gebhart/patrepeval huggingface dataset:
The Current State of Proteomics in GI Oncology (2008)

Proteomics refers to the study of the entire set of proteins in a given cell or tissue. With the extensive development of protein separation, mass spectrometry, and bioinformatics technologies, clinical proteomics has shown its potential as a powerful approach for biomarker discovery, particularly in the area of oncology. More than 130 exploratory studies have defined candidate markers in serum, gastrointestinal (GI) fluids, or cancer tissue. In this article, we introduce the commonly adopted proteomic technologies and describe results of a comprehensive review of studies that have applied these technologies to GI oncology, with a particular emphasis on developments in the last 3 years. We discuss reasons why the more than 130 studies to date have had little discernible clinical impact, and we outline steps that may allow proteomics to realize its promise for early detection of disease, monitoring of disease recurrence, and identification of targets for individualized therapy.
Asymmetric induction. Reduction, nucleophilic addition to, and ene reactions of chiral α-ketoesters (1983)

J. K. Whitesell, D. Deyo and A. Bhattacharya, J. Chem. Soc., Chem. Commun., 1983, 802 DOI: 10.1039/C39830000802
Production of high-quality amorphous silicon films by evaporative silane surface decomposition (1988)

High-quality hydrogenated amorphous silicon films (a-Si:H) have been produced by decomposition of low-pressure silane gas on a very hot surface with deposition on a nearby, typically 210 °C substrate. A high-temperature tungsten filament provides the surface for heterogeneous thermal decomposition of the low-pressure silane and subsequent evaporation of atomic silicon and hydrogen. These evaporated species (primarily) induce a-Si:H growth on nearby substrates which are temperature controlled using a novel substrate holder. The light and dark conductivities, optical band gap, deposition rates, and light-soaking effects of preliminary films are reported. The decomposition-evaporation process has been examined using a mass spectrometer to directly detect the decomposition rate and the evaporated radical species. Based on this data and other information, a simplified model for the deposition process is suggested. The excellent film quality and the attributes of the deposition process make this technique, which was originally suggested by Wiessman, viable for the fast rate, large-area deposition of a-Si:H for solar cells and other applications.
Regulation of Inflammatory Cytokine Expression in Pulmonary Epithelial Cells by Pre-B-cell Colony-enhancing Factor via a Nonenzymatic and AP-1-dependent Mechanism (2009)

Although our previous studies found Pre-B-cell colony-enhancing factor (PBEF) as a highly up-regulated gene in acute lung injury that could stimulate expressions of other inflammatory cytokines, the underlying molecular mechanisms remain to be fully elucidated. Growing evidence indicates that PBEF is a nicotinamide phosphoribosyltransferase involved in the mammalian salvage pathway of NAD synthesis. This study was designed to determine whether the effect of PBEF to stimulate expressions of inflammatory cytokines depends on its enzymatic activity. We prepared two human PBEF mutant (H247E and H247A) recombinant proteins and overexpressing constructs for their overexpressions in A549 cells and confirmed that enzymatic activities of both mutants were nearly or completely abolished. Two mutants stimulated interleukin-8 (IL-8) expression at both the mRNA level and protein level just as equally effective as the wild-type PBEF did. These effects were due to the increased transcription, not the mRNA stability, of the IL-8 gene. Reporter gene assays and gel shift experiments indicated that AP-1 transcription factor is required to mediate these effects. SB203580, a p38 MAPK pathway inhibitor, and JNK inhibitor 1 can attenuate these effects. Both PBEF mutants similarly stimulated the expression of two other inflammatory cytokines: IL-16 and CCR3. These results indicate that PBEF stimulated expression of IL-8, IL-16, and CCR3 via its non-enzymatic activity. This effect is AP-1-dependent, in part via the p38 MAPK pathway and the JNK pathway. This finding reveals a new insight, which may manifest a novel role of PBEF in the pathogenesis of acute lung injury and other inflammatory disorders.
pH and molecular weight dependence of auric acid reduction by polyethylenimine and the gene transfection efficiency of cationic gold nanoparticles thereof (2018)

Small, cationic gold nanoparticles (GNPs) are produced by the direct reduction of auric acid in a non-reducing solvent, water, with branched polyethylenimine (bPEI) in a broad pH range (3.0–9.0).
Unsaturated fatty acids suppress anti-tumor T cell function. (2016)

