gebhart/patrepeval huggingface dataset:
Cloning of a carcinoembryonic antigen gene family member expressed in leukocytes of chronic myeloid leukemia patients and bone marrow. (1990)

The carcinoembryonic antigen (CEA) gene family belongs to the immunoglobulin superfamily and can be subdivided into the CEA and pregnancy-specific glycoprotein subgroups. The basic structure of the encoded proteins consists of, in addition to a leader, one IgV-like and 2, 3, or 6 IgC-like domains. These domains are followed by varying COOH-terminal regions responsible for secretion, transmembrane anchoring, or insertion into the membrane by a glycosyl phosphatidylinositol tail. Here we report on the characterization of CGM6, a new member of the CEA gene subgroup, by complementary DNA cloning. The deduced coding region comprises 349 amino acids and consists of a leader, one IgV-like, two IgC-like domains, and a hydrophobic region, which is replaced by a glycosyl phosphatidylinositol moiety in the mature protein. CGM6 transcripts were only found thus far in leukocytes of chronic myeloid leukemia patients, in normal bone marrow, and in marginal amounts in normal granulocytes. The CGM6 gene product might, therefore, represent a myeloid marker. Analyses of CGM6 protein-expressing HeLa transfectants with monoclonal antibodies strongly indicate that the CGM6 gene codes for the CEA family member NCA-95.
Correlations between apolipoprotein E ε4 gene dose and brain-imaging measurements of regional hypometabolism (2005)

Patients with Alzheimer's disease (AD) have abnormally low positron emission tomography (PET) measurements of the cerebral metabolic rate for glucose (CMRgl) in regions of the precuneus and the posterior cingulate, parietotemporal, and frontal cortex. Apolipoprotein E (APOE) epsilon4 gene dose (i.e., the number of epsilon4 alleles in a person's APOE genotype) is associated with a higher risk of AD and a younger age at dementia onset. We previously found that cognitively normal late-middle-aged APOE epsilon4 carriers have abnormally low CMRgl in the same brain regions as patients with probable Alzheimer's dementia. In a PET study of 160 cognitively normal subjects 47-68 years of age, including 36 epsilon4 homozygotes, 46 heterozygotes, and 78 epsilon4 noncarriers who were individually matched for their gender, age, and educational level, we now find that epsilon4 gene dose is correlated with lower CMRgl in each of these brain regions. This study raises the possibility of using PET as a quantitative presymptomatic endophenotype to help evaluate the individual and aggregate effects of putative genetic and nongenetic modifiers of AD risk.
Genetic engineering of streptavidin, a versatile affinity tag (1998)

Streptavidin, a tetrameric protein produced by Streptomyces avidinii, has been used as a useful, versatile affinity tag in a variety of biological applications. The efficacy of streptavidin is derived from its extremely high binding affinity for the vitamin biotin. For the last several years, we have used genetic engineering as a primary means to enhance the properties of streptavidin and to expand the application of streptavidin as an affinity tag. In this review, we describe several genetically engineered streptavidin variants, which include a streptavidin with a reduced biotin-binding affinity, a dimeric streptavidin, and a fusion protein between streptavidin and protein A, along with their potential applications in biological science.
Additional Transduction Events after Subretinal Readministration of Recombinant Adeno-Associated Virus (2000)

Subretinal delivery of recombinant adeno-associated virus (rAAV) results in a systemic humoral response in the adult immunocompetent mouse. We characterized this response and determined whether it is possible to readminister rAAV to the subretinal space despite the presence of antibodies to the vector. A systemic humoral response to rAAV capsid proteins was induced by either unilateral subretinal injection or by intradermal administration of 1 x 10(9) infectious units of rAAV carrying the cDNA encoding green fluorescent protein (GFP), rAAV-GFP. Experiments were performed in cohorts of adult C57BL/6 mice. Assessment of systemic humoral response to viral capsid protein was performed through enzyme-linked immunoabsorbent assay (ELISA) and infection inhibition studies of serum samples 3 weeks after virus delivery. The rAAV-GFP virus was readministered by subretinal injection. GFP expression after subretinal administration was evaluated ophthalmoscopically throughout the course of the experiment and histologically at the termination of the experiment. We observed significant systemic humoral responses to viral capsid protein after subretinal delivery of rAAV. Intradermal injection resulted in a larger humoral response (with a higher percentage of neutralizing antibodies) than subretinal injection. Additional transduction events were observed after readministration of rAAV despite the presence of strong humoral response to the vector.
Nonhematopoietic tumor cell lines express stem cell factor and display c-kit receptors (1992)

