gebhart/patrepeval huggingface dataset:
P48 is a predictive marker for outcome of postoperative interferon‐α treatment in patients with hepatitis B virus infection‐related hepatocellular carcinoma (2006)

P48 was useful as a predictive marker of outcome after postoperative IFN-alpha treatment in patients with HBV-related HCC.
Regulation of creatine kinase induction in differentiating mouse myoblasts. (1985)

The regulation of creatine kinase (CK) induction during muscle differentiation was analyzed with MM14 mouse myoblasts. These cells withdraw from the cell cycle and commit to terminal differentiation when fed with mitogen-depleted medium. Myoblasts contained trace amounts of an isozyme of brain CK (designated BB-CK), but differentiation was accompanied by the induction of two other isozymes of muscle and brain CKs (designated MM-CK and MB-CK). Increased CK activity was detectable within 6 h of mitogen removal, 3 h after the first cells committed to differentiation and 6 h before fusion began. By 48 h, MM-CK activity increased more than 400-fold, MB-CK activity increased more than 150-fold, and BB-CK activity increased more than 10-fold. Antibodies prepared against purified mouse MM-CK cross-reacted with muscle and brain CKs (designated M-CK and B-CK, respectively) from a variety of species and were used to demonstrate that the increase in enzymatic activity was paralleled by an increase in the protein itself. CK antibodies were also used to aid in identifying cDNA clones to M-CK. cDNA sequences which corresponded to protein-coding regions cross-hybridized with B-CK mRNA; however, a subclone containing the 3'-nontranslated region was unique and was used to quantitate M-CK mRNA levels during myoblast differentiation. M-CK mRNA was not detectable in myoblasts, but within 5 to 6 h of mitogen withdrawal (6 to 7 h before fusion begins) it accumulated to about 30 molecules per cell. By 24 h, myotubes contained approximately 1,100 molecules per nucleus of M-CK mRNA.
Ca<sup>2+</sup>-Dependent Structural Changes in C-type Mannose-Binding Proteins<sup>,</sup> (1998)

C-type animal lectins are a diverse family of proteins which mediate cell-surface carbohydrate-recognition events through a conserved carbohydrate-recognition domain (CRD). Most members of this family possess a carbohydrate-binding activity that depends strictly on the binding of Ca2+ at two sites, designated 1 and 2, in the CRD. The structural transitions associated with Ca2+ binding in C-type lectins have been investigated by determining high-resolution crystal structures of rat serum mannose-binding protein (MBP) bound to one Ho3+ in place of Ca2+, and the apo form of rat liver MBP. The removal of Ca2+ does not affect the core structure of the CRD, but dramatic conformational changes occur in the loops. The most significant structural change in the absence of Ca2+ is the isomerization of a cis-peptide bond preceding a conserved proline residue in Ca2+ site 2. This bond adopts the cis conformation in all Ca2+-bound structures, whereas both cis and trans conformations are observed in the absence of Ca2+. The pattern of structural changes in the three loops that interact with Ca2+ is dictated in large part by the conformation of the prolyl peptide bond. The highly conserved nature of Ca2+ site 2 suggests that the transitions observed in MBPs are general features of Ca2+ binding in C-type lectins.
Phosphine-pyridonate ligands containing octahedral ruthenium complexes: access to esters and formic acid (2017)

Selective formation of esters from primary alcohols or formic acid from carbon dioxide was achieved in the presence of phosphine-pyridone containing ruthenium catalysts.
Application of Supercritical Fluid Carbon Dioxide to The Extraction And Analysis of Lipids (2012)

Supercritical carbon dioxide (SCCO(2)) is an ecofriendly supercritical fluid that is chemically inert, nontoxic, noninflammable and nonpolluting. As a green material, SCCO(2) has desirable properties such as high density, low viscosity and high diffusivity that make it suitable for use as a solvent in supercritical fluid extraction, an effective and environment-friendly analytical method, and as a mobile phase for supercritical fluid chromatography, which facilitates high-throughput, high-resolution analysis. Furthermore, the low polarity of SCCO(2) is suitable for the extraction and analysis of hydrophobic compounds. The growing concern surrounding environmental pollution has triggered the development of green analysis methods based on the use of SCCO(2) in various laboratories and industries. SCCO(2) is becoming an effective alternative to conventional organic solvents. In this review, the usefulness of SCCO(2) in supercritical fluid extraction and supercritical fluid chromatography for the extraction and analysis of lipids is described.
Surprising chiral composition changes over the Amazon rainforest with height, time and season (2020)