Abstract Remarkable progress in cancer immunotherapy has revealed the power of harnessing immunity to combat cancer. Anti-tumor T cells suppress tumor development by secreting cytotoxic cytokines and activating other immune cells. However, the tumoricidal function of tumor-infiltrating T cells is often suppressed and inefficient to combat tumors. Thus one of the key questions in the field of cancer immunology is to address what causes the immunosuppressive nature of the tumor microenvironment. Using a melanoma mouse model, we found that 1) fatty acids accumulated in the tumor microenvironment, 2) unsaturated fatty acids suppressed T cell effector function through CD36/PPAR pathway and 3) blocking FAs transportation into T cells enhanced T cell cytotoxicity and delayed tumor growth. This study has identified unsaturated fatty acid species as immunosuppressive factors in tumor, which may lead to the development of novel forms of therapy that stimulates anti-tumor immunity by manipulating fatty acid transportation and metabolism.
A General Cooperative Intrusion Detection Architecture for MANETs (2005)

Intrusion detection in MANETs is challenging because these networks change their topologies dynamically; lack concentration points where aggregated traffic can be analyzed; utilize infrastructure protocols that are susceptible to manipulation; and rely on noisy, intermittent wireless communications. We present a cooperative, distributed intrusion detection architecture that addresses these challenges while facilitating accurate detection of MANET-specific and conventional attacks. The architecture is organized as a dynamic hierarchy in which detection data is acquired at the leaves and is incrementally aggregated, reduced, and analyzed as it flows upward toward the root. Security management directives flow downward from nodes at the top. To maintain communications efficiency, the hierarchy is automatically reconfigured as needed using clustering techniques in which clusterheads are selected based on topology and other criteria. The utility of the architecture is illustrated via multiple attack scenarios.
On Minimizing Broadcast Completion Delay for Instantly Decodable Network Coding (2010)

In this paper, we consider the problem of minimizing the mean completion delay in wireless broadcast for instantly decodable network coding. We first formulate the problem as a stochastic shortest path (SSP) problem. Although finding the packet selection policy using SSP is intractable, we use this formulation to draw the theoretical properties of efficient selection algorithms. Based on these properties, we propose a simple online selection algorithm that efficiently minimizes the mean completion delay of a frame of broadcast packets, compared to the random and greedy selection algorithms with a similar computational complexity. Simulation results show that our proposed algorithm indeed outperforms these random and greedy selection algorithms.
All-Amorphous-Oxide Transparent, Flexible Thin-Film Transistors. Efficacy of Bilayer Gate Dielectrics (2010)

Optically transparent and mechanically flexible thin-film transistors (TF-TFTs) composed exclusively of amorphous metal oxide films are fabricated on plastic substrates by combining an amorphous Ta(2)O(5)/SiO(x) bilayer transparent oxide insulator (TOI) gate dielectric with an amorphous zinc-indium-tin oxide (a-ZITO) transparent oxide semiconductor (TOS) channel and a-ZITO transparent oxide conductor (TOC) electrodes. The bilayer gate dielectric is fabricated by the post-cross-linking of vapor-deposited hexachlorodisiloxane-derived films to form thin SiO(x) layers (v-SiO(x)) on amorphous Ta(2)O(5) (a-Ta(2)O(5)) films grown by ion-assisted deposition at room temperature. The a-Ta(2)O(5)/v-SiO(x) bilayer TOI dielectric integrates the large capacitance of the high dielectric constant a-Ta(2)O(5) layer with the excellent dielectric/semiconductor interfacial compatibility of the v-SiO(x) layer in a-ZITO TOS-based TF-TFTs. These all-amorphous-oxide TF-TFTs, having a channel length and width of 100 and 2000 microm, respectively, perform far better than a-Ta(2)O(5)-only devices and exhibit saturation-regime field-effect mobilities of approximately 20 cm(2)/V x s, on-currents >10(-4) A, and current on-off ratios >10(5). These TFTs operate at low voltages (approximately 4.0 V) and exhibit good visible-region optical transparency and excellent mechanical flexibility.
Analysis of Pregnancy-Associated Plasma Protein A Production in Human Adult Cardiac Progenitor Cells (2013)

