gebhart/patrepeval huggingface dataset:
Nucleolar Clustering of Dispersed tRNA Genes (2003)

Early transfer RNA (tRNA) processing events in Saccharomyces cerevisiae are coordinated in the nucleolus, the site normally associated with ribosome biosynthesis. To test whether spatial organization of the tRNA pathway begins with nucleolar clustering of the genes, we have probed the subnuclear location of five different tRNA gene families. The results show that tRNA genes, though dispersed in the linear genome, colocalize with 5S ribosomal DNA and U14 small nucleolar RNA at the nucleolus. Nucleolar localization requires tRNA gene transcription-complex formation, because inactivation of the promoter at a single locus removes its nucleolar association. This organization of tRNA genes must profoundly affect the spatial packaging of the genome and raises the question of whether gene types might be coordinated in three dimensions to regulate transcription.
Production of maltohexaose by .ALPHA.-amylase from Bacillus circulans G-6. (1982)

An α-amylase which produces maltohexaose as the main product from strach was found in the culture nitrate of Bacillus circulans G-6 which was isolated from soil and identified by the author. The enzyme was purified by means of ammonium sulfate fractionation, DEAE-Sepharose column chromatography and Sephadex G-200 column chromatography. The purified enzyme was homogeneous on disc electrophoresis. The optimum pH and temperature of the enzyme were around pH 8.0 and around 60°C, respectively. The enzyme was stable in the range of pH 5-10. Metal ions such as Hg2+, Cu2+, Zn2+, Fe2+ and Co2+ inhibited the enzyme activity. The molecular weight was about 76, 000. The yield of maltohexaose from soluble starch of DE (dextrose equivalent*) 1.8-12.6 was about 30%, and the combined action of the enzyme and pullulanase or isoamylase increased the yield of maltohexaose.
Compositing. 1. Theory (1994)

Associating a pixel's color with its opacity is the basis for a compositing function that is simple, elegant, and general. However, there are more reasons than mere prettiness to store pixels this way. One of the most important anti-aliening tools in computer graphics comes from a generalization of the simple act of storing a pixel into a frame buffer. Several people simultaneously discovered the usefulness of this operation, so it goes by several names: matting, image compositing, alpha blending, overlaying, or lerping. It was most completely codified in a previous paper by Porter and Duff (1984), where they call it the over operator. The author shows a new way to derive the over operator and describes some implementation details that he has found useful.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
REDUCING PREDATION THROUGH CHEMICALLY MEDIATED CAMOUFLAGE: INDIRECT EFFECTS OF PLANT DEFENSES ON HERBIVORES (1999)

Herbivores often specialize on particular hosts that provide both food and shelter from natural enemies. It is thus often unclear whether a plant’s value as a food or its value as a safe shelter has played a larger role in selecting for specialization. Decorator crabs offer a novel opportunity to investigate the relative effects of diet vs. natural enemies in selecting for specialization because these crabs place plant “shelter” on their backs as camouflage but need not use these plants as food, thus decoupling the plant’s value as a food from its value as a shelter. In this study, we show that juveniles of the decorator crab Libinia dubia selectively decorate with the chemically defended brown alga Dictyota menstrualis but treat this plant as a low-preference food. Common omnivorous fishes that are potential predators of Libinia avoid consuming Dictyota due to the alga’s potent chemical defenses. In the field, juvenile crabs decorated with Dictyota experience significantly less predation than crabs decorated with an alga that is not chemically noxious to local fishes, and the Dictyota metabolite that most strongly deters feeding by fishes is the specific metabolite that determines decoration choice by this crab. Thus, by behaviorally sequestering defenses from this chemically noxious plant, these small crabs reduce their susceptibility to predation. In the presence of predators, juvenile crabs reduce their rate of feeding, but not of decorating, suggesting that antipredator behavior such as decorating takes precedence over feeding. In addition, only juvenile crabs that are of a size that can be consumed by local fishes decorate at all. Adult crabs that have carapace widths exceeding the gape size of co-occurring fishes do not decorate in either the field or the laboratory. Apparently predation, rather than diet selection, drives decoration specialization in Libinia, highlighting how indirect effects of plant secondary chemistry can impact herbivore behavior, ecology, and evolution.
Long‐Term Electromyogram Recording from the Posterior Cricoarytenoid Muscle as a Potential Biological Trigger for Phrenic Pacing: Results of an Animal Study (1999)

