gebhart/patrepeval huggingface dataset:
Activation of NF-κB by TMPRSS2/ERG Fusion Isoforms through Toll-Like Receptor-4 (2010)

The TMPRSS2/ERG (T/E) fusion gene is present and thought to be an oncogenic driver of approximately half of all prostate cancers. Fusion of the androgen-regulated TMPRSS2 promoter to the ERG oncogene results in constitutive high level expression of ERG which promotes prostate cancer invasion and proliferation. Here, we report the characterization of multiple alternatively spliced T/E fusion gene isoforms which have differential effects on invasion and proliferation. We found that T/E fusion gene isoforms differentially increase NF-κB-mediated transcription, which may explain in part the differences in biological activities of the T/E fusion isoforms. This increased activity is due to phosphorylation of NF-κB p65 on Ser536. Tissue microarray immunochemistry revealed that p65 phospho-Ser536 is present in the majority of prostate cancers where it is associated with ERG protein expression. The T/E fusion gene isoforms differentially increase expression of a number of NF-κB associated genes including PAR1, CCL2, FOS, TLR3, and TLR4 (Toll-like receptor). TLR4 activation is known to promote p65 Ser536 phosphorylation and knockdown of TLR4 with shRNA decreases Ser536 phosphorylation in T/E fusion gene expressing cells. TLR4 can be activated by proteins in the tumor microenvironment and lipopolysacharide from Gram (-) bacteria. Our findings suggest that bacterial infection of the prostate and/or endogenous microenvironment proteins may promote progression of high-grade prostatic intraepithelial neoplasia and/or prostate cancers that express the T/E fusion gene, where the NF-κB pathway might be targeted as a rational therapeutic approach.
Viral Interactions in Human Lymphoid Tissue: Human Herpesvirus 7 Suppresses the Replication of CCR5-Tropic Human Immunodeficiency Virus Type 1 via CD4 Modulation (2006)

Human immunodeficiency virus (HIV) infection is often accompanied by infection with other pathogens that affect the clinical course of HIV disease. Here, we identified another virus, human herpesvirus 7 (HHV-7) that interferes with HIV type 1 (HIV-1) replication in human lymphoid tissue, where critical events of HIV disease occur. Like the closely related HHV-6, HHV-7 suppresses the replication of CCR5-tropic (R5) HIV-1 in coinfected blocks of human lymphoid tissue. Unlike HHV-6, which affects HIV-1 by upregulating RANTES, HHV-7 did not upregulate any CCR5-binding chemokine. Rather, the inhibition of R5 HIV-1 by HHV-7 was associated with a marked downregulation of CD4, the cellular receptor shared by HHV-7 and HIV-1. HHV-7-induced CD4 downregulation was sufficient for HIV-1 inhibition, since comparable downregulation of CD4 with cyclotriazadisulfonamide, a synthetic macrocycle that specifically modulates expression of CD4, resulted in the suppression of HIV infection similar to that seen in HHV-7-infected tissues. In contrast to R5 HIV-1, CXCR4-tropic (X4) HIV-1 was only minimally suppressed by HHV-7 coinfection. This selectivity in suppression of R5 and X4 HIV-1 is explained by a suppression of HHV-7 replication in X4- but not in R5-coinfected tissues. These results suggest that HIV-1 and HHV-7 may interfere in lymphoid tissue in vivo, thus potentially affecting the progression of HIV-1 disease. Knowledge of the mechanisms of interaction of HIV-1 with HHV-7, as well as with other pathogens that modulate HIV-1 replication, may provide new insights into HIV pathogenesis and lead to the development of new anti-HIV therapeutic strategies.
Subspace identification of linear parameter-varying systems with innovation-type noise models driven by general inputs and a measurable white noise time-varying parameter vector (2008)

In this article, we introduce an iterative subspace system identification algorithm for MIMO linear parameter-varying systems with innovation-type noise models driven by general inputs and a measurable white noise time-varying parameter vector. The new algorithm is based on a convergent sequence of linear deterministic–stochastic state-space approximations, thus considered a Picard-based method. Such methods have proven to be convergent for the bilinear state-space system identification problem. Their greatest strength lies on the dimensions of the data matrices that are comparable to those of a linear subspace algorithm, thus avoiding the curse of dimensionality.
Dependence of Fuel Properties During Blending of Iso-Paraffinic Kerosene and Petroleum-Derived Jet Fuel (2008)

