gebhart/patrepeval huggingface dataset:
Cloning, Expression, and Characterization of a DNA Binding Domain of gpNu1, a Phage λ DNA Packaging Protein (1998)

Terminase is an enzyme from bacteriophage lambda that is required for insertion of the viral genome into an empty pro-capsid. This enzyme is composed of the viral proteins gpNu1 (20.4 kDa) and gpA (73.3 kDa) in a holoenzyme complex. Current models for terminase assembly onto DNA suggest that gpNu1 binds to three repeating elements within a region of the lambda genome known as cosB which, in turn, stimulates the assembly of a gpA dimer at the cosN subsite. This prenicking complex is the first of several stable nucleoprotein intermediates required for DNA packaging. We have noted a hydrophobic region within the primary amino acid sequence of the terminase gpNu1 subunit and hypothesized that this region constitutes a protein-protein interaction domain required for cooperative assembly at cosB and that is also responsible for the observed aggregation behavior of the isolated protein. We therefore constructed a mutant of gpNu1 in which this hydrophobic "domain" has been deleted in order to test these hypotheses. The deletion mutant protein, gpNu1DeltaK, is fully soluble and, unlike full-length protein, shows no tendency toward aggregation; However, the protein is a dimer under all experimental conditions examined as determined by gel permeation and sedimentation equilibrium analysis. The truncated protein is folded with evidence of secondary and tertiary structural elements by circular dichroism and NMR spectroscopy. While physical and biological assays demonstrate that gpNu1DeltaK does not interact with the terminase gpA subunit, the deletion mutant binds with specificity to cos-containing DNA. We have thus constructed a deletion mutant of the phage lambda terminase gpNu1 subunit which constitutes a highly soluble DNA binding domain of the protein. We further propose that the hydrophobic amino acids found between Lys100 and Pro141 define a self-association domain that is required for the assembly of stable nucleoprotein packaging complexes and that the C-terminal tail of the protein defines a distinct gpA-binding site that is responsible for terminase holoenzyme formation.
mRNAs biotinylated within the 5′ cap and protected against decapping: new tools to capture RNA–protein complexes (2018)

The 5'-terminus of eukaryotic mRNAs comprises a 7-methylguanosine cap linked to the first transcribed nucleotide via a 5'-5' triphosphate bond. This cap structure facilitates numerous interactions with molecules participating in mRNA processing, turnover and RNA translation. Here, we report the synthesis and biochemical properties of a set of biotin-labelled cap analogues modified within the triphosphate bridge and increasing mRNA stability while retaining biological activity. Successful co-transcriptional incorporation of the cap analogues allowed for the quantification of cap-dependent translation efficiency, capping efficiency and the susceptibility to decapping by Dcp2. The utility of such cap-biotinylated RNAs as molecular tool was demonstrated by ultraviolet-cross-linking and affinity capture of protein-RNA complexes. In conclusion, RNAs labelled with biotin via the 5' cap structure can be applied to a variety of biological experiments based on biotin-avidin interaction or by means of biotin-specific antibodies, including protein affinity purification, pull-down assays, <i>in vivo</i> visualization, cellular delivery and many others.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
YPR139c/LOA1encodes a novel lysophosphatidic acid acyltransferase associated with lipid droplets and involved in TAG homeostasis (2011)

For many years, lipid droplets (LDs) were considered to be an inert store of lipids. However, recent data showed that LDs are dynamic organelles playing an important role in storage and mobilization of neutral lipids. In this paper, we report the characterization of LOA1 (alias VPS66, alias YPR139c), a yeast member of the glycerolipid acyltransferase family. LOA1 mutants show abnormalities in LD morphology. As previously reported, cells lacking LOA1 contain more LDs. Conversely, we showed that overexpression results in fewer LDs. We then compared the lipidome of loa1Δ mutant and wild-type strains. Steady-state metabolic labeling of loa1Δ revealed a significant reduction in triacylglycerol content, while phospholipid (PL) composition remained unchanged. Interestingly, lipidomic analysis indicates that both PLs and glycerolipids are qualitatively affected by the mutation, suggesting that Loa1p is a lysophosphatidic acid acyltransferase (LPA AT) with a preference for oleoyl-CoA. This hypothesis was tested by in vitro assays using both membranes of Escherichia coli cells expressing LOA1 and purified proteins as enzyme sources. Our results from purification of subcellular compartments and proteomic studies show that Loa1p is associated with LD and active in this compartment. Loa1p is therefore a novel LPA AT and plays a role in LD formation.
Effect of oxygen plasma etching on graphene studied using Raman spectroscopy and electronic transport measurements (2011)

