gebhart/patrepeval huggingface dataset:
Specific RNA binding by Q.beta. coat protein (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSpecific RNA binding by Q.beta. coat proteinGary W. Witherell and Olke C. UhlenbeckCite this: Biochemistry 1989, 28, 1, 71–76Publication Date (Print):January 10, 1989Publication History Published online1 May 2002Published inissue 10 January 1989https://pubs.acs.org/doi/10.1021/bi00427a011https://doi.org/10.1021/bi00427a011research-articleACS PublicationsRequest reuse permissionsArticle Views385Altmetric-Citations77LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Monitoring formation of high intensity focused ultrasound (HIFU) induced lesions using backscattered ultrasound (2004)

Backscattered radio frequency (RF) data collected in a series of in vitro experiments, in which HIFU lesions were created in bovine liver tissue, were analyzed using two signal processing approaches to visualize temporal evolution of lesion formation. Change in round-trip travel time provides information related to temperature change during and after therapy. Changes in the RF spectrum related to changes in scattering properties of the heated region were observed before visible changes appeared on B-mode images. Effect of increased attenuation in the necrosed tissue region was also observed. Results demonstrate potential for these two techniques in imageguided HIFU therapy.
Simonsen Lecture. Synthetic approaches to vitamin D and its relatives (1980)

B. Lythgoe, Chem. Soc. Rev., 1980, 9, 449 DOI: 10.1039/CS9800900449
Construction and Analysis of a Library for Random Insertional Mutagenesis in Streptococcus pneumoniae : Use for Recovery of Mutants Defective in Genetic Transformation and for Identification of Essential Genes (1999)

To explore the use of insertion-duplication mutagenesis (IDM) as a random gene disruption mutagenesis tool for genomic analysis of Streptococcus pneumoniae, a large mutagenic library of chimeric plasmids with 300-bp inserts was constructed. The library was large enough to produce 60,000 independent plasmid clones in Escherichia coli. Sequencing of a random sample of 84 of these clones showed that 85% of the plasmids had inserts which were scattered widely over the genome; 80% of these plasmids had 240- to 360-bp inserts, and 60% of the inserts targeted internal regions of apparent open reading frames. Thus, the library was both complex and highly mutagenic. To evaluate the randomness of mutagenesis during recombination and to test the usefulness of the library for obtaining specific classes of nonessential genes, this library was used to seek competence-related genes by constructing a large pneumococcal transformant library derived from 20,000 mutagenic plasmids. After we screened the mutants exhaustively for transformation defects, 114 competence-related insertion mutations were identified. These competence mutations hit most previously known genes required for transformation as well as a new gene with high similarity to the Bacillus subtilis competence gene comFA. Mapping of the mutation sites at these competence loci showed that the mutagenesis was highly random, with no apparent hot spots. The recovery of a high proportion of competence genes and the absence of hot spots for mutational hits together show that such a transformant library is useful for finding various types of nonessential genes throughout the genome. Since a promoterless lacZ reporter vector was used for the construction of the mutagenic plasmid library, it also serves as a random transcriptional fusion library. Finally, use of a valuable feature of IDM, directed gene targeting, also showed that essential genes, which can be targets for new drug designs, could be identified by simple sequencing and transformation reactions. We estimate that the IDM library used in this study could readily achieve about 90% genome coverage.
Detection of allelic variations of human gene expression by polymerase colonies (2004)

We were able to reproduce the results of allelic variation in gene expression using an accurate technology known as polymerase colonies. Therefore, we have demonstrated the utility of this method in human gene expression analysis.
A human protein containing a “cold shock” domain binds specifically to H-DNA upstream from the human gamma-globin genes. (1994)