Abstract Human stem cell factor (SCF) acts in the presence of other growth factors to stimulate the growth of primitive hematopoietic progenitor cells. These effects are performed by activation of the SCF receptor, c- kit. Because of the potential use of SCF in patients undergoing chemotherapy and bone marrow transplantation, the effect of SCF on nonhematopoietic tumors requires investigation. To determine whether human tumor cell lines display c-kit receptors, we performed binding experiments with 125I-SCF on a breast carcinoma cell line (Du4475), a gastric carcinoma cell line (KATO III), a melanoma cell line (HTT144), as well as two small cell lung carcinoma cell lines (H69 and H128). The biologic effect of SCF on tumor cell lines was assessed by its ability to stimulate tritiated thymidine uptake and to enhance colony growth in methylcellulose. The breast carcinoma cell line, Du4475, as well as two small cell lung carcinoma cell lines, H69 and H128, exhibit high- affinity c-kit receptors with approximate binding affinities of 40, 100, and 90 pmol/L, respectively. The number of high-affinity receptors per cell ranged from 700 to 9,500. The gastric carcinoma cell line, as well as the melanoma cell line, showed trace binding of 125I-SCF. In the presence of SCF alone, or in combination with granulocyte- macrophage colony-stimulating factor or interleukin-3, there was less than a 17% increase in the colony growth of Du4475, H69, or H128 cell lines. Postulating that the lack of growth response could be secondary to endogenous SCF production by the tumor cell lines, we used an RNAse protection assay to determine whether the tumor cell lines contain SCF messenger RNA (mRNA). In addition, we tested tumor cell line supernatants for the presence of secreted SCF protein by enzyme immunoassay, and analyzed the tumor cell lines for membrane-bound SCF by indirect immunofluorescence. Our results show that the Du4475, H69, and H128 cell lines, as well as a melanoma cell line (HTT144), have multiple copies of SCF mRNA. Soluble SCF protein was detected in the cell supernatants in the Du4475 and H69 cell lines and SCF was found on the surface of all four cell lines. These data show that some human solid tumor cell lines display high-affinity c-kit receptors and produce SCF, which can be detected on the cell surface. These results suggest the possibility that autocrine production of SCF by c-kit receptor-bearing tumor cells may enhance cell growth in tumor cell lines.
Light-sensitive glycosides. I. 6-Nitroveratryl .beta.-D-glucopyranoside and 2-nitrobenzyl .beta.-D-glucopyranoside (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLight-sensitive glycosides. I. 6-Nitroveratryl .beta.-D-glucopyranoside and 2-nitrobenzyl .beta.-D-glucopyranosideUri Zehavi, Boaz Amit, and Abraham PatchornikCite this: J. Org. Chem. 1972, 37, 14, 2281–2285Publication Date (Print):July 1, 1972Publication History Published online1 May 2002Published inissue 1 July 1972https://pubs.acs.org/doi/10.1021/jo00979a016https://doi.org/10.1021/jo00979a016research-articleACS PublicationsRequest reuse permissionsArticle Views809Altmetric-Citations67LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Regnase-1 Is an Endoribonuclease Essential for the Maintenance of Immune Homeostasis (2017)

Regnase-1, also known as Zc3h12a or MCPIP1, is responsible for endonucleolytic cleavage of mRNAs encoding proteins involved in inflammatory responses. Furthermore, Regnase-1-mediated mRNA decay (RMD) is critical for the maintenance of immune homeostasis. Regnase-1 controls the magnitude of innate and adaptive immune responses, and thereby dysfunction of this protein in mice leads to the development of spontaneous systemic inflammation. During the last several years, advances have been made in understanding molecular mechanisms of RMD. In this article, unique functions of Regnase-1 in controlling inflammation are discussed.
Non-invasive amino acid turnover predicts human embryo developmental capacity (2002)

