gebhart/patrepeval huggingface dataset:
Phenotypic heterogeneity among stromal cell lines from mouse bone marrow disclosed in their extracellular matrix composition and interactions with normal and leukemic cells (1985)

Study of a series of stromal cell lines from mouse bone marrow (MBA) verified and extended their classification as phenotypically distinct subtypes. Production of extracellular matrix proteins was examined using specific antibodies. Fibronectin and laminin were detected in all of the cell lines tested, yet 14F1.1 adipocytes exhibited particularly prominent extracellular deposition. This cell line and MBA-13.2 cells were positive to both collagen types I and IV, whereas MBA-1 and MBA-2.1 were stained with anticollagen type I antibodies only. Coculture experiments revealed differences among the lines in their effects on normal myeloid cells and leukemic cell lines. In promoting the in vitro accumulation of myeloid progenitors (CFU-C), 14F1.1 cells surpassed the others. The MBA-2.1 cell line was particularly inhibitory to MPC-11 plasmacytoma and Friend erythroleukemia cells. However, the latter were refractory to other stromal cell lines, whereas MPC-11 cells were inhibited to various degrees by virtually all of the cell lines. Physical separation between the interacting cells reduced the inhibition in some but not all cases, and no inhibitory activity was detected in conditioned media. The MBA-13 stromal cells synergistically promoted the differentiation of dimethylsulfoxide (Me2SO)-induced Friend erythroleukemia. The latter cells themselves, at high concentrations, as well as some of the stromal cell lines and unrelated adherent cells, antagonized the Me2SO effect, revealing possible reversible stages in the Friend cell differentiation pathway.
One-dimensional Steeplechase for Electrons Realized (2002)

We report growth of one-dimensional semiconductor nanocrystals, nanowhiskers, in which segments of the whisker with different composition are formed, illustrated by InAs whiskers containing segments of InP. Our conditions for growth allow the formation of abrupt interfaces and heterostructure barriers of thickness from a few monolayers to 100s of nanometers, thus creating a one-dimensional landscape along which the electrons move. The crystalline perfection, the quality of the interfaces, and the variation in the lattice constant are demonstrated by high-resolution transmission electron microscopy, and the conduction band off-set of 0.6 eV is deduced from the current due to thermal excitation of electrons over an InP barrier.
Rotary Suspension Culture Enhances the Efficiency, Yield, and Homogeneity of Embryoid Body Differentiation (2007)

Embryonic stem (ES) cells hold great promise as a robust cell source for cell-based therapies and as a model of early embryonic development. Current experimental methods for differentiation of ES cells via embryoid body (EB) formation are either inherently incapable of larger-scale production or exhibit limited control over cell aggregation during EB formation and subsequent EB agglomeration. This report describes and characterizes a novel method for formation of EBs using rotary orbital motion that simultaneously addresses both concerns. EBs formed under rotary suspension conditions were compared with hanging-drop and static EBs for efficiency of EB formation, cell and EB yield, homogeneity of EB size and shape, and gene expression. A 20-fold enhancement in the number of cells incorporated into primitive EBs in rotary versus static conditions was detected after the first 12 hours, and a fourfold increase in total cell yield was achieved by rotary culture after 7 days. Morphometric analysis of EBs demonstrated formation and maintenance of a more uniform EB population under rotary conditions compared with hanging-drop and static conditions. Quantitative gene expression analysis indicated that rotary EBs differentiated normally, on the basis of expression of ectoderm, endoderm, and mesoderm markers. Increased levels of endoderm gene expression, along with cystic EB formation, indicated by histological examination, suggested that differentiation was accelerated in rotary EBs. Thus, the rotary suspension culture method can produce a highly uniform population of efficiently differentiating EBs in large quantities in a manner that can be easily implemented by basic research laboratories conducting ES cell differentiation studies.
Circumvention of drug resistance in cancer cells by a new fluoropyrimidine analogue (1996)

