gebhart/patrepeval huggingface dataset:
Binding specificity and stability of duplexes formed by modified oligonucleotides with a 4096-hexanucleotide microarray (2001)

The binding of oligodeoxynucleotides modified with adenine 2'-O-methyl riboside, 2,6-diaminopurine 2'-O-methyl riboside, cytosine 2'-O-methyl riboside, 2,6-diaminopurine deoxyriboside or 5-bromodeoxyuridine was studied with a microarray containing all possible (4096) polyacrylamide-bound hexadeoxynucleotides (a generic microchip). The generic microchip was manufactured by using reductive immobilization of aminooligonucleotides in the activated copolymer of acrylamide, bis-acrylamide and N-(2,2-dimethoxyethyl) acrylamide. The binding of the fluorescently labeled modified octanucleotides to the array was analyzed with the use of both melting profiles and the fluorescence distribution at selected temperatures. Up to three substitutions of adenosines in the octamer sequence by adenine 2'-O-methyl ribosides (A(m)), 2,6-diaminopurine 2'-O-methyl ribosides (D(m)) or 2,6-diaminopurine deoxyribosides (D) resulted in increased mismatch discrimination measured at the melting temperature of the corresponding perfect duplex. The stability of complexes formed by 2'-O-methyl-adenosine-modified oligodeoxynucleotides was slightly decreased with every additional substitution, yielding approximately 4 degrees C of total loss in melting temperature for three modifications, as followed from microchip thermal denaturation experiments. 2,6-Diaminopurine 2'-O-methyl riboside modifications led to considerable duplex stabilization. The cytosine 2'-O-methyl riboside and 5-bromodeoxyuridine modifications generally did not change either duplex stability or mismatch resolution. Denaturation experiments conducted with selected perfect duplexes on microchips and in solution showed similar results on thermal stabilities. Some hybridization artifacts were observed that might indicate the formation of parallel DNA.
Utilidad de la relación Sao2/Fio2 en la evaluación del grado de compromiso pulmonar en pacientes críticos (2002)

Introducción: La mezcla arteriovenosa pulmonar y la relación PaO2/FiO2 han sido tomadas tradicionalmente como indicadores de la función pulmonar. Dado que la SaO2 refleja en esencia lo mismo que la PaO2, es decir, el oxígeno aportado, es de esperarse que la relación PaO2/FiO2 pueda ser sustituida con la relación SaO2/FiO2. Objetivos: Establecer si existe una correlación confiable entre PaO2/FiO2 y SaO2/FiO2. Validar la correlación encontrada en un estudio anterior entre la estimación de la mezcla arteriovenosa por métodos "no invasivos" e "invasivos". Métodos: En una cohorte de 107 pacientes hospitalizados con diversas patologías en una Unidad de Cuidados Intensivos se recogieron un total de 507 muestras de gases arteriales, venosos centrales y SaO2 por oximetria de pulso. Los datos así medidos de PaO2/FiO2, SaO2/FiO2 y mezcla arteriovenosa de oxígeno por métodos invasivos y no invasivos, fueron correlacionados mediante análisis de regresión simple. Resultados: Se encontró una buena correlación entre PaO2/FiO2 y SaO2/FiO2. (R2--0.81, R=Ü.9). La correlación entre la mezcla arteriovenosa por métodos "invasivos" y "no invasivos" se confirmó (R2=0.75, R=Ü.86). Se establecieron cinco grupos de severidad de compromiso pulmonar según el nivel de SaO2/FiO2, a los cuales se les asignó un puntaje de 0 a 4, similares a los del índice de injuria pulmonar de Murray y de falla multisistémica de Marshall. Finalmente se sustituyeron los puntajes de PaO2/FiO2 por los de Sa en tales índices, y se compararon los resultados mediante análisis de regresión. Se encontró una buena correlación entre el LIS calculado con PaO2/FiO2 y con SaO2/FiO2 (R2=0.94, R=0.96) y entre el índice de Marshall calculado con PaO2/FiO2 y con SaO2/FiO2. (R2=0.85, R=0.92). La correlación se mantuvo aún cuando se hizo un análisis estratificado por severidad de la lesión. Conclusiones: La SaO2/FiO2 es un indicador útil de la función de oxigenación, equiparable a la PaO2/FiO2. Puede ser incorporado al cálculo de LIS y del Marshall sin alterar los resultados. Adicionalmente, se confirma la utilidad del cálculo de mezcla arteriovenosa por métodos no invasivos.
Field-Induced Single Molecule Magnetic Behavior of Mononuclear Cobalt(II) Schiff Base Complex Derived from 5-Bromo Vanillin (2022)

