gebhart/patrepeval huggingface dataset:
Mouse IgA heavy chain gene sequence: implications for evolution of immunoglobulin hinge axons. (1981)

The complete nucleotide sequence of the gene and mRNA coding for the constant (C) region of the secreted form of the BALB/c mouse IgA immunoglobulin alpha heavy (H) chain has been determined. As in other immunoglobulins, the three C region domains of the alpha protein, C alpha 1, C alpha 2, and C alpha 3 are coded in separate exons. However, the hinge region of C alpha is not coded on a separate exon as it is in other hinge-containing immunoglobulins. Instead, the alpha hinge is coded as a 5' extension of the C alpha 2 exon, and we suggest that it may have evolved by duplication leading to incorporation of an acceptor RNA splice site into the coding portion of the C alpha 2 exon. Extensions of this concept could provide an explanation for duplications in the human alpha 1 chain.
The Relation between the Minor Components of Whole Normal Human Adult Hemoglobin as Isolated by Chromatography and Starch Block Electrophoresis (1961)

Three hemoglobin components may be separated from hemolysates of normal adult red blood cells by starch block electrophoresis: the main component, A_1, moves at a position intermediate between the most slowly moving component, A_2, and the most rapidly moving component, A_3. By chromatography, eight hemoglobin components may be detected: five (A_(Ia), A_(Ib), A_(Ic), A_(Id) and A_(Ie)) move down the column more rapidly than the main component (An) and two move more slowly&#13;\n(Ania and Amb). Non-heme containing proteins are also present. The present investigation has determined the correspondence&#13;\nbetween the components as isolated by the two methods: A_I contains A_I(c), A_(Id) and A_(Ie), and A_(II); A_2 contains&#13;\nA_(IIIb) and non-heme protein(s); A_3 contains A_(Ia), A(Ib) and non-heme protein(s).
Sustained correction of B-cell development and function in a murine model of X-linked agammaglobulinemia (XLA) using retroviral-mediated gene transfer (2004)

X-linked agammaglobulinemia (XLA) is a human immunodeficiency caused by mutations in Bruton tyrosine kinase (Btk) and characterized by an arrest in early B-cell development, near absence of serum immunoglobulin, and recurrent bacterial infections. Using Btk- and Tec-deficient mice (BtkTec(-/-)) as a model for XLA, we determined if Btk gene therapy could correct this disorder. Bone marrow (BM) from 5-fluorouracil (5FU)-treated BtkTec(-/-) mice was transduced with a retroviral vector expressing human Btk and transplanted into BtkTec(-/-) recipients. Mice engrafted with transduced hematopoietic cells exhibited rescue of both primary and peripheral B-lineage development, recovery of peritoneal B1 B cells, and correction of serum immunoglobulin M (IgM) and IgG(3) levels. Gene transfer also restored T-independent type II immune responses, and B-cell antigen receptor (BCR) proliferative responses. B-cell progenitors derived from Btk-transduced stem cells exhibited higher levels of Btk expression than non-B cells; and marking studies demonstrated a selective advantage for Btk-transduced B-lineage cells. BM derived from primary recipients also rescued Btk-dependent function in secondary hosts that had received a transplant. Together, these data demonstrate that gene transfer into hematopoietic stem cells can reconstitute Btk-dependent B-cell development and function in vivo, and strongly support the feasibility of pursuing Btk gene transfer for XLA.
THE myc ONCOGENE: ITS ROLE IN TRANSFORMATION AND DIFFERENTIATION (1986)

We have made rapid progress in recent years in identifying the genetic causes of many human diseases. However, despite this recent progress, our mechanistic understanding of these diseases is often incomplete. This is a problem because it limits our ...Read More
A Baculovirus (Bombyx mori Nuclear Polyhedrosis Virus) Repeat Element Functions as a Powerful Constitutive Enhancer in Transfected Insect Cells (1997)