Abstract Many biogenic volatile organic compounds (BVOC) are chiral, existing in two mirror image forms called enantiomers. The most abundant atmospheric chiral BVOC is α-pinene (C 10 H 16 ), whose enantiomeric ratio has been reported to be regiospecific. Here we show with measurements made on a 325 m tower in the Amazon rainforest that the enantiomeric ratio varies unexpectedly (by a factor of ten) with (+)-α-pinene dominating at canopy level and (−)-α-pinene at tower top. The ratio is independent of wind direction, speed and sunlight but shows diurnal temperature dependent enrichment in the (−)-α-pinene enantiomer at the lowest 80 m height. These effects cannot be caused by atmospheric reaction with oxidants , or aerosol uptake. The reversal of chiral ratio at 80 m reveals the presence of a potent uncharacterized local (+)-α-pinene rich source, possibly linked to herbivory and termites. These results suggest the presence of a strong uncharacterized BVOC source that is overlooked in current emission models.
3D-DXA: Assessing the Femoral Shape, the Trabecular Macrostructure and the Cortex in 3D from DXA images (2016)

The 3D distribution of the cortical and trabecular bone mass in the proximal femur is a critical component in determining fracture resistance that is not taken into account in clinical routine Dual-energy X-ray Absorptiometry (DXA) examination. In this paper, a statistical shape and appearance model together with a 3D-2D registration approach are used to model the femoral shape and bone density distribution in 3D from an anteroposterior DXA projection. A model-based algorithm is subsequently used to segment the cortex and build a 3D map of the cortical thickness and density. Measurements characterising the geometry and density distribution were computed for various regions of interest in both cortical and trabecular compartments. Models and measurements provided by the "3D-DXA" software algorithm were evaluated using a database of 157 study subjects, by comparing 3D-DXA analyses (using DXA scanners from three manufacturers) with measurements performed by Quantitative Computed Tomography (QCT). The mean point-to-surface distance between 3D-DXA and QCT femoral shapes was 0.93 mm. The mean absolute error between cortical thickness and density estimates measured by 3D-DXA and QCT was 0.33 mm and 72 mg/cm<sup>3</sup>. Correlation coefficients (R) between the 3D-DXA and QCT measurements were 0.86, 0.93, and 0.95 for the volumetric bone mineral density at the trabecular, cortical, and integral compartments respectively, and 0.91 for the mean cortical thickness. 3D-DXA provides a detailed analysis of the proximal femur, including a separate assessment of the cortical layer and trabecular macrostructure, which could potentially improve osteoporosis management while maintaining DXA as the standard routine modality.
Photo and dark conductivity of doped amorphous silicon (1977)

Abstract The photo and dark conductivity of boron‐ and phosphorus‐doped amorphous silicon is measured in the temperature range from 100 to 400 K, for various doping levels. Increasing doping generally decreases the activation energy of dark conductivity, down to 0.2 eV, and also decreases the σ 0 ‐value (extrapolation of dark conductivity for T → ∞). This lowering of σ 0 is explained by a temperature shift of the Fermi level plus a change in the conduction mechanism. The activation energy of photoconductivity is also lowered, at least by phosphorus doping, which is understood by an influence of doping on the tailing of the bands.
Impact of Legal Threats on Online Music Sharing Activity: An Analysis of Music Industry Legal Actions (2006)