Diaphragm pacing has been used to restore respiration in approximately 1,000 patients worldwide suffering from high quadriplegia or from central alveolar hypoventilation syndrome. Compared with conventional mechanical ventilation, electrophrenic respiration (EPR) reduces the risk of pulmonary infections and increases the mobility of patients. Voluntary activation of the pacemaker during speech would improve patients' quality of life and allow application of EPR in a more physiological way. An animal study was performed to investigate the electromyogram (EMG) of the posterior cricoarytenoid (PCA) muscle and the movement of the glottis via impedance measurement (electroglottography) with the aim to examine reproducibility and stability of the recordings from the PCA muscle as a potential biological trigger for a phrenic pacemaker. The EMG of the PCA muscle was recorded via implanted electrodes for a 200 day period. The EMG signal proved stable for that period, artifacts caused by movements can be suppressed, and swallowing can be detected. In contrast, impedance measurement to detect movement of the glottis proved not useful. Based on the results of this study, the use of the PCA EMG as a biological trigger for a phrenic pacemaker has to be considered a realistic option.
Utilization of the herpes simplex virus type 1 latency-associated regulatory region to drive stable reporter gene expression in the nervous system (1997)

The ability of herpes simplex virus type 1 (HSV-1) to establish a lifelong, transcriptionally active, latent infection in neurons has led to much interest in developing HSV-based vectors for gene delivery to the nervous system. A prerequisite of such vectors is that they should be capable of directing long-term transgene expression in latently infected neurons. The continued transcription of HSV-1 latency-associated transcripts (LATs) during neuronal latency suggests that regulatory sequences which mediate expression of LATs could be utilized for long-term expression of heterologous genes in the mammalian nervous system. In addition to upstream regulatory elements which are important for LAT promoter-mediated transcription during neuronal latency, there is growing evidence that sequences downstream of the LAT transcription start site play an important role in facilitating long-term latent-phase transcription. In order to maintain the integrity of both upstream and downstream regulatory elements of the LAT promoter, we constructed viruses which contained the lacZ and lacZ-neo reporter genes linked to the encephalomyocarditis virus internal ribosomal entry site (IRES) (viruses LbetaA and LbetaB, respectively) inserted approximately 1.5 kb downstream of the LAT transcription start site. These viruses expressed low levels of beta-galactosidase in lytically infected Vero cells and in cervical dorsal root ganglion neurons during the acute stage of infection in vivo. In contrast, at later times postinfection and consistent with the establishment of latency, increases both in the numbers of neurons expressing beta-galactosidase and in the intensity of staining were observed. Examination of the brain stems and spinal cords of animals latently infected with LbetaA, sampled at time points from 72 to 307 days postinfection, revealed the stable expression of beta-galactosidase within neurons located in facial and hypoglossal nerve nuclei and the upper cervical spinal cord. We conclude that the insertion of an IRES linked to a reporter gene 1.5 kb downstream from the LAT transcription start site does not disrupt elements of the LAT promoter necessary for long-term gene expression and, in both the peripheral and central nervous systems, facilitates beta-galactosidase expression in a wide variety of neurons.
Phase Noise and Jitter in CMOS Ring Oscillators (2006)

A simple, physically based analysis illustrate the noise processes in CMOS inverter-based and differential ring oscillators. A time-domain jitter calculation method is used to analyze the effects of white noise, while random VCO modulation most straightforwardly accounts for flicker (1/f) noise. Analysis shows that in differential ring oscillators, white noise in the differential pairs dominates the jitter and phase noise, whereas the phase noise due to flicker noise arises mainly from the tail current control circuit. This is validated by simulation and measurement. Straightforward expressions for period jitter and phase noise enable manual design of a ring oscillator to specifications, and guide the choice between ring and LC oscillator
Cyclen-Based Phenylboronate Ligands and Their Eu3+ Complexes for Sensing Glucose by MRI (2004)