A mononuclear Co(II) complex of a Schiff base ligand derived from 5-Bromo-vanillin and 4-aminoantipyrine, that has a compressed tetragonal bipyramidal geometry and exhibiting field-induced slow magnetic relaxation, has been synthesized and characterized by single crystal X-ray diffraction, elemental analysis and molecular spectroscopy. In the crystal packing, a hydrogen-bonded dimer structural topology has been observed with two distinct metal centers having slightly different bond parameters. The complex has been further investigated for its magnetic nature on a SQUID magnetometer. The DC magnetic data confirm that the complex behaves as a typical S = 3/2 spin system with a sizable axial zero-field splitting parameter D/hc = 38 cm−1. The AC susceptibility data reveal that the relaxation time for the single-mode relaxation process is τ = 0.16(1) ms at T = 2.0 K and BDC = 0.12 T.
Systemic Inflammation Modulates Fc Receptor Expression on Microglia during Chronic Neurodegeneration (2011)

Chronic neurodegeneration is a major worldwide health problem, and it has been suggested that systemic inflammation can accelerate the onset and progression of clinical symptoms. A possible explanation is that systemic inflammation "switches" the phenotype of microglia from a relatively benign to a highly aggressive and tissue-damaging phenotype. The current study investigated the molecular mechanism underlying this microglia phenotype "switching." We show in mice with chronic neurodegeneration (ME7 prion model) that there is increased expression of receptors that have a key role in macrophage activation and associated signaling pathways, including TREM-2, Siglec-F, CD200R, and FcγRs. Systemic inflammation induced by LPS further increased protein levels of the activating FcγRIII and FcγRIV, but not of other microglial receptors, including the inhibitory FcγRII. In addition to these changes in receptor expression, IgG levels in the brain parenchyma were increased during chronic neurodegeneration, and these IgG levels further increased after systemic inflammation. γ-Chain-deficient mice show modified proinflammatory cytokine expression in the brain after systemic inflammation. We conclude that systemic inflammation during chronic neurodegeneration increases the expression levels of activating FcγR on microglia and thereby lowers the signaling threshold for Ab-mediated cell activation. At the same time, IgG influx into the brain could provide a cross-linking ligand resulting in excessive microglia activation that is detrimental to neurons already under threat by misfolded protein.
A Comparison of Fatigue Failure Morphology Between TiN Coated and Uncoated Lubricated Rollers (1991)

In this study two series of morphological fatigue tests were con-ducted with a two disk machine for TiN coated rollers as well as uncoated rollers. Surface examinations showed that 1 mu;m TiN coated surfaces underwent principally elastic deformation without coating debonding. However, uncoated surfaces were heavily deformed even after a shorter contact cycle. For the uncoated rollers, cross-sectional micrographs revealed the presence of many near-surface microcracks at an asperity scale nearly parallel to the surface. It is believed that these microcracks are initiated by asperity interaction. Metallographic examinations of the uncoated subsurface revealed a. thin layer of dark etching region corresponding to the microcrack failure region. For the coated roller, few cracks were found and the dark etching region was absent. The hard coating minimizes the surface distress and suppresses the initiation of microcracks. This explains why the fatigue life is enhanced with a thin hard coating. Cross-sectional transmission electron microscopy (XTEM) study showed a. coherent interface structure for the coated specimens. The interface after rolling and sliding contact exhibited no clear boundary compared to that of the as-deposited coating. This may indicate that a good coating adhesion can be maintained during the current concentrated contact tests.
Editorial: Neue Technologien (2014)

In der diesjährigen Dezemberausgabe der Klinischen Monatsblätter wollen wir unter der Überschrift „Neue Technologien“ einige zukunftsträchtige Konzepte aus dem Bereich der apparativen Diagnostik und Therapie vorstellen, die bisher wenig Aufmerksamkeit gefunden haben. Wir denken jedoch, dass zukünftig gerade auch in diesen Bereichen Fortschritte zu erwarten sind.
Jueces, premios y castigos en el Más Allá de Plutarco (2014)

