gebhart/patrepeval huggingface dataset:
Construction and characterization of a normalized cDNA library. (1994)

We have developed a simple procedure based on reassociation kinetics that can reduce effectively the high variation in abundance among the clones of a cDNA library that represent individual mRNA species. For this normalization, we used as a model system a library of human infant brain cDNAs that were cloned directionally into a phagemid vector and, thus, could be easily converted into single-stranded circles. After controlled primer extension to synthesize a short complementary strand on each circular template, melting and reannealing of the partial duplexes at relatively low C0t, and hydroxyapatite column chromatography, unreassociated circles were recovered from the flow through fraction and electroporated into bacteria, to propagate a normalized library without a requirement for subcloning steps. An evaluation of the extent of normalization has indicated that, from an extreme range of abundance of 4 orders of magnitude in the original library, the frequency of occurrence of any clone examined in the normalized library was brought within the narrow range of only 1 order of magnitude.
PRESENILE DEMENTIA AND ALZHEIMER'S DISEASE IN MONGOLISM (1969)

Journal Article PRESENILE DEMENTIA AND ALZHEIMER'S DISEASE IN MONGOLISM Get access MARY I. OLSON, MARY I. OLSON Laboratory of Neuropathology, Department of Pathology, University of Washington Medical SchoolSeattle, Washington 98105 Search for other works by this author on: Oxford Academic PubMed Google Scholar CHENG-MEI SHAW CHENG-MEI SHAW Laboratory of Neuropathology, Department of Pathology, University of Washington Medical SchoolSeattle, Washington 98105 Search for other works by this author on: Oxford Academic PubMed Google Scholar Brain, Volume 92, Issue 1, March 1969, Pages 147–156, https://doi.org/10.1093/brain/92.1.147 Published: 01 March 1969 Article history Received: 18 July 1968 Published: 01 March 1969
Ribosomal movement impeded at a pseudoknot required for frameshifting. (1992)

Translational frameshifting sometimes occurs when ribosomes encounter a "shift" site preceding a region of unusual secondary structure, which in at least three cases is known to be a pseudoknot. We provide evidence that ribosomes have a decreased rate of movement through a pseudoknot required for frameshifting. These paused ribosomes are directly situated over the shift sequence. Ribosomal pausing appears to be necessary but not sufficient for frameshifting.
Media design considerations for a PRML channel (1993)

The requirements placed on the recording media by the partial-response maximum-likelihood (PRML) detection channel are examined in order to obtain optimum readback performance. It is noted that the use of a partial response (PR) data channel leads to somewhat different requirements for the recording media than are found for a conventional peak detector channel. The high transition density of current PR codes changes both the nonlinear behavior and the noise level in thin film media. Consequences of the different equalization techniques and sensor types have been explored. A by-product of the amplitude-sampling PR channel is a range of useful recording test functions which can be built into the channel and which can be used in a self-diagnostic mode.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Postoperative obstructive sleep apnoea (1991)

A 74-year-old man presenting for aortic reconstructive surgery showed severe, previously undiagnosed obstructive sleep apnoea during overnight oximetry monitoring before operation. Postoperatively, in the first 4 hours following extubation, he suffered 238 episodes of respiratory obstruction. These events were associated with frequent arousals, large fluctuations in systolic and diastolic blood pressure. Administration of nasal continuous positive airways pressure abolished the obstructions and allowed an uninterrupted night's sleep, with a significantly reduced blood pressure. Subsequent dips in oxygen saturation as a result of respiratory obstruction recurred on the fifth postoperative night. We conclude that pre-operative overnight oximetry may be useful in identifying those patients at risk of postoperative upper airway obstruction. Use of nasal continuous positive airway pressure may prevent the occurrence of early postoperative obstruction and the associated haemodynamic changes.
Distinct Mutations in IRAK-4 Confer Hyporesponsiveness to Lipopolysaccharide and Interleukin-1 in a Patient with Recurrent Bacterial Infections (2003)