Novel cyclen-based phenylboronate ligands and their corresponding Eu(3+) complexes have been examined as glucose sensors using chemical exchange saturation transfer (CEST) MR imaging for detection. Two isomeric bis-phenylboronate complexes, Eu(4) and Eu(10), and a mono-phenylboronate complex, Eu(12), had been prepared and characterized by UV and circular dichroism spectroscopy, mass spectrometry, and CEST imaging. Both the free ligands and their Eu(3+) complexes bind to simple sugars, but their selectivity and binding affinities vary with sugar structure. Interestingly, the free ligands, 4 and 10, are selective for fructose over glucose, but this selectivity order switches in the respective Eu(3+) complexes. Of the complexes examined, Eu(4) shows the highest selectivity and binding affinity for glucose (2275 +/- 266 M(-)(1) at pH 10.2 and 339 +/- 29 M(-)(1) at pH 7). Glucose acts as a "capping"moiety in the Eu(4).glucose binary complex and modulates water exchange between a single Eu(3+)-bound water molecule and bulk water, an effect that can be detected by CEST imaging. Thus, Eu(4) represents a new class of metabolite-specific imaging agents that may allow mapping of metabolites by MRI of the bulk water signal.
Attachment of Mycoplasma pneumoniae to hamster tracheal organ cultures, tracheal outgrowth monolayers, human erythrocytes, and WiDr human tissue culture cells (1982)

Virulent strains of Mycoplasma pneumoniae, PI-1428 and M129, were radiolabeled wtih [3H]palmitic acid or [3H]thymidine and examined for attachment to hamster tracheal organ cultures, tracheal outgrowth monolayers, human O-positive erythrocytes, and human WiDr carcinoma cell cultures. Although attachment to each cell substrate was readily detected, the WiDr cell culture monolayers provided the most satisfactory substrate for quantitating mycoplasma attachment. Serious technical limitations were encountered with each of the other substrates that we examined; these limitations interfered with reproducibility or sensitivity and rendered tracheal organ cultures and erythrocyte suspensions unsuitable for routine attachment and attachment inhibition assays. Moreover, the WiDr cell monolayer was the most sensitive substrate for determining attachment inhibition activity in protein-containing extracts prepared from M. pneumoniae. The significance of these findings is discussed.
Measurements of pulmonary gas exchange efficiency using expired gas and oximetry: results in normal subjects (2018)

We are developing a novel, noninvasive method for measuring the efficiency of pulmonary gas exchange in patients with lung disease. The patient wears an oximeter, and we measure the partial pressures of oxygen and carbon dioxide in inspired and expired gas using miniature analyzers. The arterial Po<sub>2</sub> is then calculated from the oximeter reading and the oxygen dissociation curve, using the end-tidal Pco<sub>2</sub> to allow for the Bohr effect. This calculation is only accurate when the oxygen saturation is <94%, and therefore, these normal subjects breathed 12.5% oxygen. When the procedure is used in patients with hypoxemia, they breathe air. The Po<sub>2</sub> difference between the end-tidal and arterial values is called the "oxygen deficit." Preliminary data show that this index increases substantially in patients with lung disease. Here we report measurements of the oxygen deficit in 20 young normal subjects (age 19 to 31 yr) and 11 older normal subjects (47 to 88 yr). The mean value of the oxygen deficit in the young subjects was 2.02 ± 3.56 mmHg (means ± SD). This mean is remarkably small. The corresponding value in the older group was 7.53 ± 5.16 mmHg (means ± SD). The results are consistent with the age-related trend of the traditional alveolar-arterial difference, which is calculated from the calculated ideal alveolar Po<sub>2</sub> minus the measured arterial Po<sub>2</sub>. That measurement requires an arterial blood sample. The present study suggests that this noninvasive procedure will be valuable in assessing the degree of impaired gas exchange in patients with lung disease.
Ground- and Excited-State Dynamics of Aluminum and Gallium Corroles (2009)