It has been previously reported that baculovirus homologous regions, the regions of baculovirus genomes that contain the origins of DNA replication, can augment the expression of a small number of baculovirus genes in vitro. We are now reporting that a region of the genome of Bombyx mori nuclear polyhedrosis virus (BmNPV) containing the homologous region 3 (HR3) acts as an enhancer for the promoter of a nonviral gene, the cytoplasmic actin gene of the silkmoth B. mori. Incorporation of the HR3 sequences of BmNPV into an actin promoter-based expression cassette results in an augmentation of transgene expression in transfected cells by two orders of magnitude relative to the control recombinant expression cassette. This increase is due to a corresponding increase in the rate of transcription from the actin promoter and not to replication of the expression cassette and occurs only when the HR3 element is linked to the expression cassette in cis. A comparable degree of enhancement in the activity of the silkworm actin promoter occurs also in heterologous lepidopteran cells. Concomitant supplementation of transfected cells with the BmIE1 trans-activator, which was previously shown to be capable of functioning in vitro as a transcriptional co-activator of the cytoplasmic actin gene promoter, results in more than a 1,000-fold increase in the level of expression of recombinant proteins placed under the control of the actin gene promoter. These findings provide the foundation for the development of a nonlytic insect cell expression system for continuous high-level expression of recombinant proteins. Such a system should provide levels of expression of recombinant proteins comparable to those obtained from baculovirus expression systems and should also have the additional advantage of continuous production in a cellular environment that, in contrast to that generated by a baculovirus infection, supports continuously proper posttranslational modifications of recombinant proteins and the capability of expression of proteins from genomic as well as cDNA sequences.
Protein Identification with a Single Accurate Mass of a Cysteine-Containing Peptide and Constrained Database Searching (2000)

A method for rapid and unambiguous identification of proteins by sequence database searching using the accurate mass of a single peptide and specific sequence constraints is described. Peptide masses were measured using electrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry to an accuracy of 1 ppm. The presence of a cysteine residue within a peptide sequence was used as a database searching constraint to reduce the number of potential database hits. Cysteine-containing peptides were detected within a mixture of peptides by incorporating chlorine into a general alkylating reagent specific for cysteine residues. Secondary search constraints included the specificity of the protease used for protein digestion and the molecular mass of the protein estimated by gel electrophoresis. The natural isotopic distribution of chlorine encoded the cysteine-containing peptide with a distinctive isotopic pattern that allowed automatic screening of mass spectra. The method is demonstrated for a peptide standard and unknown proteins from a yeast lysate using all 6118 possible yeast open reading frames as a database. As judged by calculation of codon bias, low-abundance proteins were identified from the yeast lysate using this new method but not by traditional methods such as tandem mass spectrometry via data-dependent acquisition or mass mapping.
Carboxyl-terminal Domains in the Avian β1-Adrenergic Receptor That Regulate Agonist-promoted Endocytosis (1995)

Most G protein-coupled receptors, including the mammalian beta 2-adrenergic receptor, are endocytosed to an intracellular, vesicular compartment upon continued exposure to agonist. The long form of the avian beta 1-adrenergic receptor, which contains a carboxyl-terminal 59-amino acid extension, does not undergo agonist-promoted endocytosis. We constructed and expressed turkey beta 1-adrenergic receptor cDNAs with regularly spaced carboxyl-terminal truncations and studied their agonist-promoted endocytosis. Removal of 34-86 amino acids from the carboxyl terminus of the turkey receptor allowed its efficient endocytosis, with optimal endocytosis observed upon removal of 59 residues. Removal of only 18 residues allowed some endocytosis. A receptor that lacks the entire carboxyl-terminal region (124 residues) was not endocytosed. We also constructed a chimeric hamster beta 2-adrenergic receptor with the added 59-residue carboxyl-terminal domain of the turkey receptor. The chimera was not significantly endocytosed. These data indicate that residues 450-465 in the carboxyl-terminal region of the beta 1-adrenergic receptor can act independently to block agonist-promoted endocytosis and that other carboxyl-terminal structures nearer to the seventh membrane span are required for endocytosis.
Synthesis, Structure, and Photochemistry of Exceptionally Stable Synthetic DNA Hairpins with Stilbene Diether Linkers (2002)