We identified previously a patient with recurrent bacterial infections who failed to respond to gram-negative LPS in vivo, and whose leukocytes were profoundly hyporesponsive to LPS and IL-1 in vitro. We now demonstrate that this patient also exhibits deficient responses in a skin blister model of aseptic inflammation. A lack of IL-18 responsiveness, coupled with diminished LPS and/or IL-1-induced nuclear factor-kappaB and activator protein-1 translocation, p38 phosphorylation, gene expression, and dysregulated IL-1R-associated kinase (IRAK)-1 activity in vitro support the hypothesis that the defect lies within the signaling pathway common to toll-like receptor 4, IL-1R, and IL-18R. This patient expresses a "compound heterozygous" genotype, with a point mutation (C877T in cDNA) and a two-nucleotide, AC deletion (620-621del in cDNA) encoded by distinct alleles of the IRAK-4 gene (GenBank/EMBL/DDBJ accession nos. AF445802 and AY186092). Both mutations encode proteins with an intact death domain, but a truncated kinase domain, thereby precluding expression of full-length IRAK-4 (i.e., a recessive phenotype). When overexpressed in HEK293T cells, neither truncated form augmented endogenous IRAK-1 kinase activity, and both inhibited endogenous IRAK-1 activity modestly. Thus, IRAK-4 is pivotal in the development of a normal inflammatory response initiated by bacterial or nonbacterial insults.
Expression of activity-dependent neuroprotective protein in the brain of adult rats. (2008)

Activity-dependent neuroprotective protein (ADNP) is a VIP-regulated gene, which is essential for brain development. A synthetic peptide (NAP) derived from the ADNP sequence is highly neuroprotective, therefore it has been hypothesised that ADNP has a similar role. ADNP contains classical transcription factor motifs and nuclear localisation domains, but it has also been reported to be secreted and to co-localise with microtubules, indicating that ADNP may have multiple functions. We investigated the pattern of ADNP expression by immunohistology in normal rat brain, in order to generate a framework for future studies examining changes in ADNP expression in response to noxious stimuli or in models of disease. We found widespread ADNP-like immunoreactivity in neurons throughout the rat brain, with the highest expression in the cerebellum, and strong expression in the thalamus, mesencephalon, pons and medulla oblongata. ADNP-like immunoreactivity was mainly observed in the cytoplasm of neurons, and fibre tracts were often strongly positive as well. In addition, positive neuronal nuclei were occasionally observed. ADNP-like immunoreactivity was lost in degenerating "dark" neurons, whereas it appeared to locate to the nucleus in some of the morphologically unaltered adjacent cells. Occasional astrocyte and microglial cells were also positive. We suggest that the widespread expression of ADNP may correlate with the wide-ranging protective effects of NAP, and that the cytoplasmic and axonal localisation of ADNP-like immunoreactivity suggests additional, non-transcriptional functions of ADNP.
Bone marrow transplantation corrects osteopetrosis in the carbonic anhydrase II deficiency syndrome (2001)

Carbonic anhydrase II (CAII), found in renal tubules, brain, and osteoclasts, is critical in acid-base homeostasis and bone remodeling. Deficiency of CAII gives rise to a syndrome of osteopetrosis, renal tubular acidosis (RTA), and cerebral calcification with associated developmental delay. It is inherited in an autosomal recessive fashion and found most frequently in the Mediterranean region and the Middle East. We report 2 related Irish families with clinically severe CAII deficiency in whom the gene mutation has been fully elucidated. Two children, one from each family, have undergone allogeneic bone marrow transplantation because of severe progressive visual and hearing loss. The older 2 children had already developed cerebral calcification and marked visual loss at the time of diagnosis and were treated symptomatically. Post-transplantation evaluation at 2 and 3 years demonstrates histologic and radiologic resolution of their osteopetrosis with stabilization of hearing and vision. Both children remain developmentally delayed and continue to have RTA, and the older child has now developed cerebral calcification. Allogeneic bone marrow stem cell replacement cures the osteoclast component of CAII deficiency and retards the development of cerebral calcification, but it appears to have little or no effect on the renal lesions. (Blood. 2001;97:1947-1950)
Genetic transformation of HeLa cells by Agrobacterium (2001)

