gebhart/patrepeval huggingface dataset:
Effects of fasting and insulin administration on polyribosome formation in rat epididymal fat cells. (1980)

Polyribosomes from rat epididymal fat pads may be prepared in a synthetically active state and high yield by quick-freezing the tissue in liquid nitrogen, followed by grinding to a frozen powder. The number of initiated (active) ribosomes is limiting in a cell-free protein synthesis assay derived from the frozen preparation that measures completion of nascent polypeptide chains. When starved rats are killed 30 min after a single injection of insulin (0.8 unit, subcutaneously) there is a shift in the ribosomal distribution pattern (on sucrose density gradients) in the direction of larger polyribosomes. This is accompanied by a 2-fold increase in protein synthetic activity of fat cell ribosomes as measured in vitro. When isolated epididymal fat cells are treated with insulin, with or without added glucose, a 2-fold increase in the rate of incorporation of [3H]leucine into [3H]leucine into trichloroacetic acid-insoluble protein is noted within 40 min. The parallel increases in the number of initiated ribosomes, in their synthetic activity in vitro, and in the apparent protein synthetic activity of the whole cell indicate a rapidly evolving action of insulin at the level of peptide chain initiation.
Heterogeneous antibodies against SARS-CoV-2 spike receptor binding domain and nucleocapsid with implications for COVID-19 immunity (2020)

Evaluation of potential immunity against the novel severe acute respiratory syndrome (SARS) coronavirus that emerged in 2019 (SARS-CoV-2) is essential for health, as well as social and economic recovery. Generation of antibody response to SARS-CoV-2 (seroconversion) may inform on acquired immunity from prior exposure, and antibodies against the SARS-CoV-2 spike protein receptor binding domain (S-RBD) are speculated to neutralize virus infection. Some serology assays rely solely on SARS-CoV-2 nucleocapsid protein (N-protein) as the antibody detection antigen; however, whether such immune responses correlate with S-RBD response and COVID-19 immunity remains unknown. Here, we generated a quantitative serological ELISA using recombinant S-RBD and N-protein for the detection of circulating antibodies in 138 serial serum samples from 30 reverse transcription PCR-confirmed, SARS-CoV-2-hospitalized patients, as well as 464 healthy and non-COVID-19 serum samples that were collected between June 2017 and June 2020. Quantitative detection of IgG antibodies against the 2 different viral proteins showed a moderate correlation. Antibodies against N-protein were detected at a rate of 3.6% in healthy and non-COVID-19 sera collected during the pandemic in 2020, whereas 1.9% of these sera were positive for S-RBD. Approximately 86% of individuals positive for S-RBD-binding antibodies exhibited neutralizing capacity, but only 74% of N-protein-positive individuals exhibited neutralizing capacity. Collectively, our studies show that detection of N-protein-binding antibodies does not always correlate with presence of S-RBD-neutralizing antibodies and caution against the extensive use of N-protein-based serology testing for determination of potential COVID-19 immunity.
CD40 Ligation Activates Murine Macrophages via an IFN-γ-Dependent Mechanism Resulting in Tumor Cell Destruction In Vitro (2005)

We have shown previously that agonistic anti-CD40 mAb induced T cell-independent antitumor effects in vivo. In this study, we investigated mechanisms of macrophage activation with anti-CD40 mAb treatment, assessed by the antitumor action of macrophages in vitro. Intraperitoneal injection of anti-CD40 mAb into C57BL/6 mice resulted in activation of peritoneal macrophages capable of suppressing B16 melanoma cell proliferation in vitro, an effect that was greatly enhanced by LPS and observed against several murine and human tumor cell lines. Anti-CD40 mAb also primed macrophages in vitro to mediate cytostatic effects in the presence of LPS. The tumoristatic effect of CD40 ligation-activated macrophages was associated with apoptosis and killing of tumor cells. Activation of macrophages by anti-CD40 mAb required endogenous IFN-gamma because priming of macrophages by anti-CD40 mAb was abrogated in the presence of anti-IFN-gamma mAb, as well as in IFN-gamma-knockout mice. Macrophages obtained either from C57BL/6 mice depleted of T and NK cells by Ab treatment, or from scid/beige mice, were still activated by anti-CD40 mAb to mediate cytostatic activity. These results argued against the role of NK and T cells as the sole source of exogenous IFN-gamma for macrophage activation and suggested that anti-CD40 mAb-activated macrophages could produce IFN-gamma. We confirmed this hypothesis by detecting intracytoplasmic IFN-gamma in macrophages activated with anti-CD40 mAb in vivo or in vitro. IFN-gamma production by macrophages was dependent on IL-12. Taken together, the results show that murine macrophages are activated directly by anti-CD40 mAb to secrete IFN-gamma and mediate tumor cell destruction.
Phase III Randomized Trial of 12 Versus 3 Months of Maintenance Paclitaxel in Patients With Advanced Ovarian Cancer After Complete Response to Platinum and Paclitaxel-Based Chemotherapy: A Southwest Oncology Group and Gynecologic Oncology Group Trial (2003)

