gebhart/patrepeval huggingface dataset:
Uterine Cellular Changes in 2′,5′-Oligoadenylate Synthetase during the Bovine Estrous Cycle and Early Pregnancy1 (1993)

The signal for maternal recognition of pregnancy in cattle is bovine trophoblast protein-1 (bTP-1), a Type I trophoblast interferon. One of the many functions of interferons is the induction of the 2',5'-oligoadenylate (2-5[A]) system, which is involved in cell division and selective degradation of mRNA. The present study focused on the cellular changes of 2-5(A) synthetase in bovine endometrium during the estrous cycle and early pregnancy. Ability of recombinant bTP-1 to stimulate activity of the enzyme in uterine cells throughout the estrous cycle was also evaluated in vitro. Surface epithelium, glandular epithelium, and stroma were enzymatically separated in cows on Day 5, 10, 15, or 18 postestrus and on Day 15 or 18 of pregnancy. Cell samples were lysed and frozen for determination of the endogenous cellular content of 2-5(A) synthetase. Additional cells obtained during the estrous cycle were cultured and treated with increasing doses of recombinant bovine interferon alpha (rbIFN-alpha) or recombinant bTP-1 (rbTP-1). During the estrous cycle, 2-5(A) synthetase was greatest on Day 5 and declined approximately 10-fold by Day 15 (p < 0.01). Cellular content of 2-5(A) synthetase was similar among all three endometrial cell types. In the gravid horn of pregnant animals, presence of a conceptus significantly increased (p < 0.01) 2-5(A) synthetase in all endometrial cell types compared to levels on Days 15 and 18 of the estrous cycle. On Day 18, levels of 2-5(A) synthetase were 30-fold greater (p < 0.01) in epithelium (surface and glandular) from pregnant cows compared to that from cyclic cows.(ABSTRACT TRUNCATED AT 250 WORDS)
Purification and Molecular Cloning of Plx1, a Cdc25-Regulatory Kinase from Xenopus Egg Extracts (1996)

Cdc2, the cyclin-dependent kinase that controls mitosis, is negatively regulated by phosphorylation on its threonine-14 and tyrosine-15 residues. Cdc25, the phosphatase that dephosphorylates both of these residues, undergoes activation and phosphorylation by multiple kinases at mitosis. Plx1, a kinase that associates with and phosphorylates the amino-terminal domain of Cdc25, was purified extensively from Xenopus egg extracts. Cloning of its complementary DNA revealed that Plx1 is related to the Polo family of protein kinases. Recombinant Plx1 phosphorylated Cdc25 and stimulated its activity in a purified system. Cdc25 phosphorylated by Plx1 reacted strongly with MPM-2, a monoclonal antibody to mitotic phosphoproteins. These studies indicate that Plx1 may participate in control of mitotic progression.
Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri (2010)

Going Multicellular The volvocine algae include both the unicellular Chlamydomonas and the multicellular Volvox , which diverged from one another 50 to 200 million years ago. Prochnik et al. (p. 223 ) compared the Volvox genome with that of Chlamydomonas to identify any genomic innovations that might have been associated with the transition to multicellularity. Size changes were observed in several protein families in Volvox , but, overall, the Volvox genome and predicted proteome were highly similar to those of Chlamydomonas . Thus, biological complexity can arise without major changes in genome content or protein domains.
The schlieren image of two-dimensional ultrasonic fields and cavity resonances (1997)

The schlieren technique can be used to visualize the two-dimensional ultrasonic standing wave fields associated with circular cylindrical shells under resonance conditions. However, the interpretation of the schlieren image is not simple due to the complex relationship between the acoustic and optical fields. A model for predicting the optical image in an ideal schlieren system is presented and used to investigate the influence of the acoustic pressure and optical spatial filtering on the resultant image, demonstrating the conditions under which the image is a meaningful representation of the acoustic wave field. A low-frequency (&amp;gt;100 kHz), wide-aperture, laboratory schlieren system is used to image the fluid column resonances of a circular cylindrical shell. Experimental results agree well with the predictions, validating the theory. Although the schlieren image is two-dimensional, limiting investigations to targets having translational symmetry, the technique is noninvasive and can potentially provide greater insight into the acoustic resonance behavior of more complex scattering geometries.
Interactions between Local Anesthetics and Na+ Channel Inactivation Gate Peptides in Phosphatidylserine Suspensions as Studied by 1H-NMR Spectroscopy. (2000)

