gebhart/patrepeval huggingface dataset:
Advanced Aqueous-Phase Phosphoramidation Reactions for Effectively Synthesizing Peptide–Oligonucleotide Conjugates Trafficked into a Human Cell Line (2012)

Peptide-oligonucleotide conjugates (POCs) have held promise as effective therapeutic agents in treating microbial infections and human genetic diseases including cancers. In clinical applications, POCs are especially useful to circumvent cellular delivery and specificity problems of oligonucleotides. We previously reported that nucleic acid phosphoramidation reactions performed in aqueous solutions have the potential for facile POC synthesis. Here, we carried out further studies to significantly improve aqueous-phase two-step phosphoramidation reaction yield. Optimized reactions were employed to effectively synthesize POCs for delivery into human A549 cells. We achieved optimization of aqueous-phase two-step phosphoramidation reaction and improved reaction yield by (1) determining appropriate co-solutes and co-solute concentrations to acquire higher reaction yields, (2) exploring a different nucleophilicity of imidazole and its derivatives to stabilize essential nucleic acid phosphorimidazolide intermediates prior to POC formation, and (3) enhancing POC synthesis by increasing reactant nucleophilicity. The advanced two-step phosphoramidation reaction was exploited to effectively conjugate a well-studied cell penetrating peptide, the Tat(48-57) peptide, with oligonucleotides, bridged by either no linkers or a disulfide-containing linker, to have the corresponding POC yields of 47-75%. Phosphoramidation-synthesized POCs showed no cytotoxicity to human A549 cells at studied POC concentrations after 24 h inoculation and were successfully trafficked into the human A549 cell line as demonstrated by flow cytometry, fluorescent microscopy, and confocal laser scanning microscopy study. The current report provides insight into aqueous-phase phosphoramidation reactions, the knowledge of which was used to develop effective strategies for synthesizing POCs with crucial applications including therapeutic agents for medicine.
A variant OSR1 allele which disturbs OSR1 mRNA expression in renal progenitor cells is associated with reduction of newborn kidney size and function (2011)

Human nephrons are formed during fetal life through an interaction between the branching ureteric bud and progenitor cells. The wide variation in final nephron number has been attributed to allelic variants of genes regulating ureteric bud arborization. Here, we hypothesize that dysfunctional variants of the Odd-Skipped Related 1 (OSR1) gene which compromise the renal progenitor cell pool might also limit newborn kidney size and function. We show that OSR1 is expressed in human mesenchymal stem cells, the blastemal component of Wilms tumors and CD24+/CD133+ progenitor cells isolated from the mature kidney. We identified an OSR1(rs12329305(T)) allele in 6% of normal Caucasians which alters an exon2 splice enhancer. This variant is predicted to reduce spliceosome-binding affinity and stability of the OSR1 mRNA. In cultured cells, the OSR1(rs12329305)(T) allele produced no identifiable transcript. Normal Caucasian newborns from Montreal with the OSR1(rs12329305)(T) allele had kidney volume 11.8% smaller (P= 0.006) and cord blood cystatin C levels 12.6% higher (P = 0.005) than those with wild-type genotype. Effects of the OSR1(rs12329305)(T) allele are additive with genes that alter ureteric bud branching. Kidney volume was reduced more in newborns bearing both RET(rs1800860)(A) and OSR1(rs12329305)(T) alleles (22%, P= 0.0008) and cystatin C was increased by 17% (P= 0.006) versus newborns with wild-type alleles. Although only two subjects had PAX2(rs11599825)(A) and OSR1(rs12329305)(T) alleles, kidney size was reduced by 27% and cystatin C was increased by 14% versus wild-types (P= NS).
Identification of Enterostatin, the Pancreatic Procolipase Activation Peptide in the Intestine of Rat (1993)