The structure and properties of 18 hairpin-forming bis(oligonucleotide) conjugates possessing stilbene diether linkers are reported. Conjugates possessing bis(2-hydroxyethyl)stilbene 4,4'-diether linkers form the most stable DNA hairpins reported to date. Hairpins with as few as two T:A base pairs or four noncanonical G:G base pairs are stable at room temperature. Increasing the length of the hydroxyalkyl groups results in a decrease in hairpin thermal stability. On the basis of the investigation of their circular dichroism spectra, all of the hairpins investigated adopt B-DNA structures, except for a hairpin with a short poly(G:C) stem which forms a Z-DNA structure. Both the strong fluorescence of the stilbene diether linkers and their trans-cis photoisomerization are totally quenched in hairpins possessing neighboring T:A and G:C base pairs. Quenching is attributed to an electron-transfer mechanism in which the singlet stilbene serves as an electron donor and T or C serves as an electron acceptor. In contrast, in denatured hairpins and hairpins possessing neighboring G:G base pairs the stilbene diether linkers undergo efficient photoisomerization.
The Effect of Low Molecular Weight Heparin on Survival in Patients With Advanced Malignancy (2005)

A brief course of subcutaneous low molecular weight heparin favorably influences the survival in patients with advanced malignancy and deserves additional clinical evaluation.
The treatment targets in acute decompensated heart failure. (2001)

Acute decompensated heart failure is characterized by hemodynamic abnormalities as well as neuroendocrine activation, which contribute to heart failure symptoms, progressive cardiac dysfunction, and sudden death. The therapeutic goals in patients hospitalized with decompensated heart failure are to reverse acute hemodynamic abnormalities, relieve symptoms, and initiate treatment that will slow disease progression and improve long-term survival. Traditional hemodynamic targets in acute heart failure have been reduction in left and right ventricular filling pressures, reduction in systemic vascular resistance, and increase in cardiac output. Treatments aimed at these targets in patients with acute decompensated heart failure include diuretics, vasodilators, and inotropic agents. In patients hospitalized with acute decompensated heart failure, persistently elevated left ventricular filling pressure has been shown to be highly predictive of an increased risk of fatal decompensation and sudden death. Measures of systemic perfusion, arterial pressure, and vascular resistance have not. Thus, there is a more compelling physiologic rationale for the use of vasodilators than for inotropic agents in these patients. An ideal agent for acute decompensated heart failure would be one that rapidly reduces pulmonary wedge pressure, results in balanced arterial and venous dilation, promotes natriuresis, lacks direct positive inotropic effects, and does not result in reflex neuroendocrine activation.
Autosomal dominant inheritance of early-onset breast cancer. Implications for risk prediction (1994)

These tables can be used for the purpose of counseling women at high risk of breast cancer development, that is, women with a family history of breast cancer.
Mechanical Stress-Induced Apoptosis of Endplate Chondrocytes in Organ-Cultured Mouse Intervertebral Discs (2003)

Chondrocyte apoptosis was induced using a static mechanical load especially in the cartilaginous endplate in an organ culture. Apoptosis occurred similarly to previous findings using an in vivo model. This culture system thus reflected the apoptosis demonstrated in vivo. Because biologically active reagents such as MAPK inhibitors can be simply added to culture media, this system may be a useful method for detecting factors that influence apoptosis induced by mechanical stress. Both MAPK inhibitors increased the occurrence of apoptosis. This suggests that these two MAPKs can counteract the apoptotic pathway induced by mechanical stress.
Synthesis of S-Methyl-L-cysteine (2003)

S Methyl L cysteine was synthesized with L cysteine as the starting material and trimethyl phosphate as the methylating agent. The influence of temperature and pH value on the yield and quality of product was studied. The result showed that racemization was not observed when the pH value was 7 and the reaction temperature was lower than 37°C. This method is suitable for large scale production.
UV‐B radiation microphototherapy. An elective treatment for segmental vitiligo (1999)

UV-B microphototherapy seems highly effective in restoring pigmentation in patients affected by vitiligo. As no side-effects have been observed, this could represent the treatment of choice in the limited (segmental) forms of vitiligo.
Anaerobic Hydrocarbon Degradation in Petroleum-Contaminated Harbor Sediments under Sulfate-Reducing and Artificially Imposed Iron-Reducing Conditions (1996)