Plutarch mentions in his writings the existence of three judges, Minos, Rhadamanthys, and Aeacus. They judge people in Hades and decide whether they must be condemned in Tartarus or can live happily on the Isles of the Blessed. Rewards and punishments depend on the moral behaviour of the souls during their lives. The aim of my work is to analyze the background against which Plutarch elaborates his idea of justice in the Netherworld. He suits and reworks traditional motifs but also leaves a personal mark on his netherworldly imagery.
Vision-based mobile application for supporting the user in the vehicle operation (2019)

In this paper the automatic vision-based mobile application for supporting the vehicle user is proposed. The system, using the image taken with the typical smartphone camera, recognizes three types of information located on the vehicle body: text data, displayed dashboard icons, and components in the engine compartment. The modern programming tools and recognition algorithms, including deep neural networks, were used in the implementation regarded to the limited efficiency of mobile devices. Preliminary tests using prepared database indicate on a high recognition performance. Recognition results and instructions are presented to the user in an accessible way using techniques of the augmented reality.
The in-vitro activity of doxycycline and minocycline against anaerobic bacteria (1987)

The likelihood of bacterial resistance now prevents the use of oxytetracycline in the empirical therapy of anaerobic infections. This study investigates the in-vitro activity of two semi-synthetic derivatives, doxycycline and minocycline, against a range of anaerobic bacteria. MICs for each antibiotic were determined by an agar incorporation technique. Doxycycline and minocycline were four to eight times more active against the majority of strains than oxytetracycline. With the exception of Bacteroides bivius, almost 90% of strains were inhibited by 4 mg/l of doxycycline or minocycline, but resistance to the same concentration of oxytetracycline was present in 60% of the B. fragilis group, 30% of Peptostreptococcus spp. and 24% of Clostridium perfringens. Doxycycline and minocycline represent an alternative therapy for anaerobic infections where bacterial sensitivities are known.
Capturing reaction paths and intermediates in Cre- loxP recombination using single-molecule fluorescence (2012)

Site-specific recombination plays key roles in microbe biology and is exploited extensively to manipulate the genomes of higher organisms. Cre is a well studied site-specific recombinase, responsible for establishment and maintenance of the P1 bacteriophage genome in bacteria. During recombination, Cre forms a synaptic complex between two 34-bp DNA sequences called loxP after which a pair of strand exchanges forms a Holliday junction (HJ) intermediate; HJ isomerization then allows a second pair of strand exchanges and thus formation of the final recombinant product. Despite extensive work on the Cre-loxP system, many of its mechanisms have remained unclear, mainly due to the transient nature of complexes formed and the ensemble averaging inherent to most biochemical work. Here, we address these limitations by introducing tethered fluorophore motion (TFM), a method that monitors large-scale DNA motions through reports of the diffusional freedom of a single fluorophore. We combine TFM with Förster resonance energy transfer (FRET) and simultaneously observe both large- and small-scale conformational changes within single DNA molecules. Using TFM-FRET, we observed individual recombination reactions in real time and analyzed their kinetics. Recombination was initiated predominantly by exchange of the "bottom-strands" of the DNA substrate. In productive complexes we used FRET distributions to infer rapid isomerization of the HJ intermediates and that a rate-limiting step occurs after this isomerization. We also observed two nonproductive synaptic complexes, one of which was structurally distinct from conformations in crystals. After recombination, the product synaptic complex was extremely stable and refractory to subsequent rounds of recombination.
Influence of Radiative Energy Transfer on the Thermal Behavior of Bonded InGaAs/GaAs Lasers (2009)

Temperature characteristics and thermal resistance of InGaAs/GaAs laser diode (LD) is investigated from below to beyond the lasing threshold. Spectrally-resolved emission measurements show that the heat generated in the active region is induced by the radiative energy transfer of free carriers. Below the lasing threshold, nonradiative recombination induces large heat generation in the active region. Beyond the lasing threshold, Joules heating due to the series resistance of the LD dominates the heating response. The dependence of the associated thermal resistance on different bonding configurations and its correlation with the output power is also discussed. Epi-side up and epi-side down bonding of LDs reduces the device temperature by ~ 30% and ~ 50%, respectively.
An Overlooked Effect of Glycine Betaine on Fermentation: Prevents Caramelization and Increases the L-Lysine Production (2014)