Enterostatin, the procolipase activation peptide, has been suggested in previous studies to act as a satiety signal for food intake, with a specificity for fat intake. In this study, by use of a competitive enzyme-linked immunosorbent assay with a detection limit of 4.115 nmol/L and within 6% intra- and interassay variation, the immunoreactive and chromatographic characterization of enterostatin in intestinal content was undertaken in Sprague-Dawley rats. Following intravenous infusion of cholecystokinin octapeptide (CCK-8; 200 pmol/kg/h) for 60 min, the concentration of intestinal enterostatin increased from a basal level of 2.0 +/- 0.7 microM to 5.64 +/- 1.1 microM at time point 60 min. The enterostatin level remained at 4.24 +/- 0.54 microM for 120 min after the CCK infusion had ceased. Pancreatic lipase and colipase activities in rat intestinal content also increased during the CCK-8 infusion. The enzyme activities reached the maximal level after 30 min of CCK infusion and thereafter progressively decreased to basal levels, remaining there during the following 2 h. The basal level of intestinal enterostatin in rats fed with standard pellets was found to be increased from 1.42 +/- 0.14 to 3.86 +/- 0.4, 3.17 +/- 0.54, and 5.02 +/- 1.6 microM on days 1, 3, and 7, respectively, after high-fat feeding. Parallel to the increase in intestinal enterostatin, there was a significant increase in pancreatic lipase and colipase activities in the intestine during the ingestion period of high-fat diet as compared with the control group. The estimated molecular mass of enterostatin immunoreactivity of intestinal content was similar to that of the synthetic pentapeptide. These results suggest that immunoreactive enterostatin (Val-Pro-Gly-Pro-Arg) is normally present in rat intestinal content, is significantly increased after stimulation with CCK-8, and is also increased after prolonged high-fat feeding.
Learning Non-Stationary Dynamic Bayesian Networks (2010)

Learning dynamic Bayesian network structures provides a principled mechanism for identifying conditional dependencies in time-series data. An important assumption of traditional DBN structure learning is that the data are generated by a stationary process, an assumption that is not true in many important settings. In this paper, we introduce a new class of graphical model called a non-stationary dynamic Bayesian network, in which the conditional dependence structure of the underlying data-generation process is permitted to change over time. Non-stationary dynamic Bayesian networks represent a new framework for studying problems in which the structure of a network is evolving over time. Some examples of evolving networks are transcriptional regulatory networks during an organism's development, neural pathways during learning, and traffic patterns during the day. We define the non-stationary DBN model, present an MCMC sampling algorithm for learning the structure of the model from time-series data under different assumptions, and demonstrate the effectiveness of the algorithm on both simulated and biological data.
Holographic microantenna array metrology (2005)

We describe a holographic or phaseless technique for measurement of complex antenna patterns that is particularly suited to planar antennas at very high frequencies (mm-wave thru long-wave infrared) where phase coherent detection is impractical. It has been implemented in a compact automated antenna range, and validated on a previously reported planar slot-ring antenna at 95 GHz. In the IR, the interferometric technique must be refined in order to reduce to acceptable levels the uncertainties due to positioning and alignment errors. This measurement of the complex antenna pattern is the most problematic part of a full accounting for the optical coupling efficiency budget in a microantenna-coupled, imaging sensor array.
The Di-leucine Motif of Vesicle-associated Membrane Protein 4 Is Required for Its Localization and AP-1 Binding (2001)

Heterotetrameric adaptor complexes and SNAREs play key roles in the specificity of membrane budding and fusion. Here we test the hypothesis that vesicle budding and membrane fusion are coupled by the interaction of these molecules. We investigate the role of the di-leucine motif of vesicle-associated membrane protein 4 (VAMP4) in adaptor binding and localization of VAMP4. Mutation of the di-leucine motif inhibits AP-1 binding in vitro and affects the steady state distribution of VAMP4 in vivo.
Clinical studies of antisense therapy in cancer (2000)

The ability to target and inhibit individual gene expression with antisense oligonucleotides has shown promising activity in preclinical cancer models. Recent clinical studies have tested antisense compounds directed against seven cancer related genes including p53, bcl-2, c-raf, H-ras, protein kinase C-alpha, and protein kinase A. Class specific effects of the phosphorothioate backbone common to the first generation of antisense compounds have dominated the side effects of these oligonucleotides. Inhibition of target gene expression has been modest at most, and clinical activity has been primarily anecdotal. Combinations of the antisense compounds with chemotherapy and second-generation oligonucleotides offer promise that these agents might become a standard part of future cancer therapy.
RAPID DETECTION of <i>STAPHYLOCOCCUS AUREUS</i> IN FOOD BY FLOW CYTOMETRY (1992)