Twelve cycles of single-agent paclitaxel administered to women with advanced ovarian cancer who attain a clinically defined complete response to initial platinum/paclitaxel-based chemotherapy significantly prolongs the duration of PFS.
8: Disorders of bone and mineral other than osteoporosis (2004)

Rickets in children and osteomalacia in adults are caused by undermineralisation of bone, which increases its susceptibility to bending and fracture; treatment is with calcium, vitamin D or phosphate, depending on the specific mineral or vitamin deficiency. In Paget's disease, osteoclasts are overactive and produce woven or "repair" bone, which is mechanically weaker than lamellar bone; treatment is with antiresorptive bisphosphonate drugs. Cancers can produce bone lysis through direct spread within the skeleton or production of endocrine parathyroid hormone-like factors; treatment is with a bisphosphonate, plus appropriate therapy for the cancer. Cancer can also produce hypercalcaemia if the capacity of the kidneys to excrete the calcium dissolved from bone is exceeded; treatment is with saline infusion to increase excretion and a bisphosphonate. Primary hyperparathyroidism is the other common cause of hypercalcaemia and is usually associated with a single parathyroid adenoma; it is best treated with parathyroidectomy. Hypocalcaemia may result from severe decrease in calcium absorbed or lack of parathyroid action; both are treated with calcium and vitamin D (ergocalciferol or calcitriol). These disorders range from nutritional deficiencies to complex genetic and metabolic diseases
Effect of tamoxifen and radiotherapy in women with locally excised ductal carcinoma in situ: long-term results from the UK/ANZ DCIS trial (2010)

Cancer Research UK and the Australian National Health and Medical Research Council.
Mouse embryonic stem cell-derived feeder cells support the growth of their own mouse embryonic stem cells (2006)

Feeder cells are usually used in culturing embryonic stem cells (ESCs) to maintain their undifferentiated and pluripotent status. To test whether mouse embryonic stem cells (mESCs) may be a source of feeder cells to support their own growth, 48 fibroblast-like cell lines were isolated from the same mouse embryoid bodies (mEBs) at three phases (10th day, 15th day, 20th day), and five of them, mostly derived from 15th day mEBs, were capable of maintaining mESCs in an undifferentiated and pluripotent state over 10 passages, even up to passage 20. mESCs cultured on the feeder system derived from these five cell lines expressed alkaline phosphatase and specific mESCs markers, including SSEA-1, Oct-4, Nanog, and formed mEBs in vitro and teratomas in vivo. These results suggest that mEB-derived fibroblasts (mEB-dFs) could serve as feeder cells that could sustain the undifferentiated growth and pluripotency of their own mESCs in culture. This study not only provides a novel feeder system for mESCs culture, avoiding a lot of disadvantages of commonly used mouse embryonic fibroblasts as feeder cells, but also indicates that fibroblast-like cells derived from mESCs take on different functions. Investigating the molecular mechanisms of these different functional fibroblast-like cells to act on mESCs will contribute to the understanding of the mechanisms of mESCs self-renewal.
Out-of-Sample Extensions for LLE, Isomap, MDS, Eigenmaps, and Spectral Clustering (2003)

