gebhart/patrepeval huggingface dataset:
Overexpression of the MicroRNA hsa-miR-200c Leads to Reduced Expression of Transcription Factor 8 and Increased Expression of E-Cadherin (2007)

MicroRNAs are approximately 22-nucleotide sequences thought to interact with multiple mRNAs resulting in either translational repression or degradation. We previously reported that several microRNAs had variable expression in mammalian cell lines, and we examined one, miR-200c, in more detail. A combination of bioinformatics and quantitative reverse transcription-PCR was used to identify potential targets and revealed that the zinc finger transcription factor transcription factor 8 (TCF8; also termed ZEB1, deltaEF1, Nil-2-alpha) had inversely proportional expression levels to miR-200c. Knockout experiments using anti-microRNA oligonucleotides increased TCF8 levels but with nonspecific effects. Therefore, to investigate target predictions, we overexpressed miR-200c in select cells lines. Ordinarily, the expression level of miR-200c in non-small-cell lung cancer A549 cells is low in contrast to normal human bronchial epithelial cells. Stable overexpression of miR-200c in A549 cells results in a loss of TCF8, an increase in expression of its regulatory target, E-cadherin, and altered cell morphology. In MCF7 (estrogen receptor-positive breast cancer) cells, there is endogenous expression of miR-200c and E-cadherin but TCF8 is absent. Conversely, MDA-MB-231 (estrogen receptor-negative) cells lack detectable miR-200c and E-cadherin (the latter reportedly due to promoter region methylation) but express TCF8. The ectopic expression of miR-200c in this cell line also reduced levels of TCF8, restored E-cadherin expression, and altered cell morphology. Because the down-regulation of E-cadherin is a crucial event in epithelial-to-mesenchymal transition, loss of miR-200c expression could play a significant role in the initiation of an invasive phenotype, and, equally, miR-200c overexpression holds potential for its reversal.
Design, Synthesis, and Evaluation of Latent Alkylating Agents Activated by Glutathione S-Transferase (1996)

In search of compounds with improved specificity for targeting the important cancer-associated P1-1 glutathione S-transferase (GST) isozyme, new analogs 4 and 5 of the previously reported glutathione S-transferase (GST)-activated latent alkylating agent gamma-glutamyl-alpha-amino-beta-[[[2-[[bis[bis(2-chloroethyl)amino]ph osp horyl]oxy]ethyl]sulfonyl]propionyl]-(R)-(-)-phenylglycine (3) have been designed, synthesized, and evaluated. One of the diastereomers of 4 exhibited good selectivity for GST P1-1. The tetrabromo analog 5 of the tetrachloro compound 3 maintained its specificity and was found to be more readily activated by GSTs than 3. The GST activation concept was further broadened through design, synthesis, and evaluation of a novel latent urethane mustard 8 and its diethyl ester 9. Interestingly, 8 showed very good specificity for P1-1 GST. Cell culture studies were carried out on 4, 5, 8, and 9 using cell lines engineered to have varying levels of GST P1-1 isozyme. New analogs 4 and 5 exhibited increased toxicity to cell lines with overexpressed GST P1-1 isozyme. The urethane mustard 8 and its diethyl ester 9 were found to be not as toxic. However, they too exhibited more toxicity to a cell line engineered to have elevated P1-1 levels, which was in agreement with the observed in vitro specificity of 8 for P1-1 GST isozyme. Mechanistic studies on alkaline as well as enzyme-catalyzed decomposition of latent mustard 3 provided experimental proof for the hypothesis that 3 breaks down into an active phosphoramidate mustard and a reactive vinyl sulfone. The alkylating nature of the decomposition products was further demonstrated by trapping those transient species as relatively stable diethyldithiocarbamic acid adducts. These results substantially extend previous efforts to develop drugs targeting GST and provide a paradigm for development of other latent drugs.
Tumor Regression After Adoptive Transfer of Effector T Cells Is Independent of Perforin or Fas Ligand (APO-1L/CD95L) (1999)