In this paper, we report a study of graphene and graphene field effect devices after their exposure to a series of short pulses of oxygen plasma. Our data from Raman spectroscopy, back-gated field-effect and magnetotransport measurements are presented. The intensity ratio between Raman 'D' and 'G' peaks, I-D/I-G (commonly used to characterize disorder in graphene), is observed to initially increase almost linearly with the number (N-e) of plasma-etching pulses, but later decreases at higher N-e values. We also discuss the implications of our data for extracting graphene crystalline domain sizes from I-D/I-G. At the highest N-e value measured, the '2D' peak is found to be nearly suppressed while the 'D' peak is still prominent. Electronic transport measurements in plasma-etched graphene show an up-shifting of the Dirac point, indicating hole doping. We also characterize mobility, quantum Hall states, weak localization and various scattering lengths in a moderately etched sample. Our findings are valuable for understanding the effects of plasma etching on graphene and the physics of disordered graphene through artificially generated defects.
A new radiological index for assessing asphericity of the femoral head in cam impingement (2007)

Femoroacetabular cam impingement is thought to be a cause of premature osteoarthritis of the hip. The presence of cam malformation was determined in 2803 standardised anteroposterior (AP) pelvic radiographs from the Copenhagen Osteoarthritis Study by measuring the alpha (alpha) angle and the triangular index, a new measure of asphericity of the femoral head. In addition, the alpha-angle and the triangular index were assessed on the AP and lateral hip radiographs of 82 men and 82 women randomly selected from patients scheduled for total hip replacement (THR). The influence of varying femoral rotation on the alpha angle and the triangular index was also determined in femoral specimens under experimental conditions. From the 2803 radiographs the mean AP alpha-angle was 55 degrees (30 degrees to 100 degrees ) in men and 45 degrees (34 degrees to 108 degrees ) in women. Approximately 6% of men and 2% of women had cam malformation. The alpha-angle and triangular index were highly inter-related. Of those patients scheduled for THR, 36 men (44%) and 28 women (35%) had cam malformation identifiable on the AP radiographs. The triangular index proved to be more reliable in detecting cam malformation when the hip was held in varying degrees of rotation. The combination of the alpha-angle and the triangular index will allow examination of historical radiographs for epidemiological purposes in following the natural history of the cam deformity.
A High-Affinity Native Human Antibody Neutralizes Human Cytomegalovirus Infection of Diverse Cell Types (2014)

Human cytomegalovirus (HCMV) is the most common infection causing poor outcomes among transplant recipients. Maternal infection and transplacental transmission are major causes of permanent birth defects. Although no active vaccines to prevent HCMV infection have been approved, passive immunization with HCMV-specific immunoglobulin has shown promise in the treatment of both transplant and congenital indications. Antibodies targeting the viral glycoprotein B (gB) surface protein are known to neutralize HCMV infectivity, with high-affinity binding being a desirable trait, both to compete with low-affinity antibodies that promote the transmission of virus across the placenta and to displace nonneutralizing antibodies binding nearby epitopes. Using a miniaturized screening technology to characterize secreted IgG from single human B lymphocytes, 30 antibodies directed against gB were previously cloned. The most potent clone, TRL345, is described here. Its measured affinity was 1 pM for the highly conserved site I of the AD-2 epitope of gB. Strain-independent neutralization was confirmed for 15 primary HCMV clinical isolates. TRL345 prevented HCMV infection of placental fibroblasts, smooth muscle cells, endothelial cells, and epithelial cells, and it inhibited postinfection HCMV spread in epithelial cells. The potential utility for preventing congenital transmission is supported by the blockage of HCMV infection of placental cell types central to virus transmission to the fetus, including differentiating cytotrophoblasts, trophoblast progenitor cells, and placental fibroblasts. Further, TRL345 was effective at controlling an ex vivo infection of human placental anchoring villi. TRL345 has been utilized on a commercial scale and is a candidate for clinical evaluation.
Convergence Analysis of Serial Message-Passing Schedules for LDPC Decoding (2006)