The potentiation of antitumor drugs by their analogues is one of strategies for overcoming cellular resistance to chemotherapy. In attempts to improve the efficacy of 5-fluorouracil (5-FU) and overcome 5-FU resistance, we synthesized new 5- FU derivatives and evaluated the potentiation effect on 5-FU cytotoxicity. 5-Fluorouracil-1-yl-3-butanone (5-FUBO), a newly synthesized 5-FU derivative, significantly potentiated the cytotoxic effect of 5-FU, and the potentiation of 5-FU by 5-FUBO in 5-FU resistant cells was higher than in their drugsensitive parental cells. Surprisingly, it potentiated the cytotoxicities of vincristine and vinblastine. The potentiation of these drugs by 5-FUBO in mutidrugresistant (MDR) cells was more than in their drugsensitive parental cells. It was also shown that 5-FUBO increased the intracellular accumulation of [3H]vincristine in P388/M cells, and this is related with increased cytotoxicity of vincristine. Northern blot analysis showed that the potentiation effect of MDR-related antitumor drugs by 5-FUBO was caused by inhibition of MDRl gene expression. Also, 5-FUBO cytotoxicity in K562 cells was increased significantly upon transformation with c-Ha-ras.
3′ Untranslated Region in a Light Neurofilament (NF-L) mRNA Triggers Aggregation of NF-L and Mutant Superoxide Dismutase 1 Proteins in Neuronal Cells (2004)

The pathogenesis of neurodegenerative diseases is believed to involve abnormal aggregation of proteins, but the mechanisms initiating protein aggregation are unclear. Here we report a novel phenomenon that could be instrumental in triggering protein aggregation in neurodegenerative diseases. We show that the 3' untranslated region (3'UTR) of a light neurofilament (NF-L) transcript enhances the reactivity of its own translated product and leads to loss of solubility and aggregation of NF-L protein and to coaggregation of mutant superoxide dismutase 1 (SOD1) protein. Full-length mouse NF-L cDNAs, with and without NF-L 3'UTR, were fused to the C terminus of a green fluorescent protein (GFP) reporter gene, and the GFP-tagged NF-L proteins were examined in transfected Neuro2a cells. The GFP-tagged NF-L protein expressed from the transgene containing NF-L 3'UTR, but not from the transgene lacking NF-L 3'UTR, colocalizes with endogenous heavy neurofilament protein and, at high-level expression, leads to loss of solubility and aggregation of GFP-tagged NF-L protein. Aggregation of GFP-tagged NF-L protein triggers coaggregation and loss of solubility of coexpressed DsRed-tagged mutant (G93A) SOD1 protein but not wild-type SOD1 protein. Deletional mutagenesis maps the RNA sequence causing aggregation of GFP-tagged NF-L protein to the proximal 45 nucleotides of NF-L 3'UTR. This is the site of a major destabilizing element in NF-L RNA and binding site for RNA-binding proteins. Our findings support a working model whereby NF-L RNA, or cognate RNA-binding factors, enhances the reactivity of NF-L protein and provides a triggering mechanism leading to aggregation of NF-L and other proteins in neurodegenerative diseases.
TGD4 involved in endoplasmic reticulum‐to‐chloroplast lipid trafficking is a phosphatidic acid binding protein (2012)

The synthesis of galactoglycerolipids, which are prevalent in photosynthetic membranes, involves enzymes at the endoplasmic reticulum (ER) and the chloroplast envelope membranes. Genetic analysis of trigalactosyldiacylglycerol (TGD) proteins in Arabidopsis has demonstrated their role in polar lipid transfer from the ER to the chloroplast. The TGD1, 2, and 3 proteins resemble components of a bacterial-type ATP-binding cassette (ABC) transporter, with TGD1 representing the permease, TGD2 the substrate binding protein, and TGD3 the ATPase. However, the function of the TGD4 protein in this process is less clear and its location in plant cells remains to be firmly determined. The predicted C-terminal β-barrel structure of TGD4 is weakly similar to proteins of the outer cell membrane of Gram-negative bacteria. Here, we show that, like TGD2, the TGD4 protein when fused to DsRED specifically binds phosphatidic acid (PtdOH). As previously shown for tgd1 mutants, tgd4 mutants have elevated PtdOH content, probably in extraplastidic membranes. Using highly purified and specific antibodies to probe different cell fractions, we demonstrated that the TGD4 protein was present in the outer envelope membrane of chloroplasts, where it appeared to be deeply buried within the membrane except for the N-terminus, which was found to be exposed to the cytosol. It is proposed that TGD4 is either directly involved in the transfer of polar lipids, possibly PtdOH, from the ER to the outer chloroplast envelope membrane or in the transfer of PtdOH through the outer envelope membrane.
Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research (2015)