The steady-state absorption and emission spectra and the temporal fluorescence decay profiles of two metallocorroles, Al(tpfc)(py)(n) and Ga(tpfc)(py)(n) (n = 1,2), have been measured in a noncoordinating solvent, benzene, in a coordinating solvent, pyridine, and in mixed benzene-pyridine solutions. The ground-state spectra reveal that an equilibrium between the pentacoordinate corrole (n = 1) and the hexacoordinate corrole (n = 2) is established in the mixed benzene-pyridine solutions. The ground-state equilibrium constants are 135 M(-1) and 1.0 M(-1) at 295 K for the Al and Ga species, respectively. The excited-state radiative and nonradiative decay constants of the pentacoordinate and the hexacoordinate species have been obtained from measurements of the fluorescence quantum yields and monoexponential fluorescence decay times in pure benzene and pure pyridine. Temporal fluorescence decays of the gallium system in a mixed benzene-pyridine solution are biexponential due to dissociation of the hexacoordinate species in the excited state leading to the establishment of a dissociation-association equilibrium. The rate constants for the pyridine association and dissociation processes for the gallium corrole in the excited state have been measured, k(a)* = 2.3 x 10(8) M(-1) s(-1) and k(d)* = 2.9 x 10(8) s(-1), respectively, leading to a value for the excited-state association equilibrium constant of K(a)* = 0.78 M(-1).
Residual stresses in polycrystalline silicon sheet and their relation to electron-hole lifetime (2006)

This letter summarizes research on the characterization of residual stresses and electron-hole lifetimes of polycrystalline silicon sheet for photovoltaic applications. Full-field polariscopy, scanning room temperature photoluminescence, and surface photovoltage are used to characterize the polycrystalline silicon sheet. An orientation dependent stress-optic coefficient has been developed and used to extract the in-plane residual stresses from analysis of transmitted near-infrared light. The characteristics of the spatial distribution and the quantitative correlation between the residual stresses and the electron-hole lifetime are presented.
Quantification of RNA integrity and its use for measurement of transcript number (2012)

RNA degradation can distort or prevent measurement of RNA transcripts. A mathematical model for degradation was constructed, based on random RNA damage and exponential polymerase chain reaction (PCR) amplification. Degradation, measured as the number of lesions/base, can be quantified by amplifying several sequences of a reference gene, calculating the regression of C(t) on amplicon length and determining the slope. Reverse transcriptase-quantitative PCR (RT-qPCR) data can then be corrected for degradation using lesions/base, amplicon length(s) and the relevant equation obtained from the model. Several predictions of the model were confirmed experimentally; degradation in a sample quantified using the model correlated with degradation quantified using an additional control sample and the ΔΔCt method and application of the model corrected erroneous results for relative quantification resulting from degradation and differences in amplicon length. Compared with RIN, the method was quantitative, simpler, more sensitive and spanned a wider range of RNA damage. The method can use either random or specifically primed complementary DNA and it enables relative and absolute quantification of RNA to be corrected for degradation. The model and method should be applicable to many situations in which RNA is quantified, including quantification of RNA by methods other than nucleic acid amplification.
Cutting Edge: Signal-Regulatory Protein β1 Is a DAP12-Associated Activating Receptor Expressed in Myeloid Cells (2000)

Signal-regulatory proteins (SIRPs) are cell-surface glycoproteins expressed on myeloid and neural cells that have been shown to recruit SH2 domain-containing protein phosphatase 1 (SHP-1) and SHP-2 and to regulate receptor tyrosine kinase-coupled signaling. One SIRP of unknown function, designated SIRP beta 1, contains a short cytoplasmic domain that lacks sequence motifs capable of recruiting SHP-1 and SHP-2. Using a SIRP-specific mAb, we show that SIRP beta 1 is expressed in monocytes and dendritic cells and associates with the signal transduction molecule DAP12. SIRP beta 1/DAP12 complex formation was required for efficient cell-surface expression of SIRP beta 1. Stimulation of this complex induced tyrosine phosphorylation, mitogen-activated protein kinase activation, and cellular activation. Thus, SIRP beta 1 is a new DAP12-associated receptor involved in the activation of myeloid cells.
TheFrancisellaPathogenicity Island Protein PdpD Is Required for Full Virulence and Associates with Homologues of the Type VI Secretion System (2008)

