gebhart/patrepeval huggingface dataset:
The Hydrophobic Pocket Contributes to the Structural Stability of the N-Terminal Coiled Coil of HIV gp41 but Is Not Required for Six-Helix Bundle Formation (2003)

In models of HIV fusion, the glycoprotein gp41 is thought to form a six-helix bundle during viral fusion with the target cell. This bundle is comprised of three helical regions (from the heptad repeat 2, or HR2, region of gp41) bound to an inner, trimeric, coiled-coil core (from the HR1 region). Although much has been learned about the structure and thermodynamics of this complex, the energetics of the isolated HR1 self-associated oligomer remain largely unknown. By systematically studying self-association through a series of truncations based on a 51-mer HR1 peptide (T865), we have identified amino acid segments which contribute significantly to the stability of the oligomeric HR1 complex. Biophysical characterization of C-terminal truncations of T865 identifies a 10-15-amino acid region that is essential for HR1 oligomerization. This region coincides with a hydrophobic pocket that provides important contacts for the interaction of HR2 helices. Complete removal of this pocket abolishes HR1 oligomerization. Despite the dramatic reduction in stability, the monomeric HR1 peptides are still able to form stable six-helix bundles in the presence of HR2 peptides. Truncations on the N-terminal side of T865 have little effect on oligomerization but significantly reduce the stability of the HR1-HR2 six-helix bundle. Unlike the HR2 binding site, which extends along a hydrophobic groove on the HR1 oligomer, the residues that are critical for HR1 oligomerization are concentrated in a 10-15-amino acid region. These results demonstrate that there are localizations of binding energy, or "hot spots", in the self-association of peptides derived from the HR1 region of gp41.
Leptin-mediated ion channel regulation: PI3K pathways, physiological role, and therapeutic potential (2016)

Leptin is produced by adipose tissue and identified as a "satiety signal," informing the brain when the body has consumed enough food. Specific areas of the hypothalamus express leptin receptors (LEPRs) and are the primary site of leptin action for body weight regulation. In response to leptin, appetite is suppressed and energy expenditure allowed. Beside this hypothalamic action, leptin targets other brain areas in addition to neuroendocrine cells. LEPRs are expressed also in the hippocampus, neocortex, cerebellum, substantia nigra, pancreatic β-cells, and chromaffin cells of the adrenal gland. It is intriguing how leptin is able to activate different ionic conductances, thus affecting excitability, synaptic plasticity and neurotransmitter release, depending on the target cell. Most of the intracellular pathways activated by leptin and directed to ion channels involve PI3K, which in turn phosphorylates different downstream substrates, although parallel pathways involve AMPK and MAPK. In this review we will describe the effects of leptin on BK, KATP, KV, CaV, TRPC, NMDAR and AMPAR channels and clarify the landscape of pathways involved. Given the ability of leptin to influence neuronal excitability and synaptic plasticity by modulating ion channels activity, we also provide a short overview of the growing potentiality of leptin as therapeutic agent for treating neurological disorders.
Zusammenfassung (1958)

Die Bildsamkeit des Systems Kalk-Wasser ist eine technisch äußerst wichtige Eigenschaft, deren Erscheinung und Ursache geklärt werden sollen.
Improved Expression for Estimation of Leakage Inductance in <i>E</i> Core Transformer Using Energy Method (2012)

This paper proposes a simpler and more accurate expression for estimation of leakage inductance in E core transformer, which is the most widely used transformer structure. The derived expression for leakage inductance accounts for the flux extending into air. The finite element method (FEM) analysis is made on the secondary shorted transformer to observe the H -field pattern. The results obtained from FEM analysis are used for approximating the field that is extending into air to derive an expression for leakage inductance. This expression is experimentally validated on prototype transformers of different core dimensions.
Modeling the short-channel threshold voltage of a novel vertical heterojunction pMOSFET (1999)