We previously determined that a region between positions -228 and -189 upstream from the human gamma-globin genes can form an intramolecular triplex (H-DNA) in supercoiled plasmids. To identify proteins that might interact with this DNA structure, we performed expression cloning using an adult bone marrow cDNA library and the single-stranded region of the H-DNA structure as a probe. We cloned molecules very similar to two previously identified cDNAs, dbpA and dbpB. The dbpB-like protein (called BP-8 in this study) interacts specifically (KD approximately 4 nM) with two homopyrimidine "half-sites" in the single-stranded gamma-228 to -189 probe, but binds to double-stranded DNA containing the same sequence with 100-fold less affinity. We have also shown that supercoiled plasmids containing the gamma-228 to -189 region contain a high affinity binding site for BP-8 that is stabilized by factors that stabilize H-DNA; two HPFH point mutations (-202 C-->G or C-->T) that destabilize the secondary DNA structure abolish the high affinity binding site. Collectively, these data show that dbpB/BP-8 binds specifically to homopyrimidine half-sites in single-stranded DNA, and that it also binds to H-DNA structures that contain homopyrimidine tracts in the single-stranded and triple-stranded regions.
High expression of AKR1C1 is associated with proliferation and migration of small-cell lung cancer cells (2016)

AKR1C1 is a member of the AKR1C family, which not only plays an important role in hormone metabolism but is believed to be involved in carcinogen metabolism. Our previous study demonstrated that AKR1C1 was highly expressed in lung tumor tissues as compared with the tumor-adjacent tissues. Small-cell lung cancer (SCLC) is a special type of lung cancer. Surgical treatment of SCLC is usually difficult due to the high degree of malignancy and early metastasis, and difficulty in obtaining clinical specimens. There is not much basic or clinical research on SCLC in the People's Republic of China even in recent years. To investigate the mechanism of AKR1C1 in the pathogenesis of SCLC, the present study used H446 cell line to see whether AKR1C1 could affect the proliferation or migration of SCLC cells, and used a lentivirus to build the AKR1C1 overexpression and under-expression cell lines. The results indicated that AKR1C1 was an important inducement in the proliferation and migration of H446 cells. AKR1C1 promoted cell proliferation and played a vital role in the migration of SCLC cells. These results were also verified in nude mice in vivo. In conclusion, AKR1C1 plays an important role in the development and progression of SCLC and may represent an independent biomarker for assessment of the primary prognosis and therapy of SCLC.
Microphase Separation in Model 4-Miktoarm Star Copolymers of the AB3 Type (1997)

The order−disorder transition has been studied in two AB3 miktoarm stars of styrene and isoprene with SAXS and rheology. A mean-field theory has been developed to treat the most general case of miktoarm stars: AmBn (m ≠ n) which provides the phase stability criteria and the static structure factor in the disordered phase. The theory predicts a maximum in the critical value of χNt (Nt = NA + nNB) as a function of the number of arms n in ABn, for n = 3. This maximum arises from a delicate balance between the stretching free energies of the A and B blocks forming the miktoarm stars. The theoretical predictions for the phase stability and the structure factor have been tested experimentally, using SAXS, and the interaction parameter has been extracted. The latter exhibits a weak T-dependence which is consistent with fluctuation effects near the transition. Further evidences for the existence of fluctuations at temperatures above and below the transition are provided by (i) the nonlinearity of the inverse peak intensity vs inverse temperature, in the disordered state, and (ii) the existence of metastable states in the ordered state. All SAXS peak parameters were discontinuous at the order-to-disorder transition, revealing a first-order transition.
Molecular Dynamics andab initioTotal Energy Calculations (1986)

Received 4 February 1986DOI:https://doi.org/10.1103/PhysRevLett.56.2656©1986 American Physical Society
Diagnostic Limitations of Spontaneous Growth Hormone Measurements in Normally Growing Prepubertal Children (1989)

