gebhart/patrepeval huggingface dataset:
Differential regulation of GDNF, neurturin, and their receptors in primary cultures of rat glial cells (2001)

Glial cell line-derived neurotrophic factor (GDNF) and neurturin (NTN) bind to GFR alpha-1 and GFR alpha-2 receptors, respectively, and their neurotrophic activity is mediated by the tyrosine kinase receptor, Ret. All these molecules were found to be expressed in primary cultures of rat glial cells, which were largely composed of astrocytes and maintained in serum-free medium. Although GDNF, NTN and Ret mRNA levels were at the limit of detection, RNase protection assays revealed relatively high amounts of GFR alpha-1 and GFR alpha transcripts. To characterize signals controlling their expression, glial cells were exposed to serum or treated with hormones acting through nuclear receptors and by activators of the cAMP or protein kinase C (PKC)-dependent pathways. Retinoic acid or 1,25-dihydroxyvitamin D3 appeared ineffective. In contrast, the 5-fold increase in GFR alpha-2 mRNA after 24 hr of treatment with 10(-10) M of tri-iodothyronine, suggests a physiological role of thyroid hormone in the regulation of this receptor in vivo. The serum induced a 7-fold increase in GFR alpha-1 mRNA levels. These changes may be mediated by the cAMP or PKC pathways because both forskolin and TPA up-regulated the GFR alpha-1 gene. Interestingly, only TPA led to a coordinated increase in the levels of GDNF, GFR alpha-1 and GFR alpha-2 mRNAs. On the other hand, NTN transcripts remained constant, irrespective of the culture conditions. Taken together, these results indicate that GDNF family ligands and their receptors are regulated in glial cells by common or independent transductional pathways, which could modulate their specific expression during brain development or in the case of trauma.
Presence of a C4-Binding Protein (C4-bp) in Human Serum (1978)

Abstract As published elsewhere (Ferreira et al., J. Exp. Med., in press) mouse serum contains a 10S β-globulin which specifically binds to fluid phase activated Ss (C4) protein. This new protein was named Ss-bp or C4-bp. A search was made in human serum for the presence of a protein with similar properties. Human serum was incubated at 37°C with washed immune precipitates and centrifuged. Activated C4 was isolated from the supernatant by precipitation with a monospecific antiserum to C4, and injected into rabbits. The resulting antiserum was tested against whole human serum by crossed-immunoelectrophoresis. It reacted only against C4 and an additional serum component with properties very similar to those of mouse C4-bp. Human C4-bp is a heat stable β-globulin which is found in the exclusion volume after filtration of serum or EDTA-plasma through a Sephadex G-200 column. It has a sedimentation coefficient of 13S as determined by sucrose gradient ultracentrifugation of serum from a patient with hereditary angioedema (HAE) with low levels of C4. However, after addition of pure C4 to the HAE serum, the sedimentation coefficient of C4-bp increased to 17S. Moreover, the isolated, faster sedimenting C4-bp moieties could be quantitatively precipitated with antisera monospecific to C4.
Sensitive PCR Analysis of Animal Tissue Samples for Fragments of Endogenous and Transgenic Plant DNA (2004)

An optimized DNA extraction protocol for animal tissues coupled with sensitive PCR methods was used to determine whether trace levels of feed-derived DNA fragments, plant and/or transgenic, are detectable in animal tissue samples including dairy milk and samples of muscle (meat) from chickens, swine, and beef steers. Assays were developed to detect DNA fragments of both the high copy number chloroplast-encoded maize rubisco gene (rbcL) and single copy nuclear-encoded transgenic elements (p35S and a MON 810-specific gene fragment). The specificities of the two rbcL PCR assays and two transgenic DNA PCR assays were established by testing against a range of conventional plant species and genetically modified maize crops. The sensitivities of the two rbcL PCR assays (resulting in 173 and 500 bp amplicons) were similar, detecting as little as 0.08 and 0.02 genomic equivalents, respectively. The sensitivities of the p35S and MON 810 PCR assays were approximately 5 and 10 genomic equivalents for 123 bp and 149 bp amplicons, respectively, which were considerably less than the sensitivity of the rbcL assays in terms of plant cell equivalents, but approximately similar when the higher numbers of copies of the chloroplast genome per cell are taken into account. The 173 bp rbcL assay detected the target plant chloroplast DNA fragment in 5%, 15%, and 53% of the muscle samples from beef steers, broiler chickens, and swine, respectively, and in 86% of the milk samples from dairy cows. Reanalysis of new aliquots of 31 of the pork samples that were positive in the 173 bp rbcL PCR showed that 58% of these samples were reproducibly positive in this same PCR assay. The 500 bp rbcL assay detected DNA fragments in 43% of the swine muscle samples and 79% of the milk samples. By comparison, no statistically significant detections of transgenic DNA fragments by the p35S PCR assay occurred with any of these animal tissue samples.
Capsid protein structure in Zika virus reveals the flavivirus assembly process (2020)

