gebhart/patrepeval huggingface dataset:
NF-E2-related Factor-2 Mediates Neuroprotection against Mitochondrial Complex I Inhibitors and Increased Concentrations of Intracellular Calcium in Primary Cortical Neurons (2003)

NF-E2-related factor-2 (Nrf2) regulates the gene expression of phase II detoxification enzymes and antioxidant proteins through an enhancer sequence referred to as the antioxidant-responsive element (ARE). In this study, we demonstrate that Nrf2 protects neurons in mixed primary neuronal cultures containing both astrocytes ( approximately 10%) and neurons ( approximately 90%) through coordinate up-regulation of ARE-driven genes. Nrf2-/- neurons in this mixed culture system were more sensitive to mitochondrial toxin (1-methyl-4-phenyl-1,2,5,6-tetrahydropyridine or rotenone)-induced apoptosis compared with Nrf2+/+ neurons. To understand the underlying mechanism of this observed differential sensitivity, we compared the gene expression profiles using oligonucleotide microarrays. Microarray data showed that Nrf2+/+neuronal cultures had higher expression levels of genes encoding detoxification enzymes, antioxidant proteins, calcium homeostasis proteins, growth factors, neuron-specific proteins, and signaling molecules compared with Nrf2-/- neuronal cultures. As predicted from the microarray data, Nrf2-/- neurons were indeed more vulnerable to the cytotoxic effects of ionomycin- and 2,5-di-(t-butyl)-1,4-hydroquinone-induced increases in intracellular calcium. Finally, adenoviral vector-mediated overexpression of Nrf2 recovered ARE-driven gene expression in Nrf2-/- neuronal cultures and rescued Nrf2-/- neurons from rotenone- or ionomycin-induced cell death. Taken together, these findings suggest that Nrf2 plays an important role in protecting neurons from toxic insult.
Intraarticular injection of high molecular weight hyaluronan for osteoarthritis of the knee - prediction of effectiveness with biological markers. (2006)

It has been reported that the concentration of aggrecan-derived fragments in synovial fluid decreases with advancement of the OA stage, reflecting decreases in the amount of residual cartilage and suppression of chondrocyte metabolism. Our findings suggested that HA injection exhibits a greater clinical effect in cases with a high intraarticular aggrecan fragment concentration, i.e., cases in which a high amount of residual cartilage and chondrocyte metabolic activity remain. The biological markers were useful in predicting the effectiveness of HA injection for OA of the knee.
[Advances in interleukin-6 therapy]. (1999)

Interleukin-6 (IL-6) exhibits multiple biologic activities such as regulation of immunological responses and hematopoiesis, promotion of acute inflammation, and stimulation of some malignant and non-malignant cell growth. The IL-6 receptor system consists of an IL-6 specific binding molecule, IL-6R and a signal transducer, gp130. Following gp130 dimerization, IL-6 activates multiple signaling pathways (Ras dependent MAPk cascade, STAT1-STAT3 heterodimer pathway, and STAT3 homodimer pathway). Several other cytokines including oncostatin M, IL-11, leukemia inhibitory factor (LIF), ciliary neurotrophic factor (CNTF) and cardiotropin-1 (CT-1) use gp130 as a common signal transducing molecule and therefore have similar biological activities. Two major in vivo functions of IL-6 are reported. Firstly, IL-6 acts as a growth factor of some malignant and non-malignant cells such as malignant plasma cells in multiple myeloma, mesangial cells in the kidney, and keratinocytes. Secondly, IL-6 mediates inflammatory and immune responses in rheumatoid arthritis, Castleman disease, psoriasis, cardiac myxoma, cachexia, and other inflammatory conditions. Recently, a humanized anti-IL-6 receptor antibody was developed. Neutralization of IL-6 activity by the humanized anti-IL-6 receptor antibody may be a new therapeutic approach for IL-6 related diseases such as multiple myeloma, Castleman disease and rheumatoid arthritis.
Deregulation of microRNA involved in hematopoiesis and the immune response in HTLV-I adult T-cell leukemia (2009)

