gebhart/patrepeval huggingface dataset:
Immunohistochemical studies on vitronectin in elastic tissue disorders, cutaneous amyloidosis, lichen ruber planus and porphyria. (1988)

Vitronectin, identical with serum-spreading factor and S-protein of complement, is a glycoprotein present in both plasma and tissue. It stimulates cell adhesion and spreading and affects the complement and coagulation pathways. Vitronectin immunoreactivity was recently found in conjunction with dermal and renal elastic fibres, in renal amyloid deposits in cases of AL- and AA-amyloidosis, and in sclerotic glomerular lesions. Skin specimens from lesions of patients with selected skin diseases were investigated with an avidin-biotin peroxidase technique using both monoclonal and polyclonal anti-vitronectin antibodies and an alkaline phosphatase anti-alkaline phosphatase technique using monoclonal anti-vitronectin antibodies. Vitronectin immunoreactivity was found in association with the abnormal elastic tissue in solar elastosis and pseudoxanthoma elasticum. It was also found in conjunction with dermal amyloid deposits in primary localized cutaneous amyloidosis and in Civatte bodies in cases of lichen ruber planus. In cases of erythropoietic protoporphyria and porphyria cutanea tarda, hyaline perivascular deposits also demonstrated positive vitronectin immunoreactivity. The presence of vitronectin immunoreactivity not only in normal and degenerated elastic fibres but also in various pathological tissue deposits suggests that vitronectin occurs both in elastic fibres and in different types of abnormal protein deposits.
연구논문 / 제주해협의 해수유동특성에 관한 연구 (1997)

제주해협내에 설정한 3개의 남북 단면상에 배열한 13개의 관측정점과 기타 4개의 제주항 부근의 연안정점에서 1986-1989년까지 실시한 해류계에 의한 해류조사결과와 1981-1987년 사이에 실시된 해류판 추적조사, 일반해양관측 등에 의하여 얻어진 자료들을 종합적으로 분석하여 정리한 제주해협의 유황을 요약하면 다음과 같다.
1. 제주해협내에는 주로 동-북동류의 항류가 있어, 해협 서쪽 입구의 전단면을 통하여 해협내로 유입된 해수가 동쪽 입구의 전단면을 통하여 유출되고 있으며, 이 항류의 유속은 10m층에서 5.2㎝/sec-30㎝/sec이고, 중·저층은 1.3-24㎝/sec로 대체로 해협의 심소 및 제주도 북측에 강류대가 있고, 추자도 및 보길도 부근의 연안 천소에 약한 항류가 있다.
2. 제주해협 서쪽 입구의 전단면에서 실측한 항류의 하계 평균유속은 6.93㎝/sec로, 이것을 기초로 계산한 이 단면의 해수수송량은 0.384×10^6㎥/sec(Sv)이며, 단면의 항류분포와 지형류 유속 분포간에는 많은 차를 보였다.
3. 추자도 북서쪽의 전선 역에서는 밀물 때는 북향류에 의해 고온·고염분의 외해수가 5mile정도 연안역으로 이동 하지만, 썰물 때는 북상 거리만큼 다시 남하하지 않고 동-남동향류 때문에, 연안수와 혼합하면서 전선 북쪽의 연안역으로 이동하므로, 결과적으로 추자도 북서해역은 제주도 서방해역으로부터 북상해온 외해수가 한국남해연안수내로 유입하는 창구가 되며, 이것을 일으키는 주된 작용은 항류가 아닌 조류이다.
Oxygen isotopic signature of CO 2 from combustion processes (2011)

Abstract. For a comprehensive understanding of the global carbon cycle precise knowledge of all processes is necessary. Stable isotope (13C and 18O) abundances provide information for the qualification and the quantification of the diverse source and sink processes. This study focuses on the δ18O signature of CO2 from combustion processes, which are widely present both naturally (wild fires), and human induced (fossil fuel combustion, biomass burning) in the carbon cycle. All these combustion processes use atmospheric oxygen, of which the isotopic signature is assumed to be constant with time throughout the whole atmosphere. The combustion is generally presumed to take place at high temperatures, thus minimizing isotopic fractionation. Therefore it is generally supposed that the 18O signature of the produced CO2 is equal to that of the atmospheric oxygen. This study, however, reveals that the situation is much more complicated and that important fractionation effects do occur. From laboratory studies fractionation effects on the order of up to 26%permil; became obvious in the derived CO2 from combustion of different kinds of material, a clear differentiation of about 7‰ was also found in car exhausts which were sampled directly under ambient atmospheric conditions. We investigated a wide range of materials (both different raw materials and similar materials with different inherent 18O signature), sample geometries (e.g. texture and surface-volume ratios) and combustion circumstances. We found that the main factor influencing the specific isotopic signatures of the combustion-derived CO2 and of the concomitantly released oxygen-containing side products, is the case-specific rate of combustion. This points firmly into the direction of (diffusive) transport of oxygen to the reaction zone as the cause of the isotope fractionation. The original total 18O signature of the material appeared to have little influence, however, a contribution of specific bio-chemical compounds to individual combustion products released from the involved material became obvious.
A Paradigm Case for the Merging of Glycal and Enzymatic Assembly Methods in Glycoconjugate Synthesis: A Highly Efficient Chemo‐Enzymatic Synthesis of GM3 (1996)