Structures of flavivirus (dengue virus and Zika virus) particles are known to near-atomic resolution and show detailed structure and arrangement of their surface proteins (E and prM in immature virus or M in mature virus). By contrast, the arrangement of the capsid proteins:RNA complex, which forms the core of the particle, is poorly understood, likely due to inherent dynamics. Here, we stabilize immature Zika virus via an antibody that binds across the E and prM proteins, resulting in a subnanometer resolution structure of capsid proteins within the virus particle. Fitting of the capsid protein into densities shows the presence of a helix previously thought to be removed via proteolysis. This structure illuminates capsid protein quaternary organization, including its orientation relative to the lipid membrane and the genomic RNA, and its interactions with the transmembrane regions of the surface proteins. Results show the capsid protein plays a central role in the flavivirus assembly process.
Invasive and metastatic potential induced by ras-transfection into mouse BW5147 T-lymphoma cells. (1987)

Noninvasive, nonmetastatic BW5147 T-lymphoma cells were transfected with the activated human c-Ha-ras oncogene and were examined subsequently for the acquisition of invasive properties in vitro and of metastatic potential in vivo. It was found that several transfectants harboring the ras gene had become invasive in vitro, as assessed in hepatocyte cultures, and metastatic after tail vein injection into syngeneic AKR mice. The induced level of both invasive and metastatic potential appeared to depend on the level of expression of the transfected ras gene. Those transfectants exhibiting an elevated level of ras expression, mostly cells containing a high copy number of the ras gene, showed the highest invasiveness (up to 30-fold increase) and produced widespread metastasis in all mice tested. Transfectants with a low level of ras expression were less invasive and formed metastases in a few mice only, limited to a few organs or even to a single deposit in one organ. Untransfected BW cells, control transfected cells without the ras gene, and ras transfectants that did not express the gene were noninvasive and nonmetastatic. No changes in number of ras gene copies were found between isolated metastases and the transfectants from which they were derived. However, RNA analysis of the cells from the isolated metastases revealed similar, as well as elevated or diminished levels of ras transcription when compared to the corresponding cell lines prior to injection, suggesting that a persistent high expression of the ras gene is not necessarily needed for the independent growth at the secondary site. Our results indicate that the activated human ras oncogene may confer metastatic potential onto lymphoid tumor cells, probably due to the induction of invasiveness.
Using the structure of Web sites for automatic segmentation of tables (2004)

Many Web sites, especially those that dynamically generate HTML pages to display the results of a user's query, present information in the form of list or tables. Current tools that allow applications to programmatically extract this information rely heavily on user input, often in the form of labeled extracted records. The sheer size and rate of growth of the Web make any solution that relies primarily on user input is infeasible in the long term. Fortunately, many Web sites contain much explicit and implicit structure, both in layout and content, that we can exploit for the purpose of information extraction. This paper describes an approach to automatic extraction and segmentation of records from Web tables. Automatic methods do not require any user input, but rely solely on the layout and content of the Web source. Our approach relies on the common structure of many Web sites, which present information as a list or a table, with a link in each entry leading to a detail page containing additional information about that item. We describe two algorithms that use redundancies in the content of table and detail pages to aid in information extraction. The first algorithm encodes additional information provided by detail pages as constraints and finds the segmentation by solving a constraint satisfaction problem. The second algorithm uses probabilistic inference to find the record segmentation. We show how each approach can exploit the web site structure in a general, domain-independent manner, and we demonstrate the effectiveness of each algorithm on a set of twelve Web sites.
A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. (1992)

