gebhart/patrepeval huggingface dataset:
Differences between 99mTc-sestamibi and 99mTc-tetrofosmin uptake in thyroid and salivary glands: comparison with 99mTc-pertechnetate in 86 subjects (2003)

Tc-tetrofosmin seems to show a prolonged thyroid retention when compared with Tc-sestamibi; this may explain its poorer performance in the dual-phase parathyroid scintigraphy. In order to verify objectively whether and to what extent Tc-sestamibi and Tc-tetrofosmin uptake and retention differ in the thyroid gland, we performed a head-to-head comparison between the tracers in 86 euthyroid subjects enrolled in five centres. Data were compared with those of Tc-pertechnetate obtained from the same subjects. For comparison purposes, quantitative data from the salivary glands were also obtained. Tc-sestamibi showed a higher early thyroid uptake (2.26+/-0.52 vs. 2.01+/-0.49, respectively; P<0.002) and a lower retention (1.4+/-0.37 vs. 1.65+/-0.58, respectively; P<0.002) when compared with Tc-tetrofosmin. This finding provides an objective basis for the poorer results of Tc-tetrofosmin in dual-phase parathyroid scintigraphy. Delayed Tc-tetrofosmin salivary gland uptake was unexpectedly high and approached the Tc-pertechnetate value (2.29+/-0.56 vs. 2.46+/-0.75, respectively; P =not significant). This finding should be kept in mind in order to avoid interpretation pitfalls in thyroid and parathyroid imaging with Tc-tetrofosmin, as well as in other oncological imaging of the neck region. This study definitely establishes that Tc-tetrofosmin and Tc-sestamibi are not twin but rather sibling tracers.
Mutations Affecting the Different Transport Systems for Isoleucine, Leucine, and Valine in Escherichia coli K-12 (1974)

Uptake of isoleucine, leucine, and valine in Escherichia coli K-12 is due to several transport processes for which kinetic evidence has been reported elsewhere. A very-high-affinity transport process, a high-affinity transport process, and three different low-affinity transport processes were described. In this paper the existence of these transport processes is confirmed by the isolation and preliminary characterization of mutants altered in one or more of them. The very-high-affinity transport process is missing either in strains carrying the brnR6(am) mutation or in strains carrying the brn-8 mutation. This appears to be a pleiotropic effect since other transport systems are also missing. Mutant analysis shows that more than one transport system with high affinity is present. One of them, high-affinity 1, which needs the activity of a protein produced by the brnQ gene, transports isoleucine, leucine, and valine and is unaffected by threonine. The other, high-affinity 2, which needs the activity of a protein produced by the brnS gene, transports isoleucine, leucine, and valine; this uptake is inhibited by threonine which probably is a substrate. Another protein, produced by the brnR gene, is required for uptake through both high-affinity 1 and high-affinity 2 transport systems. The two systems therefore appear to work in parallel, brnR being a branching point. The brnQ gene is located close to phoA at 9.5 min on the chromosome of E. coli, the brnR gene is located close to lac at 9.0 min, and the brnS gene is close to pdxA at 1 min. A mutant lacking the low-affinity transport system for isoleucine was isolated from a strain in which the high-affinity system was missing because of a brnR mutation. This strain also required isoleucine for growth because of an ilvA mutation. The mutant lacking the low-affinity transport system was unable to grow on isoleucine but could grow on glycylisoleucine. This mutant had lost the low-affinity transport for isoleucine, whereas those for leucine and valine were unaffected. A pleiotropic consequence of this mutation (brn-8) was a complete absence of the very-high-affinity transport system due either to the alteration of a common gene product or to any kind of secondary interference which inhibits it. Mutants altered in isoleucine-leucine-valine transport were isolated by taking advantage of the inhibition that valine exerts on the K-12 strain of E. coli. Mutants resistant both to valine inhibition (Val(r)) and to glycylvaline inhibition are regulatory mutants. Val(r) mutants that are sensitive to glycylvaline inhibition are transport mutants. When the very-high-affinity transport process is repressed (for example by methionine) the frequency of transport mutants among Val(r) mutants is higher, and it is even higher if the high-affinity transport process is partially inhibited by leucine.
Reversible maleimide–thiol adducts yield glutathione-sensitive poly(ethylene glycol)–heparin hydrogels (2012)