The adoptive transfer of tumor-specific effector T cells can result in complete regression and cure mice with systemic melanoma, but the mechanisms responsible for regression are not well characterized. Perforin- and Fas ligand (APO-1/CD95 ligand)-mediated cytotoxicity have been proposed as mechanisms for T cell-mediated tumor destruction. To determine the role of perforin and Fas ligand (FasL) in T cell-mediated tumor regression in a murine melanoma model, B16BL6-D5 (D5), we generated D5-specific effector T cells from tumor vaccine-draining lymph nodes of wild type (wt), perforin knock out (PKO), or FasL mutant (gld) mice and treated established D5 metastases in mice with the same genotype. Effector T cells from wt, PKO and gld mice induced complete regression of pulmonary metastases and significantly prolonged survival of the treated animals regardless of their genotype. Complete tumor regression induced by PKO effector T cells was also observed in a sarcoma model (MCA-310). Furthermore, adoptive transfer of PKO and wt effector T cells provided long-term immunity to D5. Therapeutic T cells from wt, PKO, or gld mice exhibit a tumor-specific type 1 cytokine profile; they secrete IFN-gamma, but not IL-4. In these models, T cell-mediated tumor regression and long-term antitumor immunity are perforin and FasL independent.
Glossary of class names of organic compounds and reactivity intermediates based on structure (IUPAC Recommendations 1995) (1995)

Article Glossary of class names of organic compounds and reactivity intermediates based on structure (IUPAC Recommendations 1995) was published on January 1, 1995 in the journal Pure and Applied Chemistry (volume 67, issue 8-9).
Serum Lipopolysaccharide Binding Protein Levels Predict Severity of Lung Injury and Mortality in Patients with Severe Sepsis (2009)

Serial LBP serum measurements may offer a clinically useful biomarker for identification of patients with severe sepsis having the worst outcomes and the highest probability of developing sepsis-induced ARDS.
Serum levels of soluble CD4 and CD8 in patients with chronic viral hepatitis. (1994)

The blood levels of soluble CD8 (sCD8) and soluble CD4 (sCD4) were measured in patients with various liver diseases, and their significance was studied. The levels of sCD8 were significantly higher in patients with chronic active hepatitis (CAH), autoimmune hepatitis (AIH), primary biliary cirrhosis (PBC), acute hepatitis (AH), fulminant hepatitis (FH) and liver cirrhosis (LC) as compared with the normal controls (NC), and correlated positively with those of GPT (r = 0.67, p < 0.001). In addition, a comparison of the exacerbation of CAH with remission showed that the sCD8 levels were significantly higher in the former. On the other hand, there was no significant rise in the level of sCD4 in patients with any liver disease, except FH, no definite relationship between sCD4 and sGPT, and no consistant tendency in sCD4 levels between exacerbation and remission. The reason for an insignificant elevation of the sCD4 level is the fact that in hepatitis the CD8-positive cells, which are cytotoxic T cells, are directly involved in hepatocyte damage; therefore the CD8-positive cells are predominantly activated, while the activity of the CD4-positive cells is considered to be lower. Instead of determining the number of CD4-positive cells and CD8-positive cells in the mononuclear cells of peripheral blood, serum sCD4 and sCD8 levels can be measured simply and inexpensively. Thus, these levels may be useful immune markers.
Tumor-Infiltrating Foxp3−CD4+CD25+ T Cells Predict Poor Survival in Renal Cell Carcinoma (2007)

Increased presence of CD4(+)CD25(+)Foxp3(+) T cells was not significantly associated with RCC death. In contrast, CD4(+)CD25(+)Foxp3(-) T cells, which may represent a unique set of Tregs or activated helper T cells, was significantly associated with outcome.
Interactions of Sertoli Cells with Myoid Cells in vitro (1980)

formation characteristic of tubule morphogenesis.
Longer Nanotubes at Lower Temperatures:  The Influence of Effective Activation Energies on Carbon Nanotube Growth by Thermal Chemical Vapor Deposition (2007)