Human T-cell leukemia virus type-I (HTLV-I) is the etiologic agent of adult T-cell leukemia (ATL), an aggressive lymphoproliferative disease. MicroRNAs (miRNAs) are differentially expressed during hematopoiesis and lineage commitment of hematopoietic stem cell progenitors (HSCPs). Here, we report aberrant expression of hematopoietic-specific miR-223, miR-181a, miR-150, miR-142.3p, and miR-155 in HTLV-I-infected cells in vitro and uncultured ex vivo ATL cells. Our results suggest that HTLV-I-infected cells have an unbalanced expression of miRNA that favors T-cell differentiation. We also found altered expression of miRNA previously recognized as innate immunity regulators: miR-155, miR-125a, miR-132, and miR-146. Strikingly, our data also revealed significant differences between ex vivo ATL tumor cells and in vitro HTLV-I cell lines. Specifically, miR-150 and miR-223 were up-regulated in ATL patients but consistently down-regulated in HTLV-I cell lines, suggesting that ATL cells and in vitro-established cells are derived from distinct cellular populations.
Low-cost multiple degrees-of-freedom optical tracking for 3D interaction in head-mounted display virtual reality (2009)

Abstract Interacting with the 3D content present in games and virtual environments generally involves some form of 3D interaction. As such, the design and development of 3D spatial interaction devices are important in creating more realistic and immersive user experiences in 3D virtual environment applications through natural and intuitive human expression. In general, current commercially available 3D input devices for virtual reality applications like data gloves, multiple DOF sensors and trackers, etc. typically come with a heavy price tag. The objective of this research is to investigate an approach to setting up an inexpensive 6-DOF optical tracking system using Wii Remotes, which is adequate for 3D interaction in an interactive Head-Mounted Display (HMD) virtual reality system. For the purpose of HMD virtual reality, a user should ideally be able to use a 3D interaction device in a space surrounding the user. This cannot be achieved when using this game controller in the conventional manner. Also, normal usage of the controller only allows for relative positioning and cannot reliably track 6-DOF. This paper outlines a method of using Wii Remotes for 3D spatial interaction in an area surrounding the user. This paper also presents experimental results conducted in order to benchmark the accuracy of the system, by comparing the systems position and orientation estimates with the readings obtained from a commercial 6-DOF magnetic tracker. Index Terms 3D input device, optical tracking, virtual
Epidemiology and Predictors of Mortality in Cases of Candida Bloodstream Infection: Results from Population-Based Surveillance, Barcelona, Spain, from 2002 to 2003 (2005)

We conducted population-based surveillance for Candida bloodstream infections in Spain to determine its incidence, the extent of antifungal resistance, and risk factors for mortality. A case was defined as the first positive blood culture for any Candida spp. in a resident of Barcelona, from 1 January 2002 to 31 December 2003. We defined early mortality as occurring between days 3 to 7 after candidemia and late mortality as occurring between days 8 to 30. We detected 345 cases of candidemia, for an average annual incidence of 4.3 cases/100,000 population, 0.53 cases/1,000 hospital discharges, and 0.73 cases/10,000 patient-days. Outpatients comprised 11% of the cases, and 89% had a central venous catheter (CVC) at diagnosis. Overall mortality was 44%. Candida albicans was the most frequent species (51% of cases), followed by Candida parapsilosis (23%), Candida tropicalis (10%), Candida glabrata (8%), Candida krusei (4%), and other species (3%). Twenty-four isolates (7%) had decreased susceptibility to fluconazole (MIC > or = 16 microg/ml). On multivariable analysis, early death was independently associated with hematological malignancy (odds ratio [OR], 3.5; 95% confidence interval [CI], 1.1 to 10.4). Treatment with antifungals (OR, 0.05; 95% CI, 0.01 to 0.2) and removal of CVCs (OR, 0.3; 95% CI, 0.1 to 0.9) were protective factors for early death. Receiving adequate treatment, defined as having CVCs removed and administration of an antifungal medication (OR, 0.2; 95% CI, 0.08 to 0.8), was associated with lower odds of late mortality; intubation (OR, 7.5; 95% CI, 2.6 to 21.1) was associated with higher odds. The incidence of candidemia and prevalence of fluconazole resistance are similar to other European countries, indicating that routine antifungal susceptibility testing is not warranted. Antifungal medication and catheter removal are critical in preventing mortality.
Testable Signatures of Quantum Nonlocality in a Two-Dimensional Chiralp-Wave Superconductor (2008)