We have recently reported that retro Michael-type addition reactions can be employed for producing labile chemical linkages with tunable sensitivity to physiologically relevant reducing potentials. We reasoned that such strategies would also be useful in the design of glutathione-sensitive hydrogels for a variety of targeted delivery and tissue engineering applications. In this report, we describe hydrogels in which maleimide-functionalized low molecular weight heparin (LMWH) is crosslinked with various thiol-functionalized poly(ethylene glycol) (PEG) multi-arm star polymers. Judicious selection of the chemical identity of the thiol permits tuning of degradation <i>via</i> previously unstudied, but versatile chemical methods. Thiol <i>p</i>K<sub>a</sub> and hydrophobicity affected both the gelation and degradation of these hydrogels. Maleimide-thiol crosslinking reactions and retro Michael-type addition reactions were verified with <sup>1</sup>H NMR during the crosslinking and degradation of hydrogels. PEGs esterified with phenylthiol derivatives, specifically 4-mercaptophenylpropionic acid or 2,2-dimethyl-3-(4-mercaptophenyl)propionic acid, induced sensitivity to glutathione as shown by a decrease in hydrogel degradation time of 4-fold and 5-fold respectively, measured via spectrophotometric quantification of LMWH. The degradation proceeded through the retro Michael-type addition of the succinimide thioether linkage, with apparent pseudo-first order reaction constants derived from oscillatory rheology experiments of 0.039 ± 0.006 h<sup>-1</sup> and 0.031 ± 0.003 h<sup>-1</sup>. The pseudo-first order retro reaction constants were approximately an order of magnitude slower than the degradation rate constants for hydrogels crosslinked via disulfide linkages, indicating the potential use of these Michael-type addition products for reduction-mediated release and/or degradation, with increased blood stability and prolonged drug delivery timescales compared to disulfide moieties.
The genetic basis of myelodysplasia and its clinical relevance (2013)

Myelodysplasia is a diagnostic feature of myelodysplastic syndromes (MDSs) but is also found in other myeloid neoplasms. Its molecular basis has been recently elucidated by means of massive parallel sequencing studies. About 90% of MDS patients carry ≥1 oncogenic mutations, and two thirds of them are found in individuals with a normal karyotype. Driver mutant genes include those of RNA splicing (SF3B1, SRSF2, U2AF1, and ZRSR2), DNA methylation (TET2, DNMT3A, and IDH1/2), chromatin modification (ASXL1 and EZH2), transcription regulation (RUNX1), DNA repair (TP53), signal transduction (CBL, NRAS, and KRAS), and cohesin complex (STAG2). Only 4 to 6 genes are consistently mutated in ≥10% MDS patients, whereas a long tail of ∼50 genes are mutated less frequently. At presentation, most patients typically have 2 or 3 driver oncogenic mutations and hundreds of background mutations. MDS driver genes are also frequently mutated in other myeloid neoplasms. Reliable genotype/phenotype relationships include the association of the SF3B1 mutation with refractory anemia with ring sideroblasts, TET2/SRSF2 comutation with chronic myelomonocytic leukemia, and activating CSF3R mutation with chronic neutrophilic leukemia. Although both founding and subclonal driver mutations have been shown to have prognostic significance, prospective clinical trials that include the molecular characterization of the patient's genome are now needed.
Ion Optics of Submicron Ion Beams (1986)

An electrostatic objective lens for focusing ion beams to very small diameters on a plane, conducting sample surface was designed. The lens can focus ions of either polarity in the decel-accel or accel-decel mode and collect and collimate secondary charged particles of either polarity emitted with low initial energy. Moreover, a microscopic mirror objective for visual observation of the sample surface in situ is incorporated in the electrostatic optics.
QoS based routing in networks with inaccurate information: theory and algorithms (2002)

