gebhart/patrepeval huggingface dataset:
MR contrast probes that trace gene transcripts for cerebral ischemia in live animals (2007)

The aim of this research was to validate transcription magnetic resonance (MR) imaging (MRI) for gene transcript targeting in acute neurological disorders in live subjects. We delivered three MR probe variants with superparamagnetic iron oxide nanoparticles (SPION, a T2 susceptibility agent) linked to a phosphorothioate-modified oligodeoxynucleotide (sODN) complementary to c-fos mRNA (SPION-cfos) or beta-actin mRNA (SPION-beta-actin) and to sODN with random sequence (SPION-Ran). Each probe (1 microg Fe in 2 microl) was delivered via intracerebroventricular infusion to the left cerebral ventricle of male C57Black6 mice. We demonstrated SPION retention, measured as decreased T2* signal or increased R2* value (R2* = 1/T2*). Animals that received the SPION-beta-actin probe exhibited the highest R2* values, followed (in descending order) by SPION-cfos and SPION-Ran. SPION-cfos retention was localized in brain regions where SPION-cfos was present and where hybrids of SPION-cfos and its target c-fos mRNA were detected by in situ reverse transcription PCR. In animals that experienced cerebral ischemia, SPION-cfos retention was significantly increased in locations where c-fos mRNA increased in response to the ischemic insult; these elevations were not observed for SPION-beta-actin and SPION-Ran. This study should enable MR detection of mRNA alteration in disease models of the central nervous system.
Conformational analysis of organic carbonyl compounds. Part 4. A 1H and 13C nuclear magnetic resonance study of formyl and acetyl derivatives of benzo[b]furan (1984)

A conformational study of formyl and acetyl derivatives of benzo[b] furan provides evidence that in the case of 2- and 7-derivatives the E,Z-conformational mixture is solvent dependent, the Z-form prevailing in solvents with higher polarity. The presence of the same substituents in the 3- and 4-position gives compounds with predominantly Z-conformation and no change is caused by solvents. These results show an interestingly different behaviour by carbonyl derivatives of benzo[b] furan with respect to the same benzo[b] thiophene derivatives. The conformational analysis was carried out by the n.m.r. method by employing 1H and 13C chemical shifts, long-range proton–proton coupling constants, and lanthanide-induced shifts (LIS) simulation. For the derivatives substituted in position 7, the LIS method is not a suitable approach for the determination of conformer populations since, in solution, a chelate is formed where bonding of Eu to the oxygen atoms of the carbonyl and of the heterocyclic ring stabilizes the Z-form. A quantitative approach for determining the relative conformer populations of benzo[b] furan-7-carbaldehyde was set up by statistical manipulation of long-range proton–proton coupling constants, proton chemical shifts, and the classical theory of dielectrics.
Library 2.0: Web 2.0 Applications in Libraries (2009)

The web technology has profound impact on the functioning of library and information centers across the globe. The application of Web 2.0 technologies for library resources and services led to emergence of a new librarianship called as library 2.0. This paper discusses the principles of Web 2.0 and Library 2.0 and also the application of web 2.0 technologies for the development of Library 2.0 services.
Macromolecular transport across arterial and venous endothelium in rats. Studies with Evans blue-albumin and horseradish peroxidase. (1990)