Abstract : The studies and analysis performed in this report were made to improve the understanding of blending an Iso-Paraffinic Kerosene (IPK) produced from natural gas via Fischer-Tropsch (FT) synthesis with several petroleum-derived fuels on the resulting chemical, physical and Fit-For-Purpose (FFP) properties. The IPK had a similar distillation range to a typical jet fuel and high iso-/normal alkane ratio. Blending showed a linear dependence in the specification and non-specification properties with blend ratio. Determination and understanding of this dependence allows for the prediction of anticipated fuel properties during blending and for statistical analysis using historical fuel property distribution data to be performed to investigate expected fuel properties and variability as a function of blend ratio.
Disulfide Reactivity and In Vitro Protein Digestibility of Different Thermal-Treated Milk Samples and Whey Proteins (1997)

The susceptibility of disulfides to reduction and the in vitro protein digestibility were analyzed in raw, pasteurized, ultrahigh-temperature (UHT)-treated, and sterilized milk samples and whey proteins. Both parameters increased from raw or pasteurized to UHT-treated or sterilized milk samples. Whey proteins had impaired digestibility compared with that of the corresponding whole milk samples, especially when extracted from UHT-treated and sterilized milk samples. The amino acid composition of proteins in whey indicated that the ratio of whey proteins to casein gradually decreased in the extracts from raw or pasteurized to sterilized milk samples. Disulfide reactivity of whey proteins was inversely related to the intensity of thermal treatment of milk. The results were consistent with the progressive heat-induced increase in the amount of highly stable proteins in whey from raw to sterilized milk samples. Stability of whey proteins was likely either intrinsic in the native conformation or conferred during heating by thiol−disulfide interchange reactions also involving k-casein. The possibility of using disulfide reactivity as a parameter in the characterization of thermal-treated milk is considered. Keywords: Milk; whey proteins; disulfide reactivity; protein digestibility; thermal treatment
The preparation of diazine derivatives containing the ferroin group (1968)

Abstract With the idea of providing new compounds capable of chelation with metal ions, certain derivatives of diazines, containing the ferroin (NCCN) group have been prepared.
Dietary glycine blunts lung inflammatory cell influx following acute endotoxin (2000)

Mortality associated with endotoxin shock is likely mediated by Kupffer cells, alveolar macrophages, and circulating neutrophils. Acute dietary glycine prevents mortality and blunts increases in serum tumor necrosis factor-alpha (TNF-alpha) following endotoxin in rats. Furthermore, acute glycine blunts activation of Kupffer cells, alveolar macrophages, and neutrophils by activating a glycine-gated chloride channel. However, in neuronal tissue, glycine rapidly downregulates chloride channel function. Therefore, the long-term effects of a glycine-containing diet on survival following endotoxin shock were investigated. Dietary glycine for 4 wk improved survival after endotoxin but did not improve liver pathology, decrease serum alanine transaminase, or effect TNF-alpha levels compared with animals fed control diet. Interestingly, dietary glycine largely prevented inflammation and injury in the lung following endotoxin. Surprisingly, Kupffer cells from animals fed glycine for 4 wk were no longer inactivated by glycine in vitro; however, isolated alveolar macrophages and neutrophils from the same animals were sensitive to glycine. These data are consistent with the hypothesis that glycine downregulates chloride channels on Kupffer cells but not on alveolar macrophages or neutrophils. Importantly, glycine diet for 4 wk protected against lung inflammation due to endotoxin. Chronic glycine improves survival by unknown mechanisms, but reduction of lung inflammation is likely involved.
Purification and Characterization of Protease Inhibitors from Peanuts (Arachis hypogaea)1 (1982)