The music industry has repeatedly expressed concerns over potentially devastating impacts of online music sharing. Initial attempts to control online file sharing have been primarily through consumer education and legal action against the operators of networks that facilitated file sharing. Recent legal action against individual file sharers marked an unprecedented shift in the industry’s strategy. The focus now is on well‐publicized legal threats and actions on a relatively small group of individuals to discourage overall music file sharing. To determine the resulting impact of these legal threats, we passively tracked online file‐sharing behavior of over 2,000 individuals. We found that individuals who share a substantial number of music files react to legal threats differently from those who share a lesser number of files. Importantly, our analysis indicates that even after these legal threats and the resulting lowered levels of file sharing, the availability of music files on these networks remains substantial.
Nano-Indentation and Tribological Studies of Ultrahigh Strength Carbon Nitride Thin Films (1994)

Carbon nitride (CNX) thin films were prepared by DC magnetron sputtering of a graphite target in a nitrogen ambient onto Si(100) and M2 steel substrates held at ambient temperatures. All CNx coatings grown to a thickness of 1.5 μm are adherent and smooth. Nanoindentation studies showed that amorphous CNx thin films have hardness and effective Young's modulus comparable to those of amorphous hard carbon. In dry sliding against 52100 steel, CNx-coated M2 substrates give initial friction coefficients ˜0.1, rising to around 0.5 in the steady state. The wear life of coated M2 steels varies inversely with normal load, rising to about two orders of magnitude higher than that of uncoated M2 at a normal load of 1.3N and a sliding speed of 0.12 m/s. This improvement is attributed to the high yield strength of carbon nitride coatings.
Selection of therapeutic H5N1 monoclonal antibodies following IgVH repertoire analysis in mice (2016)

The rapid rate of influenza virus mutation drives the emergence of new strains that inflict serious seasonal epidemics and less frequent, but more deadly, pandemics. While vaccination provides the best protection against influenza, its utility is often diminished by the unpredictability of new pathogenic strains. Consequently, efforts are underway to identify new antiviral drugs and monoclonal antibodies that can be used to treat recently infected individuals and prevent disease in vulnerable populations. Next Generation Sequencing (NGS) and the analysis of antibody gene repertoires is a valuable tool for Ab discovery. Here, we describe a technology platform for isolating therapeutic monoclonal antibodies (MAbs) by analyzing the IgVH repertoires of mice immunized with recombinant H5N1 hemagglutinin (rH5). As an initial proof of concept, 35 IgVH genes were selected using a CDRH3 search algorithm and co-expressed in a murine IgG2a expression vector with a panel of germline murine kappa genes. Culture supernatants were then screened for antigen binding. Seventeen of the 35 IgVH MAbs (49%) bound rH5VN1203 in preliminary screens and 8 of 9 purified MAbs inhibited 3 heterosubtypic strains of H5N1 virus when assayed by HI. Two of these MAbs demonstrated prophylactic and therapeutic activity in virus-challenged mice. This is the first example in which an NGS discovery platform has been used to isolate anti-influenza MAbs with relevant therapeutic activity.
Microservices: Granularity vs. Performance (2017)

Microservice Architectures (MA) have the potential to increase the agility of software development. In an era where businesses require software applications to evolve to support software emerging requirements, particularly for Internet of Things (IoT) applications, we examine the issue of microservice granularity and explore its effect upon application latency. Two approaches to microservice deployment are simulated; the first with microservices in a single container, and the second with microservices partitioned across separate containers. We observed a neglibible increase in service latency for the multiple container deployment over a single container.
Regulation of arousal via online neurofeedback improves human performance in a demanding sensory-motor task (2019)

Our state of arousal can significantly affect our ability to make optimal decisions, judgments, and actions in real-world dynamic environments. The Yerkes-Dodson law, which posits an inverse-U relationship between arousal and task performance, suggests that there is a state of arousal that is optimal for behavioral performance in a given task. Here we show that we can use online neurofeedback to shift an individual's arousal from the right side of the Yerkes-Dodson curve to the left toward a state of improved performance. Specifically, we use a brain-computer interface (BCI) that uses information in the EEG to generate a neurofeedback signal that dynamically adjusts an individual's arousal state when they are engaged in a boundary-avoidance task (BAT). The BAT is a demanding sensory-motor task paradigm that we implement as an aerial navigation task in virtual reality and which creates cognitive conditions that escalate arousal and quickly results in task failure (e.g., missing or crashing into the boundary). We demonstrate that task performance, measured as time and distance over which the subject can navigate before failure, is significantly increased when veridical neurofeedback is provided. Simultaneous measurements of pupil dilation and heart-rate variability show that the neurofeedback indeed reduces arousal. Our work demonstrates a BCI system that uses online neurofeedback to shift arousal state and increase task performance in accordance with the Yerkes-Dodson law.
Event processing of monitoring data of large hi-tech manufacturing equipment (2012)