The modulation of DNA-protein interactions by methylation of protein-binding sites in DNA and the occurrence in genomic imprinting, X chromosome inactivation, and fragile X syndrome of different methylation patterns in DNA of different chromosomal origin have underlined the need to establish methylation patterns in individual strands of particular genomic sequences. We report a genomic sequencing method that provides positive identification of 5-methylcytosine residues and yields strand-specific sequences of individual molecules in genomic DNA. The method utilizes bisulfite-induced modification of genomic DNA, under conditions whereby cytosine is converted to uracil, but 5-methylcytosine remains nonreactive. The sequence under investigation is then amplified by PCR with two sets of strand-specific primers to yield a pair of fragments, one from each strand, in which all uracil and thymine residues have been amplified as thymine and only 5-methylcytosine residues have been amplified as cytosine. The PCR products can be sequenced directly to provide a strand-specific average sequence for the population of molecules or can be cloned and sequenced to provide methylation maps of single DNA molecules. We tested the method by defining the methylation status within single DNA strands of two closely spaced CpG dinucleotides in the promoter of the human kininogen gene. During the analysis, we encountered in sperm DNA an unusual methylation pattern, which suggests that the high methylation level of single-copy sequences in sperm may be locally modulated by binding of protein factors in germ-line cells.
Synthesis of antigenic carbohydrate polymers recognized by lectins and antibodies (1988)

The alkene group of allyl α-L-rhamnopyranoside has been converted to an N-acryloyl spacer arm which was copolymerized with acrylamide to afford water soluble carbohydrate copolymers; these have antigenic properties demonstrated by their binding to Ricinus communis lectin and to the antisera to the capsular polysaccharide of Streptococcus pneumoniae type 23.
Interaction of Frizzled Related Protein (FRP) with Wnt Ligands and the Frizzled Receptor Suggests Alternative Mechanisms for FRP Inhibition of Wnt Signaling (1999)

Frizzled related proteins (FRPs) comprise a family of secreted molecules that contain an N-terminal cysteine-rich domain (CRD) highly similar to the CRDs of the frizzled family of membrane-anchored Wnt receptors. FRPs have been shown to interact with Wnt proteins and antagonize Wnt signaling in a Xenopus developmental model. We demonstrated that FRP antagonizes the Wnt-induced increase in uncomplexed beta-catenin in both transient cotransfection and stable transformation models, where Wnt-induced morphological alterations are inhibited as well. We showed further that FRP inhibits Wnt signaling in a paracrine mode using a T-cell factor luciferase reporter to measure Wnt function. Investigation of the mechanisms responsible for FRP inhibition revealed that FRP forms complexes with WNT-1 or WNT-2 through its CRD domain. Transfection analysis with FRPs containing different tags revealed that FRP itself forms complexes and that this ability is conferred by its CRD domain. Finally, we demonstrated by cotransfection that FRP forms complexes with a prototype frizzled. All of these findings are consistent with a model by which FRP inhibits Wnt signaling through interactions with Wnt and/or formation of nonfunctional complexes with the frizzled receptor.
Finite difference time-domain calculation of transients in antennas with nonlinear loads (1993)

Transient currents for an antenna with a nonlinear load are calculated using finite-difference-time-domain (FDTD) methods. The FDTD electric field across the nonlinear load (which determines the voltage across the load) is calculated by solving a nonlinear equation at each time step. This allows the time step to be at the Courant limit, and is more efficient than reducing the time step size in all the FDTD cells to maintain stability in just the cell containing the nonlinear load. The stability of this approach relative to a simpler approach of approximating the diode as a variable resistor is demonstrated. As a validation of the method the transient current in a long dipole antenna with a nonlinear load excited by a pulsed plane wave is computed and compared with calculated results obtained by another method. The approach given here extends the applicability of the FDTD method to problems involving radiation and scattering from antennas including nonlinear loads.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A novel DFNA5 mutation, IVS8+4 A>G, in the splice donor site of intron 8 causes late‐onset non‐syndromic hearing loss in a Chinese family (2007)