Five protease inhibitors were isolated from peanut seeds and named A-I, A-II, B-I, B-II, and B-III. These inhibitors seemed to be Bowman-Birk type inhibitors judging from their low molecular weights and high cystine contents. All the inhibitors inhibited both bovine trypsin and chymotrypsin at ratios of 1:2 and 1:1, respectively, but not simultaneously. The complexes of the inhibitors and trypsin no longer inhibit chymotrypsin. On the other hand, their complexes with chymotrypsin inhibit trypsin with a slow release of chymotrypsin.
Optical control of NMDA receptors with a diffusible photoswitch (2015)

N-methyl-D-aspartate receptors (NMDARs) play a central role in synaptic plasticity, learning and memory, and are implicated in various neuronal disorders. We synthesized a diffusible photochromic glutamate analogue, azobenzene-triazole-glutamate (ATG), which is specific for NMDARs and functions as a photoswitchable agonist. ATG is inactive in its dark-adapted trans-isoform, but can be converted into its active cis-isoform using one-photon (near UV) or two-photon (740 nm) excitation. Irradiation with violet light photo-inactivates ATG within milliseconds, allowing agonist removal on the timescale of NMDAR deactivation. ATG is compatible with Ca(2+) imaging and can be used to optically mimic synaptic coincidence detection protocols. Thus, ATG can be used like traditional caged glutamate compounds, but with the added advantages of NMDAR specificity, low antagonism of GABAR-mediated currents, and precise temporal control of agonist delivery.
Subunits Coupling H+ Transport and ATP Synthesis in the Escherichia coli ATP Synthase (1995)

Second site suppressor mutations at position 31 of F1 subunit epsilon recouple ATP-driven H+ translocation in the uncoupled Q42E mutant of subunit c of the Escherichia coli F1F0 ATP synthase (Zhang, Y., Oldenburg, M., and Fillingame, R. H. (1994) J. Biol. Chem. 269, 10221-10224). This finding suggests a functional interaction between subunit c and subunit epsilon during the coupling of H+ transport through F0 to ATP synthesis of F1. However, the physical proximity of the two subunits remained to be defined. In this study, Cys residues were introduced into residues in the polar loop region of subunit c surrounding Gln42 and at position 31 of subunit epsilon to see whether the subunits could be cross-linked. Disulfide bridge formation between subunit c and subunit epsilon was observed in membranes of three double mutants, i.e. cA40C/epsilon E31C, cQ42C/epsilon E31C, and cP43C/epsilon E31C, but not in wild type membranes or in membranes of the cA39C/epsilon E31C double mutant. These results indicate that the polar loop of subunit c and the region around residue 31 of subunit epsilon are physically close to each other in the F1F0 complex and support the hypothesis that these two subunits interact directly in the coupling of H+ transport to ATP synthesis. Disulfide cross-linking of the Q42C subunit c and E31C subunit epsilon leads to inhibition of ATPase coupled H+ transport, as might be expected in a model where the catalytic sites of the F1 ATPase alternate during H+ transport-coupled ATP hydrolysis/synthesis. However, a quantitative relationship between the extent of inhibition of transport and the extent of cross-linking could not be established by the methods used here, and the possibility remains that the epsilon-c cross-linked F1F0 complex retains residual H+ transporting activity.
Comparison of Selected Properties of Barrier Textile Materials Used in Durable, Moisture Repellent Protective Clothing (1994)

Abstract The needs of workers in hazardous environments are extremely varied. The choice of textile materials must be made on the basis of end use and critical characteristics needed for protection, comfort, and performance of the workers. The purpose of this study was to conduct a series of experiments in order to provide scientific data on the qualities and characteristics of several barrier textile massenals. These materials would be suitable for garments for off-shore oil riggers, pesticide applicators, forestry personnel, hazardous waste disposal workers, military personnel, skiers, hikers, and pilots. The following properties were evaluated: stiffness, drape, abrasion resistance, air permeability, water resistance, tear resistance, breaking force and elongation, oil repellency, and soil release. These data provide a range of information on various properties that users of fabrics for prosective clothing need to be aware of in the selection of fabrics for garments.
Level ordered transaction scheduler (LOTS) for concurrency control. (2000)

