules as a new class of potent small-molecule inhibitors of the murine double minute 2-p53 interaction. Structure-based or fragment-based drug design approaches have been particularly successful for protein systems where there is a good structural understanding of the key elements for recognition, affinity, and selectivity. The evidence so far demonstrates that finding bromodomain (BD) inhibitors outside of the BET family is achievable, whether in silico predictions deem the BDs to be difficult, intermediate, or druggable. The catalytic activity of many enzymes is modulated by PPIs, providing opportunities for drug discovery. Many protein complexes are dynamic, and pharmacological modulation can be achieved not only by PPI inhibition but also through their stabilization.