Cancer cell lines are used extensively to study cancer biology and to test hypotheses in translational research. The relevance of cell lines is dependent on how closely they resemble the tumors being studied. Relating tumors and cell lines, and recognizing their similarities and differences are thus very important for translational research. Rapid advances in genomics have led to the generation of large volumes of genomic and transcriptomic data for a diverse set of primary cancer samples, normal tissue samples and cancer cell lines. Hepatocellular Carcinoma (HCC) is one of the most common tumors worldwide, with high occurrence in Asia and sub-Saharan regions. The current effective treatments of HCC remain limited. In this work, we compared the gene expression measurements of 200 HCC tumor samples from The Cancer Genome Atlas and over 1000 cancer cell lines including 25 HCC cancer cell lines from Cancer Cell Line Encyclopedia. We showed that the HCC tumor samples correlate closely with HCC cell lines in comparison to cell lines derived from other tumor types. We further demonstrated that the most commonly used HCC cell lines resemble HCC tumors, while we identified nearly half of the cell lines that do not resemble primary tumors. Interestingly, a substantial number of genes that are critical for disease development or drug response are either expressed at low levels or absent among highly correlated cell lines; additional attention should be paid to these genes in translational research. Our study will be used to guide the selection of HCC cell lines and pinpoint the specific genes that are differentially expressed in either tumors or cell lines.
Chromosome abnormalities in human embryos (1998)

The presence of numerical chromosome abnormalities in human embryos was studied using fluorescence in-situ hybridization with four or more chromosome-specific probes. When most cells of an embryo are analysed, this technique allows differentiation to be made between aneuploidy, mosaicism, haploidy and polyploidy. Abnormal types of fertilization, such as unipronucleated, tripronucleated zygotes and zygotes with uneven pronuclei, were studied using this technique. We have found a strong correlation between some types of dysmorphism with chromosomal abnormalities. In addition, the more impaired the development of an embryo, the more chromosomal abnormalities were detected in those embryos. Maternal age and other factors were linked to an increase in chromosome abnormalities (hormonal regimes, temperature changes), but not to intracytoplasmic sperm injection.
Sutterella stercoricanis sp. nov., isolated from canine faeces (2004)

Morphological, biochemical and molecular genetic studies were carried out on an unknown non-spore-forming, Gram-negative, rod-shaped bacterium which was isolated from dog faeces. The bacterium grew under anaerobic conditions, was asaccharolytic, resistant to 20 % (v/v) bile and was oxidase- and urease-negative. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that the unidentified bacterium clustered with Sutterella wadsworthensis, although a sequence divergence of >5 % indicated that the bacterium from dog faeces represented a previously unrecognized subline within the genus. On the basis of the presented findings, a novel species, Sutterella stercoricanis sp. nov., is described. The type strain of Sutterella stercoricanis is 5BAC4T (= CCUG 47620T = CIP 108024T).
Spectroscopic properties of an engineered maltose binding protein (1997)

The maltose binding protein (MBP) has been site specifically labelled with a nitrobenzoxadiazole (NBD) group following mutation of a serine to a cysteine residue at position 337. The resulting protein shows a large ligand (maltose or beta-cyclodextrin) dependent increase in its steady-state fluorescence intensity. Analysis of the static (intensity and anisotropy) and dynamic (lifetime distributions) fluorescence of the NBD label as well as the tryptophan residues in both ligand-bound and ligand-free states of this molecule reveals complex multi-component decays that are interpreted in terms of a ligand-induced solvent shielding mechanism. In the context of the known crystal structures of the various forms of the maltose-binding protein (MBP), ligand-dependent changes in both the fluorescence parameters as well as the circular dichroism spectra of the NBD group are interpreted by a twisted intramolecular charge-transfer (TICT) mechanism, wherein ligand binding locks the NBD group into a conformation that prevents efficient relaxation of the excited state.
BDNF protection of basal forebrain cholinergic neurons after axotomy (1993)