Growth of carbon nanotubes (CNTs) by metal-catalyzed thermal chemical vapor deposition (CVD) upon flat silicon substrates is studied as a function of growth temperature. It is found that the CNT growth rate at a given temperature is constant for a certain amount of growth time, after which growth ceases; the product of the growth rate and the growth time gives the ultimate length of the CNTs. Both the growth rate and the growth time are found to depend on the CVD temperature, and this dependence is such that the ultimate CNT length increases as temperature decreases; that is, longer CNTs can be grown at lower temperatures than at higher temperatures. This surprising and counter-intuitive result reflects the interaction of competing factors affecting the CNT growth: the rate at which carbon is incorporated into growing CNTs versus the rate at which catalytic metal particles become inactive. Both of these rates are found to have an Arrhenius form of temperature dependence, with activation energies of 2.0 and 3.4 eV, respectively, when an Al2O3 diffusion barrier layer is used. These energies are interpreted as “effective” activation barriers arising from activation energy contributions from multiple chemical processes. CNT bundles as long as one millimeter have been grown at a temperature of 600 °C.
MRI Study on Reversible and Irreversible Electroporation Induced Blood Brain Barrier Disruption (2012)

Electroporation, is known to induce cell membrane permeabilization in the reversible (RE) mode and cell death in the irreversible (IRE) mode. Using an experimental system designed to produce a continuum of IRE followed by RE around a single electrode we used MRI to study the effects of electroporation on the brain. Fifty-four rats were injected with Gd-DOTA and treated with a G25 electrode implanted 5.5 mm deep into the striata. MRI was acquired immediately after treatment, 10 min, 20 min, 30 min, and up to three weeks following the treatment using: T1W, T2W, Gradient echo (GE), serial SPGR (DCE-MRI) with flip angles ranging over 5-25°, and diffusion-weighted MRI (DWMRI). Blood brain barrier (BBB) disruption was depicted as clear enhancement on T1W images. The average signal intensity in the regions of T1-enhancement, representing BBB disruption, increased from 1887±83 (arbitrary units) immediately post treatment to 2246±94 20 min post treatment, then reached a plateau towards the 30 min scan where it reached 2289±87. DWMRI at 30 min showed no significant effects. Early treatment effects and late irreversible damage were clearly depicted on T2W. The enhancing volume on T2W has increased by an average of 2.27±0.27 in the first 24-48 hours post treatment, suggesting an inflammatory tissue response. The permanent tissue damage, depicted as an enhancing region on T2W, 3 weeks post treatment, decreased to an average of 50±10% of the T2W enhancing volumes on the day of the treatment which was 33±5% of the BBB disruption volume. Permanent tissue damage was significantly smaller than the volume of BBB disruption, suggesting, that BBB disruption is associated with RE while tissue damage with IRE. These results demonstrate the feasibility of applying reversible and irreversible electroporation for transient BBB disruption or permanent damage, respectively, and applying MRI for planning/monitoring disruption volume/shape by optimizing electrode positions and treatment parameters.
The gene for the human architectural transcription factor HMGI-C consists ofn five exons each coding for a distinct functional element (1995)

The gene on chromosome 12 coding for the human protein HMGI-C has been cloned and partially sequenced. It consists of five exons, the first and last of which include long untranslated regions. The 5' UTR includes a (CA/T)n tract and a polymorphic (CT)n tract. Exons II, III and IV (87, 51 and 33 bp) are dispersed over > 30 kb. Exons I-III separately encode the three basic DNA binding domains ('A-T hooks'), exon IV encodes an 11 amino acid sequence characteristic of HMGI-C and absent from the human HMGI(Y) gene [Friedmann, M., Holth, L. T., Zoghbi, H. Y. and Reeves, R. (1993) Nucleic Acids Res., 21, 4259-4267], whilst exon V encodes the acidic C-terminal domain, which is subject to multiple phosphorylation. The HMGI-C gene is thus a striking example of the separation of functional protein elements into different coding exons.
Double Dissociation between the Effects of Peri-Postrhinal Cortex and Hippocampal Lesions on Tests of Object Recognition and Spatial Memory: Heterogeneity of Function within the Temporal Lobe (2004)