Abstract A concise, regio‐ and stereoselective synthesis of the ganglioside GM 3 has been achieved. Use of an α‐1,2‐oxirane derived from lactal facilitated installation of the anomeric β‐ceramide side chain. Introduction of the sialic acid residue at C 3 , of the lactose was accomplished regiospecifically by enzymatically mediated sialyl transfer from CMP‐Neu‐5‐Ac.
Human Ig heavy chain CDR3 regions in adult bone marrow pre-B cells display an adult phenotype of diversity: evidence for structural selection of DH amino acid sequences (1997)

Ig repertoires generated at various developmental stages differ markedly in diversity. It is well documented that Ig H chain genes in human fetal liver are limited with regard to N-regional diversity and use of diversity elements. It is unclear whether these characteristics persist in pre-B cell H chain genes of adult bone marrow. Using Ig H chain CDR3 fingerprinting and sequence analysis, we analyzed the diversity of Ig H chain third complementarity determining regions (HCDR3) in adult bone marrow pre-B and mature B lymphocytes. Pre-B cell HCDR3 sequences exhibited adult characteristics with respect to HCDR3 size, distribution of N regions and usage of diversity elements. This suggested that pre-B cells in adults are distinct from fetal B cell precursors with regard to Ig H chain diversification mechanisms. At the DNA sequence level, HCDR3 diversity in mature B cells was similar to that in pre-B cells. Pre-B HCDR3s, however, frequently contained a consecutive stretch of hydrophobic amino acids, which were rare in mature B cells. We propose that highly hydrophobic pre-B HCDR3s may be negatively selected on the basis of structural limitations imposed by the antigen binding site. At the same time, usage of hydrophilic HCDR3 sequences (thought to support HCDR3 loop formation) may be promoted by positive selection.
Inhibition of AP-1 binding and transcription by gold and selenium involving conserved cysteine residues in Jun and Fos. (1995)

Gold(I) salts and selenite, which have diverse therapeutic and biological effects, are noted for their reactivity with thiols. Since the binding of Jun-Jun and Jun-Fos dimers to the AP-1 DNA binding site is regulated in vitro by a redox process involving conserved cysteine residues, we hypothesized that some of the biological actions of gold and selenium are mediated via these residues. In electrophoretic mobility-shift analyses, AP-1 DNA binding was inhibited by gold(I) thiolates and selenite, with 50% inhibition occurring at approximately 5 microM and 1 microM, respectively. Thiomalic acid had no effect in the absence of gold(I), and other metal ions inhibited at higher concentrations, in a rank order correlating with their thiol binding affinities. Cysteine-to-serine mutants demonstrated that these effects of gold(I) and selenite require Cys272 and Cys154 in the DNA-binding domains of Jun and Fos, respectively. Gold(I) thiolates and selenite did not inhibit nonspecific protein binding to the AP-1 site and were at least an order of magnitude less potent as inhibitors of sequence-specific binding to the AP-2, TFIID, or NF1 sites compared with the AP-1 site. In addition, 10 microM gold(I) or 10 microM selenite inhibited expression of an AP-1-dependent reporter gene, but not an AP-2-dependent reporter gene. These data suggest a mechanism regulating transcription factor activity by inorganic ions which may contribute to the known antiarthritic action of gold and cancer chemoprevention by selenium.
Spatio‐temporal analysis of mitotic activity with a labile cyclin–GUS fusion protein (1999)