To evaluate whether the measurement of the spontaneous overnight growth hormone secretion in prepubertal children clearly separated normal children from subjects with growth hormone deficiency, we studied 45 prepubertal normally growing children (10 with normal height and 35 with constitutional growth delay) and compared their overnight growth hormone secretion with that of a group of subjects with either isolated growth hormone deficiency or neurosecretory dysfunction. Peak growth hormone levels (greater than or equal to 10 ng/mL) following oral clonidine administration were normal in individuals with normal height, constitutional growth delay, and neurosecretory dysfunction, as was the basal somatomedin C concentration; subjects with growth hormone deficiency had low peak growth hormone levels (less than 10 ng/mL) following oral clonidine administration as well as low basal somatomedin C values. The mean 9-hour overnight growth hormone concentration, total growth hormone output, total number of nocturnal pulses, and the mean peak growth hormone response during nocturnal sampling were similar in the normal height and constitutional growth delay groups and significantly greater than those seen in subjects with either growth hormone deficiency or neurosecretory dysfunction. Twelve (26.6%) of 45 normally growing children (4 to 10 normal height and 8 of 35 constitutional growth delay), however, had low overnight growth hormone levels (less than 3 ng/mL), which overlapped results obtained in the growth hormone-deficient or neurosecretory dysfunction groups. Frequent overnight growth hormone (GH) sampling does not always separate normal-growing children from those with partial or complete GH deficiency. In our this study over one quarter of the normally growing children had overnight GH levels in the range of children with either GH deficiency or neurosecretory dysfunction. These findings, in addition to the cost and difficulty in performing this test, do not support the measurement of spontaneous GH as a routine test in short but normally growing prepubertal children.
Ras gene mutation and amplification in human nonmelanoma skin cancers (1991)

Our previous studies have shown that human skin cancers occurring on sun-exposed body sites frequently contain activated Ha-ras oncogenes capable of inducing morphologic and tumorigenic transformation of NIH 3T3 cells. In this study, we analyzed human primary squamous cell carcinomas (SCCs) and basal cell carcinomas (BCCs) occurring on sun-exposed body sites for mutations in codons 12, 13, and 61 of Ha-ras, Ki-ras, and N-ras oncogenes by amplification of genomic tumor DNAs by the polymerase chain reaction, followed by dot-blot hybridization to synthetic oligonucleotide probes designed to detect single base-pair mutations. In addition to the primary human skin cancers, we also analyzed Ha-ras-positive NIH 3T3 transformants for mutations in the Ha-ras oncogene. The results indicated that all three NIH 3T3 transformants, 11 of 24 (46%) SCCs, and 5 of 16 (31%) BCCs contained mutations at the second position of Ha-ras codon 12 (GGC----GTC), predicting a glycine-to-valine amino acid substitution, whereas only 1 of 40 skin cancers (an SCC) displayed a mutation in the first position of Ki-ras codon 12 (GGT----AGT), predicting a glycine-to-serine amino acid change. In addition, three of the SCCs contained highly amplified copies of the N-ras oncogene in their genomic DNA. Interestingly, two of the SCCs containing amplified N-ras sequences also had G----T mutations in codon 12 of the Ha-ras oncogene. These studies demonstrate that mutations in codon 12 of the Ha-ras oncogene occurred at a high frequency in human skin cancers originating on sun-exposed body sites, whereas mutation in codon 12 of Ki-ras or amplification of N-ras occurred at a low frequency. Since the mutations in the Ha-ras and Ki-ras oncogenes were located opposite potential pyrimidine dimer sites (C-C), it is likely that these mutations were induced by ultraviolet radiation present in sunlight.
c-Myc is crucial for the expression of LAT1 in MIA Paca-2 human pancreatic cancer cells (2012)