Agrobacterium tumefaciens is a soil phytopathogen that elicits neoplastic growths on the host plant species. In nature, however, Agrobacterium also may encounter organisms belonging to other kingdoms such as insects and animals that feed on the infected plants. Can Agrobacterium, then, also infect animal cells? Here, we report that Agrobacterium attaches to and genetically transforms several types of human cells. In stably transformed HeLa cells, the integration event occurred at the right border of the tumor-inducing plasmid's transferred-DNA (T-DNA), suggesting bona fide T-DNA transfer and lending support to the notion that Agrobacterium transforms human cells by a mechanism similar to that which it uses for transformation of plants cells. Collectively, our results suggest that Agrobacterium can transport its T-DNA to human cells and integrate it into their genome.
Particulate Systems as Adjuvants and Carriers for Peptide and Protein Antigens (2006)

The most common feature for antigen-delivery systems is their particulate nature. Together with a certain depot effect, it is the particulate nature that primarily dictates whether the antigen-delivery system will be successful in inducing a certain type and strength of immune response. In this article, we will summarize recent data on particulate delivery systems for peptide and protein antigens with a main focus on lipid or polymer-based particles, all of which possess high potential as both preventive and therapeutic vaccines for parenteral, nasal, and possibly oral administration.
Effects of in vivo treatment with PIXY321 (GM-CSF/IL-3 fusion protein) on proliferation kinetics of bone marrow and blood myeloid progenitor cells in patients with sarcoma. (1995)

PIXY321, a stimulator of multipotent colony-forming units (CFU-GEMM), burst-forming unit-erythroid (BFU-E), and colony-forming units granulocyte/macrophage (CFU-GM) progenitor cell proliferation in vitro, is currently being assessed in phase-I/-II clinical trials. We evaluated kinetics of CFU-GEMM, BFU-E, and CFU-GM proliferation in bone marrow (BM), blood, and granulocyte (CFU-G) and macrophage (CFU-M) progenitors in BM of chemotherapy-naive patients with sarcoma-administered PIXY321 (25 to 1000 micrograms/m2/day subcutaneously for 14 days). BM and/or blood cells from three to four patients at each dosage were assessed before, during, 1 to 2 days, and 7 days following treatment with PIXY321. Cells were pulse-treated in vitro with or without high-specific activity tritiated thymidine (3H-dThr) (to assess the percentage of progenitors in S-phase of cell cycle) and cultured for immature and more mature subsets of CFU-GEMM, BFU-E, CFU-GM, and for CFU-G and CFU-M. Despite heterogeneity in baseline cycling status of progenitors in BM, administration of 125 to 500 micrograms PIXY321 to patients at least doubled (p < 0.001) cycling rates of all BM progenitors. The cycling rates of blood progenitors increased from a slow or non-cycling state to > 38% cells in cycle. Within 1 to 2 days after cessation of PIXY321 infusion, all progenitors were in a slow or noncycling phase below that of many of the pre-BM samples (immature and mature CFU-GM and mature BFU-E) or were back to background levels (CFU-G, CFU-M, CFU-GEMM, and immature BFU-E). These cycling effects were similar to those previously noted for BM CFU-GM and BFU-E in patients on clinical trial with GM-CSF. In contrast, higher dosages of PIXY321, especially 1000 micrograms, increased cycling of BM and blood progenitor cells early during treatment, but cycling rates decreased while patients were still being administered PIXY321; decreased cycling was maintained after cessation of PIXY321. PIXY321 is thus highly active in vivo as a stimulator of multipotential and more lineage-restricted progenitors. The kinetics of progenitor cell proliferation noted in this study highlight differences seen with GM-CSF and G-CSF. The effects described here could be of relevance in design of future clinical trials using PIXY321 as an adjunct treatment in patients undergoing cytoreductive therapy.
Considerations of Solid-Phase DNA Amplification (2010)