The subject of DEBS 2012 Grand Challenge is to implement an automatic event-monitoring system that traces the state of Chem Additive sensors and their associated valves and records the energy consumption of the manufacturing equipment. As solutions for the problem, we compare three different approaches. The first one is a custom solution using optimal technologies, such as lock-free queue and minimum heap-list. The second one is a rule-based solution using JBoss Drools Expert. The third one is a CEP-enhanced rule-based solution using JBoss Drools Fusion. After evaluating the event processing performance among these three implementation methods in terms of throughput and latency, we finally conclude this paper with the discussion of implications of our solution methods including non-performance factors.
Physical interventions to interrupt or reduce the spread of respiratory viruses: systematic review (2007)

Routine long term implementation of some physical measures to interrupt or reduce the spread of respiratory viruses might be difficult but many simple and low cost interventions could be useful in reducing the spread.
Long Noncoding RNAs and MicroRNAs in Cardiovascular Pathophysiology (2015)

RNAs not encoding proteins have gained prominence over the last couple of decades as fundamental regulators of cellular function. Not surprisingly, their dysregulation is increasingly being linked to pathology. Here, we review recent reports investigating the pathophysiological relevance of this species of RNA for the cardiovascular system, concentrating mainly on recent findings on long noncoding RNAs and microRNAs in cardiac hypertrophy and failure.
Ovarian Follicular Steroidogenic Acute Regulatory Protein, Low-Density Lipoprotein Receptor, and Cytochrome P450 Side-Chain Cleavage Messenger Ribonucleic Acids in Cattle Undergoing Superovulation1 (1997)

Ovarian hyperstimulation with eCG in cattle results in increased plasma estradiol and progesterone concentrations, whereas hyperstimulation with FSH increases only estradiol concentrations. This study tested the hypothesis that eCG, compared to FSH, increases mRNA abundance for steroidogenic acute regulatory protein (StAR), low-density lipoprotein receptor (LDL-R), and/or cytochrome P450 cholesterol side-chain cleavage (P450scc), the main elements of the progesterone biosynthetic pathway. Heifers were stimulated with eCG (n = 10) or commercial FSH (n = 10), and ovaries were removed by colpotomy the day before and at 12 and 24 h after luteolysis was induced with prostaglandin (PG) F2alpha. RNA was extracted from individual follicles, and relative abundance of StAR, LDL-R, and P450scc mRNA was assessed by slot blots. In ovaries of abattoir origin, StAR mRNA was detected in all follicles and was present in the theca but not the granulosa cell layer, as shown by Northern blotting. Levels of StAR mRNA increased 2-fold (p < 0.05) after PGF2alpha injection in small (< 6 mm) follicles from eCG-treated but not from FSH-treated animals. After PGF2alpha, injection, StAR mRNA levels were 2- to 3-fold higher (p < 0.01) in large (> 9 mm) and medium (6-9 mm) follicles in eCG- compared with FSH-treated heifers. In contrast, P450scc and LDL-R mRNA levels did not consistently differ according to treatments. We show that StAR is expressed in the theca cells of bovine follicles and that stimulation with eCG increases follicular accumulation of StAR mRNA in comparison to stimulation with FSH.
Rapid Detection of the ACMG/ACOG-Recommended 23 CFTR Disease-Causing Mutations Using Ion Torrent Semiconductor Sequencing (2012)