Serial decoding schedules for low-density parity-check (LDPC) codes are described and analyzed. Conventionally, in each iteration all the variable nodes and subsequently all the check nodes send messages to their neighbors (“flooding schedule”). In contrast, in the considered methods, the updating of the nodes is implemented according to a serial schedule. The evolution of the decoding algorithm’s computation tree under serial scheduling is analyzed. The analysis shows that it grows twice as fast in comparison to the flooding schedule’s computation tree, indicating that the serial schedule propagates information twice as fast in the code’s underlying graph. Furthermore, asymptotic analysis of the serial schedule’s convergence rate is done using the Density Evolution (DE) algorithm. Applied to various ensembles of LDPC codes, it shows that when working near the ensemble’s threshold, for long enough codes the serial schedule is expected to converge in half the number of iterations compared to the standard flooding schedule. This observation is generally proved for the Binary Erasure Channel (BEC) under some likely assumptions. Finally, an accompanying concentration theorem is proved, justifying the asymptotic DE analysis assumptions. 1
Cell-penetrating peptides as noninvasive transmembrane vectors for the development of novel multifunctional drug-delivery systems (2016)

Unique characteristics, such as nontoxicity and rapid cellular internalization, allow the cell-penetrating peptides (CPPs) to transport hydrophilic macromolecules into cells, thus, enabling them to execute biological functions. However, some CPPs have limitations due to nonspecificity and easy proteolysis. To overcome such defects, the CPP amino acid sequence can be modified, replaced, and reconstructed for optimization. CPPs can also be used in combination with other drug vectors, fused with their preponderances to create novel multifunctional drug-delivery systems that increase the stability during blood circulation, and also develop novel preparations capable of targeted delivery, along with sustainable and controllable release. Further improvements in CPP structure can facilitate the penetration of macromolecules into diverse biomembrane structures, such as the blood brain barrier, gastroenteric mucosa, and skin dermis. The ability of CPP to act as transmembrane vectors improves the clinical application of some biomolecules to treat central nervous system diseases, increase oral bioavailability, and develop percutaneous-delivery dosage form.
Water fluoridation, osteoporosis, fractures—recent developments (2001)

These studies provide a substantial body of evidence that fluoride at up to 1ppm does not have an adverse effect on bone strength, bone mineral density or fracture incidence.
Optical and microstructural characterization of chemically synthesized gallium nitride nanopowders (1997)

Thermal decomposition of an amido precursor; [Ga2(NMe2)6, Me=CH3] in an ammonia atmosphere yielded nanostructured gallium nitride powder. The x-ray diffraction spectrum of the nanosized gallium nitride exhibited reflections corresponding to the lattice planes of fcc (zinc blende) GaN. High resolution transmission electron microscopy confirmed the cubic structure of the material and evidence of stacking faults within the fcc structure. Infrared spectra showed the characteristic Ga–N stretch at 550 cm−1. Transmission electron microscope measurements indicated that the GaN consisted of ≈50 nm sized particles which in turn are agglomerates of smaller particles with ≈5 nm domain sizes. The photoluminescence (PL) emission spectrum of the GaN was found to be sensitive to the excitation wavelength exhibiting peaks at 378 and 317 nm. The PL excitation spectrum showed resonances in the 200–300 nm region. These PL results suggest the effect of quantum confinement in these GaN particles.
Bermudagrass Freezing Tolerance Associated with Abscisic Acid Metabolism and Dehydrin Expression during Cold Acclimation (2008)