Francisella tularensis is a highly infectious, facultative intracellular bacterial pathogen that is the causative agent of tularemia. Nearly a century ago, researchers observed that tularemia was often fatal in North America but almost never fatal in Europe and Asia. The chromosomes of F. tularensis strains carry two identical copies of the Francisella pathogenicity island (FPI), and the FPIs of North America-specific biotypes contain two genes, anmK and pdpD, that are not found in biotypes that are distributed over the entire Northern Hemisphere. In this work, we studied the contribution of anmK and pdpD to virulence by using F. novicida, which is very closely related to F. tularensis but which carries only one copy of the FPI. We showed that anmK and pdpD are necessary for full virulence but not for intracellular growth. This is in sharp contrast to most other FPI genes that have been studied to date, which are required for intracellular growth. We also showed that PdpD is localized to the outer membrane. Further, overexpression of PdpD affects the cellular distribution of FPI-encoded proteins IglA, IglB, and IglC. Finally, deletions of FPI genes encoding proteins that are homologues of known components of type VI secretion systems abolished the altered distribution of IglC and the outer membrane localization of PdpD.
The Largest Penal Experiment in American History (2003)

This chapter argues that California's Three Strikes is the most important effort to achieve an abrupt increase in criminal punishments in modern times. Three Strikes legislation in the federal system and most American states was designed to have maximum symbolic impact while not making major changes in case outcomes. The Washington initiative that launched Three Strikes had somewhat larger practical ambitions but was limited in its impact to defendants with three serious felony convictions. The California Three Strikes initiative was designed to use the Three Strikes label and logic to require long-mandatory prison terms for criminal defendants with one prior designated felony conviction and any current felony offense. Its two major innovations are the use of mandatory sentences after a single predicate felony and second- and third-strike sanctions following any subsequent felony conviction.
Connexin43 mimetic peptide reduces vascular leak and retinal ganglion cell death following retinal ischaemia (2012)

Connexin43 gap junction protein is expressed in astrocytes and the vascular endothelium in the central nervous system. It is upregulated following central nervous system injury and is recognized as playing an important role in modulating the extent of damage. Studies that have transiently blocked connexin43 in spinal cord injury and central nervous system epileptic models have reported neuronal rescue. The purpose of this study was to investigate neuronal rescue following retinal ischaemia-reperfusion by transiently blocking connexin43 activity using a connexin43 mimetic peptide. A further aim was to evaluate the effect of transiently blocking connexin43 on vascular permeability as this is known to increase following central nervous system ischaemia. Adult male Wistar rats were exposed to 60 min of retinal ischaemia. Treatment groups consisted of no treatment, connexin43 mimetic peptide and scrambled peptide. Retinas were then evaluated at 1-2, 4, 8 and 24 h, and 7 and 21 days post-ischaemia. Evans blue dye leak from retinal blood vessels was used to assess vascular leakage. Blood vessel integrity was examined using isolectin-B4 labelling. Connexin43 levels and astrocyte activation (glial fibrillary acidic protein) were assessed using immunohistochemistry and western blot analysis. Retinal whole mounts and retinal ganglion cell counts were used to quantify neurodegeneration. An in vitro cell culture model of endothelial cell ischaemia was used to assess the effect of connexin43 mimetic peptide on endothelial cell survival and connexin43 hemichannel opening using propidium iodide dye uptake. We found that retinal ischaemia-reperfusion induced significant vascular leakage and disruption at 1-2, 4 and 24 h following injury with a peak at 4 h. Connexin43 immunoreactivity was significantly increased at 1-2, 4, 8 and 24 h post ischaemia-reperfusion injury co-localizing with activated astrocytes, Muller cells and vascular endothelial cells. Connexin43 mimetic peptide significantly reduced dye leak at 4 and 24 h. In vitro studies on endothelial cells demonstrate that endothelial cell death following hypoxia can be mediated directly by opening of connexin43 hemichannels in endothelial cells. Blocking connexin43 mediated vascular leakage using a connexin43 mimetic peptide led to increased retinal ganglion cell survival at 7 and 21 days to levels of uninjured retinas. Treatment with scrambled peptide did not result in retinal ganglion cell rescue. Pharmacological targeting of connexin43 gap junction protein by transiently blocking gap junction hemichannels following injury provides new opportunities for treatment of central nervous system ischaemia.