We report here the clinical, genetic, and molecular characteristics of a large Chinese family exhibiting non-syndromic, late-onset autosomal dominant sensorineural hearing loss. Clinical evaluation revealed variable phenotypes of hearing loss in terms of severity and age-at-onset of disease in these subjects. Genome-wide linkage analysis mapped the disease gene to the DFNA5 locus with a maximum two-point log odds score of 5.39 at [theta] = 0 for marker D7S2457. DNA sequencing of DFNA5 revealed a novel heterozygous IVS8+4 A>G substitution in the splice donor site of intron 8. Reverse transcriptase-polymerase chain reaction (RT-PCR) showed skipping of exon 8 in the mutant transcript. This mutation faithfully cosegregated with hearing loss in the family. In addition, the mutation was absent in 100 unrelated control DNA samples of Chinese origin. The IVS8+4 A>G mutation is predicted to create a shift in the reading frame and introduce a stop codon at position 372, thereby resulting in a prematurely truncated DFNA5 protein. Up to date, a total of four mutations in DFNA5 have been reported to lead to hearing impairment, all of them result in skipping of exon 8 at the mRNA level. Our findings provide further support for the hypothesis that DFNA5-associated hearing loss is caused by a very specific gain-of-function mutation.
Monolithic 3D integration of SRAM and image sensor using two layers of single grain silicon (2010)

In this paper we report the monolithic integration of two single grain silicon layers for SRAM and image sensor applications. A 12 × 28 silicon lateral photodiode array with a 25_μm pixel size prepared on top of a three transistor readout circuit with individual outputs for every pixel is demonstrated. 6T SRAM cells with two layers of stacked transistors were prepared to compare the performance and area of each cell in different configurations.
Biosynthesis of Chondroitin/Dermatan Sulfate (2002)

Chondroitin sulfate and dermatan sulfate are synthesized as galactosaminoglycan polymers containing N-acetylgalactosmine alternating with glucuronic acid. The sugar residues are sulfated to varying degrees and positions depending upon the tissue sources and varying conditions of formation. Epimerization of any of the glucuronic acid residues to iduronic acid at the polymer level constitutes the formation of dermatan sulfate. Chondroitin/dermatan glycosaminoglycans are covalently attached by a common tetrasaccharide sequence to the serine residues of core proteins while they are adherent to the inner surface of endoplasmic reticulum/Golgi vesicles. Addition of the first sugar residue, xylose, to core proteins begins in the endoplasmic reticulum, followed by the addition of two galactose residues by two distinct glycosyl transferases in the early cis/medial regions of the Golgi. The linkage tetrasaccharide is completed in the medial/trans Golgi by the addition of the first glucuronic acid residue, followed by transfer of N-acetylgalactosamine to initiate the formation of a galactosaminoglycan rather than a glucosaminoglycan. This specific N-acetylgalactosaminyl transferase is different from the chondroitin synthase involved in generation of the repeating disaccharide units to form the chondroitin polymer. Sulfation of the chondroitin polymer by specific sulfotransferases occurs as the polymer is being formed. All the enzymes in the pathway for synthesis have been cloned, with the exception of the glucuronyl to iduronyl epimerase involved in the formation of dermatan residues.
Feedback Regulation of Cholesterol Uptake by the LXR–IDOL–LDLR Axis (2012)

Inducible degrader of the low-density lipoprotein receptor (IDOL) is an E3 ubiquitin ligase that mediates the ubiquitination and degradation of the low-density lipoprotein receptor (LDLR). IDOL expression is controlled at the transcriptional level by the cholesterol-sensing nuclear receptor liver X receptor (LXR). In response to rising cellular sterol levels, activated LXR induces IDOL production, thereby limiting further uptake of exogenous cholesterol through the LDLR pathway. The LXR-IDOL-LDLR mechanism for feedback inhibition of cholesterol uptake is independent of and complementary to the sterol regulatory element-binding protein pathway. Since the initial description of the LXR-IDOL pathway, biochemical studies have helped to define the structural basis for both IDOL target recognition and LDLR ubiquitin transfer. Recent work has also suggested links between IDOL and human lipid metabolism.
Requirement of Rsk-2 for Epidermal Growth Factor-Activated Phosphorylation of Histone H3 (1999)