We investigate the problem of routing connections with QoS requirements across one or more networks, when the information available for making routing decisions is inaccurate and expressed in some probabilistic manner. This uncertainty about the actual state of a node or network arises naturally in a number of different environments, that are reviewed in the paper. The main focus is to determine the impact of such inaccuracies on the path selection process, whose goal is then to identify the path that is most likely to satisfy the QoS requirements.
Method for reduction of background artifacts of images in scanning holography with a Fresnel-zone-plate coded aperture (2004)

Near-infrared scanning holography with a Fresnel zone plate (FZP) coded aperture has potential applications in imaging through turbid media. However, the nonnegative intensity-distribution function of the FZP coded aperture introduces the background artifacts into the reconstructed images, reducing the contrast and the signal-to-noise ratio (SNR) of the images. A novel method termed as the composite hologram is proposed to reduce the artifacts. The computer simulations showed that the contrast and the SNR of the reconstructed images had improvements of at least 50.2% and 5.58-dB, respectively, compared with the conventional method. The composite hologram of a metal ring with a 6.0-mm diameter made by a wire with a 0.4-mm diameter immersing in 1% intralipid solution was recorded, and the reconstruction was performed numerically. The experimental results demonstrated that the contrast and the SNR of the reconstructed image had improvements of at least 32.3% and 2.51-dB, respectively.
Alternatively spliced androgen receptor variants (2011)

Alternative splicing is an important mechanism for increasing functional diversity from a limited set of genes. Deregulation of this process is common in diverse pathologic conditions. The androgen receptor (AR) is a steroid receptor transcription factor with functions critical for normal male development as well as the growth and survival of normal and cancerous prostate tissue. Studies of AR function in androgen insensitivity syndrome (AIS) and prostate cancer (PCa) have demonstrated loss-of-function AR alterations in AIS and gain-of-function AR alterations in PCa. Over the past two decades, AR gene alterations have been identified in various individuals with AIS, which disrupt normal AR splicing patterns and yield dysfunctional AR protein variants. Recently, altered AR splicing patterns have been identified as a mechanism of PCa progression and resistance to androgen depletion therapy. Several studies have described the synthesis of alternatively spliced transcripts encoding truncated AR isoforms that lack the ligand-binding domain, which is the ultimate target of androgen depletion. Many of these truncated AR isoforms function as constitutively active, ligand-independent transcription factors that can support androgen-independent expression of AR target genes, as well as the androgen-independent growth of PCa cells. In this review, we will summarize the various alternatively spliced AR variants that have been discovered, with a focus on their role and origin in the pathologic conditions of AIS and PCa.
Integration and expression of alpha-amylase and endoglucanase genes in the Lactobacillus plantarum chromosome (1989)

A commercial grass silage starter strain of Lactobacillus plantarum was transformed by high-frequency electroporation with plasmids containing an alpha-amylase gene from Bacillus stearothermophilus and an endoglucanase gene from Clostridium thermocellum. Both genes were expressed from their native regulatory signals, and active enzymes were found in the supernatant. However, the segregational stability of the transforming plasmids was rather low. Therefore, the transforming genes were inserted in the L. plantarum chromosome by means of single homologous recombination. In the majority of the transformants, this led to extremely stable segregation and expression of the transforming genes, without generating secondary mutations in the host. Increased selective pressure led to tandem amplification of the transforming DNA. The transformed strains demonstrated the ability of L. plantarum to express heterologous gene products; they can be used to detect the inoculum in silage ecology studies; and they demonstrate the feasibility of engineering truly cellulolytic silage starter bacteria.
Regulation of a Novel Gene Encoding a Lysyl Oxidase-related Protein in Cellular Adhesion and Senescence (1997)

