gebhart/patrepeval huggingface dataset:
Restriction Site-Free Insertion of PCR Products Directionally into Vectors (2000)

A restriction site-free cloning method has been developed for inserting a PCR product into a vector flexibly and precisely at any desired location with high efficiency. The method uses a pair of DNA integration primers with two portions. The 3' portion isolates the inserts by PCR, and the 5' portion integrates the PCR products into the homologous region of the vector. For mutagenesis, a third portion of mutation-generating sequences can be placed in between the 3' and 5' portions. This method has been used to clone the E. coli gene that codes for peptidyl-tRNA hydrolase, expressing it as a native protein and as a glutathione S-transferase fusion protein. It was also applied to convert a construct of the E. coli fatty acid biosynthesis protein with an N-terminal hexa-histidine tag into a construct with a C-terminal hexa-histidine tag.
Development of a Highly Sensitive Immuno-PCR Assay for the Measurement of α-Galactosidase A Protein Levels in Serum and Plasma (2013)

Fabry disease is an X-linked genetic disorder caused by defects in the α-galactosidase A (GLA) gene, and heterogeneous mutations lead to quantitative and/or qualitative defects in GLA protein in male patients with Fabry disease. Random X-chromosomal inactivation modifies the clinical and biochemical features of female patients with Fabry disease. Functional polymorphisms have been frequently reported in recent times, and these increase the difficulty of understanding the pathogenetic basis of the disease. To date, GLA protein level has been measured using an enzyme-linked immunosorbent assay (ELISA). However, ELISA is not highly sensitive due to the high background noise. In this paper, we introduce a novel application of the immuno-polymerase chain reaction (PCR) method (termed Multiple Simultaneous Tag [MUSTag]) for measurement of the GLA protein level in blood samples. We compared the sensitivities of the MUSTag method with plates or magnetic beads with those of ELISA for recombinant human GLA and found that the apparent maximal sensitivity was higher for the former than for the latter. We then measured the GLA concentrations in serum and plasma from male patients with classic Fabry disease (Male Fabry), females with Fabry disease (Female Fabry), male subjects harboring the functional polymorphism p.E66Q (E66Q), and control (Control) subjects. Our results revealed that compared to the MUSTag plate and ELISA, the MUSTag beads assay afforded a clearer estimation of the GLA protein levels in the serum and plasma with minimal or no background noise, although all the methods could differentiate between the Male Fabry, E66Q, and Control groups. The Female Fabry group showed characteristic heterogeneity, which was consistent with the X-linked inheritance. This novel method is expected to be useful for the sensitive determination of GLA level in blood and elucidation of the pathogenetic basis of Fabry disease.
The role of AMPK in psychosine mediated effects on oligodendrocytes and astrocytes: implication for Krabbe Disease (2008)

Krabbe disease (KD) is an inherited neurological disorder caused by the deficiency of galactocerebrosidase activity resulting in accumulation of psychosine, which leads to energy depletion, loss of oligodendrocytes, induction of gliosis, and inflammation by astrocytes in CNS. In this study, for the first time, we report the regulation of 'cellular energy switch,' AMP-activated protein kinase (AMPK), by psychosine in oligodendrocytes and astrocytes. Psychosine treatment significantly down-regulated AMPK activity, resulting in increased biosynthesis of lipids including cholesterol and free fatty acid in oligodendrocytes cell line (MO3.13) and primary astrocytes. Pharmacological activator of AMPK, 5-aminoimidazole-4-carboxamide-1-beta-4-ribofuranoside (AICAR) attenuated the psychosine-mediated down-regulation of AMPK and restored altered biosynthesis of lipids. AICAR treatment also down-regulated psychosine induced expression of proinflammatory cytokines and inducible nitric oxide synthase in primary astrocytes. However, AICAR treatment had no effect on psychosine induced-reactive oxygen species generation, arachidonic acid release, and death of oligodendrocytes; suggesting the specific role of AMPK in regulation of psychosine-mediated inflammatory response of astrocytes but not in cell death of oligodendrocytes. This study delineates an explicit role for AMPK in psychosine induced inflammation in astrocytes without directly affecting the cell death of oligodendrocytes. It also suggests that AMPK activating agents act as anti-inflammatory agents and can hold a therapeutic potential in Krabbe disease/twitcher disease, particularly when used in combination with drugs, which protect oligodendrocyte cell loss, such as sPLA2 inhibitor [Giri et al., J. Lipid Res. 47 (2006), 1478].
Photodynamic therapy using Lu-Tex induces apoptosis in vitro, and its effect is potentiated by angiostatin in retinal capillary endothelial cells. (2000)