IGF-binding proteins (IGFBPs) and their proteases regulate IGFs bioavailability in multiple tissues. Pregnancy-associated plasma protein A (PAPP-A) is a protease acting by cleaving IGFBP2, 4, and 5, regulating local bioavailability of IGFs. We have previously shown that IGFs and IGFBPs are produced by human adult cardiac progenitor cells (haCPCs) and that IGF-1 exerts paracrine therapeutic effects in cardiac cell therapy with CPCs. Using immunofluorescence and enzyme immunoassays, we firstly report that PAPP-A is produced and secreted in surprisingly high amounts by haCPCs. In particular, the homodimeric, enzymatically active, PAPP-A is secreted in relevant concentrations in haCPC-conditioned media, while the enzymatically inactive PAPPA/proMBP complex is not detectable in the same media. Furthermore, we show that both homodimeric PAPP-A and proMBP can be detected as cell associated, suggesting that the previously described complex formation at the cell surface does not occur easily, thus positively affecting IGF signalling. Therefore, our results strongly support the importance of PAPP-A for the IGFs/IGFBPs/PAPP-A axis in CPCs biology.
Exploring the thermodynamics of a rubber band (2012)

We describe an upper-division experiment in thermal physics where students measure the tension of a rubber band as a function of temperature and length and use a Maxwell relation to find the change in internal energy and entropy for an isothermal stretch. This allows students to experimentally check the predictions of the entropic spring model for elastomers and observe that the entropy does indeed decrease as a rubber band is stretched.
Valuing Credit Default Swaps I (2000)

One of the fastest growing areas of both derivatives trading and research right now is in contracts based on credit risk. The credit default swap is a standard instrument, offering the possibility of hedging against default by the issuer of an underlying bond. Several existing valuation methodologies differ in their assumptions about the payoff in case of a credit event. In this article, Hull and White present an approach based on the realistic assumption that the amount bondholders will claim in a default is based on the difference between the bond&amp;’s post-default market value and its face value. An important contribution of this article is to use the term structure of risk-neutral implied default probabilities obtained from market prices for a set of bonds of the same issuer. The dependence of swap values on assumed recovery rates and the shape of the yield curve are explored.
Strategies for migration from C to Java (2003)

With the growing popularity of the Java programming language for both client and server side applications in network centric computing, there is a rising need for programming libraries that can be easily integrated into Java programs. Many mature programming libraries exist for the C programming language. The paper surveys approaches to the migration of C source code to Java and evaluates their usefulness with respect to the integration of the migrated code into Java programs.
Supplementary Table 2 from Impact of Intrinsic Affinity on Functional Binding and Biological Activity of EGFR Antibodies (2023)

&lt;p&gt;PDF file, 56KB, Kinetic parameters used in the computational model of antibody binding.&lt;/p&gt;
Application of positron age-momentum correlation measurement to the study of defects in electron irradiated synthetic silica glass (1994)

Age-momentum measurements and positron lifetime measurements were carried out in order to investigate vacancy-type defects produced in 3 MeV electron irradiated synthetic silica glasses, in which 1 ppm and 300 ppm of –OH bonds were contained. A high formation probability of positronium (Ps) was found for unirradiated specimens. These Ps atoms were considered to be formed in open-volume defects (∼7×10−2 nm3). The formation probability of Ps was drastically decreased by the electron irradiation, especially for the specimens which contained 1 ppm of –OH bonds, even though the size of the open-volume defects and the momentum distribution of electrons at the open-volume defects are independent on the –OH concentration and on the electron irradiation. Since the values of second lifetime components of positron lifetime spectra were ∼300 ps and very close to the estimated value of the lifetime of the positrons which are considered to be trapped in the mono- or divacancies, the decrease of formation probability of Ps can be attributed to an increase of positron annihilation in vacancy-type defects generated by the electron irradiation. Positrons were suspected to be trapped in such defects.
When to ask male adolescents to provide semen sample for fertility preservation? (2014)

It is appropriate to consider a request for semen specimens by masturbation from teenagers at one year and six months after the onset of puberty; the onset age of puberty plus 1.5 years is an important predictor of ejaculation and sample collection for cryopreservation.
Non-invasive in vivo thrombus imaging in patients with ischaemic stroke or transient ischaemic attack (2023)