Interactions between local anesthetics and a sodium channel inactivation gate peptide (Ac-GGQDIFMTEEQK-NH2, MP-1A), which was dissected from the cytoplasmic linker between domains III and IV of the sodium channel alpha-subunit (G1484-K1495 in rat brain type IIA), have been studied by 1H-NMR spectroscopy. Changes in 1H-NMR chemical shifts of the aromatic proton resonances of dibucaine (pH 7.0) and lidocaine (pH 6.0 and 9.0) in phosphatidylserine (PS) suspensions were observed. The effects of substitution of glutamine (F1489Q; MP-2A) or D-phenylalanine (MP-1A') for L-phenylalanine (F1489) in MP-1A and the effects of substitution of neutral amino acid residues for the corresponding acidic amino acid residues (D1487N, MP-1NA; E1492Q, MP-IQEA; E1493Q, MP-IEQA) in MP-1A, on the aromatic 1H-NMR chemical shift changes of dibucaine and lidocaine were also investigated. From these results it was concluded that: the aromatic ring of phenylalanine of MP-1A and the aromatic ring of the cationic form of dibucaine or lidocaine are interacting by pi-pi stacking; the tertiary amine nitrogen of dibucaine is interacting electrostatically with D1487, whereas that of lidocaine is interacting with E1492.
A new method for detecting state changes in the EEG: exploratory application to sleep data (1998)

A new statistical method is described for detecting state changes in the electroencephalogram (EEG), based on the ongoing relationships between electrode voltages at different scalp locations. An EEG sleep recording from one NREM-REM sleep cycle from a healthy subject was used for exploratory analysis. A dimensionless function defined at discrete times ti, u(ti), was calculated by determining the log-likelihood of observing all scalp electrode voltages under the assumption that the data can be modeled by linear combinations of stationary relationships between derivations. The u(ti), calculated by using independent component analysis, provided a sensitive, but non-specific measure of changes in the global pattern of the EEG. In stage 2, abrupt increases in u(ti) corresponded to sleep spindles. In stages 3 and 4, low frequency (approximately equal to 0.6 Hz) oscillations occurred in u(ti) which may correspond to slow oscillations described in cellular recordings and the EEG of sleeping cats. In stage 4 sleep, additional irregular very low frequency (approximately equal to 0.05-0.2 Hz) oscillations were observed in u(ti) consistent with possible cyclic changes in cerebral blood flow or changes of vigilance and muscle tone. These preliminary results suggest that the new method can detect subtle changes in the overall pattern of the EEG without the necessity of making tenuous assumptions about stationarity.
Lexicon modeling for query understanding (2011)

Lexicons are important resources for semantic tagging. However, commonly used lexicons collected from entity databases suffer from multiple problems, such as ambiguity, limited coverage and lack of relative importance. In this work we present a lexicon modeling technique that automatically expands the lexicon and assigns weights to its elements. For lexicon expansion, we use a generative model to extract patterns from query logs using known lexicon seeds, and discover new lexicon elements using the learned patterns. For lexicon weighting, we propose two approaches based on generative and discriminative models to learn the relative importance of lexicon elements from user click statistics. Experiments on text queries in multiple domains show that our lexicon modeling technique can significantly improve semantic tagging performance.
UDP-GlcNAc concentration is an important factor in the biosynthesis of 1,6-branched oligosaccharides: regulation based on the kinetic properties of N-acetylglucosaminyltransferase V (2002)