Recent advances in bermudagrass [ Cynodon dactylon (L.) Pers. var. dactylon ] breeding and cultural management practices have enabled its use as a sports surface in U.S. Department of Agriculture cold hardiness zones 5 and 6. Use of these more cold-hardy bermudagrass cultivars further into transition- and cool-season zones increases the probability of freezing injury and increases the need for an improved understanding of physiological responses to chilling and freezing temperatures. Abscisic acid (ABA) has been shown to increase during cold acclimation (CA) and play a role in dehydration tolerance. This study investigated changes in ABA metabolism and dehydrin expression during CA and their association with freezing tolerance in four bermudagrass cultivars. Two cold-tolerant (‘Patriot’ and ‘Riviera’) and two relatively cold-sensitive (‘Tifway’ and ‘Princess’) cultivars were either subjected to CA at 8 °C day/4 °C night with a light intensity of 250 μmol·m −2 ·s −1 over a 10-h photoperiod for 21 days or maintained at 28 °C day/24 °C night over a 12-h photoperiod. In a separate study, exogenous ABA at 0, 50, 100, and 150 μ m was applied to ‘Patriot’ bermudagrass without CA. ABA content in leaf and stolon tissues increased substantially during the first week of CA and remained relatively stable thereafter. ‘Patriot’ and ‘Riviera’ had greater ABA content and less stolon electrolyte leakage (EL) relative to ‘Tifway’ and ‘Princess’. Expression of a 25 kDa dehydrin protein increased during CA in all four cultivars. A significant correlation was found between ABA content and freezing tolerance. Exogenously applying ABA to ‘Patriot’ at 50, 100, and 150 μ m significantly increased endogenous ABA content and the 25 kDa dehydrin expression and reduced stolon EL. The results suggest that alteration of ABA metabolism during CA is closely associated with freezing tolerance. Selection and use of cultivars with substantial accumulation of ABA and certain dehydrins during CA or in response to exogenous ABA could improve bermudagrass persistence in transition zone climates.
Ursodeoxycholic Acid for Treatment of Primary Sclerosing Cholangitis: A Placebo–Controlled Trial (1992)

The efficacy and safety of ursodeoxycholic acid for the treatment of primary sclerosing cholangitis were evaluated in a prospective, randomized, double-blind, placebo-controlled trial. Fourteen patients with primary sclerosing cholangitis documented by cholestatic serum enzyme pattern, liver histological appearance and endoscopic retrograde cholangiography were included in the trial. Six patients received ursodeoxycholic acid (13 to 15 mg/kg body wt/day), and eight patients received placebo. Two patients had to be withdrawn from the study, one because of UDCA-related diarrhea and the other because of worsening of the disease during placebo treatment. Patients in the ursodeoxycholic acid group improved significantly during 1 yr of treatment with respect to serum levels of bilirubin (median = -50%), alkaline phosphatase (median = -67%), gamma-glutamyltransferase (median = -53%), AST (median = -54%) and ALT (median = -36%) compared with the placebo group, but not with respect to serum levels of hydrophobic bile acids. During ursodeoxycholic acid treatment, histopathological features also improved significantly, as evaluated by multiparametric score. Expression of human leukocyte antigen class I molecules appeared to be markedly reduced on liver cells after ursodeoxycholic acid treatment. We conclude that ursodeoxycholic acid is beneficial in reducing disease activity in patients with primary sclerosing cholangitis.
Carrier-frequency estimation for transmissions over selective channels (2000)

This paper deals with carrier-frequency estimation for burst transmissions over frequency-selective channels. Three estimation schemes are proposed, all based on the use of known training sequences. The first scheme employs an arbitrary sequence and provides joint maximum-likelihood (ML) estimates of the carrier frequency and the channel response. Its implementation complexity is relatively high but its accuracy achieves the Cramer-Rao bound. The second scheme is still based on the ML criterion, but the training sequence is periodic, which helps to reduce the computational load. The third scheme also employs periodic sequences, but its structure comes from heuristic reasoning. Theoretical analysis and simulations are employed to assess the performance of the three schemes.
Practical mobile robot self-localization (2002)

A map-making robot integrates accumulated sensor data into a data structure that can be used for future localization or planning operations. Localization is the process of determining the robot's location within its environment. This paper describes experiments in which a robot simultaneously makes a map and localizes to that map. The map is a collection of tangent vectors constructed from stored sonar readings localized to a series of estimated poses. The vectors retain sensed surface normal information to improve accuracy. The localization scheme is a Hough transform into a space described by the robot's current sonar scan. The Hough transform finds a best fit in the presence of both sporadic sensor noise and discretization error.
The Expression Pattern of the Transcription Factor Phox2 Delineates Synaptic Pathways of the Autonomic Nervous System (1996)