Tumor cells take up a massive amount of nutrition compared to normal cells for increased metabolism. Therefore, special transporters for organic materials are required to satisfy the powerful consumption of nutrition in tumor cells. L-type amino acid transporter 1 (LAT1) incorporates large neutral amino acids, most of which are also categorized as essential amino acids, into cells in a Na+-independent manner. Because of its high expression levels in a variety of cancer cells, it is speculated that LAT1 functions as a key transporter for highly effective delivery of essential amino acids into cancer cells. In this regard, LAT1 inhibitor is expected to have clinical benefit for cancer therapy. However, the molecular mechanism of enrichment of LAT1 in cancer cells remains poorly understood. Here, we show that a proto-oncogene, c-Myc, is a critical positive regulator of LAT1 expression in MIA Paca-2 human pancreatic cancer cells. The uptake of leucine, a representative neutral amino acid, was strictly dependent on LAT1 in MIA Paca-2 cells, and siRNA-mediated knockdown of LAT1 inhibited cell proliferation. Diminished c-Myc expression with siRNA resulted in severe reduction of LAT1 protein levels as well as mRNA levels, which, in turn, led to a significant defect of leucine incorporation. The LAT1 promoter has a canonical c-Myc binding sequence and overexpression of c-Myc increased LAT1 promoter activity, whereas mutation of c-Myc binding site diminished this effect. Our results suggest biological significance of LAT1 in tumor growth and molecular machinery that could explain why LAT1 is preferentially expressed in cancer cells.
Gremlin is Overexpressed in Lung Adenocarcinoma and Increases Cell Growth and Proliferation in Normal Lung Cells (2012)

Our data suggest that Gremlin acts in an oncogenic manner in lung adenocarcinoma and could hold promise as a new diagnostic marker or potential therapeutic target in lung AD or general thoracic malignancies.
Genetic diversity in Treponema pallidum: Implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws (2011)

Pathogenic uncultivable treponemes, similar to syphilis-causing Treponema pallidum subspecies pallidum, include T. pallidum ssp. pertenue, T. pallidum ssp. endemicum and Treponema carateum, which cause yaws, bejel and pinta, respectively. Genetic analyses of these pathogens revealed striking similarity among these bacteria and also a high degree of similarity to the rabbit pathogen, Treponema paraluiscuniculi, a treponeme not infectious to humans. Genome comparisons between pallidum and non-pallidum treponemes revealed genes with potential involvement in human infectivity, whereas comparisons between pallidum and pertenue treponemes identified genes possibly involved in the high invasivity of syphilis treponemes. Genetic variability within syphilis strains is considered as the basis of syphilis molecular epidemiology with potential to detect more virulent strains, whereas genetic variability within a single strain is related to its ability to elude the immune system of the host. Genome analyses also shed light on treponemal evolution and on chromosomal targets for molecular diagnostics of treponemal infections.
Proteomics-based Target Identification (2003)

LAF389 is a synthetic analogue of bengamides, a class of marine natural products that produce inhibitory effects on tumor growth in vitro and in vivo. A proteomics-based approach has been used to identify signaling pathways affected by bengamides. LAF389 treatment of cells resulted in altered mobility of a subset of proteins on two-dimensional gel electrophoresis. Detailed analysis of one of the proteins, 14-3-3gamma, showed that bengamide treatment resulted in retention of the amino-terminal methionine, suggesting that bengamides directly or indirectly inhibited methionine aminopeptidases (MetAps). Both known MetAps are inhibited by LAF389. Short interfering RNA suppression of MetAp2 also altered amino-terminal processing of 14-3-3gamma. A high resolution structure of human MetAp2 co-crystallized with a bengamide shows that the compound binds in a manner that mimics peptide substrates. Additionally, the structure reveals that three key hydroxyl groups on the inhibitor coordinate the di-cobalt center in the enzyme active site.
Pose Invariant Face Recognition Using Neuro-Biologically Inspired Features (2012)

A face recognition algorithm using biologically inspired C2 standard model features is proposed. The C2 feature extraction system, which is based on the standard model of the ventral stream of visual cortex, is modified for the extraction of facial features. The S2 units in the learning stage are tuned to frontal and profile views of the faces to provide pose invariant recognition. A new learning function is utilized to extract discriminative facial features. The spatial invariance is limited both in the local and global pooling stages. The reduced spatial invariance in the local pooling preserves the minute shape and texture details of the facial components, whereas that in the global pooling stage preserves the component location information. The faces are classified using a support vector machines classifier with linear kernel. The proposed algorithm is tested using two face datasets (MIT-CBCL, FEI) with wide variations in profiles, and compared with existing algorithms (the original C2 feature extraction algorithm and MPCALDA algorithm). The experimental results provide evidence of the better performance of the proposed approach for pose invariant face recognition, by at least 6.5%.
Transition of Methotrexate Polyglutamate Drug Monitoring Assay from Venipuncture to Capillary Blood-Based Collection Method in Rheumatic Diseases (2019)