This report describes the detection of Staphylococcus aureus in buffer and in several kinds of food by flow cytometry. Fluorescein isothiocyanate conjugated anti‐protein A antibodies were used in a 4‐h procedure to label cells, 10 5 ‐10 6 cells/mL are needed. the use of single parameter, green fluorescence, enabled specific differentiation of S. aureus from other bacteria including 11 Staphylococcus species. the flow cytometric method can detect S. aureus in food samples after 48‐h enrichment in trypticase soy broth with 10% NaCl. As low as 2 S. aureus cells present in 10 mL enrichment broth could grow to a population density detectable by the flow cytometric method after enrichment. This method was faster and less laborious than the conventional BAM (Bacteriological Analytical Manual) or AOAC (Association of Official Analytical Chemists) methods, and could be automated for analysis of S. aureus in food.
Synthesis of psilocin labelled with <sup>14</sup>C and <sup>3</sup>H (1986)

Abstract 14 C‐ and 3 H‐Labelled psilocin (4‐hydroxy‐N,N‐dimethyl‐tryptamine), the principal, active agent of hallucinogenic mushrooms, was synthesized from 2‐methyl‐3‐nitrophenol via 4‐benzyloxyindole. 14 C‐Labelled potassium cyanide was reacted with 4‐benzyloxygramine (obtained from 4‐benzyloxyindole) to give 14 C‐4‐benzyloxy‐3‐indole acetic acid, an intermediate for 14 C‐psilocin synthesis. 3 H‐Labelled lithium aluminium hydride was used to react with 4‐benzyloxy‐3‐indole‐N,N‐dimethyl‐glyoxylamide (obtained from 4‐benzyloxyindole) to give 3 H‐4‐benzyloxy‐psilocin which was debenzylated to form 3 H‐psilocin.
OPC UA based Field Device Integration (2008)

Today the two technologies electronic device description language and field device tool exist for device integration. This paper describes a concept that integrates the advantages of both technologies into a single consistent concept. The new concept defines a model for device integration and a client-server architecture that makes use of the various advantages of OPC Unified Architecture. The authors validated the concept by setting up a comprehensive prototype including different field devices from process and factory automation. The positive results of the evaluation show that the described concept is a sustainable basis for device integration.
Transforming Growth Factor Beta-Releasing Scaffolds for Cartilage Tissue Engineering (2013)

The maintenance of a critical threshold concentration of transforming growth factor beta (TGF-β) for a given period of time is crucial for the onset and maintenance of chondrogenesis. Thus, the development of scaffolds that provide temporal and/or spatial control of TGF-β bioavailability has appeal as a mechanism to induce the chondrogenesis of stem cells in vitro and in vivo for articular cartilage repair. In the past decade, many types of scaffolds have been designed to advance this goal: hydrogels based on polysaccharides, hyaluronic acid, and alginate; protein-based hydrogels such as fibrin, gelatin, and collagens; biopolymeric gels and synthetic polymers; and solid and hybrid composite (hydrogel/solid) scaffolds. In this study, we review the progress in developing strategies to deliver TGF-β from scaffolds with the aim of enhancing chondrogenesis. In the future, such scaffolds could prove critical for tissue engineering cartilage, both in vitro and in vivo.
Managing routing tables for URL routers in content distribution networks (2004)

Abstract Large‐scale content distribution networks (CDNs) can be built using URL routers to redirect client HTTP requests to the nearest content source. URL routers employ very large routing tables. To improve the manageability of CDNs, we propose to use URL signatures to reduce the size of routing tables and aggressive hashing to speed‐up routing look‐ups. Copyright © 2004 John Wiley & Sons, Ltd.
[Low dose heparin for the prevention of hepatic veno-occlusive disease after allogeneic hematopoietic stem cell transplantation]. (2007)