Human beta1,6-N-acetylglucosaminyltransferase V (GnT-V) was expressed by baculovirus-insect cell system, and the purified recombinant enzyme was kinetically characterized. The data obtained were used to establish the kinetic basis of the substrate specificity toward donor nucleotide sugars, and also revealed that K(m) values for the donors are much higher compared to those of other GlcNAc transferases, the kinetic properties of which have been reported. Because this exceptionally higher K(m) suggests that GnT-V is physiologically present at far from saturated conditions, it would appear that the production of beta1,6-branched oligosaccharide, which is formed by GnT-V, could be regulated in vivo by the concentration of the donor, UDP-GlcNAc, as well as the expression levels of the enzyme. When B16 melanoma cells, which express high levels of GnT-V, were incubated with GlcNAc, the beta1,6-branched oligosaccharide levels were increased, as judged by a lectin blot analysis, in conjunction with an increase in intracellular UDP-GlcNAc. These findings suggest that the level of UDP-GlcNAc can be a critical factor in the production of beta1,6-branched oligosaccharides, for example, by tumor cells, which have been thought to be closely associated with tumor progression and metastasis.
Channel Noise is Essential for Perithreshold Oscillations in Entorhinal Stellate Neurons (2005)

Previous experimental and computational work (for review, see White et al., 2000) has suggested that channel noise, generated by the stochastic flicker of voltage-gated ion channels, can be a major contributor to electrical membrane noise in neurons. In spiny stellate neurons of the entorhinal cortex, we remove the primary source of channel noise by pharmacologically blocking the native persistent Na+ conductance. Via the dynamic-clamp technique (Robinson and Kawai, 1993; Sharp et al., 1993), we then introduce virtual persistent Na+ channels into the membranes of the stellate neurons. By altering the mathematical properties of these virtual "knock-ins," we demonstrate that stochastic flicker of persistent Na+ channels is necessary for the existence of slow perithreshold oscillations that characterize stellate neurons. Channel noise also alters the ability of stellate neurons to phase lock to weak sinusoidal stimuli. These results provide the first direct demonstration that physiological levels of channel noise can produce qualitative changes in the integrative properties of neurons.
Directed Mutation of the Rubisco Large Subunit of Tobacco Influences Photorespiration and Growth (1999)

The gene for the large subunit of Rubisco was specifically mutated by transforming the chloroplast genome of tobacco (Nicotiana tabacum). Codon 335 was altered to encode valine instead of leucine. The resulting mutant plants could not grow without atmospheric CO2 enrichment. In 0.3% (v/v) CO2, the mutant and wild-type plants produced similar amounts of Rubisco but the extent of carbamylation was nearly twice as great in the mutants. The mutant enzyme's substrate-saturated CO2-fixing rate and its ability to distinguish between CO2 and O2 as substrates were both reduced to 25% of the wild type's values. Estimates of these parameters obtained from kinetic assays with the purified mutant enzyme were the same as those inferred from measurements of photosynthetic gas exchange with leaves of mutant plants. The Michaelis constants for CO2, O2, and ribulose-1,5-bisphosphate were reduced and the mutation enhanced oxygenase activity at limiting O2 concentrations. Consistent with the reduced CO2 fixation rate at saturating CO2, the mutant plants grew slower than the wild type but they eventually flowered and reproduced apparently normally. The mutation and its associated phenotype were inherited maternally. The chloroplast-transformation strategy surmounts previous obstacles to mutagenesis of higher-plant Rubisco and allows the consequences for leaf photosynthesis to be assessed.
Triggered amplification by hybridization chain reaction (2004)

We introduce the concept of hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment. In the simplest version of this process, two stable species of DNA hairpins coexist in solution until the introduction of initiator strands triggers a cascade of hybridization events that yields nicked double helices analogous to alternating copolymers. The average molecular weight of the HCR products varies inversely with initiator concentration. Amplification of more diverse recognition events can be achieved by coupling HCR to aptamer triggers. This functionality allows DNA to act as an amplifying transducer for biosensing applications.
Structural analysis of parathormone fragments elaborated by cells cultured from a hyperplastic human parathyroid gland. (1986)