Solid-phase (SP) polymerase chain reaction (PCR) is an increasingly popular tool used to produce immobilized DNA for a variety of applications, including high-throughput DNA sequencing and SNP analysis. Despite its usefulness, the mechanism of DNA amplification using immobilized primers has not been thoroughly explored. Herein, we describe a SP-PCR process that was designed to explore and better understand some limitations of SP-DNA amplification. The rate of SP-DNA amplification was measured, and the ability to exponentially amplify DNA on a surface was demonstrated. Approximately 50 amol of DNA was amplified to detectable levels using SP-PCR. The mechanism and some limitations of the reaction were investigated by measuring the density of the primer on the surface prior to amplification and the amount of immobilized amplicon produced after SP-PCR. This enabled some of the practical limitations of the reaction to be addressed within a logical theoretical framework.
Amygdala–Hippocampal Involvement in Human Aversive Trace Conditioning Revealed through Event-Related Functional Magnetic Resonance Imaging (1999)

Previous functional neuroimaging studies have characterized brain systems mediating associative learning using classical delay conditioning paradigms. In the present study, we used event-related functional magnetic resonance imaging to characterize neuronal responses mediating aversive trace conditioning. During conditioning, neutral auditory tones were paired with an aversive sound [unconditioned stimulus (US)]. We compared neuronal responses evoked by conditioned (CS+) and nonconditioned (CS-) stimuli in which a 50% pairing of CS+ and the US enabled us to limit our analysis to responses evoked by the CS+ alone. Differential responses (CS+ vs CS-), related to conditioning, were observed in anterior cingulate and anterior insula, regions previously implicated in delay fear conditioning. Differential responses were also observed in the amygdala and hippocampus that were best characterized with a time x stimulus interaction, indicating rapid adaptation of CS+-specific responses in medial temporal lobe. These results are strikingly similar to those obtained with a previous delay conditioning experiment and are in accord with a preferential role for medial temporal lobe structures during the early phase of conditioning. However, an additional activation of anterior hippocampus in the present experiment supports a view that its role in trace conditioning is to maintain a memory trace between the offset of the CS+ and the delayed onset of the US to enable associative learning in trace conditioning.
Colon-targeted delivery of live bacterial cell biotherapeutics including microencapsulated live bacterial cells (2008)

There has been an ample interest in delivery of therapeutic molecules using live cells. Oral delivery has been stipulated as best way to deliver live cells to humans for therapy. Colon, in particular, is a part of gastrointestinal (GI) tract that has been proposed to be an oral targeted site. The main objective of these oral therapy procedures is to deliver live cells not only to treat diseases like colorectal cancer, inflammatory bowel disease, and other GI tract diseases like intestinal obstruction and gastritis, but also to deliver therapeutic molecules for overall therapy in various diseases such as renal failure, coronary heart disease, hypertension, and others. This review provides a comprehensive summary of recent advancement in colon targeted live bacterial cell biotherapeutics. Current status of bacterial cell therapy, principles of artificial cells and its potentials in oral delivery of live bacterial cell biotherapeutics for clinical applications as well as biotherapeutic future perspectives are also discussed in our review.
Sequence of the Streptococcus pneumoniae bacteriophage HB-3 amidase reveals high homology with the major host autolysin (1990)

We have sequenced a DNA fragment containing the pneumococcal bacteriophage HB-3 hbl gene, which codes for the phage lytic amidase. A remarkable nucleotide similarity (87.1%) between the lytA gene, coding for the pneumococcal amidase, the major autolysin of Streptococcus pneumoniae, and the hbl gene was found. This similarity completely disappeared outside the open reading frames coding for both amidases. The hbl gene transformed amidase-deficient strains of S. pneumoniae to the wild-type phenotype, and Southern blotting experiments provided evidence for recombination between donor and recipient genes. A comprehensive evaluation of these and previous results on the peptidoglycan hydrolases of S. pneumoniae and its bacteriophages suggested that recombination mechanisms participate in the evolution of the genes coding for these enzymes.
π-dimers of oligothiophene cations (2000)

The structure and stability of dimers of quaterthiophene radical cations are studied using density functional calculations. Several dimer structures are identified that are metastable in vacuum, in which the cations are stacked coplanarly. Evidence for a weak chemical dimer bonding is found from the binding energy curves and the singlet–triplet splittings. Introducing solvent or solid-state effects by embedding the dimer in a dielectric medium results in stabilizing the dimer, as is observed experimentally. An infinite stack of quaterthiophene cations shows a weak spontaneous dimerization.
Comparison of Penetratin and Other Homeodomain-Derived Cell-Penetrating Peptides:  Interaction in a Membrane-Mimicking Environment and Cellular Uptake Efficiency (2006)