Plant growth responds rapidly to developmental and environmental signals, but the underlying changes in cell division activity are poorly understood. A labile cyclin-GUS reporter was developed to facilitate the spatio-temporal analysis of cell division patterns. The chimeric reporter protein is turned over every cell cycle and hence its histochemical activity accurately reports individual mitotic cells. Using Arabidopsis plants transformed with cyclin-GUS, we visualized patterns of mitotic activity in wounded leaves which suggest a role for cell division in structural reinforcement.
Gas phase pyrolysis of heterocyclic compounds, part 3. Flow pyrolysis and annulation reactions of some nitrogen heterocycles. A product oriented study (2000)

Continuous flow pyrolysis (CFP) and annulation reactions of pyrrole (1), its benzo-annulated derivatives indole (2) and carbazole (3), pyridine (4), quinoline (5), and isoquinoline (6) have been investigated at 900 o C. While for 1, 2, 4-6 between 15 and 24 products were identified by GC-MS, 3 is rather stable under the reaction conditions and naphthalene (18) was found as the only substantial product. Except for 3, about 10 compounds were always present in the pyrolysate, benzonitrile (14) (6-24%) and naphthalene (18) (2-21%) being the most prominent products. Compounds 4-6 have even 16 common pyrolysis products. Among the major products are nitrogen heterocycles like quinoline (5) (4-13%), isoquinoline (6) (0-8%), and indole (2) (0.5-3%), cyano-substituted aromatic hydrocarbons like 14, 1-cyanonaphthalene (17) (0-16%), and 9-cycanoanthracene (19) (0-6%), as well as the corresponding unsubstituted parent compounds like 18, phenanthrene (31) (2-10%), pyrene (38) (1-5%), and fluoranthene (22) (2-8%). In addition to the volatile products, several heavy compounds were identified by direct inlet MS. Possible routes of product formation are outlined. The relative amounts of unreacted starting material clearly indicate that benzo-annulation of pyrrole and pyridine causes considerable increase of thermal stability.
A guide to the design and use of mismatched and degenerate primers. (1994)

Roche Molecular Systems, Inc., Alameda, California 94501 Although simple in concept, PCR requires a myriad of complex interactions between template, primers, deoxynucleoside triphosphates, and DNA polymerase to successfully accomplish targeted amplification. Primer design in conjunct ion with changes in the concentrat ions of reaction components and thermal cycling parameters provides a versatility available in no other molecular technique. For example, PCR can be employed to accommodate mismatches in the pr imertemplate duplex, thereby permit t ing amplification not only of related sequences but also of uncharacterized sequences. It can also be designed to amplify selectively a small number of mutan t genes with single base alterations in a vast background of normal genes. The flexibiliW of PCR has greatly simplified molecular manipulat ions. Procedures for altering a particular template sequence, which in the past required several steps, can now be performed with only a few manipulat ions. Because 3' and internal mismatches between pr imertemplate duplexes are tolerated under appropriate conditions, point mutat ions and desired restriction endonuclease sites can be directly introduced into the primers. Likewise, nucleotide insertions and deletions can be similarly introduced into the amplified product via the primers. Degenerate primers have made it possible to amplify related but distinct nucleic acid sequences as well as to amplify targets for which only amino acid sequences are available. The range of possible applications precludes providing detailed protocols for each. Instead, the delineation of the critical parameters and a guide for representative use will be summarized. Depending on the application, a subset of these recommendat ions or suggestions may suffice.
MBOC: The New Optimized Spreading Modulation Recommended for GALILEO L1 OS and GPS L1C (2006)

This paper describes the Multiplexed Binary Offset Carrier (MBOC) spreading modulation that has been recommended by the GPS-GALILEO Working Group on Interoperability and Compatibility. The MBOC(6,1,1/11) power spectral density is a mixture of BOC(1,1) spectrum and BOC(6,1) spectrum, that would be used by GALILEO for its Open Service (OS) signal at L1 frequency, and also by GPS for its modernized L1 Civil (L1C) signal. A number of different time waveforms can produce the MBOC(6,1,1/11) spectrum, allowing flexibility in implementation, although interoperable waveforms remains an objective for GALILEO and GPS. The time-multiplexed BOC (TMBOC) implementation interlaces BOC(6,1) and BOC(1,1) spreading symbols in a regular pattern, whereas composite BOC (CBOC) uses multilevel spreading symbols formed from the weighted sum of BOC(1,1) and BOC(6,1) spreading symbols, interplexed to form a constant modulus composite signal. This paper provides information on the history, motivation, and construction of MBOC signals. It then shows various performance characteristics, and summarizes their status in GALILEO and GPS signal design.
Sensitive Detection of Mono- and Polyclonal ESR1 Mutations in Primary Tumors, Metastatic Lesions, and Cell-Free DNA of Breast Cancer Patients (2015)