Capillary blood MTXPG<sub>3</sub> levels can be used to guide MTX dosing in TDM practice.
Identifying driver mutations from sequencing data of heterogeneous tumors in the era of personalized genome sequencing (2013)

Distinguishing driver mutations from passenger mutations is critical to the understanding of the molecular mechanisms of carcinogenesis and for identifying prognostic and diagnostic markers as well as therapeutic targets. We reviewed the current approaches and software for identifying driver mutations from passenger mutations including both biology-based approaches and machine-learning-based approaches. We also reviewed approaches to identify driver mutations in the context of pathways or gene sets. Finally, we discussed the challenges of predicting driver mutations considering the complexities of inter- and intra-tumor heterogeneity as well as the evolution and progression of tumors.
Thermoelectric Power in Bilayer Graphene Device with Ionic Liquid Gating (2016)

The quest for materials showing large thermoelectric power has long been one of the important subjects in material science and technology. Such materials have great potential for thermoelectric cooling and also high figure of merit ZT thermoelectric applications. We have fabricated bilayer graphene devices with ionic-liquid gating in order to tune its band gap via application of a perpendicular electric field on a bilayer graphene. By keeping the Fermi level at charge neutral point during the cool-down, we found that the charge puddles effect can be greatly reduced and thus largely improve the transport properties at low T in graphene-based devices using ionic liquid gating. At (Vig, Vbg) = (-1 V, +23 V), a band gap of about 36.6 ± 3 meV forms, and a nearly 40% enhancement of thermoelectric power at T = 120 K is clearly observed. Our works demonstrate the feasibility of band gap tuning in a bilayer graphene using ionic liquid gating. We also remark on the significant influence of the charge puddles effect in ionic-liquid-based devices.
The MTA family proteins as novel histone H3 binding proteins (2013)

Together our study reveals a novel histone H3-binding activity for the MTA family proteins and provides evidence that the MTA family proteins mediate the in vitro specific binding of H3 tail peptide by NURD complex. However, multiple mechanisms are likely to contribute to the chromatin association of NURD complex in cells. Our finding also raises the possibility that the MTA family proteins may exert their diverse biological functions at least in part through their direct interaction with H3 tail.
Dual Endothelin-A/Endothelin-B Receptor Blockade and Cardiac Remodeling in Heart Failure With Preserved Ejection Fraction (2016)

These findings indicate that dual ET-A/ET-B receptor inhibition improves HFpEF by abrogating adverse cardiac remodeling via antihypertrophic mechanisms and by reducing stiffness. Additional studies are needed to explore the role of dual ET-1 receptor antagonists in patients with HFpEF.
Improvements in clinical and functional vision and perceived visual disability after first and second eye cataract surgery (1997)

Significant improvements in clinical, functional, and perceived vision are obtained by cataract surgery. The improvements in objective measures of functional vision found in this study support previous findings of improvements in patients' perceived functional vision. In addition, these data provide support to the necessity of second eye surgery in some patients to improve certain aspects of visual function to age matched normal levels.
Technology evaluation: CpG-7909, Coley. (2003)

Coley Pharmaceutical (formerly CpG ImmunoPharmaceuticals) is developing CpG-7909 (ProMune) for use in the potential treatment of cancer and as a vaccine adjuvant. By April 2000, CpG-7909 had entered phase I/II trials for cancer and in March 2002, Coley initiated a phase I trial in non-Hodgkin's lymphoma in combination with rituximab (Rituxan). By October 2002, CpG-7909 was in phase II trials as a vaccine adjuvant. Cpg-7909 is currently also undergoing phase II trials for melanoma.