A class of topological excitations-the odd-winding number vortices-in a spinless 2D chiral p-wave (px+ipy) superconductor traps Majorana fermion states in the vortex cores. For a dilute gas of such vortices, the lowest energy fermionic eigenstates are intrinsically nonlocal. We predict two testable signatures of this unusual quantum nonlocality in quasiparticle tunneling experiments. We discuss why the associated teleportationlike phenomenon does not imply the violation of causality.
Three-dimensional tissue constructs built by bioprinting (2006)

Bioprinting is an evolving tissue engineering technology. It utilizes computer controlled three-dimensional printers for rapid and high-precision construction of three-dimensional biological structures. We employed discrete and continuous bioprinting to build three-dimensional tissue constructs. In the former case bioink particles - spherical cell aggregates composed of many thousands of cells - are delivered one by one into biocompatible scaffolds, the biopaper. Structure formation takes place by the subsequent fusion of the bioink particles due to their liquid-like and self-assembly properties. In the latter case a mixture of cells and scaffold material is extruded from the biocartridge akin to toothpaste to arrive at the desired construct. Specifically, we built rectangular tissue blocks of several hundred microns in thickness as well as tubular structures of several millimeters in height. The physical basis of structure formation was studied by computer simulations.
An analysis of CDMA 3G wireless communications standards (2003)

This paper gives a high level overview of the development status of the next generation standards, particularly in the convergence of major CDMA 3G standards proposals. Major technical characteristics of the physical layer of key next generation (3G) CDMA wireless communications standards proposals in the ITU are discussed. General attributes and major forward and reverse link features are compared and analyzed. Key differences of the seven CDMA terrestrial radio transmission technology physical layers are highlighted, and a technical discussion for convergence of major parameters is given. Focus has been given to the most controversial issues such as the chip rate, the downlink pilot structure, and synchronized vs asynchronized system operations. Finally the author wishes to point out that while it is technically possible to achieve global harmonization with major impacts on system performance, other nontechnical factors are blocking the progress as well.
Vagotomy Blocks the Induction of Interleukin-1β (IL-1β) mRNA in the Brain of Rats in Response to Systemic IL-1β (1998)

There is considerable interest in the mechanisms by which systemic cytokines signal the CNS to elicit centrally controlled biological actions. This study determined the effects of intraperitoneal injections of interleukin-1beta (IL-1beta) on IL-1beta mRNA and IL-1 receptor accessory protein (IL-1RAP) mRNA production in rat liver and brain using the reverse transcription-PCR. Saline or IL-1beta (0.5 microg/kg) was injected intraperitoneally in subdiaphragmatically vagotomized and sham-operated (SHAM) rats. All injections were performed at dark onset, and rats were killed 2 hr after the injection. In SHAM rats, IL-1beta increased IL-1beta mRNA levels in the liver, hypothalamus, hippocampus, and brainstem. Subdiaphragmatic vagotomy blocked the IL-1beta-induced increase in IL-1beta mRNA in the brainstem and hippocampus and significantly attenuated the increase in the hypothalamus. Vagotomy did not affect IL-1beta-induced IL-1beta mRNA production in the liver. IL-1RAP mRNA was highly expressed in each region examined; however, no significant differences in IL-1RAP mRNA production were found in any region after IL-1beta injection. The current results indicate that the vagus nerve is involved in transmitting cytokine signals to the brain and suggest that the induction of brain cytokines is a critical step in the pathway by which vagal-mediated signals result in centrally controlled symptoms of the acute phase response.
Self-Pulsing Regime of DC Electric Discharge in Dielectric Tube Filled With Water Containing Gas Bubble (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Effective generation of biochemically active species inside a liquid can be performed by an electric discharge in small gas bubbles admixed from outside into the liquid. In such a case, active species are produced by a gas discharge plasma inside bubbles and then transported due to diffusion into the liquid. This paper presents experimental data of electric discharges in small bubbles inserted into a thin dielectric tube filled with water. A low-frequency regime of periodic electrical breakdowns is revealed and described. </para>
Antisense Expression of a Cell Wall-Associated Protein Kinase, WAK4, Inhibits Cell Elongation and Alters Morphology (2001)

David Lally, Peter Ingmire, Hong-Yun Tong, Zheng-Hui He, Antisense Expression of a Cell Wall-Associated Protein Kinase, WAK4, Inhibits Cell Elongation and Alters Morphology, The Plant Cell, Vol. 13, No. 6 (Jun., 2001), pp. 1317-1331
Production of unmodified human adult hemoglobin in Escherichia coli. (1993)