: In time stamp ordering method, transactions (txns) access data by the order of timestamp. This makes concurrency control (CC) simple but decreases the degree of concurrency. On the other hand, standard locking grants locks on data items to txns by their request order. It increases concurrency but brings dead lock. In this paper, we propose a new approach called level ordered txn scheduler (LOTS), which can optimize txns execution order and maximize the degree of concurrency. Two links, D_Link and T_Link, are implemented in LOTS to support its internal quick computing. Each txn has a lever number (LNo). A txn can commit only when its LNo is 0. As shown in this paper, LOTS provides flexible control mechanisms on CC. And the depth of cascading aborts can be controlled. In the presence of heavy conflict frequency, LOTS has no system &quot;thrashing&quot;. Performance analysis also shows that it&apos;s a promising CC with reasonable small overhead.
Focal modulation microscopy (2008)

We report a novel light microscopy method for high resolution molecular imaging of thick biological tissues with one photon excited fluorescence. Effective optical sectioning and diffraction limited spatial resolution are achieved when imaging deep inside a multiple-scattering medium by the use of focal modulation, a technique for suppressing the background fluorescence signal excited by scattered light. Our method has been validated with animal tissue and an imaging depth around 600 microns has been demonstrated.
The complete nucleotide sequence of the gene coding for the human aldolase C (1988)

Journal Article The complete nucleotide sequence of the gene coding for the human aldolase C Get access P. Buono, P. Buono Istituto di Scienze Biochimiche, II Facoltà di Medicina e Chirurgia, Università degli Studi di NapoliVia Sergio, Pansini 5, 80131 Napoli, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar G. Paolella, G. Paolella Istituto di Scienze Biochimiche, II Facoltà di Medicina e Chirurgia, Università degli Studi di NapoliVia Sergio, Pansini 5, 80131 Napoli, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar F.P. Mancini, F.P. Mancini Istituto di Scienze Biochimiche, II Facoltà di Medicina e Chirurgia, Università degli Studi di NapoliVia Sergio, Pansini 5, 80131 Napoli, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar P. Izzo, P. Izzo Istituto di Scienze Biochimiche, II Facoltà di Medicina e Chirurgia, Università degli Studi di NapoliVia Sergio, Pansini 5, 80131 Napoli, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar F. Salvatore F. Salvatore Istituto di Scienze Biochimiche, II Facoltà di Medicina e Chirurgia, Università degli Studi di NapoliVia Sergio, Pansini 5, 80131 Napoli, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 10, 25 May 1988, Page 4733, https://doi.org/10.1093/nar/16.10.4733 Published: 25 May 1988 Article history Accepted: 09 March 1988 Published: 25 May 1988
Progress in high resolution atomic force microscopy in biology (1995)

The atomic force microscope (AFM) was invented by Binnig, Quate and Gerber less than 10 years ago (Binnig et al . 1986). In their first prototype, a piece of goldfoil was used as the cantilever, with a crushed diamond tip mounted at the end. On the back of the cantilever, a tunnelling junction was used to monitor the deflection of the cantilever (the gold-foil) when the specimen was scanned with the tip in contact with the surface. Thus, the surface topography of the specimen was obtained with a resolution critically dependent on the sharpness of the tip provided the deformation of the specimen was not serious. Even with such a crude set-up, they managed to obtain a lateral resolution of ˜ 30 Å and a vertical resolution of better than 1 Å on an amorphous A1 2 O 3 surface. The operating principle of such an instrument is deceptively simple. However, such an arrangement was inconvenient for routine operations and unsuitable for imaging hydrated specimens, because the tunnelling junction is easily contaminated in air and works poorly in aqueous solutions (Alexander et al . 1989). As a result, the application of this type of AFM to biological samples was rare (Engel, 1991).
COMPUTATIONAL INTELLIGENCE IN NUCLEAR ENGINEERING (2005)