Parathyroid cells were obtained by collagenase digestion of 2 g of human parathyroid tissue obtained at surgery from a patient with end stage renal failure and hypercalcemia. Cells were placed into monolayer culture in supplemented Waymouth's MB752/1. Secretion of parathyroid hormone (PTH) from monolayer cultures was inhibited for 3 weeks by 2.5 mM compared to 0.5 mM calcium. The inhibition was 50% on day 3 of culture, and decreased to 19% by day 21. When cultures were incubated with [3H]leucine, radioactive PTH and COOH-terminal PTH fragments were secreted. Sequence analyses were performed on material in radioactive and immunoreactive peaks following gel filtration and high performance liquid chromatography of media. The results indicated that cleavage of PTH or fragments thereof occurred at the 23-24, 27-28, and 33-34 peptide bonds. NH2-terminal fragments of PTH were not detected in media.
Janus kinase 3 (Jak3) is essential for common cytokine receptor γ chain (γc)-dependent signaling: comparative analysis of γc, Jak3, and γc and Jak3 double-deficient mice (2000)

The common cytokine receptor gamma chain (gamma(c)) is an essential receptor component for IL-2, IL-4, IL-7, IL-9 and IL-15, and thereby gamma(c)-deficient mice exhibit impaired T cell and B cell development. The Janus family tyrosine kinase 3 (Jak3) is known to be associated with gamma(c), and the reported phenotypes of gamma(c)-deficient (gamma(c)(-)) and Jak3-deficient (Jak3(-)) mice are similar, indicating that Jak3 is an essential transducer of gamma(c)-dependent signals. Nevertheless, certain differences have been suggested related to the range of actions of gamma(c) and Jak3. To clarify whether gamma(c)-dependent cytokines can partially transduce their signals without Jak3, we compared lymphocyte development in gamma(c)(-), Jak3(-), and gamma(c) and Jak3 double-deficient (gamma(c)(-)Jak3(-)) mice in the same genetic background. With the exception that T and B cells in Jak3(-) mice express high levels of gamma(c), the defects in thymocyte and peripheral T cell and B cell development are indistinguishable among gamma(c)(-), Jak3(-) and gamma(c)(-)Jak3(-) mice. Interestingly, although Bcl-2 induction was previously suggested to be Jak3-independent, IL-7 cannot induce Bcl-2 expression in CD4 single-positive (SP) thymocytes in either gamma(c)(-) or Jak3(-) mice nor can IL-7 rescue CD4 SP thymocytes from dexamethasone-induced cell death in gamma(c)(-) or Jak3(-) mice. These results indicate that Jak3 is absolutely essential for gamma(c)-dependent T cell and B cell development, and for gamma(c)-dependent prevention of thymocyte apoptosis.
CD8 + T Lymphocyte-Mediated Inhibition of HIV-1 Long Terminal Repeat Transcription: A Novel Antiviral Mechanism (1993)

HIV-1 infection evokes a vigorous antiviral response that may participate in resolving the initial peak of plasma viremia and maintenance of the asymptomatic state. CD8+ T lymphocytes of HIV-1-infected individuals play a critical role in the cellular anti-HIV response. In agreement with previous reports, we observed a potent suppressive effect on HIV-1 production from autologous CD4+ T lymphocytes by CD8+ T lymphocytes from asymptomatic HIV-1-infected individuals. To elucidate the mechanism(s) of the nonlytic suppressive antiviral activity, we examined the effect of CD8+ T lymphocytes on the transcriptional activity of the HIV-1 promoter (HIV-LTR). CD8+ lymphocytes from HIV-1-infected asymptomatic individuals suppressed tat-mediated HIV-LTR transcription in CD4+ lymphocytes. HIV-LTR transcriptional activity was suppressed by CD8 lymphocytes to an extent similar to tat-mediated transcription whereas CMV immediate early gene promoter activity was not affected. In contrast to the suppressive effect seen with CD8+ lymphocytes from HIV-1-infected individuals, CD8+ lymphocytes from uninfected individuals did not significantly inhibit tat-mediated or HIV-LTR transcription. The transcriptional inhibitory activity was not MHC class I restricted and could be mediated by a soluble factor(s). Supernatants from some CD8+ T lymphocyte cultures from HIV-1+ individuals exerted an inhibitory effect on tat-mediated HIV-LTR transcription comparable to that seen with CD8+ cells. In conclusion, CD8+ lymphocytes from asymptomatic HIV-1+ individuals could suppress virus production by inhibiting HIV-1 gene expression.(ABSTRACT TRUNCATED AT 250 WORDS)
A mechanism for dynamic lateral polarization in CdZnTe under high flux x-ray irradiation (2008)