We have constructed a plasmid (pHE2) in which the synthetic human alpha- and beta-globin genes and the methionine aminopeptidase (Met-AP) gene from Escherichia coli are coexpressed under the control of separate tac promoters. The Hbs were expressed in E. coli JM109 and purified by fast protein liquid chromatography, producing two major components, a and b. Electrospray mass spectrometry shows that at least 98% and about 90% of the expressed alpha and beta chains of component a, respectively, have the expected masses. The remaining 10% of the beta chain in component a corresponds in mass to the beta chain plus methionine. In component b, both alpha and beta chains have the correct masses without detectable N-terminal methionine (< 2%). These results have been confirmed by Edman degradation studies of the amino-terminal sequences of the alpha and beta chains of these two recombinant Hb (rHb) samples. rHbs from components a and b exhibit visible optical spectra identical to that of human normal adult Hb (Hb A). Component a and Hb A have very similar oxygen-binding properties, but component b shows somewhat altered oxygen binding, especially at low pH values. 1H-NMR spectra of component a and Hb A are essentially identical, whereas those of component b exhibit altered ring current-shifted and hyperfine-shifted proton resonances, indicating altered heme conformation in the beta chain. These altered resonance patterns can be changed to those of Hb A by converting component b to the ferric state and then to the deoxy state and finally back to either the carbonmonoxy or oxy form. Thus, our E. coli expression system produces native, unmodified Hb A in high yield and can be used to produce desired mutant Hbs.
Robust and Fast Whole Brain Mapping of the RF Transmit Field B1 at 7T (2012)

In-vivo whole brain mapping of the radio frequency transmit field B(1) (+) is a key aspect of recent method developments in ultra high field MRI. We present an optimized method for fast and robust in-vivo whole-brain B(1) (+) mapping at 7T. The method is based on the acquisition of stimulated and spin echo 3D EPI images and was originally developed at 3T. We further optimized the method for use at 7T. Our optimization significantly improved the robustness of the method against large B(1) (+) deviations and off-resonance effects present at 7T. The mean accuracy and precision of the optimized method across the brain was high with a bias less than 2.6 percent unit (p.u.) and random error less than 0.7 p.u. respectively.
Mutagenically separated PCR (MS-PCR): a highly specific one step procedure for easy mutation detection (1993)

With increasing knowledge about the causal role of genetic defects in clinical diseases the necessity is apparent to have procedures for rapid diagnosis of point mutations. We developed a PCR-based technique, whereby both normal and mutant alleles can be amplified in the same reaction tube, using different length allele-specific primers. Furthermore the allele-specific primers introduce additional deliberate differences into the allelic PCR-products that drastically reduce crossreactions in subsequent cycles. This mutagenesis separates the amplification reactions of the alleles performed in the same tube. Subsequent identification of the PCR-products is done by gel electrophoresis and shows at least one of the two allelic products. Therefore, in addition to simple handling, MS-PCR provides a within-assay quality control for the exclusion of false negative results. The feasibility of this technique has been tested using six different mutations. The high sensitivity of MS-PCR also allows screening for mutation carriers in pooled DNA samples.
Computation of the right-inverse of G ( D ) and the left-inverse of H t ( D ) (1990)

Useful column and row operations are given for the computation of the right-inverse G−(D) of an k × n generator matrix G(D) and the left-inverse [H(D)]−1 of the transpose of an (n — k) × n parity-check matrix H(D). The methods are illustrated with two examples.
Lasting safe interruption of endarterectomy thrombosis by transiently infused antithrombin peptide D-Phe-Pro-ArgCH2Cl in baboons (1993)