Non-invasive amino acid profiling has the potential to select developmentally competent single embryos for transfer, thereby increasing the success rate and eliminating multiple births in IVF.
Inherited bone marrow failure syndromes: considerations pre- and posttransplant (2017)

Patients with inherited bone marrow failure syndromes are usually identified when they develop hematologic complications such as severe bone marrow failure, myelodysplastic syndrome, or acute myeloid leukemia. They often have specific birth defects or other physical abnormalities that suggest a syndrome, and sequencing of specific genes or next-generation sequencing can determine or confirm the particular syndrome. The 4 most frequent syndromes are Fanconi anemia, dyskeratosis congenita, Diamond Blackfan anemia, and Shwachman Diamond syndrome. This review discusses the major complications that develop as the patients with these syndromes age, as well as additional late effects following hematopoietic stem cell transplantation. The most common complications are iron overload in transfused patients and syndrome-specific malignancies in untransplanted patients, which may occur earlier and with higher risks in those who have received transplants.
ChemInform Abstract: Synthesis via Vinyl Sulfones. Part 38. Total Synthesis of the Cephalotaxus Alkaloids dl‐Cephalotaxine, dl‐11‐Hydroxycephalotaxine, and dl‐Drupacine. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
<title>Navigation studies utilizing the NRL-801 experiment and the ARGOS satellite</title> (1993)

The NRL-801 (USA) experiment and other systems on the ARGOS (P91-1) satellite to be launched in 1995 can be used as a testbed for satellite navigational techniques, to explore unconventional means of measuring a satellite's position, velocity, acceleration, attitude and the local time. One way this is done is with measurements made using x-ray sensors. Parameters can be estimated onboard and verified through redundant determinations. The ARGOS satellite is being built under the Air Force Space Test Program. It carries eight experiments, three of which utilize far-ultraviolet (FUV) or extreme-ultraviolet (EUV) sensors and one of which (NRL-801) is an x-ray sensor. Among the ARGOS experiments NRL-801 uniquely has satellite navigation experiments as one of its prime objectives, with special design features supporting that purpose.
Increased coronary heart disease in Japanese-American men with mutation in the cholesteryl ester transfer protein gene despite increased HDL levels. (1996)

Plasma high density lipoprotein (HDL) levels are strongly genetically determined and show a general inverse relationship with coronary heart disease (CHD). The cholesteryl ester transfer protein (CETP) mediates the transfer of cholesteryl esters from HDL to other lipoproteins and is a key participant in the reverse transport of cholesterol from the periphery to the liver. A high prevalence of two different CETP gene mutations (D442G, 5.1%; intron 14G:A, 0.5%), was found in 3,469 men of Japanese ancestry in the Honolulu Heart Program and mutations were associated with decreased CETP (-35%) and increased HDL chol levels (+10% for D442G). However, the overall prevalence of definite CHD was 21% in men with mutations and 16% in men without mutations. The relative risk (RR) of CHD was 1.43 in men with mutations (P < .05); after adjustment for CHD risk factors, the RR was 1.55 (P = .02); after additional adjustment for HDL levels, the RR was 1.68 (P = .008). Similar RR values were obtained for the D442G mutation alone. Increased CHD in men with mutations was primarily observed for HDL chol 41-60 mg/dl; for HDL chol > 60 mg/dl men with and without mutations had low CHD prevalence. Thus, genetic CETP deficiency appears to be an independent risk factor for CHD, primarily due to increased CHD prevalence in men with the D442G mutation and HDL cholesterol between 41 and 60 mg/dl. The findings suggest that both HDL concentration and the dynamics of cholesterol transport through HDL (i.e., reverse cholesterol transport) determine the anti-atherogenicity of the HDL fraction.
Single M13 bacteriophage tethering and stretching (2007)