To elucidate the role of brain derived neurotrophic factor (BDNF) in the protection of cholinergic neurons in the basal forebrain, recombinant human BDNF and as a positive control, human recombinant nerve growth factor (NGF), were infused for 20 days into the lateral ventricle of adult rats with fimbrial transections. BDNF and NGF administration protected cholinergic basal forebrain cells from degenerative changes after axotomy, as assessed with immunohistochemical analysis of the two cholinergic marker proteins ChAT and p75NGFR. Both BDNF and NGF treatment completely prevent the lesion induced loss of p75NGFR-positive cells in the septal area of animals with fimbrial transections. This finding contrasts with the result obtained with ChAT immunohistochemistry, where BDNF treatment protects only part of the population of neurons which disappear following the transections. These findings are compatible with the view that there is a cascade of events induced in cholinergic neurons by the transections, so that ChAT expression is lost before p75NGFR expression, and that BDNF reduces degenerative events in the entire population of cholinergic neurons, maintaining some of them as p75NGFR-positive but ChAT-negative cells.
Exercise and Regional Dosimetry: An Overview (1989)

Regional respiratory tract dosimetry is an important consideration when examining susceptibility to inhaled gases and particles. In this overview, an orientation is provided on the major anatomical ventilatory and physiologic factors that affect regional respiratory tract dosimetry. The influence of these factors and the physical laws governing deposition exhibit complex relationships for the extrathoracic, tracheobronchial, and pulmonary regions of the respiratory tract. Specific examples of regional dosimetry of insoluble and hygroscopic particles and an oxidant gas are presented to help identify critical issues and research areas related to susceptibility to inhaled pollutants.
Cellular and Mitochondrial Remodeling upon Defects in Iron-Sulfur Protein Biogenesis (2008)

Biogenesis of iron-sulfur (Fe/S) proteins in eukaryotes is an essential process involving the mitochondrial iron-sulfur cluster (ISC) assembly and export machineries and the cytosolic iron/sulfur protein assembly (CIA) apparatus. To define the integration of Fe/S protein biogenesis into cellular homeostasis, we compared the global transcriptional responses to defects in the three biogenesis systems in Saccharomyces cerevisiae using DNA microarrays. Depletion of a member of the CIA machinery elicited only weak (up to 2-fold) alterations in gene expression with no clear preference for any specific cellular process. In contrast, depletion of components of the mitochondrial ISC assembly and export systems induced strong and largely overlapping transcriptional responses of more than 200 genes (2-100-fold changes). These alterations were strikingly similar, yet not identical, to the transcriptional profiles developed upon iron starvation. Hence, mitochondria and their ISC systems serve as primary physiological regulators exerting a global control of numerous iron-dependent processes. First, ISC depletion activates the iron-responsive transcription factors Aft1/2p leading to increased cellular iron acquisition. Second, respiration and heme metabolism are repressed ensuring the balanced utilization of iron by the two major iron-consuming processes, iron-sulfur protein and heme biosynthesis. Third, the decreased respiratory activity is compensated by induction of genes involved in glucose acquisition. Finally, transcriptional remodeling of the citric acid cycle and the biosyntheses of ergosterol and biotin reflect the iron dependence of these pathways. Together, our data suggest a model in which mitochondria perform a global regulatory role in numerous cellular processes linked to iron homeostasis.
Molecular Targeting of Lymph Nodes with L-Selectin Ligand-specific US Contrast Agent: A Feasibility Study in Mice and Dogs (2004)

Use of an intravenously administered L-selectin ligand-specific US contrast agent is feasible for active lymph node targeting in mice and dogs.
Synthesis and biological activity of certain 8-mercaptopurine and 6-mercaptopyrimidine S-nucleosides (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and biological activity of certain 8-mercaptopurine and 6-mercaptopyrimidine S-nucleosidesDennis A. Shuman, Alexander Bloch, Roland K. Robins, and Morris J. RobinsCite this: J. Med. Chem. 1969, 12, 4, 653–657Publication Date (Print):July 1, 1969Publication History Published online1 May 2002Published inissue 1 July 1969https://pubs.acs.org/doi/10.1021/jm00304a021https://doi.org/10.1021/jm00304a021research-articleACS PublicationsRequest reuse permissionsArticle Views156Altmetric-Citations11LEARN 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
Meta-Analysis of 4 Coronary Heart Disease Genome-Wide Linkage Studies Confirms a Susceptibility Locus on Chromosome 3q (2003)