It is widely believed that declarative memory is mediated by a medial temporal lobe memory system consisting of several distinct structures, including the hippocampus and perirhinal cortex. The strong version of this view assumes a high degree of functional homogeneity and serial organization within the medial temporal lobe, such that double dissociations between individual structures should not be possible. In the present study, we tested for a functional double dissociation between the hippocampus and peri-postrhinal cortex in a single experiment. Rats with bilateral excitotoxic lesions of either the hippocampus or peri-postrhinal cortex were assessed in tests of spatial memory (radial maze) and object recognition memory. For the latter, the spontaneous object recognition task was conducted in a modified apparatus designed to minimize the potentially confounding influence of spatial and contextual factors. A clear functional double dissociation was observed: rats with hippocampal lesions were impaired relative to controls and those with peripostrhinal cortex lesions on the spatial memory task, whereas rats with peri-postrhinal lesions were impaired relative to the hippocampal and control groups in object recognition. These results provide strong evidence in favor of heterogeneity and independence of function within the temporal lobe.
In vivodeployment of mechanically adaptive nanocomposites for intracortical microelectrodes (2011)

We recently introduced a series of stimuli-responsive, mechanically adaptive polymer nanocomposites. Here, we report the first application of these bio-inspired materials as substrates for intracortical microelectrodes. Our hypothesis is that the ideal electrode should be initially stiff to facilitate minimal trauma during insertion into the cortex, yet become mechanically compliant to match the stiffness of the brain tissue and minimize forces exerted on the tissue, attenuating inflammation. Microprobes created from mechanically reinforced nanocomposites demonstrated a significant advantage compared to model microprobes composed of neat polymer only. The nanocomposite microprobes exhibit a higher storage modulus (E' = ~5 GPa) than the neat polymer microprobes (E' = ~2 GPa) and can sustain higher loads (~12 mN), facilitating penetration through the pia mater and insertion into the cerebral cortex of a rat. In contrast, the neat polymer microprobes mechanically failed under lower loads (~7 mN) before they were capable of insertion into cortical tissue. Further, we demonstrated the material's ability to morph while in the rat cortex to more closely match the mechanical properties of the cortical tissue. Nanocomposite microprobes that were implanted into the rat cortex for up to eight weeks demonstrated increased cell density at the microelectrode-tissue interface and a lack of tissue necrosis or excessive gliosis. This body of work introduces our nanocomposite-based microprobes as adaptive substrates for intracortical microelectrodes and potentially for other biomedical applications.
Isolation of Genomic Clones Containing the amdS Gene of Aspergillus nidulans and Their Use in the Analysis of Structural and Regulatory Mutations (1983)

Previous analysis of the amdS gene of Aspergillus nidulans has identified multiple regulatory circuits mediated by trans-acting regulatory genes, cis-acting mutations have been identified and shown to specifically affect individual regulatory circuits. Fine-structure genetic mapping of the amdS regions showed that these cis-acting mutations occur in a complex controlling region adjacent to the amdS structural gene. The amdS gene was cloned by differential hybridization, using cDNA probes derived from a high-level-producing strain and from a strain with a large amdS deletion mutation. RNA blotting experiments showed that a single RNA species of 1,600 to 1,700 base pairs is transcribed from the amdS gene. DNA blotting experiments on a large number of amdS mutant strains, including deletions and translocations, allowed the genetic and physical maps of the gene to be correlated. The controlling region of the gene is situated at the 5' end of the gene and the direction of transcription is toward the centromere of chromosome III. The regulatory mutations in the controlling region were found to be due to small-scale alterations in the DNA rather than to large-scale rearrangements resulting in gene fusions.
Growth Requirements of Virus-Resistant Mutants of Escherichia Coli Strain “B” (1946)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
A Monoclonal Antibody against the Ligand Binding Site of the Receptor for Mouse Interferon-γ (1989)

A rat monoclonal IgG2a antibody, GR-20, has been produced against the receptor for mouse interferon-gamma (MuIFN-gamma). Comparison of competitive binding studies performed with either 125I-labeled GR-20 or recombinant (r) MuIFN-gamma, as well as a variety of other studies, suggested that the epitope recognized by the monoclonal antibody (mAb) is in the domain of the receptor that binds ligand. The binding of GR-20 to cells of the monomyelocytic line WEHI-3 was of high affinity (1-2 nM). Approximately 20,000 binding sites were found per cell, a value that is in close agreement with the number of MuIFN-gamma receptors quantified on cells of the same type by ligand binding studies. The mAb also bound to a variety of other mouse cells, suggesting that the same epitope is shared by receptors for MuIFN-gamma, regardless of cell type. The epitope was not detected on two human cell types that were tested, while cells of a rat cell line shown to be minimally responsive to rMuIFN-gamma gave equivocal binding results when they were interacted with GR-20. Binding of the mAb to the receptor did not mimic the effects of ligand. In fact, the opposite was true: binding blocked the induction of three biological effects of MuIFN-gamma, including priming of macrophages for tumor cell killing, upregulation of the expression of class II major histocompatibility antigens (Ia) on the same cell type, and induction of antiviral activity in L cells. Following intravenous injection, initial removal of GR-20 was precipitous, followed after 1 h by a phase which was more gradual, resulting in 5-10% of biologically active mAb remaining in the circulation after 24 h. Such retention should make this mAb useful in a variety of studies in vivo.
A Novel Fully Human Anti-CD40 Monoclonal Antibody, 4D11, for Kidney Transplantation in Cynomolgus Monkeys (2007)