The potential use of iron(III) oxide to stimulate in-situ hydrocarbon degradation in anaerobic petroleum-contaminated harbor sediments was investigated. Previous studies have indicated that Fe(III)-reducing bacteria (FeRB) can oxidize some electron donors more effectively than sulfate-reducing bacteria (SRB). In contrast to previous results in freshwater sediments, the addition of Fe(III) to marine sediments from San Diego Bay, CA did not switch the terminal electron-accepting process (TEAP) from sulfate reduction to Fe(III) reduction. Addition of Fe(III) also did not stimulate anaerobic hydrocarbon oxidation. Exposure of the sediment to air [to reoxidize Fe(II) to Fe(III)] followed by anaerobic incubation of the sediments, resulted in Fe(III) reduction as the TEAP, but contaminant degradation was not stimulated and in some instances was inhibited. The difference in the ability of FeRB to compete with the SRB in the different sediment treatments was related to relative population sizes. Although the addition of Fe(III) did not stimulate hydrocarbon degradation, the results presented here as well as other recent studies demonstrate that there may be significant anaerobic hydrocarbon degradation under sulfate-reducing conditions in harbor sediments.
Characterization of the human cell line TE671 (1989)

The cell line TE671 has been widely used as a model of human medulloblastoma. In the present study we have demonstrated that transfection of DNA from this cell line into NIH 3T3 cells reveals the presence of an activated N-ras gene. Using oligonucleotide probes we have shown that the N-ras gene is activated by a point mutation at the third base of codon 61 resulting in the substitution of histidine for glutamine in the p21 ras gene product. We noted that this relatively uncommon activating mutation is also present in the human rhabdomyosarcoma cell line RD. Based on this finding and on the observation that several of the phenotypic characteristics of TE671, such as the presence of muscle-type nicotinic acetylcholine receptors and the intermediate filament protein desmin, are suggestive of myoid origin we investigated the possible identity of these two cell lines. Cytogenetic analysis revealed the presence of marker chromosomes common to both TE671 and RD. DNA fingerprinting using both locus specific and multilocus core probes showed indistinguishable band patterns in the two cell lines. Taken together our data show that TE671 and RD are derivatives of the same cell line and we conclude that the properties of the TE671 line should be ascribed to rhabdomyosarcoma rather than medulloblastoma cells.
Low-Energy (3−24 eV) Electron Damage to the Peptide Backbone (2007)

We report the mass spectrometric measurement of anions desorbed by 3-24 eV electron impact on thin films of formamide-1-d (DCONH2) and on the self-assembled monolayer (SAM) of two different Lys amide molecules used as a molecular model of the peptide backbone. In the present SAM configuration, the amides are elevated from a gold substrate by hydrocarbon chains to remove the effects of the metal substrate. Electron irradiation produces H- and D- from the formamide-1-d film and H-, CH3-, O-, and OH- from the SAM Lys amides. Below 13 eV, the dependence of the anion yields on the incident electron energy exhibits structures indicative of the dissociative electron attachment process, which is responsible for molecular fragmentation via the initial formation of core-excited anions. Above 13 eV, anion desorption is dominated principally by non-resonant dipolar dissociation. Our results suggest that the sensitivity of the peptide backbone to secondary electrons produced by ionizing radiation depends on the chemical environment (i.e., the amino acids sequence).
The ChemFinder WebServer: Indexing Chemical Data on the Internet (1998)

The Internet offers a wealth of data on all topics, but chemical information provides unique challenges for searching. General-purpose indexing techniques are summarized, with a discussion of why those techniques are unsuited for use with chemical data. The ChemFinder WebServer, a WWW-based chemical index, addresses some of the weaknesses in nonchemical search engines.
One-Dimensional Metal−Organic Framework with Unprecedented Heptanuclear Copper Units (2006)

The reaction of copper(II) sulfate, copper(II) chloride, 3,5-diacetylamino-1,2,4-triazole, and 3-acetylamino-5-amino-1,2,4-triazole in water yields green, plate-shaped crystals of [[{Cu3(mu3-OH(1/2))L(H2O)2Cl}2{mu-Cu(H2O)2Cl2}].12H2O]n (1), where L is a new triazole-derived macrocyclic ligand. The structure of 1 consists of heptanuclear (H)OCuII(3)-CuII-CuII(3)O(H) entities linked in pairs through symmetric mu3-O...H...O-mu3 hydrogen bonds to form a double-stranded one-dimensional network. A significant overall antiferromagnetic behavior has been observed for 1.
Comparison of CyTOF assays across sites: Results of a six-center pilot study (2017)