It is suggested that low dose heparin alone is effective and safe for the prophylaxis of VOD following allo-HSCT conditioned with BU-CY regimen. Shortening the duration of administering heparin from -7 d to +21 d to -7 d to +14 d does not affect the effectiveness of low dose heparin to prevent VOD.
The Elephant in the Room of Density Functional Theory Calculations (2017)

Using multiwavelets, we have obtained total energies and corresponding atomization energies for the GGA-PBE and hybrid-PBE0 density functionals for a test set of 211 molecules with an unprecedented and guaranteed μHartree accuracy. These quasi-exact references allow us to quantify the accuracy of standard all-electron basis sets that are believed to be highly accurate for molecules, such as Gaussian-type orbitals (GTOs), all-electron numeric atom-centered orbitals (NAOs), and full-potential augmented plane wave (APW) methods. We show that NAOs are able to achieve the so-called chemical accuracy (1 kcal/mol) for the typical basis set sizes used in applications, for both total and atomization energies. For GTOs, a triple-ζ quality basis has mean errors of ∼10 kcal/mol in total energies, while chemical accuracy is almost reached for a quintuple-ζ basis. Due to systematic error cancellations, atomization energy errors are reduced by almost an order of magnitude, placing chemical accuracy within reach also for medium to large GTO bases, albeit with significant outliers. In order to check the accuracy of the computed densities, we have also investigated the dipole moments, where in general only the largest NAO and GTO bases are able to yield errors below 0.01 D. The observed errors are similar across the different functionals considered here.
Reduction of Naturally Occurring Motoneuron Death in Vivo by a Target-Derived Neurotrophic Factor (1988)

Treatment of chick embryos in ovo with crude and partially purified extracts from embryonic hindlimbs (days 8 to 9) during the normal cell death period (days 5 to 10) rescues a significant number of motoneurons from degeneration. The survival activity of partially purified extract was dose-dependent and developmentally regulated. The survival of sensory, sympathetic, parasympathetic, and a population of cholinergic sympathetic preganglionic neurons was unaffected by treatment with hindlimb extract. The massive motoneuron death that occurs after early target (hindlimb) removal was partially ameliorated by daily treatment with the hindlimb extract. These results indicate that a target-derived neurotrophic factor is involved in the regulation of motoneuron survival in vivo.
Similarity-based workflow clustering (2011)

Scientists have been using scientific workflow management systems (SWfMS) to support scientific experiments. However, SWfMS expect a modeled workflow to be represented on its workflow language to be executed. The scientist does not have an assistance or guidance to obtain a modeled workflow. Experiment lines, which are a novel approach to deal with these limitations, allow for the abstract representation and systematic composition of experiments. Since there are many scientific workflows already modeled and successfully executed, they can be used to leverage the construction of new abstract representations. These previous experiments can be helpful by identifying scientific workflow clusters that are generated according to similarity criteria. This paper proposes SimiFlow, which is an architecture for similarity-based comparison and clustering to build experiment lines following a bottom-up approach.
Arabidopsis florigen FT binds to diurnally oscillating phospholipids that accelerate flowering (2014)

Arabidopsis FT protein is a component of florigen, which transmits photoperiodic flowering signals from leaf companion cells to the shoot apex. Here, we show that FT specifically binds phosphatidylcholine (PC) in vitro. A transgenic approach to increase PC levels in vivo in the shoot meristem accelerates flowering whereas reduced PC levels delay flowering, demonstrating that PC levels are correlated with flowering time. The early flowering is related to FT activity, because expression of FT-effector genes is increased in these plants. Simultaneous increase of FT and PC in the shoot apical meristem further stimulates flowering, whereas a loss of FT function leads to an attenuation of the effect of increased PC. Specific molecular species of PC oscillate diurnally, and night-dominant species are not the preferred ligands of FT. Elevating night-dominant species during the day delays flowering. We suggest that FT binds to diurnally changing molecular species of PC to promote flowering. Daytime flowering in Arabidopsis is stimulated by the secreted protein FT. Nakamura et al. show that FT binds the lipid phosphatidylcholine (PC) in vitro, and that in plants, different PC species predominate during day and night, with daytime species stimulating flowering in a manner that is partially dependent on FT.
Inflammation, atherosclerosis, and cardiovascular risk: an epidemiologic view. (1999)