4D11 appears to be a promising agent for antirejection treatment in clinical organ transplantation.
Dissipative soliton resonance in an all-normaldispersion erbium-doped fiber laser (2009)

We report on the generation of 281.2 nJ mode locked pulses directly from an erbium-doped fiber laser mode-locked with the nonlinear polarization rotation technique. We show that apart from the conventional dissipative soliton operation, an all-normal-dispersion fiber laser can also emit square-profile dissipative solitons whose energy could increase to a very large value without pulse breaking.
Direct Regioselective Vinylation of Indoles Using Palladium (II) Chloride (1984)

Direct regioselective vinylation at C3-position of ethyl indole-2-carboxylate, its N-benzyl derivative, and Nbenzylindole with various conjugated olefins was accomplished in the presence of palladium (11) chloride and acetate salt in good to moderate yields.Applications of organopalladium chemistry to indoles have been studied extensively in recent years; those involve carbonylation,la arylation,lb allylation?c'd and v i n y l a t i ~n .~~, ~, ~ Among these reactions, the regioselective C -vinylation of 3 indoles is especially attractive, because the introduction of functionalized carbon side chain at the C3-position is very effective for the synthesis of
Low Penetrance in the Long-QT Syndrome (1999)

This study demonstrates that in some families, LQTS may appear with a very low penetrance, a finding with multiple clinical implications. The family members considered to be normal and found to be silent gene carriers are unexpectedly at risk of generating affected offspring and also of developing torsade de pointes if exposed to either cardiac or noncardiac drugs that block potassium channels. It is no longer acceptable to exclude LQTS among family members of definitely affected patients on purely clinical grounds. Conversely, it now appears appropriate to perform molecular screening in all family members of genotyped patients.
Differential expression of proteins in rice leaves cultivated with different forms of nitrogen nutrients. (2006)

Nitrate as one of the two main nitrogen source compounds, acts also as a potent signal substance in plant growth and development. It is increasingly interesting to determine whether nitrate itself or the derived metabolites acts as a signal during the regulation. Rice seedlings were treated with different nitrogen forms (NO(-)(3) vs. NH(+)(4)) and total proteins extracted either from nitrate-fed or ammonium-fed leaves were separated by two-dimensional gel electrophoresis (2-DE), and then the differentially-expressed proteins were identified by MALDI-TOF-MS or ESI-Q-TOF-MS. Twenty-six proteins were up-regulated with NO(-)(3) as the nitrogen source while 6 were up-regulated with NH(+)(4) as the nitrogen source. MS analysis, in combination with database searching, allowed for only a total of 11 proteins identified with significant probability. Among them 7 nitrate-up-regulated proteins were identified, i.e., a PSII oxygen-evolving complex protein 1 (N1), a putative CC-NBS-LRR resistance protein MLA13 (N2), a 23-kD polypeptide of PSII (N3), a translation initiation factor eIF-5A (N5), a putative PSII oxygen-evolving complex protein 2 precursor (N8), an unknown protein (N17), and the ubiquitin carrier protein UBC7 (N18). Four ammonium-up-regulated proteins were identified as the ATP synthase beta subunit (A1), the putative aminotransferase (A3), a hypothetical protein (A5), and OSJNBb0032K15.22 (A6). These results give some new insights into both the biochemical adaptation of plant to different nitrogen forms (NO(-)(3)/NH(+)(4)) and the differences in responses signaled by NO(-)(3)/NH(+)(4) in rice.