Several unsupervised learning algorithms based on an eigendecomposition provide either an embedding or a clustering only for given training points, with no straightforward extension for out-of-sample examples short of recomputing eigenvectors. This paper provides a unified framework for extending Local Linear Embedding (LLE), Isomap, Laplacian Eigenmaps, Multi-Dimensional Scaling (for dimensionality reduction) as well as for Spectral Clustering. This framework is based on seeing these algorithms as learning eigenfunctions of a data-dependent kernel. Numerical experiments show that the generalizations performed have a level of error comparable to the variability of the embedding algorithms due to the choice of training data. 1
Excess putrescine accumulation inhibits the formation of modified eukaryotic initiation factor 5A (eIF-5A) and induces apoptosis (1997)

DH23A cells, an alpha-difluoromethylornithine-resistant variant of the parental hepatoma tissue culture cells, express high levels of stable ornithine decarboxylase. Aberrantly high expression of ornithine decarboxylase results in a large accumulation of endogenous putrescine and increased apoptosis in DH23A cells when alpha-difluoromethylornithine is removed from the culture. Treatment of DH23A cells with exogenous putrescine in the presence of alpha-difluoromethylornithine mimics the effect of drug removal, suggesting that putrescine is a causative agent or trigger of apoptosis. Accumulation of excess intracellular putrescine inhibits the formation of hypusine in vivo, a reaction that proceeds by the transfer of the butylamine moiety of spermidine to a lysine residue in eukaryotic initiation factor 5A (eIF-5A). Treatment of DH23A cells with diaminoheptane, a competitive inhibitor of the post-translational modification of eIF-5A, causes both the suppression of eIF-5A modification in vivo and induction of apoptosis. These data support the hypothesis that rapid degradation of ornithine decarboxylase is a protective mechanism to avoid cell toxicity from putrescine accumulation. Further, these data suggest that suppression of modified eIF-5A formation is one mechanism by which cells may be induced to undergo apoptosis.
ChemInform Abstract: REACTION OF CINNAMYLIDENEMALONIC ESTERS OR CINNAMYLIDENE CYANOACETIC ESTERS AND THE CORRESPONDING MALONONITRILES WITH DIAZOMETHANE, THERMOLYSIS OF THE CORRESPONDING PYRAZOLINES (1978)

Abstract Durch Kondensation der betreffenden Ketone mit Cyanessigester, Dialkylmalonat bzw. Malodinitril werden nach bekannten Verfahren die Cinnamyliden‐Derivate (I) bis (V) dargestellt (Ausb. 60‐100%).
On the simultaneous binding of eukaryotic DNA topoisomerase II to a pair of double-stranded DNA helices (1993)

Stabilization of crossings of pairs of DNA helices by binding of eukaryotic DNA topoisomerase II was studied by two types of experiments. In one, mixtures of yeast DNA topoisomerase II and supercoiled DNA were incubated with vaccinia virus topoisomerase, and the linking numbers of the DNA products were measured to quantitate supercoils that were constrained by the stoichiometrically bound yeast enzyme molecules; in parallel, the same yeast enzyme-supercoiled DNA mixtures were incubated with a nonhydrolyzable ATP analog AMPPNP (adenosine 5'-(beta, gamma-imido)triphosphate) instead of the vaccinia enzyme, and DNA linking number changes following the addition of AMPPNP were measured to monitor DNA transport mediated by the yeast enzyme and AMPPNP. In the second type of experiments, formation of knotted DNA rings by the addition of AMPPNP to mixtures of yeast DNA topoisomerase II and different topological forms of DNA rings was studied. These experiments indicate that binding of yeast DNA topoisomerase II to DNA crossings is significant, especially in low salt media containing Mg(II), and that this mode of binding strongly affects DNA knotting. It appears, however, that stabilization of DNA crossovers by the eukaryotic type II enzyme is not directly related to its DNA transport activity.
Congenital Disorders of Glycosylation (2001)

Congenital disorders of glycosylation (CDG) are a rapidly growing group of genetic diseases that are due to defects in the synthesis of glycans and in the attachment of glycans to other compounds. Most CDG are multisystem diseases that include severe brain involvement. The CDG causing sialic acid deficiency of N-glycans can be diagnosed by isoelectrofocusing of serum sialotransferrins. An efficient treatment, namely oral D-mannose, is available for only one CDG (CDG-Ib). In many patients with CDG, the basic defect is unknown (CDG-x). Glycan structural analysis, yeast genetics, and knockout animal models are essential tools in the elucidation of novel CDG. Eleven primary genetic glycosylation diseases have been discovered and their basic defects identified: six in the N-glycan assembly, three in the N-glycan processing, and two in the O-glycan (glycosaminoglycan) assembly. This review summarizes their clinical, biochemical, and genetic characteristics and speculates on further developments in this field.
Determinants of efficacy of immunotherapy with tumor-derived heat shock protein gp96. (2001)