The combination of angiostatin and Lu-Tex/PDT potentiates the cytotoxic effect of Lu-Tex/PDT on BRCE but not on RPE cells. This may provide a strategy to increase the selectivity of PDT in damaging capillary endothelial cells with less damage to RPE cells. Lu-Tex/PDT induces rapid caspase-dependent apoptosis in BRCE and RPE cells. Furthermore, Lu-Tex/PDT induces apoptosis through selective modulation of members of the Bcl-2 family and differs between BRCE and RPE cells.
A locus for febrile seizures (FEB3) maps to chromosome 2q23-24 (1999)

Febrile seizures are the most common form of childhood seizures, occurring in 2% to 5% of North American children. We report a large Utah family with 21 members affected by febrile seizures inherited as an autosomal dominant trait. All had generalized tonic-clonic seizures with onset associated with fever, consistent with the consensus febrile seizure phenotype, and none had febrile seizures beyond 6 years of age. Eighteen affected individuals had recurrent febrile seizures. Eight individuals developed afebrile seizures between ages 5 and 13 years. Afebrile seizures consisted of generalized tonic-clonic, generalized tonic, generalized atonic, simple partial, and partial complex seizure types and were associated with abnormal electroencephalographic findings in 5 individuals, all of whom were intellectually normal. We undertook linkage analysis in this family, defining the disease phenotype as febrile seizures alone. Linkage analysis in epilepsy candidate gene/loci regions failed to show evidence for linkage to febrile seizures. However, a genomewide scan and subsequent fine mapping revealed significant evidence for a new febrile seizure locus (FEB3) on chromosome 2q23-24 with linkage to the marker D2S2330 (LOD score 8.08 at theta = 0.001). Haplotype analysis defined a critical 10-cM region between markers D2S141 and D2S2345 that contains the FEB3 locus.
Microbial control of pests and plant diseases 1970-1980 (1981)

Microbial control of pests and plant diseases 1970-1980 , Microbial control of pests and plant diseases 1970-1980 , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Cytoprotection and regulation of heat shock proteins induced by heat shock in human breast cancer T47‐D cells: role of [Ca 2+ ] i and protein kinases (1998)

Overexpression of heat shock protein 70 kDa alters the susceptibility of tumor cells to chemotherapeutic agents. We conducted experiments to study the regulation of expression of heat shock proteins (HSPs) in heat shock-treated T47-D cells, a human breast cancer cell line that expresses estrogen receptors. Cells exposed to heat shock at 44 degreesC displayed increased expression of heat shock protein 72 kDa (HSP-72), glucose-regulated protein 78 kDa (GRP-78), and GRP-94 in a time-dependent manner, as shown by [35S]methionine incorporation and Western blotting experiments. The maximal rate of synthesis occurred between 2 and 4 h after heat shock. Removal of external Ca2+ inhibited the synthesis of the heat shock-induced GRP-78 but not of HSP-72 and GRP-94, whereas treatment of cells with BAPTA (a Ca2+ chelator) inhibited HSP-72 and GRP-78. Treatment with H89 (a protein kinase A inhibitor) blocked the heat shock-induced GRP-78 synthesis, whereas GF-109203X (a protein kinase C inhibitor) attenuated the heat shock-induced HSP-72 synthesis and completely blocked synthesis of GRP-78 but not of GRP-94. These results indicate that protein kinase C is involved in regulation of the heat shock-induced synthesis of HSP-72, whereas PKA and PKC are involved in the regulation of GRP-78 synthesis. Cells overexpressing HSP-72 and GRPs after heat shock displayed resistance against lethal temperature (47 degreesC for 50 min) -induced death, which was diminished after removal of external Ca2+ and treatment with GF-109203X. Heat shock increased intracellular free Ca2+ concentration ([Ca2+]i) in a temperature- and heating duration-dependent fashion, and the increase was inhibited in the absence of external [Ca2+]i and significantly reduced by pretreatment with H89 and GF-109203X. The results suggest that different pathways are involved in the induction of synthesis of HSP-72, GRP-78, and GRP-94 by heat shock. It is highly likely that only HSP-72 and GRP-78 are involved in the process of cytoprotection from the thermal injury.
Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008 (2010)