Based on laboratory and experimental evidence, it has been hypothesized that inflammation plays a fundamental role in atherogenesis and acute thrombosis. From an epidemiologic perspective, corroboration of this hypothesis has been provided by a series of prospective cohort studies which demonstrate that inflammatory parameters (such as fibrinogen, C reactive protein, and serum amyloid A), cellular adhesion molecules [such as intercellular adhesion molecule (ICAM)-1], and cytokines (such as interleukin-6) are all elevated at baseline among patients at risk for future coronary occlusion. Furthermore, data deriving from randomized clinical trials suggest that the efficacy of common preventive agents such as aspirin and hydroxy-methylglutaryl (HMG) CoA reductase inhibition may derive in part from interactions with the inflammatory system. Taken together, these data raise the possibility that therapies targeting chronic low-grade inflammation may provide novel future strategies for cardiovascular disease prevention.
Main memory and cache performance of intel sandy bridge and AMD bulldozer (2014)

Application performance on multicore processors is seldom constrained by the speed of floating point or integer units. Much more often, limitations are caused by the memory subsystem, particularly shared resources such as last level caches or memory controllers. Measuring, predicting and modeling memory performance becomes a steeper challenge with each new processor generation due to the growing complexity and core count. We tackle the important aspect of measuring and understanding undocumented memory performance numbers in order to create valuable insight into microprocessor details. For this, we build upon a set of sophisticated benchmarks that support latency and bandwidth measurements to arbitrary locations in the memory subsystem. These benchmarks are extended to support AVX instructions for bandwidth measurements and to integrate the coherence states (O)wned and (F)orward. We then use these benchmarks to perform an indepth analysis of current ccNUMA multiprocessor systems with Intel (Sandy Bridge-EP) and AMD (Bulldozer) processors. Using our benchmarks we present fundamental memory performance data and illustrate performance-relevant architectural properties of both designs.
Btk inhibitor ibrutinib reduces inflammatory myeloid cell responses in the lung during murine pneumococcal pneumonia (2019)

Taken together, these data indicate that the Btk inhibitor ibrutinib reduces inflammatory myeloid cell responses during acute pulmonary inflammation evoked by LTA and antibiotic-treated pneumococcal pneumonia and suggest that ibrutinib has the potential to inhibit ongoing lung inflammation in an acute infectious setting.
A GaAs 4 kbit SRAM with direct coupled FET logic (1984)

A GaAs 4-kb static RAM with enhancement/depletion direct coupled FET logic was designed and successfully fabricated by self-aligned implantation for n/SUP +/-layer technology (SAINT). The aim of the RAM circuit was to attain an access time of 2 ns with a power dissipation of less than 1 W. Statistical circuit simulation clarified the allowable scattering tolerance for FET threshold voltage of 45 mW. In-process monitoring was made wafer-to-wafer and chip-to-chip. A minimum address access time of 2.8 ns was measured with a power consumption of 1.2 W. Write and read operations were completely confirmed with a minimum write pulse width of 2 ns.
Rapid distributed data collection with arrays ? the next step beyond full waveform capture (2006)

Ultrasonic C-scanning is widely used for large-area flaw detection but acquiring the full RF waveform for each surface point - Full Waveform Capture (FWC) - offers many advantages. A system that used phased arrays to achieve this without loss of area coverage rate has been reported (1) . FWC allows many signal processing operations, previously only possible at acquisition, to be performed off-line. Multiple or time-consuming algorithms can be performed on the same data set without compromising inspection speed but some, such as steering and focusing, must still be performed at acquisition. Although ultrasonic arrays are now widely accepted in imaging systems, their full capability will only be realised when viewed as distributed data collection devices (2) . The modular array hardware of DSL's 'Flawlnspecta' can now achieve this at real-time rates, significantly extending the post-processing operations that can be performed. These include steering and focusing adjustments, data-dependent adaptive focusing, and multi-array data collection and processing. A flexible data formatting has been devised to provide an interface for end-users to develop customised algorithms. The paper reports on the distributed data acquisition architecture and the data storage format. Specific post-processing operations are covered elsewhere (3) but some typical options will be outlined.