We report here a novel cDNA clone with a predicted protein sequence similar to lysyl oxidase. This full-length cDNA clone of 3432 base pairs (WS9-14) was isolated from human fibroblasts on the basis of its overexpression in senescent cells. It encodes an 87-kDa polypeptide, whose protein is a member of the scavenger receptor cysteine-rich family, because it contains four scavenger receptor cysteine-rich domains that are found in several secreted or cell surface proteins. The WS9-14 protein has a 48% identity with both lysyl oxidase and lysyl oxidase-like protein at a region corresponding to exons 2-6, implying the existence of a lysyl oxidase gene family. The pattern of WS9-14 gene expression by fibroblasts parallels pro-collagen I-alpha1 expression. Its mRNA level is induced by transforming growth factor beta-1 and indomethacin and inhibited by phorbol ester and retinoic acid. WS9-14 is abundantly expressed in all tumor cell lines examined that attach to culture dishes but not in cell lines that grow in suspension and is also up-regulated in senescent fibroblasts. These results suggest that WS9-14 gene encodes an extracellular protein that may be specifically involved in cell adhesion and senescence.
Successive refinement for the Wyner-Ziv problem and layered code design (2005)

We examine successive refinement for the Wyner-Ziv problem described in a recent paper by Steinberg and Merhav, where the authors showed that if the side information for all stages is identical, then the jointly Gaussian source with squared error distortion measure is successively refinable. We first extend this result to the case where the difference between the source and the side information is Gaussian and independent of the side information. As a byproduct, we give an alternative proof that the Wyner-Ziv problem for these sources has no rate loss-a result that was recently shown by Pradhan et al. through invoking the duality between the Gaussian Wyner-Ziv problem and the Costa problem. We then perform layered Wyner-Ziv code design for this general type of source based on nested scalar quantization, bit-plane coding, and low-density parity check (LDPC) code-based Slepian-Wolf coding (source coding with side information). We show that density evolution can be used to analyze the Slepian-Wolf code performance, provided that certain symmetry conditions, which have been dubbed dual symmetry, are satisfied by the hypothetical channel between the source and the side information. We also show that the dual symmetry condition is indeed satisfied by the hypothetical channel in our Slepian-Wolf coding setup. This justifies the use of density evolution in our LDPC code-based Slepian-Wolf code design for Wyner-Ziv coding. For the jointly Gaussian source, our layered coder performs 1.29 to 3.45 dB from the Wyner-Ziv bound for rates ranging from 0.47 to 4.68 bits per sample. When the side information is Laplacian and the source equals the side information plus an independent Gaussian noise term, our layered coder performs 1.33 to 3.90 dB from the Wyner-Ziv bound for rates ranging from 0.48 to 4.64 bits per sample.
A glucose-responsive transcription factor that regulates carbohydrate metabolism in the liver (2001)

Carbohydrates mediate their conversion to triglycerides in the liver by promoting both rapid posttranslational activation of rate-limiting glycolytic and lipogenic enzymes and transcriptional induction of the genes encoding many of these same enzymes. The mechanism by which elevated carbohydrate levels affect transcription of these genes remains unknown. Here we report the purification and identification of a transcription factor that recognizes the carbohydrate response element (ChRE) within the promoter of the L-type pyruvate kinase (LPK) gene. The DNA-binding activity of this ChRE-binding protein (ChREBP) in rat livers is specifically induced by a high carbohydrate diet. ChREBP's DNA-binding specificity in vitro precisely correlates with promoter activity in vivo. Furthermore, forced ChREBP overexpression in primary hepatocytes activates transcription from the L-type Pyruvate kinase promoter in response to high glucose levels. The DNA-binding activity of ChREBP can be modulated in vitro by means of changes in its phosphorylation state, suggesting a possible mode of glucose-responsive regulation. ChREBP is likely critical for the optimal long-term storage of excess carbohydrates as fats, and may contribute to the imbalance between nutrient utilization and storage characteristic of obesity.
Personalized genomic analyses for cancer mutation discovery and interpretation (2015)