Estimates of the worldwide incidence and mortality from 27 cancers in 2008 have been prepared for 182 countries as part of the GLOBOCAN series published by the International Agency for Research on Cancer. In this article, we present the results for 20 world regions, summarizing the global patterns for the eight most common cancers. Overall, an estimated 12.7 million new cancer cases and 7.6 million cancer deaths occur in 2008, with 56% of new cancer cases and 63% of the cancer deaths occurring in the less developed regions of the world. The most commonly diagnosed cancers worldwide are lung (1.61 million, 12.7% of the total), breast (1.38 million, 10.9%) and colorectal cancers (1.23 million, 9.7%). The most common causes of cancer death are lung cancer (1.38 million, 18.2% of the total), stomach cancer (738,000 deaths, 9.7%) and liver cancer (696,000 deaths, 9.2%). Cancer is neither rare anywhere in the world, nor mainly confined to high-resource countries. Striking differences in the patterns of cancer from region to region are observed.
DNA lesions induced by UV A1 and B radiation in human cells: Comparative analyses in the overall genome and in thep53tumor suppressor gene (2005)

The UV components of sunlight (UVA and UVB) are implicated in the etiology of human skin cancer. The underlying mechanism of action for UVB carcinogenicity is well defined; however, the mechanistic involvement of UVA in carcinogenesis is not fully delineated. We investigated the genotoxicity of UVA1 versus UVB in the overall genome and in the p53 tumor suppressor gene in normal human skin fibroblasts. Immuno-dot blot analysis identified the cis-syn cyclobutane pyrimidine-dimer (CPD) as a distinctive UVB-induced lesion and confirmed its formation in the genomic DNA of UVA1-irradiated cells dependent on radiation dose. HPLC/tandem MS analysis showed an induction of 8-oxo-7,8-dihydro-2'-deoxyguanosine in the genomic DNA of UVA1-irradiated cells only. Mapping of DNA damages by terminal transferase-dependent PCR revealed preferential, but not identical, formation of polymerase-blocking lesions and/or strand breaks along exons 5-8 of the p53 gene in UVB- and UVA1-irradiated cells. The UVB-induced lesions detected by terminal transferase-PCR were almost exclusively mapped to pyrimidine-rich sequences; however, the UVA1-induced lesions were mapped to purine- and pyrimidine-containing sequences along the p53 gene. Cleavage assays with lesion-specific DNA repair enzymes coupled to ligation-mediated PCR showed preferential, but not identical, formation of CPDs along the p53 gene in UVB- and UVA1-irradiated cells. Additionally, dose-dependent formation of oxidized and ring-opened purines and abasic sites was established in the p53 gene in only UVA1-irradiated cells. We conclude that UVA1 induces promutagenic CPDs and oxidative DNA damage at both the genomic and nucleotide resolution level in normal human skin fibroblasts.
Dose-dependent pharmacokinetics of telithromycin after intravenous and oral administration to rats: contribution of intestinal first-pass effect to low bioavailability. (2007)

The low F of telithromycin at a dose of 50 mg/kg was mainly due to considerable intestinal first-pass effect, approximately 63.4% of oral dose, in rats.
GSPN: Generative Shape Proposal Network for 3D Instance Segmentation in Point Cloud (2018)