Analytical modeling of the threshold voltage of a Si/sub 1-x/Ge/sub x//Si heterojunction pMOSFET has been performed using a quasi-two-dimensional (quasi-2-D) approach for the calculation of the potential. It is shown that the use of Si/sub 1-x/Ge/sub x/ in the source region leads to an improvement in the short-channel behavior of deep submicron pMOSFETs. The V/sub T/ roll-off can be substantially decreased by introducing a material dependent barrier between source and channel. Furthermore it will be proven that this advantage will become stronger when channel lengths are decreased toward the deep submicron regime.
A Long‐Lived Mononuclear Cyclopentadienyl Ruthenium Complex Grafted onto Anatase TiO<sub>2</sub> for Efficient CO<sub>2</sub> Photoreduction (2016)

This work shows a novel artificial donor-catalyst-acceptor triad photosystem based on a mononuclear C5 H5 -RuH complex oxo-bridged TiO2 hybrid for efficient CO2 photoreduction. An impressive quantum efficiency of 0.56 % for CH4 under visible-light irradiation was achieved over the triad photocatalyst, in which TiO2 and C5 H5 -RuH serve as the electron collector and CO2 -reduction site and the photon-harvester and water-oxidation site, respectively. The fast electron injection from the excited Ru(2+) cation to TiO2 in ca. 0.5 ps and the slow backward charge recombination in half-life of ca. 9.8 μs result in a long-lived D(+) -C-A(-) charge-separated state responsible for the solar-fuel production.
The impact of avatar realism and eye gaze control on perceived quality of communication in a shared immersive virtual environment (2003)

This paper presents an experiment designed to investigate the impact of scommunication in an immersive virtual environment.Participants were paired by gender and were randomly assigned to a CAVE-like system or a head-mounted display. Both were represented by a humanoid avatar in the shared 3D environment. The visual appearance of the avatars was either basic and genderless (like a match-stick figure), or more photorealistic and gender-specific. Similarly, eye gaze behavior was either random or inferred from voice, to reflect different levels of behavioral realism.Our comparative analysis of 48 post-experiment questionnaires confirms earlier findings from non-immersive studies using semi-photorealistic avatars, where inferred gaze significantly outperformed random gaze. However responses to the lower-realism avatar are adversely affected by inferred gaze, revealing a significant interaction effect between appearance and behavior. We discuss the importance of aligning visual and behavioral realism for increased avatar effectiveness.
Protective Role of Interleukin-6 during<i>Yersinia enterocolitica</i>Infection Is Mediated through the Modulation of Inflammatory Cytokines (2004)

ABSTRACT Yersinia enterocolitica is a gram-negative enteric pathogen responsible for a number of gastrointestinal disorders. A striking feature of the pathology of a Y. enterocolitica infection is inflammation. Recently, we demonstrated a role for interleukin-1α (IL-1α) in the establishment of intestinal inflammation in response to a Y. enterocolitica infection. A cytokine directly affected by IL-1 levels is IL-6. A previous report suggested that IL-6 plays an anti-inflammatory role during Y. enterocolitica infection, and in other systems IL-6 has been shown to be proinflammatory. Therefore, a closer examination of the roles of IL-6 and inflammatory cytokines in the control of Y. enterocolitica infection in IL-6 −/− mice was undertaken. Y. enterocolitica organisms were more virulent in the IL-6 −/− mice (60-fold decreased 50% lethal dose) and colonized systemic tissues more rapidly and to a higher level than in the wild-type mice. One role of IL-6 during a Y. enterocolitica infection may be the downmodulation of the inflammatory response. The IL-6 −/− mice have a more robust T H 1 T-cell response, as well as hyperinflammatory pathologies. These phenotypes appear to be due to the misregulation of tumor necrosis factor alpha, monocyte chemotactic protein 1, IL-10, transforming growth factor β1, and gamma interferon in the IL-6 −/− mouse. These data provide further insight into the intricate cytokine signaling pathways involved in the regulation of inflammatory responses and the control of bacterial infections.
Formación práctica de los estudiantes de pedagogía en las Universidades Españolas (2004)