Immunotherapy with gp96 was highly effective in mice bearing methylcholanthrene-induced fibrosarcomas (Meth A tumors) when treatment began 7 days or less after tumor challenge, but significantly less effective if the treatment began 9 days after challenge. Immunotherapy of pre-existing tumors showed all the hallmarks of specificity of gp96 and dose-restriction observed previously with prophylactic studies. When mice with large primary Meth A tumors were treated with surgery alone, or with surgery followed by therapy with Meth A-derived gp96, the mice that received surgery and immunotherapy did significantly better than those receiving surgery alone. The relationship between the time of initiation of immunotherapy with gp96 and its efficacy was also tested in a metastatic model of the Lewis lung carcinoma. In this model, immunotherapy with gp96 was very effective if treatment began up to 31 days after tumor challenge, but significantly less so if therapy was initiated day 33 post-tumor challenge. These observations suggest that the regulatory phenomena that interfere with immunotherapy gather momentum with surprising speed.
Localization of Human Immunodeficiency Virus Type 1 Gag and Env at the Plasma Membrane by Confocal Imaging (2000)

Budding of lentiviruses occurs at the plasma membrane, but the preceding steps involved in particle assembly are poorly understood. Since the Gag polyprotein mediates virion assembly and budding, studies on the localization of Gag within the cell should provide insight into the mechanism of particle assembly. Here, we utilize biochemical fractionation techniques as well as high-resolution confocal imaging of live cells to demonstrate that Gag is localized at the plasma membrane in a striking punctate pattern. Mutation of the N-terminal myristoylation site results in the formation of large cytosolic complexes, whereas mutation of the N-terminal basic residue cluster in the matrix domain redirects the Gag protein to a region partially overlapping the Golgi apparatus. In addition, we show that Gag and Env colocalize at the plasma membrane and that mistargeting of a mutant Gag to the Golgi apparatus alters the pattern of surface expression of Env.
Differentiation of follicular dendritic cells and full antibody responses require tumor necrosis factor receptor-1 signaling. (1996)

Using mice double deficient for tumor necrosis factor (TNF) and lymphotoxin alpha (LT alpha), we demonstrated that TNF and/or LT alpha are necessary for development of a normal splenic microarchitecture and for isotype switch after immunization with sheep red blood cells (SRBC). In the present study, we extended these observations by determining which TNF receptor (TNFR) is involved in morphological and functional differentiation of the spleen. Spleen morphology and antibody response were investigated in wild-type, TNFR1-/-, TNFR2-/- and TNF/LT alpha-/- mice immunized with SRBC. TNF/LT alpha-/- mice, which have a complete disruption of the TNF/LT alpha signaling system including the LT beta-receptor pathway, displayed an abnormal microarchitecture, and isotype switch did not take place. TNFR1-/- and TNFR2-/- mice displayed a normal spleen microarchitecture and mounted an IgM and IgG antibody response to SRBC. However, the IgG production in TNFR1-/- mice was minimal, with citers leveling off 6 d after immunization. In this strain, immunofluorescence revealed a lack of follicular dendritic cells (FDC) network, detected with FDC-M1 as well as anti-CR1, and a lack of germinal centers, detected with peanut agglutinin. In conclusion, whereas normal splenic microarchitecture and isotype switch might require the LT beta receptor, differentiation of FDC network, development of germinal centers, and full IgG response depend on signaling via TNFR1.
Test-retest reliability of the halstead impairment index in hospitalized alcoholic and nonalcoholic males with mild to moderate neuropsychological impairment (1981)