Atherosclerotic lesions are characterized by lipid infiltration in regions with high rates of endothelial cell turnover. The present investigation was designed to elucidate the route of macromolecular transport across vascular endothelium. The aorta and vena cava of male Sprague-Dawley rats were perfusion-fixed after the intravenous injection of Evans-blue albumin (EBA) or horseradish peroxidase (HRP). Fluorescence microscopic examination of en face preparation of the aorta stained with hematoxylin allowed the identification of endothelial cells that underwent mitosis, together with the localization and quantification of fluorescent spots for EBA leakage. The HRP specimens were subjected to histochemical treatment, and HRP leakage was seen as brown spots under the light microscope. Silver nitrate stain was added in both EBA and HRP studies to outline cell boundaries and to visualize stigmata, stomata, and dead cells. In the aorta, almost every dividing cell showed junctional leakage to albumin and HRP, with clustering of leaky spots around the branch orifices. Time-dependent studies showed gradual increases in the diameter and number of these heterogeneously sized leaky spots, which finally fused to sizes corresponding to the "blue areas" for EBA or "brown areas" for HRP. Compared with arteries, veins had fewer mitotic cells, but more dead cells and diffuse dye-staining areas, indicating a more rapid transport of macromolecules. The leaky spots in the artery were associated mainly with mitotic cells, dead cells, and stigmata, whereas those in the vein occurred primarily at regions with dead cells. These results suggest that the preferential association of the enhanced transport of macromolecules with mitosis in the arterial as compared to venous endothelium and the differential behavior in transmural transport between arteries and veins may form the basis for the predilection of atherosclerosis in arteries.
Proteolysis of Monomeric Recombinant Rotavirus VP4 Yields an Oligomeric VP5* Core (2001)

Rotavirus particles are activated for cell entry by trypsin cleavage of the outer capsid spike protein, VP4, into a hemagglutinin, VP8*, and a membrane penetration protein, VP5*. We have purified rhesus rotavirus VP4, expressed in baculovirus-infected insect cells. Purified VP4 is a soluble, elongated monomer, as determined by analytical ultracentrifugation. Trypsin cleaves purified VP4 at a number of sites that are protected on the virion and yields a heterogeneous group of protease-resistant cores of VP5*. The most abundant tryptic VP5* core is trimmed past the N terminus associated with activation for virus entry into cells. Sequential digestion of purified VP4 with chymotrypsin and trypsin generates homogeneous VP8* and VP5* cores (VP8CT and VP5CT, respectively), which have the authentic trypsin cleavages in the activation region. VP8CT is a soluble monomer composed primarily of beta-sheets. VP5CT forms sodium dodecyl sulfate-resistant dimers. These results suggest that trypsinization of rotavirus particles triggers a rearrangement in the VP5* region of VP4 to yield the dimeric spikes observed in icosahedral image reconstructions from electron cryomicroscopy of trypsinized rotavirus virions. The solubility of VP5CT and of trypsinized rotavirus particles suggests that the trypsin-triggered conformational change primes VP4 for a subsequent rearrangement that accomplishes membrane penetration. The domains of VP4 defined by protease analysis contain all mapped neutralizing epitopes, sialic acid binding residues, the heptad repeat region, and the membrane permeabilization region. This biochemical analysis of VP4 provides sequence-specific structural information that complements electron cryomicroscopy data and defines targets and strategies for atomic-resolution structural studies.
Experimental Measurements of the Thermal Conductivity of Ash Deposits:  Part 2. Effects of Sintering and Deposit Microstructure (2000)

This paper describes an experimental study that examines the influence of sintering and microstructure on ash deposit thermal conductivity. The measurements are made using a technique developed to make in situ, time-resolved measurements of the effective thermal conductivity of ash deposits formed under conditions that closely replicate those found in the convective pass of a commercial boiler. The technique is designed to minimize the disturbance of the natural deposit microstructure. The initial stages of sintering and densification are accompanied by an increase in deposit thermal conductivity. Subsequent sintering continues to densify the deposit, but has little effect on deposit thermal conductivity. SEM analyses indicate that sintering creates a layered deposit structure with a relatively unsintered innermost layer. We hypothesize that this unsintered layer largely determines the overall deposit thermal conductivity. A theoretical model that treats a deposit as a two-layered material predicts the observed trends in thermal conductivity.
$hboxBaSm_2hboxTi_4hboxO_12$Thin Film for High-Performance Metal–Insulator–Metal Capacitors (2006)