Massively parallel sequencing approaches are beginning to be used clinically to characterize individual patient tumors and to select therapies based on the identified mutations. A major question in these analyses is the extent to which these methods identify clinically actionable alterations and whether the examination of the tumor tissue alone is sufficient or whether matched normal DNA should also be analyzed to accurately identify tumor-specific (somatic) alterations. To address these issues, we comprehensively evaluated 815 tumor-normal paired samples from patients of 15 tumor types. We identified genomic alterations using next-generation sequencing of whole exomes or 111 targeted genes that were validated with sensitivities >95% and >99%, respectively, and specificities >99.99%. These analyses revealed an average of 140 and 4.3 somatic mutations per exome and targeted analysis, respectively. More than 75% of cases had somatic alterations in genes associated with known therapies or current clinical trials. Analyses of matched normal DNA identified germline alterations in cancer-predisposing genes in 3% of patients with apparently sporadic cancers. In contrast, a tumor-only sequencing approach could not definitively identify germline changes in cancer-predisposing genes and led to additional false-positive findings comprising 31% and 65% of alterations identified in targeted and exome analyses, respectively, including in potentially actionable genes. These data suggest that matched tumor-normal sequencing analyses are essential for precise identification and interpretation of somatic and germline alterations and have important implications for the diagnostic and therapeutic management of cancer patients.
Functional reconstruction and synthetic mimicry of a conformational epitope using CLIPS™ technology (2007)

This paper describes immunization studies with CLIPS-constrained peptides covering only the major part (beta3-loop) of a structurally complex antigenic site on human Follicle Stimulating Hormone beta-subunit (FSH-beta). In cases where linear and SS-constrained peptides fail, the CLIPS-constrained peptides generate polyclonal antibodies with high neutralizing activity for hFSH. The sera were shown to be specific for hFSH over human Luteinizing Hormone (hLH) and human Chorionic Gonadotropin (hCG). ELISA-competition studies and circular dichroism (CD)-measurements illustrate clearly that activity of the peptides in antibody binding and generation relates directly to precise and appropriate fixation of the peptide conformation. Design of the CLIPS-peptides was entirely based on epitope mapping studies with two neutralizing anti-hFSH mAbs. Both mAbs were shown to bind to a conformational epitope located at the top of the beta1-beta3-loop covering the amino acid sequences Y58-P77 (beta3-loop). The results described in this paper show that CLIPS-constrained peptides covering the Y58-P77 sequence provide the minimally required structural entity necessary to generate reproducibly sera with high hFSH-neutralizing activity.
Microelectromechancial Systems (MEMS) At The UCLA Micromanufacturing Lab (1998)

Less than ten years after the first successful demonstration of micromotor (1). microelectromechanical systems (MEMS) is one of the fastest growing, most visible fields in engineering. To take the current momentum to a higher level and pass the torch to the next millennium, we should understand the engineering in microscale and adapt to the new paradigm in design and manufacturing.
PHOTOSENSITIZATION WITH A CHLORIN‐THIOBARBITURATE CONJUGATE (1994)

The photobiologic properties of a chlorin-thiobarbiturate conjugate were examined. In addition to the characteristic 670 nm chlorin absorbance, the conjugate exhibited new absorbance bands at 517 and 743 nm, but these were not a part of the fluorescence emission spectra, nor was fluorescence observed at wavelengths > 670 nm. The action spectrum indicated that the long-wavelength absorbance of the conjugate was not involved in phototoxicity in cell culture, and that only irradiation at wavelengths associated with the chlorin moiety yielded a cytotoxic effect. In vivo cytotoxicity elicited by 745 nm irradiation is attributed to thermal effects.
GoPubMed: exploring PubMed with the Gene Ontology (2005)

The biomedical literature grows at a tremendous rate and PubMed comprises already over 15 000 000 abstracts. Finding relevant literature is an important and difficult problem. We introduce GoPubMed, a web server which allows users to explore PubMed search results with the Gene Ontology (GO), a hierarchically structured vocabulary for molecular biology. GoPubMed provides the following benefits: first, it gives an overview of the literature abstracts by categorizing abstracts according to the GO and thus allowing users to quickly navigate through the abstracts by category. Second, it automatically shows general ontology terms related to the original query, which often do not even appear directly in the abstract. Third, it enables users to verify its classification because GO terms are highlighted in the abstracts and as each term is labelled with an accuracy percentage. Fourth, exploring PubMed abstracts with GoPubMed is useful as it shows definitions of GO terms without the need for further look up. GoPubMed is online at www.gopubmed.org. Querying is currently limited to 100 papers per query.