Many transcription factors, and most prominently among them, homeodomain proteins, are expressed in specific groups of cells in the developing nervous system in patterns that suggest their involvement in neural fate determination. How various aspects of neural identity are controlled by such transcription factors, or sets of them, is still mostly unknown. It has been shown previously that Phox2 is such a homeodomain protein, expressed exclusively in differentiated groups of neurons or their precursors, and that its expression correlated with that of the noradrenaline synthesis enzyme dopamine-beta-hydroxylase. Here we confirm this striking correlation at the single-cell level with the use of an anti-Phox2 antibody. Moreover, we uncover a second, nonmutually exclusive correlative clue to the Phox2 expression pattern: a high proportion of Phox2-expressing cells are involved in, or located in areas involved in, synaptic circuits, i.e., that of the medullary control reflexes of autonomic functions. This suggests that Phox2 could be involved in the establishment of these circuits.
Synergistic Neutralization of Simian-Human Immunodeficiency Virus SHIV-vpu+by Triple and Quadruple Combinations of Human Monoclonal Antibodies and High-Titer Anti-Human Immunodeficiency Virus Type 1 Immunoglobulins (1998)

We have tested triple and quadruple combinations of human monoclonal antibodies (MAbs), which are directed against various epitopes on human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins, and a high-titer anti-HIV-1 human immunoglobulin (HIVIG) preparation for their abilities to neutralize a chimeric simian-human immunodeficiency virus (SHIV-vpu+). This virus encodes the HIV-1 strain IIIB env, tat, rev, and vpu genes. The quantitative nature of the Chou-Talalay method (Adv. Enzyme Regul. 22:27-55, 1984) allows ranking of various combinations under identical experimental conditions. Of all triple combinations tested, the most potent neutralization was seen with MAbs 694/98D plus 2F5 plus 2G12 (directed against domains on V3, gp41, and gp120, respectively) as measured by the total MAb concentration required to reach 90% neutralization (90% effective concentration [EC90], 2.0 microg/ml). All triple combinations involving MAbs and/or HIVIG that were tested yielded synergy with combination index values of < 1; the dose reduction indices (DRIs) ranged from 3.1 to 26.2 at 90% neutralization. When four MAbs (the previous three plus MAb F105, directed against the CD4 binding site) were combined, higher neutralization potency (EC90 1.8 microg/ml) and a higher degree of synergy compared to any triple combination were seen. The mean DRIs of the quadruple combination were approximately twice that of the most synergistic triple combination. We conclude that human MAbs targeting different HIV-1 envelope glycoprotein epitopes exhibit strong synergy when used in combination, a fact that could be exploited clinically for passive immunoprophylaxis against HIV-1.
Chemiluminescent Third-Generation Assay (Amerlite TSH-30) of Thyroid-Stimulating Hormone in Serum or Plasma Assessed (1993)

Journal Article Chemiluminescent Third-Generation Assay (Amerlite TSH-30) of Thyroid-Stimulating Hormone in Serum or Plasma Assessed Get access Ewan Wilkinson, Ewan Wilkinson University Department of Clinical Biochemistry, Royal Infirmary, Edinburgh EH3 9YW, Scotland, UK Search for other works by this author on: Oxford Academic Google Scholar Peter W H Rae, Peter W H Rae University Department of Clinical Biochemistry, Royal Infirmary, Edinburgh EH3 9YW, Scotland, UK Search for other works by this author on: Oxford Academic Google Scholar Kristy J T Thomson, Kristy J T Thomson University Department of Medicine, Royal Infirmary, Edinburgh EH3 9YW, Scotland, UK Search for other works by this author on: Oxford Academic Google Scholar Anthony D Toft, Anthony D Toft University Department of Medicine, Royal Infirmary, Edinburgh EH3 9YW, Scotland, UK Search for other works by this author on: Oxford Academic Google Scholar Carole A Spencer, Carole A Spencer Department of Medicine, University of Southern California School of Medicine, Los Angeles, CA 90033 Search for other works by this author on: Oxford Academic Google Scholar Geoffrey J Beckett Geoffrey J Beckett University Department of Clinical Biochemistry, Royal Infirmary, Edinburgh EH3 9YW, Scotland, UK Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 39, Issue 10, 1 October 1993, Pages 2166–2173, https://doi.org/10.1093/clinchem/39.10.2166 Published: 01 October 1993 Article history Received: 26 March 1993 Accepted: 17 May 1993 Published: 01 October 1993