Abstract To evaluate the relative antithrombotic efficacy and hemostatic safety of antithrombin therapy for vascular thrombus formation at sites of mechanical vascular injury, we administered the potent and specific irreversible synthetic antithrombin D-PHE-PRO-ARG chloromethyl ketone (D-FPRCH2Cl) after performing carotid endarterectomies in baboons. The continuous intravenous infusion of D-FPRCH2Cl, 100 nmol/kg per minute for 1 hour, abolished acute carotid endarterectomy thrombosis for at least 48 hours. The plasma level of D-FPRCH2Cl during the infusion was maintained steady at 7.2 +/- 0.9 mumol/L, but decreased rapidly after discontinuing its infusion (T50 17 minutes). Platelet deposition, measured in real time using autologous 111In-platelet scintillation camera imaging, was 1.51 +/- 0.40 x 10(8) platelet/cm in the 14 treated animals 90 minutes postoperatively, compared with 11.7 +/- 1.16 x 10(8) platelet/cm in 14 heparin-treated controls (P &lt; .002). The antithrombotic benefit was equivalent for treatment begun either 5 minutes before (nine animals) or 15 minutes after (five animals) reestablishing flow in the operated vessel, ie, 1.59 +/- 0.36 x 10(8) platelet/cm versus 1.35 +/- 0.51 x 10(8) platelet/min, respectively; P &gt; .5. Endarterectomy thrombosis remained decreased for at least 48 hours postoperatively, as determined by the ratio between net 111In- platelet radioactivity at the endarterectomized site versus whole blood (ratio 0.82 +/- 0.25 in the treatment group v 3.03 +/- 0.51 in heparin controls at 90 minutes, P &lt; .005; and 0.85 +/- 0.23 v 3.25 +/- 0.48 at 48 hours, P &lt; .002). The marked reduction in endarterectomy thrombosis in treated animals at 48 hours was confirmed by scanning electron microscopy. Thrombin activity formed rapidly and became immediately bound to thrombus on thrombogenic segments in untreated control studies; treatment with D-FPRCH2Cl irreversibly inactivated the thrombus-bound thrombin. Hemostatic function, as measured by bleeding time (BT), activated partial thromboplastin time (APTT), and prothrombin time (PT) was impaired throughout the intravenous administration of D-FPRCH2Cl (BT &gt; 30 minutes, APTT &gt; 150 seconds, PT &gt; 50 seconds); BT, APTT, and PT values were normal 30 minutes after discontinuing the infusions. As expected, blood loss into the surgical wound was substantial in nine animals receiving therapy initiated before restoring flow in the operated vessel (mean 95 mL, range 45 to 130 mL). By contrast, beginning D-FPRCH2Cl therapy in five animals 15 minutes after restoring arterial flow, a time when surgical hemostasis had been achieved, prevented excessive blood loss (mean 15 mL, range 10 to 35 mL; P &lt; .01 compared with earlier treatment) without compromising the antithrombotic effects.(ABSTRACT TRUNCATED AT 400 WORDS)
High current gain hybrid lateral bipolar operation of DMOS transistors (1995)

This paper describes a new operation mode of the DMOS transistor. By utilizing the diffused channel region as base and connecting it to the gate, hybrid lateral bipolar operation is obtained in the device. Current gain higher than 2000 and a cut-off frequency of 1.6 GHz are achieved. Superior breakdown voltages were obtained compared to previously published hybrid devices. It is demonstrated that hybrid operation of a DMOS transistor is a simple way to implement a high gain lateral bipolar transistor, without complex sub-/spl mu/m processing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Increased BACE1 maturation contributes to the pathogenesis of Alzheimer's disease in Down syndrome (2006)

Almost all Down syndrome (DS) patients develop characteristic Alzheimer's disease (AD) neuropathology, including neuritic plaques and neurofibrillary tangles, after middle age. The mechanism underlying AD neuropathology in DS has been unknown. Abeta is the central component of neuritic plaques and is generated from APP by cleavage by the beta- and gamma-secretases. Here we show that beta-secretase activity is markedly elevated in DS. The ratio of mature to immature forms of BACE1 is altered in DS. DS has significantly higher levels of mature BACE1 proteins in Golgi than normal controls. Time-lapse live image analysis showed that BACE1 proteins were predominantly immobile in Golgi in DS cells, while they underwent normal trafficking in controls. Thus, overproduction of Abeta in DS is caused by abnormal BACE1 protein trafficking and maturation. Our results provide a novel molecular mechanism by which AD develops in DS and support the therapeutic potential of inhibiting BACE1 in AD and DS.
Implementing global memory management in a workstation cluster (1995)

Advances in network and processor technology have greatly changed the communication and computational power of local-area workstation clusters. However, operating systems still treat workstation clusters as a collection of loosely-connected processors,