Mostramos parte de una investigación dirigida al “análisis comparado de la\n\t\t\t\t formación práctica en el sistema universitario como base de evaluación y mejora”\n\t\t\t\t siendo el Practicum, como momento en que los estudiantes entran en contacto con el\n\t\t\t\t mundo del trabajo, el objeto de nuestro análisis. Por acotar el campo, nos centramos\n\t\t\t\t en el Practicum de la Licenciatura de Pedagogía aunque con un proceso que\n\t\t\t\t pretendemos sea transferible a otras carreras. Presentamos los resultados\n\t\t\t\t procedentes del análisis comparado de los actuales sistemas de formación práctica\n\t\t\t\t (Practicum) de diversas universidades españolas, determinando características y\n\t\t\t\t componentes esenciales.
Sub-Nyquist Distortions in Sampled One- and Two-Dimensional Signals Studied (2001)

Hardware testing frequently involves the acquisition of waveform and instrumentation signals, which are often recorded on waveform recorders, oscillographs, and video recorders. Years ago, the waveforms were viewed as analog records, as drawn by a paper strip chart pen or electron beam on a cathode ray tube screen. One of the problems in the past was that the analog electronics may not have been able to accurately display the full amplitude of a signal if the real-time signals exceeded the frequency response bandwidth of the recording device. The advent of digital oscilloscopes, waveform recorders, and video frame-grabbers solved many of the frequency response problems, though not all. A restriction on digital waveform acquisition is well known by people in the instrumentation field. Put simply, the sampling frequency must be at least twice the frequency of any signal to be sampled, or vice versa; the signals must be filtered so that none of the signal frequencies are higher than one-half the sample rate (the Nyquist Limit). Then, per Shannon's Sampling Theorem (1949, ref. 1), any sampled signal can be reconstructed for viewing on a display device. If any signals exceed the Nyquist frequency limit, error signals called aliases occur in the output display.
Observation of new polarisation dependence effect in long haul optically amplified system (1993)

Progress in the development of long haul transmission systems using erbium doped fiber amplifiers as repeaters has been very rapid, and the installation of this kind of system in undersea applications is imminent [1,2]. It is very important to understand all aspects of the optical propagation in an optically amplified link, because the noise due to the amplifiers' ASE and any distortions resulting from non-linear effects etc. accumulate through the whole length of the system. This paper reports a study into the effects of polarisation dependent loss (PDL) on the signal and ASE levels in a 3100 km amplified system, containing 69 amplified sections with 45 km repeater spacing [2]. It is known that small amounts of PDL at each section can concatenate to give a significant and variable overall PDL, which leads to fading in the signal to noise ratio [3]. We will show that there is also a previously unnoticed polarisation dependent effect which causes a net penalty in the signal to noise ratio, and we will describe how to eliminate it.
Active tamper detection circuit based on the analysis of pulse response in conductive mesh (2017)

Tamper detection circuits provide the first and most important defensive wall in protecting electronic modules containing security data. A widely used procedure is to cover the entire module with a foil containing fine conductive mesh, which detects intrusion attempts. Detection circuits are further classified as passive or active. Passive circuits have the advantage of low power consumption, however they are unable to detect small variations in the conductive mesh parameters. Since modern tools provide an upper leverage over the passive method, the most efficient way to protect security modules is thus to use active circuits. The active tamper detection circuits are typically probing the conductive mesh with short pulses, analyzing its response in terms of delay and shape. The method proposed in this paper generates short pulses at one end of the mesh and analyzes the response at the other end. Apart from measuring pulse delay, the analysis includes a frequency domain characterization of the system, determining whether there has been an intrusion or not, by comparing it to a reference (un-tampered with) spectrum. The novelty of this design is the combined analysis, in time and frequency domains, of the small variations in mesh characteristic parameters.
Solid oxide membrane-assisted controllable electrolytic fabrication of metal carbides in molten salt (2016)