This article focuses on the effects of glycine betaine on preventing caramelization, and increasing DCW and L-lysine production. The additional glycine betaine not only decreased the browning intensity (decreased 4 times), and the concentrations of 5-hydroxymethylfurfural (decreased 7.8 times) and furfural (decreased 12 times), but also increased the availability of glucose (increased 17.5%) for L-lysine production. The DCW and L-lysine production were increased by adding no more than 20 mM glycine betaine, whereas the DCW and L-lysine production were decreased with the reduction of pH values, although pH had a better response to prevent caramelization than did glycine betaine. For L-lysine production, the highest increase (40%) was observed on the media with 20 mM glycine betaine. The crucial enzymes in glycolysis and L-lysine biosynthesis pathway were investigated. The results indicated that additional glycine betaine increases the activity of enzymes in glycolysis, in contrast to the effect of pH. All the results indicated that glycine betaine can be used to prevent caramelization and increase the L-lysine production. By applying this strategy, glucose would not be have to be separated from the culture media during autoclaving so that factories can save production costs and shorten the fermentation period.
Battery pack state of charge balancing algorithm for cascaded H-Bridge multilevel converters (2016)

For most of the Multilevel Converter (MC) applications a commonly discussed issue is the maintenance of balance between the energy storage elements from the SubModules (SM). In applications where a battery pack is also part of the SM storage, such as STATCOMs or motor drives, the SM voltage is not in linear relation with the State Of Charge (SOC) of the entire battery; thus, the balancing becomes more cumbersome. A method to balance the SOC of the battery packs in a system using cascaded H-Bridge is proposed in this paper. The method uses nearest level control followed by sorting and selection based on the SOC of the battery packs. Based on the simulation results the number of switching is reduced considerably compared to the method where the phase shifted PWM is used. In addition, the time needed to achieve the balanced SOC is also reduced. The proposed method has been verified through experiments and simulations.
Interactions between Escherichia coliNucleoside-diphosphate Kinase and DNA (2002)

Nucleoside-diphosphate (NDP) kinase (NTP:nucleoside-diphosphate phosphotransferase) catalyzes the reversible transfer of gamma-phosphates from nucleoside triphosphates to nucleoside diphosphates through an invariant histidine residue. It has been reported that the high-energy phosphorylated enzyme intermediate exhibits a protein phosphotransferase activity toward the protein histidine kinases CheA and EnvZ, members of the two-component signal transduction systems in bacteria. Here we demonstrate that the apparent protein phosphotransferase activity of NDP kinase occurs only in the presence of ADP, which can mediate the phosphotransfer from the phospho-NDP kinase to the target enzymes in catalytic amounts (approximately 1 nm). These findings suggest that the protein kinase activity of NDP kinase is probably an artifact attributable to trace amounts of contaminating ADP. Additionally, we show that Escherichia coli NDP kinase, like its human homologue NM23-H2/PuF/NDP kinase B, can bind and cleave DNA. Previous in vivo functions of E. coli NDP kinase in the regulation of gene expression that have been attributed to a protein phosphotransferase activity can be explained in the context of NDP kinase-DNA interactions. The conservation of the DNA binding and DNA cleavage activities between human and bacterial NDP kinases argues strongly for the hypothesis that these activities play an essential role in NDP kinase function in vivo.
Transmission and fluorescence angular domain optical projection tomography of turbid media (2009)