Cystic fibrosis (CF) is one of the most frequently diagnosed autosomal-recessive diseases in the Caucasian population. For general-population CF carrier screening, the American College of Medical Genetics (ACMG)/American College of Obstetricians and Gynecologists (ACOG) have recommended a core panel of 23 mutations that will identify 49-98% of carriers, depending on ethnic background. Using a genotyping technology that can rapidly identify disease-causing mutations is important for high-throughput general-population carrier screening, confirming clinical diagnosis, determining treatment options, and prenatal diagnosis. Here, we describe a proof-of-concept study to determine whether the Ion Torrent Personal Genome Machine (PGM) sequencer platform can reliably identify all ACMG/ACOG 23 CF transmembrane conductance regulator (CFTR) mutations. A WT CF specimen along with mutant DNA specimens representing all 23 CFTR mutations were sequenced bidirectionally on the Ion Torrent 314 chip to determine the accuracy of the PGM for CFTR variant detection. We were able to reliably identify all of the targeted mutations except for 2184delA, which lies in a difficult, 7-mer homopolymer tract. Based on our study, we believe PGM sequencing may be a suitable technology for identifying CFTR mutations in the future. However, as a result of the elevated rate of base-calling errors within homopolymer stretches, mutations within such regions currently need to be evaluated carefully using an alternative method.
Potentiation of the activity of 1-beta-D-arabinofuranosylcytosine by the protein kinase C activator bryostatin 1 in HL-60 cells: association with enhanced fragmentation of mature DNA. (1992)

We have examined the interaction between 1-beta-D-arabinofuranosylcytosine (ara-C) and the macrocyclic lactone protein kinase C activator bryostatin 1 in the human promyelocytic leukemia cell line HL-60. Preexposure of cells to 10 nM bryostatin 1 for 24 h, followed by an additional 24-h incubation with 10 microM ara-C, resulted in greater than additive inhibitory effects toward clonogenic HL-60 cells. In a series of alkaline elution assays, cells preincubated with bryostatin 1 and prelabeled with [3H]thymidine exhibited a significant increase in DNA fragmentation following exposure to ara-C in comparison to cells exposed to ara-C alone. This increase in DNA damage was apparent at both neutral and alkaline pH and was not protein associated. In contrast, studies using cells pulse-labeled with [3H]thymidine immediately before analysis suggested that bryostatin 1 pretreatment did not increase the ability of ara-C to interfere with DNA replicative intermediates. Additional studies demonstrated that the increase in DNA fragmentation induced by bryostatin 1 and ara-C preceded both loss of cell membrane integrity (as determined by trypan blue exclusion) as well as depletion of intracellular ATP and NAD pools. Furthermore, the enhanced inhibitory effects of bryostatin 1 and ara-C toward clonogenic HL-60 cells did not appear to result from the induction of cellular differentiation. Finally, agarose gel electrophoresis of DNA obtained from cells exposed to both bryostatin 1 and ara-C revealed a pattern of integer multiples of 180- to 200-base pair fragments commonly associated with endonucleolytic cleavage; the extent of this fragmentation was considerably greater than that observed in cells exposed to ara-C alone. Taken together, these findings suggest that exposure of HL-60 cells to bryostatin 1 renders them more susceptible to ara-C-related DNA damage and that this phenomenon contributes to the cytotoxic effects of this drug combination. They also raise the possibility that bryostatin 1, perhaps through modulation of intracellular signaling events in leukemic cells, has the capacity to potentiate ara-C-related apoptosis or programmed cell death.
Small-molecule control of cytokine function: new opportunities for treating immune disorders (2014)

Manipulating cytokine function with protein-based drugs has proven effective for treating a wide variety of autoimmune and autoinflammatory disorders. However, the limited ability of protein-based drugs to modulate intracellular targets, including many implicated by studies of the genetics and physiology of these diseases, and to coordinately neutralize redundant inflammatory cytokines, suggests an important and complementary role for small molecules in immunomodulatory drug development. The recent clinical approval of Janus kinase and phosphodiesterase inhibitors, along with emerging evidence from other compound classes, firmly establish small molecules as effective tools for modulating therapeutically relevant proteins that give rise to aberrant cytokine signaling or mediate its downstream consequences.