A high capacitance density of 4.84 fF/mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and a low leakage current density of 4.28 fA/pFmiddotV were obtained for a 138-nm-thick crystalline BaSm <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Ti <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sub> (BST) film. The 100-nm-thick amorphous BST film exhibited a high capacitance density of 3.91 fF/mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and a low leakage current of 1.24 fA/pFmiddotV. The crystalline BST film had quadratic and linear voltage coefficient of capacitance (VCC) of -295 ppm/V <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2 </sup> and 684 ppm/V, respectively, and a temperature coefficient of capacitance (TCC) of -136 ppm/degC at 100 kHz. The amorphous BST film also showed quadratic and linear VCCs of 48.6 ppm/V <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and -738 ppm/V, respectively, with a low TCC of 169 ppm/degC at 100 kHz
Cost-free scan: a low-overhead scan path design (1998)

Conventional scan design imposes considerable area and delay overheads. To establish a scan chain in the test mode, multiplexers at the inputs of flip-flops and scan wires are added to the actual design. However, the functionality of the functional logic has not been utilized for the test purposes. We propose a low-overhead scan design methodology, called cost-free scan, which exploits the controllability of primary inputs to establish scan paths through the functional logic. We show how to analyze the circuit to determine all the free-scan flip-flops and select the best input vector to establish the maximum number of free-scan flip-flops for the scan chain design. Significant reduction in the scan overhead is achieved on ISCAS89 benchmarks. In full-scan designs, as many as 89% of the flip-flops are found free-scannable. In the partial-scan designs, we assume that selecting flip-flops for scan to break sequential cycles is used to increase circuit testability. Reduction can be as high as 97% in scan flip-flops needed to break sequential cycles.
Transcriptional activation by the pseudorabies virus immediate early protein. (1990)

The pseudorabies virus immediate early (IE) protein is a potent, promiscuous activator of viral and cellular gene transcription. The promiscuous action of IE protein has led to the suggestion that it functions by an unusual mechanism. Here, we show that IE protein has the two essential features of a typical cellular activator: (1) a transcriptional activation region, and (2) a separable region that directs IE protein, or an unrelated activation region, to the vicinity of the promoter. We map the IE protein activation region to 34 amino acids, demonstrate that it is comparable in strength to the strongest known activation region, and show that it is required for the transcriptional activity of the intact IE protein. The 34-amino-acid IE protein activation region is highly acidic. We provide evidence that it uses the same cellular target as an unrelated acidic activator and a different target from that of a nonacidic activator. Our results provide insight into the function of promiscuous eukaryotic transcriptional activators.
Thrombopoietin and Platelet Function (2006)

In hematopoietic stem cells and megakaryocytes, the thrombopoietin (TPO) receptor signals to control proliferation, maturation, and antiapoptosis. In the anucleated platelet, much of this signaling appears out of place. Nevertheless, platelets possess TPO receptors and the cascades for transduction of TPO signals, but the final effect has shifted from DNA regulation to control of platelet aggregation and secretion. Although at physiological concentrations, TPO is not a sufficiently strong stimulator to trigger platelet functions in the absence of a second stimulator, TPO increases the sensitivity of platelets to agonist stimulation, leading to better functions at lower stimulation.
Double Threaded Screw Fixation for Bilateral Stress Fracture of the Medial Malleolus (2014)

An 18-year-old college basketball player presented with continued ankle pain. A radiographic examination showed bilateral medial malleolus stress fractures. Considering the prolonged history and refractory nature of this injury, surgery was adopted as a treatment option. At surgery, the fracture site was percutaneously fixed using two cannulated double threaded screws. Surgery for each side was sequentially performed two months apart. Prompt bony healing was attained after surgery, and the patient could return to his previous sports level six months after the first surgery without subsequent recurrence.
Synthetic lethality of cytolytic HSV-1 in cancer cells with ATRX and PML deficiency (2019)