Approaches to several recent issues in the operation of nuclear power plants using computational intelligence are discussed. These issues include 1) noise analysis techniques, 2) on-line monitoring and sensor validation, 3) regularization of ill-posed surveillance and diagnostic measurements, 4) transient identification, 5) artificial intelligence-based core monitoring and diagnostic system, 6) continuous efficiency improvement of nuclear power plants, and 7) autonomous anticipatory control and intelligent-agents. Several changes to the focus of Computational Intelligence in Nuclear Engineering have occurred in the past few years. With earlier activities focusing on the development of condition monitoring and diagnostic techniques for current nuclear power plants, recent activities have focused on the implementation of those methods and the development of methods for next generation plants and space reactors. These advanced techniques are expected to become increasingly important as current generation nuclear power plants have their licenses extended to 60 years and next generation reactors are being designed to operate for extended fuel cycles (up to 25 years), with less operator oversight, and especially for nuclear plants operating in severe environments such as space or ice-bound locations.
A 5.8-GHz DSRC Transceiver With a 10-<formula formulatype="inline"><tex Notation="TeX">$\mu{\hbox {A}}$</tex> </formula> Interference-Aware Wake-Up Receiver for the Chinese ETCS (2014)

This paper presents a fully integrated 5.8-GHz dedicated short-range communication transceiver with a 10- μA interference-aware wake-up receiver (WuRx) for Chinese electronic toll collection system terminals that can operate with a low standby and operating current consumption. To reduce the current consumption, a high-gain RF envelope detector using a voltage-boosting method is proposed for both the WuRx and receiver (Rx) while the proposed high-power ASK modulator extends output dynamic range in low power consumption. Additionally, a delay-based bandpass filter is adopted in the WuRx to filter out interference from automotive applications, thus increasing the battery lifetime by reducing the probability of a false wake-up. The proposed transceiver is fabricated using 0.13- μm CMOS technology with a chip size of 2.8 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for the target frequency range of 5.8 GHz. The measured results demonstrate sensitivities of -44 and -61 dBm for the WuRx and Rx, dissipating currents of 10 μA and 19 mA from 3.3-V supply voltage, respectively. The transmitter exhibits a normal output power of +5 dBm at an operating current of 46 mA.
Hedgehog Antagonist<i>REN<sup>KCTD11</sup></i>Regulates Proliferation and Apoptosis of Developing Granule Cell Progenitors (2005)

During the early development of the cerebellum, a burst of granule cell progenitor (GCP) proliferation occurs in the outer external granule layer (EGL), which is sustained mainly by Purkinje cell-derived Sonic Hedgehog (Shh). Shh response is interrupted once GCPs move into the inner EGL, where granule progenitors withdraw proliferation and start differentiating and migrating toward the internal granule layer (IGL). Failure to interrupt Shh signals results in uncoordinated proliferation and differentiation of GCPs and eventually leads to malignancy (i.e., medulloblastoma). The Shh inhibitory mechanisms that are responsible for GCP growth arrest and differentiation remain unclear. Here we report that REN, a putative tumor suppressor frequently deleted in human medulloblastoma, is expressed to a higher extent in nonproliferating inner EGL and IGL granule cells than in highly proliferating outer EGL cells. Accordingly, upregulated REN expression occurs along GCP differentiation in vitro, and, in turn, REN overexpression promotes growth arrest and increases the proportion of p27/Kip1+ GCPs. REN also impairs both Gli2-dependent gene transcription and Shh-enhanced expression of the target Gli1 mRNA, thus antagonizing the Shh-induced effects on the proliferation and differentiation of cultured GCPs. Conversely, REN functional knock-down impairs Hedgehog antagonism and differentiation and sustains the proliferation of GCPs. Finally, REN enhances caspase-3 activation and terminal deoxynucleotidyl transferase-mediated biotinylated UTP nick end labeling apoptotic GCP numbers; therefore, the pattern of REN expression, its activity, and its antagonism on the Hedgehog pathway suggest that this gene may represent a restraint of Shh signaling at the outer to inner EGL GCP transitions. Medulloblastoma-associated REN loss of function might withdraw such a limiting signal for immature cell expansion, thus favoring tumorigenesis.
Thermal Heterogeneity Constitutes A Marker for the Detection of Malignant Gastric Lesions In Vivo (2003)

These findings suggest that the detection of DeltaT, between normal tissue and neoplastic lesions, could be useful in clinical practice for the differential diagnosis of stomach lesions, even in the early stages.