ESR1 mutations were detected at very low allele frequencies in some primary breast cancers, and at high allele frequency in metastases, suggesting that in some tumors rare ESR1-mutant clones are enriched by endocrine therapy. Further studies should address whether sensitive detection of ESR1 mutations in primary breast cancer and in serial blood draws may be predictive for development of resistant disease. See related commentary by Gu and Fuqua, p. 1034.
A Microdomain for Protein Secretion in Gram-Positive Bacteria (2004)

Gram-positive bacteria face unique challenges in generating biologically active conformations for their exported proteins because they lack a dedicated compartment for folding secreted polypeptides. We have discovered that protein secretion by way of the general secretory (Sec) pathway in the important human pathogen Streptococcus pyogenes proceeds through a single microdomain. Unlike other mechanisms for asymmetry involving the Sec pathway, proteins destined for secretion are targeted to a single locus distal to either cell pole that has specialized to contain the Sec translocons. This subcellular organization may represent a paradigm for secretion common to other Gram-positive pathogens with profound implications for pathogenesis.
Promoter for Sindbis virus RNA-dependent subgenomic RNA transcription (1990)

Sindbis virus is a positive-strand RNA enveloped virus, a member of the Alphavirus genus of the Togaviridae family. Two species of mRNA are synthesized in cells infected with Sindbis virus; one, the 49S RNA, is the genomic RNA; the other, the 26S RNA, is a subgenomic RNA that is identical in sequence to the 3' one-third of the genomic RNA. Ou et al. (J.-H. Ou, C. M. Rice, L. Dalgarno, E. G. Strauss, and J. H. Strauss, Proc. Natl. Acad. Sci. USA 79:5235-5239, 1982) identified a highly conserved region 19 nucleotides upstream and 2 nucleotides downstream from the start of the 26S RNA and proposed that in the negative-strand template, these nucleotides compose the promoter for directing the synthesis of the subgenomic RNA. Defective interfering (DI) RNAs of Sindbis virus were used to test this proposal. A 227-nucleotide sequence encompassing 98 nucleotides upstream and 117 nucleotides downstream from the start site of the Sindbis virus subgenomic RNA was inserted into a DI genome. The DI RNA containing the insert was replicated and packaged in the presence of helper virus, and cells infected with these DI particles produced a subgenomic RNA of the size and sequence expected if the promoter was functional. The initiating nucleotide was identical to that used for Sindbis virus subgenomic mRNA synthesis. Deletion analysis showed that the minimal region required to detect transcription of a subgenomic RNA from the negative-strand template of a DI RNA was 18 or 19 nucleotides upstream and 5 nucleotides downstream from the start of the subgenomic RNA.
Relationship between the levels of cyclic cytidine 3':5'-monophosphate, cyclic guanosine 3':5'-monophosphate, and cyclic adenosine 3':5'-monophosphate in urines and leukocytes and the type of human leukemias. (1981)

Cyclic cytidine 3':5'-monophosphate (cyclic CMP), cyclic guanosine 3':5'-monophosphate (cyclic GMP), and cyclic adenosine 3':5'-monophosphate (cyclic AMP) contents of leukocytes and urines of leukemic patients have been investigated. We have studied four types of leukemia: acute myeloblastic leukemia; chronic myelocytic leukemia; acute lymphoblastic leukemia; and chronic lymphocytic leukemia. As controls, the cyclic nucleotide content of leukocytes and urines of healthy volunteers and patients with solid tumors selected for their normal hemogram has been determined. It has also been measured in phytohemagglutinin-stimulated lymphocytes. Our data show that: (a) the concentration of cyclic CMP is always lower than that of cyclic GMP or cyclic AMP; (b) in urines, the concentrations of the three nucleotides are higher in patients than in healthy volunteers, the greatest differences being observed between the cyclic CMP concentrations of acute leukemia patients and controls; and (c) in white blood cells, cyclic AMP concentration is lower in leukemic than in normal cells. The cyclic GMP concentration is the same everywhere except in monoblastic cells and leukocytes from solid tumor patients. High cyclic CMP levels are associated only with acute leukemia, whether myeloblastic, monoblastic, or lymphoblastic, a fact which suggests that cyclic CMP could be a biochemical marker of hematopoietic stem cell malignancy.
Assembly of DNA polymerase 6 and e holoenzymes depends on the geometry of the DNA template (1994)