Cancers that utilize the alternative lengthening of telomeres (ALT) mechanism for telomere maintenance are often difficult to treat and have a poor prognosis. They are also commonly deficient for expression of ATRX protein, a repressor of ALT activity, and a component of promyelocytic leukemia nuclear bodies (PML NBs) that are required for intrinsic immunity to various viruses. Here, we asked whether ATRX deficiency creates a vulnerability in ALT cancer cells that could be exploited for therapeutic purposes. We showed in a range of cell types that a mutant herpes simplex virus type 1 (HSV-1) lacking ICP0, a protein that degrades PML NB components including ATRX, was ten- to one thousand-fold more effective in infecting ATRX-deficient cells than wild-type ATRX-expressing cells. Infection of co-cultured primary and ATRX-deficient cancer cells revealed that mutant HSV-1 selectively killed ATRX-deficient cells. Sensitivity to mutant HSV-1 infection also correlated inversely with PML protein levels, and we showed that ATRX upregulates PML expression at both the transcriptional and post-transcriptional levels. These data provide a basis for predicting, based on ATRX or PML levels, which tumors will respond to a selective oncolytic herpesvirus.
ACTIVATION OF LIVER X RECEPTOR BY SYNTHETIC AGONIST T0901317 REDUCES THE LIVER INJURY CAUSED BY LIPOPOLYSACCHARIDE IN THE RAT (2006)

Aim: We recently demonstrated that activation of Liver X receptor (LXR) by GW3965 ameliorated the liver injury casued by endotoxins by suppressing activation of Kupffer cells (YY Wang, SHOCK 2005). In the present study we wanted to examine whether another synthetic agonists of LXR (T091317) would have similar effects. Method: Male Wistar rats received intravenous administration through the jugular vein of (i) 5 μg/kg of T0901317 (N = 13), (ii) 10 μg/kg of T0901317 (N = 13), (iii) 30 μg/kg of T0901317 or (iv) vehicle (10% dimethyl sulfoxide) 30 minutes before administration of lipopolysaccharide (LPS; 6 mg/kg). Sham operated animals were injected with saline. After 6 h, rats were euthanized and plasma analyzed for markers of liver injury/dysfunction and cytokines. Results: Treatment with low doses of T0901317 (5 or 10 μg/kg) attenuated the LPS-induced increase in plasma levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), and bilirubin (P ≤ 0.05 for all) (markers of liver injury/dysfunction), whereas the highest dose was ineffective. The protective effect of LXR activation was associated with a 50% reduction in plasma levels of tumor necrosis factor alpha (TNFα), whereas interleukin-1β, IL-2, IL-6, IL-10, IL-12, or IFNγ were not significantly altered. Conclusion: Pre-treatment with two structurally distinct agonists of LXR ameliorated liver injury and dysfunction caused by LPS in the rat. Further studies are required to elucidate the role of LXR in the treatment of sepsis and shock.
20.2 A variable-conversion-ratio 3-phase resonant switched capacitor converter with 85% efficiency at 0.91W/mm<sup>2</sup> using 1.1nH PCB-trace inductors (2015)

Switched-capacitor (SC) converters have shown significant promise for monolithic integration in a variety of mobile computing applications due to the relatively high energy-densities of modern capacitor technologies and the emergence of deep-trench technology [1-4]. Compared to more traditional buck and boost topologies, the SC approach provides better utilization of active and passive components, and is especially favorable when using submicron or deep-submicron CMOS technology because low-voltage devices can be configured in cascaded or hierarchical structures to interface across wide conversion ratios [5].
D1.8.1 Base upper-level ontology (BULO) Guidance 1 (2005)

An important practical approach to ontology generation is the use of background or pre-existing knowledge in the form of a basic upper-level ontology. Such an ontology can also be used for metadata generation and as a groundwork for the overall knowledge modelling and integration strategy of a KM environment. The essential contribution of this deliverable is a basic upper-level ontology called PROTON (PROTo ONtology), which is hereby introduced and documented. It contains about 300 classes and 100 properties, providing coverage of the general concepts necessary for a wide range of tasks, including semantic annotation, indexing, and retrieval of documents. The design principles can be summarized as follows (i) domain-independence; (ii) light-weight logical definitions; (iii) alignment with popular standards; (iv) good coverage of named entities and concrete domains (i.e. people, organizations, locations, numbers, dates, addresses). The ontology is originally encoded in a fragment of OWL Lite and split into four modules: System, Top, Upper, and KM (Knowledge Management).
THE SHORT-TERM EFFECTS OF LOW-DOSE-RATE RADIATION ON EL4 LYMPHOMA CELL (2012)