Seven measures of neuropsychological functioning, the resulting Impairment Index described by Halstead, and Trails A and B were administered to drug-free alcoholic inpatients (n=91) within 7 days of their last drink and again 17 days later. Nonalcoholic medical inpatients (n=20) with similar education, age, and socioeconomic characteristics were also given these tests twice, with 2 to 3 weeks separating the test administrations. Both groups showed levels of mild to moderate impairment on the first testing and were judged to have stable brain functioning between the first and second testing. Significant Pearson's coefficients of correlation between test-retest scores indicated similar psychometric reliabilities in both groups. In contrast, the reliability of the tests was judged to be questionable when Halstead's binary classification of "normal" versus "abnormal" was used to classify individual patients. Consequently, and consistent with clinical experience, we urge caution in interpreting these clinical neuropsychological tests when they are administered repeatedly within a 2- to 3-week period to a single individual with stabilized brain functioning.
A Porous Multilayer Dye-Based Photoelectrochemical Cell That Unexpectedly Runs in Reverse (2004)

Porous dye multilayers based on cavity-containing porphyrinic molecular squares are capable of sensitizing flat indium−tin oxide (ITO) electrodes to photocurrent production with visible light. In aqueous I3-/I- solutions the sensitized electrodes unexpectedly produce cathodic photocurrents, the opposite of the anodic photocurrents generally observed with conventional dye-senstized solar cells (DSSCs). In constrast to DSSCs, which work by electron injection from a dye excited state into the photoelectrode's conduction band, the mechanism of photocurrent generation is I3- quenching of the porphyrin square excited state to produce an oxidized dye. Quenching is possible, despite the short excited state lifetime, because of ground state donor (chromophore)/acceptor (quencher) complex formation. Following quenching, ground state redox hopping through the multilayer structure delivers the oxidizing equivalent to the ITO electrode. One consequence is the photocurrent production can be systematically increased by adding dye layers and collecting more light (behavior not usually seen with DSSCs). Another is that only small photovoltages can be produced. A third is that the photocurrent production scheme is inoperable when ITO is replaced by titanium dioxide, because the electrons produced are energetically incapable of reaching the TiO2 conduction band. Perhaps most importantly, to the extent that the first part of the scheme (molecular quenching) occurs in conventional cells, the photocurrent efficiencies of these cells will be diminished.
High-Titer Human Immunodeficiency Virus Type 1-Based Vector Systems for Gene Delivery into Nondividing Cells (1998)

Previously we designed novel pseudotyped high-titer replication defective human immunodeficiency virus type 1 (HIV-1) vectors to deliver genes into nondividing cells (J. Reiser, G. Harmison, S. Kluepfel-Stahl, R. O. Brady, S. Karlsson, and M. Schubert, Proc. Natl. Acad. Sci. USA 93:15266-15271, 1996). Since then we have made several improvements with respect to the safety, flexibility, and efficiency of the vector system. A three-plasmid expression system is used to generate pseudotyped HIV-1 particles by transient transfection of human embryonic kidney 293T cells with a defective packaging construct, a plasmid coding for a heterologous envelope (Env) protein, and a vector construct harboring a reporter gene such as neo, ShlacZ (encoding a phleomycin resistance/beta-galactosidase fusion protein), HSA (encoding mouse heat-stable antigen), or EGFP (encoding enhanced green fluorescent protein). The packaging constructs lack functional Vif, Vpr, and Vpu proteins and/or a large portion of the Env coding region as well as the 5' and 3' long terminal repeats, the Nef function, and the presumed packaging signal. Using G418 selection, we routinely obtained vector particles pseudotyped with the vesicular stomatitis virus G glycoprotein (VSV-G) with titers of up to 8 x 10(7) CFU/microgram of p24, provided that a functional Tat coding region was present in the vector. Vector constructs lacking a functional Tat protein yielded titers of around 4 x 10(6) to 8 x 10(6) CFU/microgram of p24. Packaging constructs with a mutation within the integrase (IN) core domain profoundly affected colony formation and expression of the reporter genes, indicating that a functional IN protein is required for efficient transduction. We explored the abilities of other Env proteins to allow formation of pseudotyped HIV-1 particles. The rabies virus and Mokola virus G proteins yielded high-titer infectious pseudotypes, while the human foamy virus Env protein did not. Using the improved vector system, we successfully transduced contact-inhibited primary human skin fibroblasts and postmitotic rat cerebellar neurons and cardiac myocytes, a process not affected by the lack of the accessory proteins.