Silicon carbide (SiC), titanium carbide (TiC), zirconium carbide (ZrC), and tantalum carbide (TaC) have been electrochemically produced directly from their corresponding stoichiometric metal oxides/carbon (MOx/C) precursors by electrodeoxidation in molten calcium chloride (CaCl2). An assembled yttria stabilized zirconia solid oxide membrane (SOM)-based anode was employed to control the electrodeoxidation process. The SOM-assisted controllable electrochemical process was carried out in molten CaCl2 at 1000 °C with a potential of 3.5 to 4.0 V. The reaction mechanism of the electrochemical production process and the characteristics of these produced metal carbides (MCs) were systematically investigated. X-ray diffraction, scanning electron microscopy, and transmission electron microscopy analyses clearly identify that SiC, TiC, ZrC, and TaC carbides can be facilely fabricated. SiC carbide can be controlled to form a homogeneous nanowire structure, while the morphologies of TiC, ZrC, and TaC carbides exhibit porous nodular structures with micro/nanoscale particles. The complex chemical/electrochemical reaction processes including the compounding, electrodeoxidation, dissolution-electrodeposition, and in situ carbonization processes in molten CaCl2 are also discussed. The present results preliminarily demonstrate that the molten salt-based SOM-assisted electrodeoxidation process has the potential to be used for the facile and controllable electrodeoxidation of MOx/C precursors to micro/nanostructured MCs, which can potentially be used for various applications.
Selective bronchial suctioning in the adult using a curve-tipped catheter with a guide mark (1982)

Our results of previous and successive studies indicate that torque control of curve-tipped catheters is easily accomplished by placing a guide mark on the catheter. Thus, a guide mark was made on a curve-tipped 14 FG Portex suction catheter using a felt pen. The efficacy of selective bronchial suctioning using this catheter was studied in 50 patients. Directed suctioning of the left and right bronchial passages was performed in each patient 3 times and once, respectively, with the head in the midline position. The success rate of left bronchial suctioning was 92% (138/150 attempts) and success in right bronchial suctioning 98% (49/50 attempts). The curve-tipped catheter with a guide mark significantly improved the success rate of left bronchial entry over the previous rate from 50% to 92%.
The Architecture of the Adhesive Apparatus of Cultured Osteoclasts: From Podosome Formation to Sealing Zone Assembly (2007)

The sealing zone of osteoclasts cultured on bone is made of structural units clearly related to individual podosomes. It differs from individual or clustered podosomes in the higher density and degree of inter-connectivity of its building blocks, thus forming a unique continuous functional structure connecting the cell to its extracellular milieu. Through this continuous structure, signals reporting on the substrate condition may be transmitted to the whole cell, modulating the cell response under physiological and pathological conditions.
pH sensing and noise characteristics of Si nanowire ion-sensitive field effect transistors (2011)

We have fabricated Si-nanowire (Si-NW) based ion-sensitive field effect transistors (ISFETSs) for biosensing applications. The ability to prepare a large number of sensors on a wafer, standard silicon microfabrication techniques resulting in cost savings and potential sensitivity are significant advantages in favor of nanoscale ISFETs for future biosensor requirements. The Si-NW ISFETs were produced using a combination of oxide-grown Si-NWs and integrated Ag/AgCl reference electrodes. The Si-NWs were fabricated on a standard silicon-on-insulator wafer using electron-beam lithography and conventional semiconductor processing techniques. To form an Ag/AgCl reference electrode, a 250-nm thick Ag layer was deposited and later chlorinated in 100 mM KCl solution. SEM analysis reveals Si-NWs with a width of ∼50 nm and a length of 10 µm. The DC characteristics were measured by placing an ISFET with 100 Si-NWs in parallel in a 0.1× PBS buffer solution. The measured I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</inf> -V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</inf> characteristics show an n-type FET behavior with a relatively high on/off current ratio, reasonable sub-threshold swing value, and low gate-leakage current. The pH responses of the ISFETs with different pH solutions were characterized at room temperature. A lateral shift of the I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</inf> -V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</inf> curve is clearly observed by changing the pH value of the solution. The low frequency noise characteristics have been performed in order to evaluate interface quality of the devices.
Error Correction for IBM 800-bit-per-inch Magnetic Tape (1970)