When imaging through turbid media, objects are often blurred by scattered light. An optical collimator (i.e., an angular filter array) improves images by accepting only photons propagating within a narrow solid angle about the direction of the incident light. These photons are expected to participate in a limited number of small-angle scattering events, maintaining their original propagation direction and, finally, contributing to the development of a faithful image of an object within a turbid medium. The collimation method, also referred to as angular domain imaging (ADI), applies to a see-through configuration where the incident collimated light beam can be aligned with the collimator in a transillumination mode of operation. In this paper, we present angular domain optical projection tomography (ADOPT), a method that can extract depth information of optical contrast in turbid media with high longitudinal resolution based on ADI technology. The resolution of the ADI system has been tested over various depths in a 5 cm optical cuvette using a resolution target suspended in a homogeneous turbid medium. The ADOPT system reconstructed images from a series of angular domain projections collected at angular intervals. The system was used to measure the attenuation of an absorbing target in transmission mode (t-ADOPT) and to measure the light emitting from a fluorescent target (f-ADOPT). Tissue-mimicking phantoms were used to validate the performance of the method. In the t-ADOPT configuration, a background scattered light estimation and subtraction methodology was introduced to improve the imaging contrast. A target consisting of two graphite rods (0.9 mm diameter) was suspended in the cuvette by a rotation stage. An Indocyanine Green-filled glass rod was used as an imaging target in the f-ADOPT arrangement. The target was placed in a manner such that the line of laser light was perpendicular to the longitudinal axis of the rods. Several projections were collected at increments of 1.8 degrees and compiled into a sinogram. A transverse image was reconstructed from the sinogram by using filtered backprojection and image contrast was improved by experimental scatter measurements using a wedge prism and an image processing algorithm. The submillimeter target embedded in a 2 cm thick scattering medium (reduced scattering coefficient < or = 2.4 cm(-1)) was discernable in both the sinograms and the reconstructed images. In the f-ADOPT system, fluorescent line targets <1 cm in diameter embedded in a 2 cm thick scattering medium (reduced scattering coefficient < or = 0.8 cm(-1)) were discernable in both the sinograms and the reconstructed images. The proposed method could be used as the basis to construct an optical tomographic scanner for simultaneous absorption and fluorescence-based imaging of biological specimens (i.e., up to 7 mm across).
Performance of a MIMO system with overlay pilots (2002)

A multiple-input multiple-output (MIMO) indoor radio system is studied to identify the origin of a typical performance degradation. When the data and overlay pilot-sequences for the channel estimation are transmitted at the same time, an error floor at high signal-to-noise ratio is normally observed. The floor is caused by channel estimation errors due to the interfering data signal. The crosstalk between the data paths can be calculated, approximately, and it is shown that the shape of the bit error curves can be steered both with the amplitude ratio /spl eta/ between pilot and data signals and with the length L of the sequences. Near-optimum performance can be reached in this way. With L = 16383, for instance, an amplitude ratio of /spl eta/ /spl ges/ 0.15 (0.3) is sufficient for BPSK (16-QAM) modulation in a MIMO system with 8 transmit and 12 receive antennas.
SITES IN TISSUE-TYPE PLASMINOGEN ACTIVATOR INVOLVED IN THE INTERACTION WITH FIBRIN, PLASMINOGEN AND LOW MOLECULAR WEIGHT LIGANDS (1987)

Tissue-type plasminogen activator (t-PA) activates the proenzyme plasminogen to the active protease plasmin which degrades fibrin. The unique properties of t-PA, fibrin binding and stimulation of activity by fibrin make it an interesting molecule for specific thrombolysis. t-PA is thought to consist of five structural regions designated finger (F), growth factor (G), kringle 1 (Kl), kringle 2 (K2) and protease (P). Previous studies have shown that the interaction of t-PA with fibrin is mediated by the F and K2 regions. Mutated t-PA cDNA molecules were expressed in Chinese hamster ovary cells and t-PA analog proteins were purified from serum free culture media using affinity chromatography with immobilized monoclonal antibodies. Besides FGK1K2P (native t-PA) the following analogs were used GK1K2P, klK2P, K2P, P, FP and FGKlk2P (kl and k2 have partial deletions of the kringle). All the molecules comprising K2P could be stimulated in plasminogen activation activity by fibrinogen fragments comparable to normal t-PA. The activities of FP and FGKlk2P were only slightly influenced by these fragments. It was shown that the fibrin binding site in K2 was plasminogen dependent whereas that in F was not. K2 was found to contain a binding site for lysine, 6-amino-hexanoic acid but also 6-amino-hexane and thus to differ from the high affinity lysine binding sites in plasminogen. Chemical modification of lysine and arginine residues in t-PA with citraconic anhydride and cyclohexanedione respectively, revealed no involvement of these residues in interaction with lysine or analogs nor in stimulation of activity by fibrinogen fragments. Arginine modification led to inhibition of plasminogen activation activity, both in the presence and absence of fibrinogen fragments, but the amidolytic activity as measured with a tripeptide paranitroanilide was not changed. The involvement of one or more arginine residues in interaction of t-PA with plasminogen seems likely.