For more than five years, high-dimensional mass cytometry has been employed to study immunology. However, these studies have typically been performed in one laboratory on one or few instruments. We present the results of a six-center study using healthy control human peripheral blood mononuclear cells (PBMCs) and commercially available reagents to test the intra-site and inter-site variation of mass cytometers and operators. We used prestained controls generated by the primary center as a reference to compare against samples stained at each individual center. Data were analyzed at the primary center, including investigating the effects of two normalization methods. All six sites performed similarly, with CVs for both Frequency of Parent and median signal intensity (MSI) values<30%. Increased background was seen when using the premixed antibody cocktail aliquots at each site, suggesting that cocktails are best made fresh. Both normalization methods tested performed adequately for normalizing MSI values between centers. Clustering algorithms revealed slight differences between the prestained and the sites-stained samples, due mostly to the increased background of a few antibodies. Therefore, we believe that multicenter mass cytometry assays are feasible.
Targeted disruption of gene function in Drosophila by RNA interference (RNA-i): A role for nautilus in embryonic somatic muscle formation (1999)

The expression of the MyoD gene homolog, nautilus (nau), in the Drosophila embryo defines a subset of mesodermal cells known as the muscle "pioneer" or "founder" cells. These cells are thought to establish the future muscle pattern in each hemisegment. Founders appear to recruit fusion-competent mesodermal cells to establish a particular muscle fiber type. In support of this concept every somatic muscle in the embryo is associated with one or more nautilus-positive cells. However, because of the lack of known (isolated) nautilus mutations, no direct test of the founder cell hypothesis has been possible. We now have utilized toxin ablation and genetic interference by double-stranded RNA (RNA interference or RNA-i) to determine both the role of the nautilus-expressing cells and the nautilus gene, respectively, in embryonic muscle formation. In the absence of nautilus-expressing cells muscle formation is severely disrupted or absent. A similar phenotype is observed with the elimination of the nautilus gene product by genetic interference upon injection of nautilus double-stranded RNA. These results define a crucial role for nautilus in embryonic muscle formation. The application of RNA interference to a variety of known Drosophila mutations as controls gave phenotypes essentially indistinguishable from the original mutation. RNA-i provides a powerful approach for the targeted disruption of a given genetic function in Drosophila.
Overexpression of Mdm2 in mice reveals a p53-independent role for Mdm2 in tumorigenesis (1998)

The Mdm2 proto-oncogene is amplified to high copy numbers in human sarcomas and is overexpressed in a wide variety of other human cancers. Because Mdm2 protein forms a complex with the p53 tumor suppressor protein and down-regulates p53 function, the oncogenic potential of Mdm2 is presumed to be p53-dependent. To model these conditions in mice, we have used the entire Mdm2 gene, under transcriptional control of its native promoter region, as a transgene to create mice that overexpress Mdm2. The transgenic mice are predisposed to spontaneous tumor formation, and the incidence of sarcomas observed in the Mdm2-transgenic mice in the presence or absence of functional p53 demonstrates that, in addition to Mdm2-mediated inactivation of p53, there exists a p53-independent role for Mdm2 in tumorigenesis.
High-Oleate Oilseeds Fail to Develop at Low Temperature (1994)

The fad2 mutants of Arabidopsis thaliana are deficient in activity of the endoplasmic reticulum oleate desaturase that is the main enzyme responsible for polyunsaturated lipid synthesis in developing seeds of oil crops. A comparison of wild-type and fad2 seeds developing on heterozygous (FAD2/-) plants was used as a model for genetically engineered high-oleate oilseeds of species such as soybean and canola. When fad2 seeds developed at normal temperatures (22[deg]C), they showed high viability compared to wild-type seeds. When a portion of seed development took place at 6[deg]C, germination of the wild-type siblings remained high but germination of fad2 segregants declined considerably. This was true even when exposure to low temperature was limited to the final stages of seed filling and maturation. Compared to wild-type seeds, fully viable fad2 seeds produced at 22[deg]C had reduced lipid contents and were slower to germinate at 10 and 6[deg]C. Taken together, these results indicate that for some oilseed species at least, molecular genetic manipulation of oleate levels in the oil may result in plant lines with unacceptable performance in the field.