The ability to present biomolecules on the highly organized structure of M13 filamentous bacteriophage is a unique advantage. Where previously this viral template was shown to direct the orientation and nucleation of nanocrystals and materials, here we apply it in the context of single-molecule (SM) biophysics. Genetically engineered constructs were used to display different reactive species at each of the filament ends and along the major capsid, and the resulting hetero-functional particles were shown to consistently tether microscopic beads in solution. With this system, we report the development of a SM assay based on M13 bacteriophage. We also report the quantitative characterization of the biopolymer's elasticity by using an optical trap with nanometer-scale position resolution. Expanding the fluctuating rod limit of the wormlike chain to incorporate enthalpic polymer stretching yielded a model capable of accurately capturing the full range of extensions. Fits of the force-extension measurements gave a mean persistence length of approximately 1,265 nm, lending SM support for a shorter filamentous bacteriophage persistence length than previously thought. Furthermore, a predicted stretching modulus roughly two times that of dsDNA, coupled with the system's linkage versatility and load-bearing capability, makes the M13 template an attractive candidate for use in tethered bead architectures.
373. Simian Adenoviral Vector Based-Vaccine Fully Protect Against Ebola Virus Even in the Presence of Pre-Existing Immunity to Human Adenovirus (2004)

Ebola virus is one of several pathogens that cause lethal hemorrhagic fever. Most strains of Ebola are highly lethal in humans and extremely infectious. The profile of Ebola virus infections that make it such a dangerous pathogen also contribute to its utility as a potential agent of biological warfare. Adenoviral vector was the only vaccine carrier recently shown to protect cynomolgus macaques against lethal dose of Ebola virus bringing optimism towards the development of an efficient vaccine formulation for human application. However, immunity to adenoviral capsid proteins prevents vector re-administration and thus limits application of this vaccine carrier to a single dose per recipient. More problematic is that 30 to 50% of the North American population has evidence for pre-exposure to AdHu5 based on the presence of high levels of neutralizing antibodies (NAB) in serum. These levels of NAB are likely to limit efficacy of a vaccine carrier based on AdHu5. Neutralization of simian-derived adenoviral vectors by human serum is not significant suggesting that pre-existing immunity to human adenovirus could possibly be bypassed by simian adenovirus. This study evaluates specific T and B cell responses to the Ebola glycoprotein envelope (EboZGP) and response to lethal challenges of Ebola Zaire following immunization in mice. E1 deleted vaccine vectors expressing EboZGP were created from molecular clones of human adenovirus serotype 5 (AdHu5) and chimpanzee adenovirus pan7 (AdC7). The impact of preexisting immunity to AdHu5 was evaluated in vaccinated mice with human or simian adenoviral vector expressing the EboZGP antigen. Both vaccines stimulated robust T and B cell responses to EboZGP after a single administration in naive mice, which were completely protected to an otherwise lethal challenge of EboZ. Preexisting immunity to AdHu5 severely compromised efficacy of the AdHu5 vaccine but not of the AdC7 vaccine. In the presence of clinically relevant level of preexisting NAB to AdHu5, T and B cell responses to EboZGP remained similar in AdC7 vaccinated mice but were severely compromised in AdHu5 vaccinated mice. These results support the further development of simian-based vaccines.
Comprehensive genomic characterization of head and neck squamous cell carcinomas (2015)

The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations. Here we show that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1. Smoking-related HNSCCs demonstrate near universal loss-of-function TP53 mutations and CDKN2A inactivation with frequent copy number alterations including amplification of 3q26/28 and 11q13/22. A subgroup of oral cavity tumours with favourable clinical outcomes displayed infrequent copy number alterations in conjunction with activating mutations of HRAS or PIK3CA, coupled with inactivating mutations of CASP8, NOTCH1 and TP53. Other distinct subgroups contained loss-of-function alterations of the chromatin modifier NSD1, WNT pathway genes AJUBA and FAT1, and activation of oxidative stress factor NFE2L2, mainly in laryngeal tumours. Therapeutic candidate alterations were identified in most HNSCCs.
Circular permutated red fluorescent proteins and calcium ion indicators based on mCherry (2013)