To determine the biological effects of low-dose-rate radiation ( 137 Cs, 2.95 mGy/h) on EL4 lymphoma cells during 24 h, we investigated the expression of genes related to apoptosis, cell cycle arrest, DNA repair, iron transport, and ribonucleotide reductase. EL4 cells were continuously exposed to low-dose-rate radiation (total dose: 70.8 mGy) for 24 h. We analyzed cell proliferation and apoptosis by trypan blue exclusion and flow cytometry, gene expression by real-time PCR, and protein levels with the apoptosis ELISA kit. Apoptosis increased in the low-dose-rate irradiated cells, but cell number did not differ between non-(Non-IR) and low-dose-rate irradiated (LDR-IR) cells. In concordance with apoptotic rate, the transcriptional activity of ATM, p53, p21, and Parp was upregulated in the LDR-IR cells. Similarly, Phospho-p53 (Ser15), cleaved caspase 3 (Asp175), and cleaved Parp (Asp214) expression was upregulated in the LDR-IR cells. No difference was observed in the mRNA expression of DNA repair-related genes (Msh2, Msh3, Wrn, Lig4, Neil3, ERCC8, and ERCC6) between Non-IR and LDR-IR cells. Interestingly, the mRNA of Trfc was upregulated in the LDR-IR cells. Therefore, we suggest that short-term low-dose-rate radiation activates apoptosis in EL4 lymphoma cells.
The Platinum Metals as Selective Hydrogenation Catalysts (1963)

At the present time the consumption of catalytic materials by industry is increasing rapidly, and the demand is growing for catalysts that are able to promote specific or selective reactions. In practice, however, the formulation of a catalyst for a particular function is frequently empirical, at least in part. We are not yet in the position of being able to design a catalyst “on the drawing-board” for a specific complex operation with any high degree of confidence, although this is a situation which we may reasonably hope to achieve at some time in the future. Recent research at the University of Hull, most of which is unpublished as yet, has indicated that a considerable rationalisation may soon be possible in the field of the metal-catalysed hydrogenation of multiply unsaturated hydrocarbons and the hydroisomerisation of olefins. It is the purpose of this paper to present a preview of this work and to advance some of its tentative conclusions.
mTORC1 Senses Lysosomal Amino Acids Through an Inside-Out Mechanism That Requires the Vacuolar H <sup>+</sup> -ATPase (2011)

The mTOR complex 1 (mTORC1) protein kinase is a master growth regulator that is stimulated by amino acids. Amino acids activate the Rag guanosine triphosphatases (GTPases), which promote the translocation of mTORC1 to the lysosomal surface, the site of mTORC1 activation. We found that the vacuolar H(+)-adenosine triphosphatase ATPase (v-ATPase) is necessary for amino acids to activate mTORC1. The v-ATPase engages in extensive amino acid-sensitive interactions with the Ragulator, a scaffolding complex that anchors the Rag GTPases to the lysosome. In a cell-free system, ATP hydrolysis by the v-ATPase was necessary for amino acids to regulate the v-ATPase-Ragulator interaction and promote mTORC1 translocation. Results obtained in vitro and in human cells suggest that amino acid signaling begins within the lysosomal lumen. These results identify the v-ATPase as a component of the mTOR pathway and delineate a lysosome-associated machinery for amino acid sensing.
Faults and recovery methods in regional undersea OADM networks (2009)

An experimental study of faults in an important class of undersea OADM networks demonstrates that channel performance through surviving segments can be recovered by the terminal-based procedures enabled by a fault resilient network design.