Abstract Funding Acknowledgements Type of funding sources: Foundation. Main funding source(s): British Heart Foundation Life Molecular Imaging provide reagents for GP1 production free of charge. Background and Purpose 18F-GP1 is a novel positron-emitting radiotracer that has high and specific binding affinity for the activated glycoprotein IIb/IIIa receptor, a key receptor in platelet activation and thrombus formation. Preliminary studies 18F-GP1 demonstrated excellent in vivo binding properties which enabled detection of intravascular thrombosis in a range of conditions including coronary thrombosis, left ventricular thrombus, pulmonary thromboembolism, and deep vein thrombosis. In a pilot proof-of-concept study, we aimed to determine its potential clinical application in establishing the role and origin of thrombus in stroke . Methods Autoradiography of 18F-GP1 uptake was performed on post-mortem samples of infarcted brain tissue following an acute ischaemic stroke and from control brain tissue without stroke. Eleven patients with recent ischaemic stroke (n=9) or transient ischaemic attack (n=2) underwent 18F-GP1 positron emission tomography and computed tomography angiography at median of 11 (absolute range 2–21) days from symptom onset. 18F-GP1 uptake (quantified by maximum target-to-background ratio, TBRmax) was assessed in the carotid arteries and brain. Results Ex vivo autoradiography of post-mortem infarcted brain tissue showed focal uptake corresponding to intraluminal thrombus within the culprit vessel and downstream microvasculature. There was also evidence of lower diffuse uptake within some of the infarcted brain tissue reflecting microthrombi within regions of reperfusion haemorrhage. In vivo 18F-GP1 uptake was identified in 9 of 11 patients: 3 in the carotid arteries only, 3 in the brain only and 3 in both the brain and carotid arteries. In those with carotid uptake, 3 participants had &amp;gt;50% stenosis and 3 had non-stenotic disease. One case had bilateral stenotic disease (&amp;gt;70%) but only the culprit carotid artery demonstrated 18F-GP1 uptake. The average uptake was higher in the culprit (median TBRmax 1.55 [interquartile range 1.26–1.82]) compared with the contralateral non-culprit carotid artery (TBRmax 1.22 [1.19–1.6]). In those with brain 18F-GP1 uptake (TBRmax 6.45 [4.89–7.65]), areas of acute infarction on computed tomography correlated with brain 18F-GP1 uptake in 6 cases. There was no brain 18F-GP1 uptake in the 7 cases without CT-defined acute cerebral infarction. Conclusions 18F-GP1 positron emission tomography and computed tomography angiography is a novel non-invasive method of identifying in vivo cerebrovascular thrombosis which holds major promise in understanding the role and origin of thrombosis in stroke.
Expression and Anticoagulant Function of the Endothelial Cell Protein C Receptor (EPCR) in Cancer Cell Lines (2001)

Induction of procoagulant factors in malignant cells is considered to be the major cause of coagulation disorders in cancer. Thrombomodulin (TM), a negative regulator of coagulation was also found to be expressed in cancer cells. We report here evidence for another anticoagulant, the endothelial cell protein C receptor (EPCR), in cancer cells. EPCR was detected in several cell lines derived from various types of cancer. Significant levels of protein C (PC) activation were detected only with cell lines expressed both EPCR and TM. Anti-EPCR monoclonal antibodies (mAbs) specifically inhibited the activation. Thus, EPCR function appears to be important for PC activation by cancer cells. In addition, we detected EPCR expression in tumor cells from breast cancer patients, with an extremely high frequency. EPCR function may contribute to progression or pathogenesis of some types of cancer, and may explain the complexity of coagulopathy in cancer patients.
[Protective effect of Salvia on ischemia-reperfusion hepatic injury in rats]. (2010)

The rat hepatic ischemia-reperfusion increases the expressions of NF-κB and ICAM-1 and they are involved in hepatic ischemia-reperfusion injury. Salvia significantly reduces the expressions of NF-κB and ICAM-1 in ischemia-reperfusion hepatic tissue and it may effectively protect the injury of hepatic ischemia-reperfusion.
Effect of different fraction interval on tumor control in C57BL mice implanted with Lewis lung cancer (2009)