During the immediate-early response of mammalian cells to mitogens, histone H3 is rapidly and transiently phosphorylated by one or more unidentified kinases. Rsk-2, a member of the pp90rsk family of kinases implicated in growth control, was required for epidermal growth factor (EGF)-stimulated phosphorylation of H3. RSK-2 mutations in humans are linked to Coffin-Lowry syndrome (CLS). Fibroblasts derived from a CLS patient failed to exhibit EGF-stimulated phosphorylation of H3, although H3 was phosphorylated during mitosis. Introduction of the wild-type RSK-2 gene restored EGF-stimulated phosphorylation of H3 in CLS cells. In addition, disruption of the RSK-2 gene by homologous recombination in murine embryonic stem cells abolished EGF-stimulated phosphorylation of H3. H3 appears to be a direct or indirect target of Rsk-2, suggesting that chromatin remodeling might contribute to mitogen-activated protein kinase-regulated gene expression.
Platination of A GG Site on Single‐Stranded and Double‐Stranded forms of A 14‐Base Oligonucleotide with Diaqua Cisplatin followed by NMR and HPLC (1997)

Detailed studies of the kinetics of platination of the single-stranded 14-base DNA oligonucleotide d(ATACATGGTACATA) and the corresponding duplex by cis-[Pt(NH3)2(H2O)2]2+ show that HPLC and NMR are complementary methods which provide similar results. The 5'-G and 3'-G monofunctional intermediates were trapped, separated and characterized by NMR (via 15NH3 labeling) and enzymatic digestion followed by mass spectrometry. The kinetic data are compared with those for the corresponding reactions of cis-[PtCl2(NH3)2] (cisplatin) and its monohydrolysed analogue. For both single and double strands of the oligonucleotide, the aqua complex shows little selectivity for the 5'-G or the 3'-G in the initial platination step, whereas the chloro-complex preferentially platinates the 3'-G. The base on the 3' side of the GG sequence appears to play an important role in controlling this selectivity; replacement of T by C increases the selectivity of duplex platination by the diaqua complex by a factor of about 6, and the selectivity of chelation of the 3'-G monofunctional adduct by a factor of about 3. In general the reactivity of the 5'-G in a GG sequence appears to be enhanced in a duplex compared with a single-strand. For both the aqua-monoadduct and chloro-monoadduct, cis-[Pt(NH3)2(N7G)(H2O or Cl)], the 5'-G monoadduct is much longer lived (t1/2 approximately 4 h at 288 K for aqua, 80 h at 298 K for chloro) than the 3'-G monoadduct (t1/2 < or = 45 min at 288 K for aqua, 6 h at 298 K for chloro). Inspection of molecular mechanics models of the end states of various monofunctional adducts provided insight into H-bonding and destacking interactions in these adducts and the sequence selectivity observed in their formation. Such adducts may play an important role in the mechanism of action of platinum anticancer drugs.
Cross-Sectional and Longitudinal Association Between Antihypertensive Medications and Cognitive Impairment in an Elderly Population (2005)

Antihypertensive use, particularly diuretics, angiotensin-converting enzymes inhibitors, beta-blockers, and angiotensin receptor blockers, may be associated with a lower rate of cognitive decline in older adults, including those with AD. Until a randomized clinical trial confirms our results, findings of this observational study should be interpreted with caution.
Teachers’ classroom‐based action research (2011)

Teachers’ classroom‐based action research is sometimes misunderstood by those who undertake it and support it, in three respects. First, it is wrongly assumed to fall into either positivist or interpretive paradigms (or perhaps a mixture of both) or to be critical. Second, there is little understanding as to why action research is necessarily self‐reflexive, collaborative and political. Third, there is a view that classroom research studies are not suitable for dissemination because they are not generalizable. Drawing on the work of Heron and Reason, I outline a view of how teachers are positioned in their classroom to explain why teachers’ classroom‐based action research cannot be underpinned by positivist, interpretive or critical paradigms, is necessarily self‐reflexive, collaborative (albeit in a weak form) and political and is suitable for dissemination to teachers, working in similar contexts.