We introduce a novel 3D object proposal approach named Generative Shape Proposal Network (GSPN) for instance segmentation in point cloud data. Instead of treating object proposal as a direct bounding box regression problem, we take an analysis-by-synthesis strategy and generate proposals by reconstructing shapes from noisy observations in a scene. We incorporate GSPN into a novel 3D instance segmentation framework named Region-based PointNet (R-PointNet) which allows flexible proposal refinement and instance segmentation generation. We achieve state-of-the-art performance on several 3D instance segmentation tasks. The success of GSPN largely comes from its emphasis on geometric understandings during object proposal, which greatly reducing proposals with low objectness.
Dynamics of Proteins and Nucleic Acids (1988)

Share Icon Share Twitter Facebook Reddit LinkedIn Reprints and Permissions Cite Icon Cite Search Site Citation J. Andrew Mccammon, Stephen C. Harvey, Peter G. Wolynes; Dynamics of Proteins and Nucleic Acids. Physics Today 1 September 1988; 41 (9): 105–106. https://doi.org/10.1063/1.2811564 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentPhysics Today Search Advanced Search
PCR-Based Amplification of Platelet mRNA Sequences Obtained From Small-Scale Platelet Samples (2009)

Platelet transcriptome studies provide a powerful tool in the analysis of disorders affecting the megakaryocytic-platelet lineage. However, individualised platelet gene expression profiling is hampered by the exceptionally low yield of platelet mRNA. The yield of mRNA transcripts that can be obtained from small-scale platelet preparations is generally not sufficient for standard RNA-labeling reactions used in expression profiling. Furthermore, leukocyte contaminants in platelet preparations are a potential source of 'unwanted' mRNA since they contain several orders of magnitude more mRNA than platelets. To overcome these limitations a strategy that combines leukocyte filtration and a PCR-based amplification technique (SMART) has been developed and extensively evaluated.
Exon-intron organization and complete nucleotide sequence of a human major histocompatibility antigen DC beta gene. (1983)

We have determined the complete nucleotide sequence of a human class II histocompatibility antigen DC beta gene. The gene spans more than 7 kilobases and contains five exons corresponding to the different domains of the DC beta polypeptide. The exon-intron organization is thus analogous to that of class II antigen alpha-chain genes, class I antigen heavy chain genes, and the constant parts of immunoglobulin genes, emphasizing further the evolutionary relationship among these molecules. The mature polypeptide deduced from the DC beta gene shows 93% and 88% homology, respectively, to sequences derived from two DC beta cDNA clones of other haplotypes. The allelic polymorphism of DC beta chains resides predominantly in the first extracellular domain, whereas the rest of the polypeptide is virtually constant. The exons of the DC beta gene display high homology to the corresponding exons of a murine I-A beta gene. Also, the introns show significant homology. The DC beta chains lack eight amino acids in the cytoplasmic tail, as compared to DR and I-A beta chains. This is probably due to a nonfunctional splice junction of DC beta genes, causing a separate cytoplasmic exon to be nonexpressed.
Production of listeriolysin by beta-hemolytic strains of Listeria monocytogenes (1986)

Listeriolysin was isolated from target rabbit erythrocyte membranes after lysis of the cells with partially purified toxin derived from a culture supernatant of Listeria ivanovii. The membrane form of the toxin exhibited properties similar to those previously found for streptolysin O. Detergent-solubilized, delipidated listeriolysin was found to comprise a heterogeneous population of partially and fully circularized, amphiphilic oligomers whose embedment within the lipid bilayer generated large transmembrane pores. The molecular weight of the toxin monomer was estimated to be 55,000 to 60,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Immunological cross-reactions between the toxin and streptolysin O were demonstrable by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting. An immunoblot assay for detecting listeriolysin in agar-incorporated, lysed erythrocyte membranes was developed, and 28 defined, clinical isolates of Listeria monocytogenes were examined for toxin production. These isolates caused beta-hemolysis on the agar plates and had previously been regarded as listeriolysin producers. However, we found that only two isolates produced genuine listeriolysin, since the sensitive immunoblot assay entirely failed to detect the toxin in all other cases. We excluded that this finding derived from proteolytic degradation of membrane-bound toxin. Thus, the great majority of human pathogenic Listeria strains appear to produce one or several hemolysins that are immunologically and, by inference, molecularly distinct from the streptolysin O-related listeriolysin. We propose that the streptolysin O-related toxin be designated alpha-listeriolysin and that the other hemolysin(s) be termed beta-listeriolysin.
Unitary ESPRIT: how to obtain increased estimation accuracy with a reduced computational burden (1995)