Red fluorescent indicators for calcium ion (Ca(2+)) are preferable, relative to blue-shifted alternatives, for biological imaging applications due to the lower phototoxicity, lower autofluorescent background and deeper tissue penetration associated with longer wavelength light. Accordingly, we undertook the development of a genetically encoded Ca(2+) indicator based on the popular and widely utilized Discosoma-derived red fluorescent protein, mCherry. Starting from a promising but dimly fluorescent circular permutated variant of mCherry, we first engineered a 13-fold brighter variant (cp196V1.2) through directed evolution. This bright cp196V1.2 was then used as the scaffold for creation of eight distinct libraries of potential Ca(2+) indicators via permutation at different sites within the 7th and 10th β-strands, and fusion of calmodulin and M13 to the new termini. Screening of these libraries led to the conclusion that, consistent with previous investigations of homologous fluorescent proteins, the 146-145 site in β-strand 7 is the most promising permutation site for construction of useful Ca(2+) indicators. Further rounds of directed evolution ultimately led to an indicator that exhibits a 250% change in intrinsic brightness in response to Ca(2+) and an exceptionally high affinity (Kd = 6 nM) for Ca(2+).
A Vector-Perturbation Technique for Near-Capacity Multiantenna Multiuser Communication—Part I: Channel Inversion and Regularization (2005)

Recent theoretical results describing the sum capacity when using multiple antennas to communicate with multiple users in a known rich scattering environment have not yet been followed with practical transmission schemes that achieve this capacity. We introduce a simple encoding algorithm that achieves near-capacity at sum rates of tens of bits/channel use. The algorithm is a variation on channel inversion that regularizes the inverse and uses a "sphere encoder" to perturb the data to reduce the power of the transmitted signal. This work is comprised of two parts. In this first part, we show that while the sum capacity grows linearly with the minimum of the number of antennas and users, the sum rate of channel inversion does not. This poor performance is due to the large spread in the singular values of the channel matrix. We introduce regularization to improve the condition of the inverse and maximize the signal-to-interference-plus-noise ratio at the receivers. Regularization enables linear growth and works especially well at low signal-to-noise ratios (SNRs), but as we show in the second part, an additional step is needed to achieve near-capacity performance at all SNRs.
Identification of FAP Locus Genes from Chromosome 5q21 (1991)

Recent studies suggest that one or more genes on chromosome 5q21 are important for the development of colorectal cancers, particularly those associated with familial adenomatous polyposis (FAP). To facilitate the identification of genes from this locus, a portion of the region that is tightly linked to FAP was cloned. Six contiguous stretches of sequence (contigs) containing approximately 5.5 Mb of DNA were isolated. Subclones from these contigs were used to identify and position six genes, all of which were expressed in normal colonic mucosa. Two of these genes (APC and MCC) are likely to contribute to colorectal tumorigenesis. The MCC gene had previously been identified by virtue of its mutation in human colorectal tumors. The APC gene was identified in a contig initiated from the MCC gene and was found to encode an unusually large protein. These two closely spaced genes encode proteins predicted to contain coiled-coil regions. Both genes were also expressed in a wide variety of tissues. Further studies of MCC and APC and their potential interaction should prove useful for understanding colorectal neoplasia.
What is New in Wound Healing? (2004)

Wound biology is complex. Wounds which were until recently seen only as defects in tissues are now increasingly interpreted in cellular and molecular terms. Growth factors, cytokines, proteases and adhesion molecules which participate in wound healing are discussed in this article. From a clinical perspective, conceptual shifts of importance, including moist wound healing, wound bed preparation and wound assessment, are presented. The frontiers of therapeutics employed in wound healing continue to advance with an increasing array of modalities joining the ranks at a regular pace. A range of currently available as well as evolving therapies- physical (topical negative pressure therapy, warming, electrical stimulation), biological (larva therapy, skin substitutes, stem cell therapy, growth factors, gene therapy) and of a miscellaneous variety (hyperbaric oxygen, dressings)- are appraised.