To study in details the assembly of DNA polymerases delta and epsilon holoenzymes a circular double-stranded DNA template containing a gap of 45 nucleotides was constructed. Both replication factor C and proliferating cell nuclear antigen were absolutely required and sufficient for assembly of DNA polymerase delta holoenzyme complex on DNA. On such a circular DNA substrate replication protein A (or E. coli single-strand DNA binding protein) was neither required for assembly of DNA polymerase delta holoenzyme complex nor for the gap-filling reaction. A circular structure of the DNA substrate was found to be absolutely critical for the ability of auxiliary proteins to interact with DNA polymerases. The linearization of the circular DNA template resulted in three dramatic effects: (i) DNA synthesis by DNA polymerase delta holoenzyme was abolished, (ii) the inhibition effect of replication factor C and proliferating cell nuclear antigen on DNA polymerase alpha was relieved and (iii) DNA polymerase epsilon could not form any longer a holoenzyme with replication factor C and proliferating cell nuclear antigen. The comparison of the effect of replication factor C and proliferating cell nuclear antigen on DNA polymerases alpha, delta and epsilon indicated that the auxiliary proteins appear to form a mobile clamp, which can easily slide along double-stranded DNA.
The Possible Importance of Silicon in Marine Eutrophication (1980)

Diatom phytoplankton populations are the usual food for zooplankton and filter feeding fishes and contribute in a direct way to the large fishable populations in coastal zones.Flagellates, on the other hand, are frequently poor foods for most grazers and can lead to undesirable eutrophication effects.Arguments are presented that silicon is often the controlling nutrient in altering a diatom to a flagellate community.The alteration is governed by the relative magnitudes of the natural fluxes of the nutrients nitrogen, phosphorus and silicon to the receiving water body and the recycled fluxes of nitrogen and phosphorus from zooplankton grazing and phytoplankton respiration and decomposition.Examples of such alterations are presented for oceanic, estuarine and inland water bodies.
Modulation of Splicing in theDMDGene by Antisense Oligoribonucleotides (1997)

Abstract Splicing of the DMD gene pre-mRNA is being examined as a model system to study the skipping of mutant exons, especially where disrupted translational reading frames are restored. Naturally-occurring examples and induced exon skipping by specific synthetic RNA oligonucleotides are under investigation.
Measurement of Peptide‐MHC Interactions in Solution Using the Spin Column Filtration Assay (1999)

This unit describes how peptide-MHC complexes can be generated in vitro using affinity-purified MHC and synthetic peptide. The unit first describes how the interaction between peptide and MHC interaction can be measured in an accurate, quantitative biochemical assay. This procedure has been optimized for efficient separation of free peptide and MHC-bound peptide through a novel principle, termed "gradient centrifugation." The first two support protocols describe how to set up a biochemical fluid-phase binding reaction between peptide and MHC class I and class II, respectively. Also, an alternative procedure for setting up a biochemical fluid phase binding reaction between beta(2)m and MHC class I is included. Finally a more versatile inhibition assay is described. The assay is simple and robust, and has several advantages compared to the classical gel-filtration assay, including increased sensitivity and throughput. It also demands fewer resources both in terms of unique reagents and labor, and it generates less hazardous waste. Thus, the spin column gel-filtration assay is ideal for routine work.
Protein fortification of cheese milk using milk protein concentrate--yield improvement and product quality. (2006)

Spray dried milk protein concentrate (MPC) was used to fortify milk protein at two levels, 4.56 and 6.48%, for cheddar cheesemaking, one level, 5.38%, for mozzarella, and one level, 5.42%, for fetta cheesemaking. Protein retention and cheese yield are increased for fortified vats relative to control vats. The cheddar made with 4.56% protein milk and the mozzarella and fetta show no defect in sensory characteristics when comparing fortified vats to control vats. Fat retention was lower with the cheddar made from the higher protein milk (6.48%) with subsequent adverse effects on the texture.
The many faces of ubiquitinated histone H2A: insights from the DUBs (2008)

Abstract Monoubiquitination of H2A is a major histone modification in mammalian cells. Understanding how monoubiquitinated H2A (uH2A) regulates DNA-based processes in the context of chromatin is a challenging question. Work in the past years linked uH2A to transcriptional repression by the Polycomb group proteins of developmental regulators. Recently, a number of mammalian deubiquitinating enzymes (DUBs) that catalyze the removal of ubiquitin from H2A have been discovered. These studies provide convincing evidence that H2A deubiquitination is connected with gene activation. In addition, uH2A regulatory enzymes have crucial roles in the cellular response to DNA damage and in cell cycle progression. In this review we will discuss new insights into uH2A biology, with emphasis on the H2A DUBs.