The 800-bit-per-inch magnetic tape units that are components of IBM System/360 can correct error bursts of unlimited length in any one of their nine tape tracks. The correction technique employs a modified cyclic code in conjunction with a parity bit in each nine-bit character. There are nine check bits in the modified cyclic code and these form a check character at the end of every record. To perform the correction, a record in which an error has been detected must be reread. Errors involving more than one track within the same record are detected but are not correctable. This error correction technique operates during both read-forward and read-backward operations, and on records of any length.
Application to a Cartilage Targeting Strategy:  Synthesis and in Vivo Biodistribution of <sup>14</sup>C-Labeled Quaternary Ammonium−Glucosamine Conjugates (2000)

As part of a cartilage targeting program based on the affinity of the quaternary ammonium (QA) moiety for cartilage, QA derivatives of D-glucosamine (DG), an antirheumatic drug exhibiting a natural tropism for cartilaginous tissues, were designed and evaluated by pharmacokinetic studies. Two QA-DG conjugates were synthesized and labeled with (14)C by cross-linking the QA entity (trimethylammonium or pyridinium) to [(14)C]DG via an amide bond in a two-step procedure. After intravenous injection to male Sprague-Dawley rats, the two (14)C-labeled conjugates exhibited similar pharmacokinetic profiles, but their behavior clearly differed from that of unconjugated DG in several ways. (i) The tissue distribution for the conjugates was more restricted, with a decreased radioactivity level for whole tissues except for kidney, cartilage, and skin. (ii) The radioactivity concentrated more rapidly and strongly in cartilage for the conjugates than for DG for the short times after injection; on the other hand, 1 h after administration, the radioactivity level in cartilage was higher for DG, this result being consistent with the tropism already observed for this compound. (iii) Both conjugates were eliminated predominantly by the urinary route (85%); the radioactivity level in urine for DG was lower (45% of the injected dose), and significant (14)CO(2) was found in expired air, indicating metabolization and utilization of DG for energy-consuming processes. (iv) Blood and plasma kinetics studies displayed an enterohepatic cycle for DG, whereas for the QA conjugates, a rapid disappearance was observed. (v) HPLC analyses of plasma and urine indicated a low degree of metabolization for the conjugates, most of the radioactivity recovered in urine and plasma corresponding to the unchanged molecule. This study demonstrates that the introduction of the QA moiety on DG modifies its biodistribution and lends it a greater specificity for cartilage, at least for short times after injection. These findings justify further work on QA derivatives of other antirheumatic agents.
Regulatory Multitasking of Tolerogenic Dendritic Cells – Lessons Taken from Vitamin D3-Treated Tolerogenic Dendritic Cells (2013)

Tolerogenic dendritic cells (DCs) work through silencing of differentiated antigen-specific T cells, activation and expansion of naturally occurring T regulatory cells (Tregs), transfer of regulatory properties to T cells, and the differentiation of naïve T cells into Tregs. Due to an operational definition based on T cell activation assays, the identity of tolerogenic DCs has been a matter of debate and it need not represent a specialized DC subset. Human tolerogenic DCs generated in vitro using inhibitory cytokines, growth factors, natural immunomodulators, or genetic manipulation have been effective and several of these tolerogenic DCs are currently being tested for clinical use. Ex vivo generated tolerogenic DCs reduce activation of naïve T cells using various means, promote a variety of regulatory T cells and most importantly, frequently show stable inhibitory phenotypes upon repetitive maturation with inflammatory factors. Yet, tolerogenic DCs differ with respect to the phenotype or the number of regulatory mechanisms they employ to modulate the immune system. In our experience, tolerogenic DCs generated using the biologically active form of vitamin D (VD3-DCs), alone, or combined with dexamethasone are proficient in their immunoregulatory functions. These tolerogenic DCs show a stable maturation-resistant semi-mature phenotype with low expression of activating co-stimulatory molecules, no production of the IL-12 family of cytokines and high expression of inhibitory molecules and IL-10. VD3-DCs induce increased apoptosis of effector T cells and induce antigen-specific regulatory T cells, which work through linked suppression ensuring infectious tolerance. Lessons learned on VD3-DCs help understanding the contribution of different pattern-recognition receptors (PRRs) and secondary signals to the tolerogenic function and how a cross-talk between DCs and T cells translates into immune regulation.