Antennapedia and other homeoproteins have the unique ability to efficiently translocate across biological membranes, a property that is mediated by the third helix of the homeodomain. To analyze the effects of sequence divergence in the homeodomain, we have compared the cellular uptake efficiencies and interaction properties in a membrane-mimicking environment of four peptides corresponding to the third helix sequence of Antennapedia, Engrailed-2, HoxA-13, and Knotted-1. NMR studies revealed that these peptides adopt helical conformations in SDS micelles. Their localization with respect to the micelle was investigated using Mn(2+) as a paramagnetic probe. Peptides are positioned parallel to the micelle surface, but subtle differences in the depth of immersion were observed. Using a recently developed method for quantification of CPP cellular uptake based on MALDI-TOF mass spectrometry, all of these peptides were found to translocate into cells but with large differences in their uptake efficiencies. The peptide with the highest uptake efficiency was found to be the least deeply inserted within the micelle, indicating that electrostatic surface interactions may be a major determinant for membrane translocation. A new cell-penetrating peptide derived from Knotted-1 homeodomain with improved uptake properties compared to penetratin is introduced here.
The feasibility of gene expression profiling generated in fine-needle aspiration specimens from patients with follicular lymphoma and diffuse large B-cell lymphoma (2005)

Lymphoma of germinal center cell (GC) origin generally is an indolent malignancy that transforms progressively into a more aggressive disease. According to the World Health Organization classification, lymphomas of follicular center cell origin are classified as either large B-cell lymphoma (LBCL) or follicular lymphoma (FL). The authors tested the feasibility of performing gene expression profiling using amplified RNA from fine-needle aspirates (FNA) obtained from lymph nodes. Twenty-four samples from patients with a diagnosis of FL or LBCL were obtained after Institutional Review Board-approved informed consent was obtained. The diagnoses were confirmed by 2 pathologists and were classified into 2 groups (10 LBCL samples and 14 FL samples) by using conventional morphology and immunophenotyping. One hundred nanograms of total RNA were subjected to 2 cycles of standard, double-stranded complementary DNA synthesis and in vitro transcription for target amplification using a small-sample target-labeling protocol. The biotinylated cRNA from each sample was hybridized to gene chips. Gene expression profiling results were analyzed first by principal-component analysis (PCA) by using a list of 146 probe sets that represented 62 genes that are characteristic of an activated B-cell (ABC) signature or a GC signature. The analysis identified 5 LBCL samples with an ABC cell signature. Using a list of 207 probe sets that represented 113 genes involved in FL transformation, PCA analysis identified 2 overlapping clusters corresponding to FL and GC-diffuse LBCL. To improve this classification further, the authors generated a list of 72 genes that were expressed differentially between FL and GC-LBCL. Using this list of genes, PCA analysis demonstrated a clear separation between FL and GC-LBCL. However, five FL samples clustered as an intermediate group between FL and GC-DLBCL. These samples were characterized morphologically by a mixed cell pattern with relatively fewer large, noncleaved lymphocytes and more small, cleaved lymphocytes. The results support the feasibility of FNA-based transcription profiles in patients with FL or LBCL, which, in combination with morphology and immunophenotyping, can help in the subtyping of these entities.
Neutron detection with single crystal organic scintillators (2009)

Detection of high-energy neutrons in the presence of gamma radiation background utilizes pulse-shape discrimination (PSD) phenomena in organics studied previously only with limited number of materials, mostly liquid scintillators and single crystal stilbene. The current paper presents the results obtained with broader varieties of luminescent organic single crystals. The studies involve experimental tools of crystal growth and material characterization in combination with the advanced computer modeling, with the final goal of better understanding the relevance between the nature of the organic materials and their PSD properties. Special consideration is given to the factors that may diminish or even completely obscure the PSD properties in scintillating crystals. Among such factors are molecular and crystallographic structures that determine exchange coupling and exciton mobility in organic materials and the impurity effect discussed on the examples of trans-stilbene, bibenzyl, 9,10- diphenylanthracene and diphenylacetylene.