The genetic regions 3q26-27 and 2q34-37 might contain susceptibility genes for CHD. Linkage to the 3q26-qter region has previously been shown in type 2 diabetes mellitus, metabolic syndrome, cholesterol concentration in LDL size fractions, and renal function in hypertensive subjects. The 2q34-37 region lies close to the type 2 diabetes NIDDM1 locus. Both of these regions harbor several candidate genes involved in the homeostasis of glucose and lipid metabolism. These results are particularly intriguing, given the growing evidence of an association between CHD risk and metabolic abnormalities, such as insulin resistance, type 2 diabetes, abdominal obesity, and dyslipidemia.
Laguerre–Gauss and Bessel–Gauss beams propagation through turbulence: analysis of channel efficiency (2016)

As a means of increasing the channel capacity in free-space optical communication systems, two types of orbital angular momentum carrying beams, Bessel-Gauss and Laguerre-Gauss, are studied. In a series of numerical simulations, we show that Bessel-Gauss beams, pseudo-nondiffracting beams, outperform Laguerre-Gauss beams of various orders in channel efficiency and bit error rates.
[Overexpression of laminine-5( LN-5) in peritoneal lavage of colorectal cancer patients preliminary results]. (2016)

Recent studies show that interaction between LN (heterotrimeric protein formed by a3/b3/g2 chains) and cancer cells plays an important role in tumor invasion, also in colorectal cancer. The overall survival was significantly worse in patients with free peritoneal cancer cells(FPTCs): detection of FPTCs after curative surgery is a challenge, because could improve staging and prognosis. Peritoneal citology is the current standard procedure with very low sensivity. We aimed to study the expression of LN5 in the peritoneal lavage of colorectal cancer pts and in controls with semiquantitative reverse trancriptase-polymerase chain reaction (RT-PCR). LN-5 overexpression was evaluated observing PCR- products intensity at electrophoresis: high intensity is correlated to overexpression. Pre and post-operative peritoneal lavages of 30 pts with colorectal cancer (13M;17F), with median age of 69 (58-84), and of 10 controls, were analyzed by conventional cytology and a semiquantitative RT-PCR. No cancer pts showed pre/postoperative negative cytology and did not express LN-5. In cancer pts. cytology was positive in 2 pts in pre/postoperative lavage. LN-5 overexpression was observed in 56,6% preoperatively and in 76,6% postoperatively. LN-5 g 2 chain was most frequent chain. Our study suggests a relationship between LN-5 and FPTCs, as shown by the low expression of lamimine in controls. LN-5 could be a useful marker to identify a subgroup of early-stage patients at increased risk of recurrence; moreover, mortality seems to correlated to LAMB3 chain. The diagnostic accuracy could be improved by using a quantitative RT-PCR or western-blot and detecting serum laminine. Finally, to validate these findings a larger number of pts with follow-up study is required.
Ethanol Tolerance in Bacteria (1989)

The adverse effects of ethanol on bacterial growth, viability, and metabolism are caused primarily by ethanol-induced leakage of the plasma membrane. This increase in membrane leakage is consistent with known biophysical properties of membranes and ethanolic solutions. The primary actions of ethanol result from colligative effects of the high molar concentrations rather than from specific interactions with receptors. The ethanol tolerance of growth in different microorganisms appears to result in large part from adaptive and evolutionary changes in cell membrane composition. Different cellular activities vary in their tolerance to ethanol. Therefore, it is essential that the aspect of cellular function under study be specifically defined and that comparisons of ethanol tolerance among systems share this common definition. Growth is typically one of the most sensitive cellular activities to inhibition by ethanol, followed by survival, or loss of reproductive ability. Glycolysis is the most resistant of these three activities. Since glycolysis is an exergonic process, a cell need not be able to grow or remain viable for glycolysis to occur.