ESPRIT is a high-resolution signal parameter estimation technique based on the translational invariance structure of a sensor array. Previous ESPRIT algorithms do not use the fact that the operator representing the phase delays between the two subarrays is unitary. The authors present a simple and efficient method to constrain the estimated phase factors to the unit circle, if centro-symmetric array configurations are used. Unitary ESPRIT, the resulting closed-form algorithm, has an ESPRIT-like structure except for the fact that it is formulated in terms of real-valued computations throughout. Since the dimension of the matrices is not increased, this completely real-valued algorithm achieves a substantial reduction of the computational complexity. Furthermore, Unitary ESPRIT incorporates forward-backward averaging, leading to an improved performance compared to the standard ESPRIT algorithm, especially for correlated source signals. Like standard ESPRIT, Unitary ESPRIT offers an inexpensive possibility to reconstruct the impinging wavefronts (signal copy). These signal estimates are more accurate, since Unitary ESPRIT improves the underlying signal subspace estimates. Simulations confirm that, even for uncorrelated signals, the standard ESPRIT algorithm needs twice the number of snapshots to achieve a precision comparable to that of Unitary ESPRIT. Thus, Unitary ESPRIT provides increased estimation accuracy with a reduced computational burden.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Replicon Particle Porcine Reproductive and Respiratory Syndrome Virus Vaccine Provides Partial Protection from Challenge (2009)

Replicon particles (RPs) expressing the GP5 and Matrix structural proteins of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) were created and compared to inactivated PRRSV in a challenge study. Pigs that received the RP vaccine had lower live virus titers and showed lower IDEXX ELISA values following challenge when compared to other groups. These results show that the RP vaccine provided partial protection against challenge with virulent PRRSV. Also, the RP vaccine allows for differentiation between vaccinated and naturally infected animals.
Synthesis of cyclobutane lignans via an organic single electron oxidant–electron relay system (2013)

A direct method to synthesize lignan cyclobutanes and analogs <i>via</i> photoinduced electron transfer is presented. A variety of oxygenated alkenes are employed to furnish terminal or substituted cyclobutane adducts with complete regiocontrol, yielding cycloadducts with <i>trans</i> stereochemistry. Key to minimizing competing cycloreversion is the inclusion of an aromatic electron relay (ER). This method has been adapted to the synthesis of the natural products magnosalin and pellucidin A.
Preliminary Studies on a Magneto-Optical Procedure for Aligning RHIC Magnets (1994)

Colloid dispersions of magnetite were used at SLAC and KEK to locate multipole magnet centers. We study the possible adaption of this method, to align RHIC magnets. A procedure for locating magnetic centers with respect to external fiducial markers, using electronic coordinate determination and digital TV image processing is described.
Psychophysics of Remembering: The Discrimination Hypothesis (2002)

In a psychophysical approach to remembering, the events to be remembered are discriminated from other possibilities at the time of remembering, and not at the time of encoding or learning. The discrimination is specific to the retention interval at which remembering occurs, as shown by experiments demonstrating that discriminability and response bias are delay–specific. This article discusses a discrimination model for remembering that emphasizes the individual's history of learning about reward payoffs in similar experiences in the past. This model predicts the two characteristics of forgetting functions, initial discriminability and rate of forgetting.
1.5-V Operating fully-depleted amorphous oxide thin film transistors achieved by 63-mV/dec subthreshold slope (2008)

Thin film transistors (TFTs) with a small subthreshold slope (SS) are urgently required for low-voltage operating circuits on large-area and flexible substrates. Using InGaZnO deposited at room temperature (RT), we achieved 63 mV/dec, the smallest-ever SS reported for oxide semiconductor TFTs. To achieve the small SS as well as small I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> , a fully-depleted off-state was employed by thinning the channel layer to 6 nm. Scalability down to L = 2 mum was confirmed. For V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> = 0 to 1.5 V operation, I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> <10-17 A/mum and on/off ratio > 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sup> were obtained.