Objective To study the effect of different fraction interval with same total radiation dose on tumor growth delay and survival in C57BL mice implanted with lewis lung cancer,and to determine whether prolonged fraction interval will decrease the tumor response to radiation. Methods Forty-eight mice were implanted with lewis lung cancer in the back legs.When the diameter of transplanted tumor reached 0.8 to 1 cm,the mice were randomized into 6 groups:normal control group,single fraction of 18 Gy group,18 Gy in 2 fractions of 9 Gy at 30 min interval group,18 Gy in 7 fractions of 2.57 Gy at 5 min inter val group,18 Gy in 2 fractions of 9 Gy at 60 min interval group and 18 Gy in 7 fractions of 2.57 Gy at 10 rain interval group.The maximal and minimal diameters of the tumor were measured and record every other day to study the tumor growth tendency,the tumor growth delay and the mice survival time. Results The tumor growth delay of groups at prolonged fraction interval was shorter than the group with single fraction of 18 Gy (P 0.05).The mice survival time of the groups with prolonged fraction interval was shortened when omparing to the group with single fraction of 18 Gy.While the difference was not significant between the groups at fraction interval of 30 min and 60 min. Conclusions The pro longed fraction interval but same total radiation dose shortens the tumor growth delay and survival time in the mice implanted with Lewis lung cancer.The longer fraction interval impairs the tumor control more signifi candy.However the difference of the effect on mice survival time is not significant between the groups at fraction interval of 30 min and 60 min.

Key words: 
Lewis lung cancer/irradiation; Fraction interval time; Mouse
Escherichia coli phosphoenolpyruvate dependent phosphotransferase system. Copurification of HPr and .alpha.1-6 glucan (1979)

A rapid, high-yield procedure has been developed for the purification of HPr from the Escherichia coli phosphoenolpyruvate dependent phosphotransferase system. During this procedure, the protein copurifies with a 2500-dalton homopolysaccharide which we have identified as alpha 1-6 glucan. The results of steady-state kinetic measurements of the phosphotransferase activity demonstrate that the polysaccharide works as an activator of the phosphotransferase system probably at the level of the HPr:P-E1 complex or the P-HPr:E11 complex.
Enhancement of Cellular and Humoral Immunity in Young Broilers by the Dietary Supplementation of β-Hydroxy-β-Methylbutyrate (1999)

As a dietary supplement, beta-Hydroxy-beta-Methylbutyrate (HMB), a catabolite of leucine, has been shown to reduce broiler mortality. In a series of experiments, male broilers (Experiments 1 and 2, n = 576) were grown for 21 days on diets that contained HMB at 0, 0.01. 0.05, and 0.10% of diet. In Experiment 3 (n = 240), chicks were fed diets containing 0, 0.05, 0.075, and 0.10% HMB. HMB dietary supplementation did not significantly affect broiler weight gain in any experiment. However, a trend toward increased mean broiler weight gain per bird was observed in Experiments 1 and 3 when HMB was consumed at 0.10% of the diet. Mean feed to gain ratio was not affected by the inclusion of HMB in broiler diets. In Experiment 3, HMB supplemented diets did not affect bursa of Fabricius, thymus, and spleen weights at 21 days of age. Cutaneous basophilic hypersensitivity response against pokeweek mitogen was higher (P < or = 0.05) at 48 and 72 hours post-injection in chicks on 0.05% dietary HMB (Experiment 1). In Experiment 2, this increase occurred 24 hours post-injection in chicks fed HMB at 0.01% of the diet. On the contrary, the T-cell mediated response against PHA-P mitogen was comparable between all dietary treatments in multiple experiments. Macrophage function profiles were determined at 21 days of age. All chicks in experiments 1 and 2 on HMB supplemented diets showed an increase in the recruitment of Sephadex-G50-elicited abdominal exudate cells (AEC). A 2-fold increase in AEC numbers occurred at the 0.10% HMB level (Experiment 1, P < or = 0.05). Although HMB supplementation did not significantly affect the phagocytic potential of the abdominal macrophages, nitrite levels in the macrophage culture supernatants were higher in 0.01% and 0.05% treatment groups as compared to the controls (Experiment 2, P < or = 0.04; Experiment 3, P < or = 0.05). HMB supplementation did not alter the bird's ability to clear Escherichiacoli or Salmonella arizona from the bloodstream. Beginning 7 days post-hatch, chicks were injected i.v. with a 7% sheep red blood cells suspension. Serum samples were collected to determine the primary and secondary antibody response. Chicks receiving the 0.1% HMB diet in Experiments 1 and 2 exhibited increased IgG and total anti-sheep red blood cell (SRBC) antibody levels during the primary response. During the secondary response, birds consuming the 0.10% HMB diet had elevated IgM levels as well as increased total anti-SRBC levels over the controls in Experiments 1 and 3. These studies show that HMB supplementation improves several immunological functions in young broilers, and such improvement may result in decreased mortality.