It has been observed that pixillated CdZnTe detectors fabricated from crystals with low hole transport properties (μhτh&amp;lt;10−5cm2V−1) experience a dynamic lateral polarization when exposed to a high flux of x-rays. In this effect, counts are transferred from pixels near the edge of the irradiated region to pixels in the interior. In this letter, we propose a mechanism capable of explaining the observed dynamical effect. The mechanism is based on a transverse electric field that is generated due to space charge that builds within the material. This transverse field, in turn, is responsible for the altered carrier trajectories toward the center of the irradiated region.
Solutions preparing for total parenteral nutrition for children (2006)

Abstract: The article describes the methodology for the preparation of paediatric parenteral nutrition with the intention of meeting the physical needs of patients for the duration of 24 hours, and to protect the organism from the effects of starvation. The methodology involves planning, and optimal preparation of standardised solutions and basic solutions of concentrated electrolytes, which must constitute a safe product of adequate quality and efficiency. Key – words: biology, paediatrics, parenteral nutrition, components, methodology of preparation of solutions, demands 1
Multicompartment Polymersomes from Double Emulsions (2011)

Versatile chambers: A microfluidic technique is used to generate polymersomes with multiple compartments using double emulsions with different morphology as templates (see scheme). The polymersomes could be utilized for encapsulation of multiple substances and as reaction vessels that enable triggered reaction with controlled stoichometry of the reactants. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
BRACHYURY and CDX2 Mediate BMP-Induced Differentiation of Human and Mouse Pluripotent Stem Cells into Embryonic and Extraembryonic Lineages (2011)

BMP is thought to induce hESC differentiation toward multiple lineages including mesoderm and trophoblast. The BMP-induced trophoblast phenotype is a long-standing paradox in stem cell biology. Here we readdressed BMP function in hESCs and mouse epiblast-derived cells. We found that BMP4 cooperates with FGF2 (via ERK) to induce mesoderm and to inhibit endoderm differentiation. These conditions induced cells with high levels of BRACHYURY (BRA) that coexpressed CDX2. BRA was necessary for and preceded CDX2 expression; both genes were essential for expression not only of mesodermal genes but also of trophoblast-associated genes. Maximal expression of the latter was seen in the absence of FGF but these cells coexpressed mesodermal genes and moreover they differed in cell surface and epigenetic properties from placental trophoblast. We conclude that BMP induces human and mouse pluripotent stem cells primarily to form mesoderm, rather than trophoblast, acting through BRA and CDX2.
Secretion of tears in patients with hemifacial spasm. (1990)

Hemifacial spasm can cause abnormal tear secretion on the affected side. Thirty patients with this disease were examined using the Schirmer's test without topical anesthetic. Twelve of them showed more tear secretion on the affected side than on the unaffected side. The average Schirmer test value was 30.4 +/- 12.3 mm (+/- SD) on the affected side in the patients and 17.4 +/- 10.9 mm (n = 148) in the control subjects (P less than 0.001). Microvascular decompression surgery reduced the hypersecretion of tears. The results suggest that compression of the facial nerve by a blood vessel causes an excitatory stimulus for tear secretion in patients with hemifacial spasm.
Fringe scanning speckle-pattern interferometry (1985)

Digital speckle-pattern interferometry systems for automatic measurement of deformations of a diffuse object are presented, which are based on a fringe scanning method with phase-shifted speckle interferograms. A digital speckle pattern before deformation of an object is recorded in the mass storage device of a computer facility. After deformation, four digital speckle patterns are recorded as changing the phase of reference light such as 0, π/2, π, and 3π/2, respectively. Four speckle interferograms, whose phases are shifted by 0, π/2, π, and 3π/2, are generated by calculating the square of the differences between speckle patterns before and after deformation. These interferograms are low-pass filtered to reduce speckle noise. The calculation of the arctangent with four phase-shifted speckle interferograms gives the optical path difference which is proportional to the deformation. A correction of the discontinuity of the calculated phase gives the numerical data of the deformation in the whole object area. Some experimental results for the measurement of out-of-plane, in-plane, and 3-D deformations are presented.