gebhart/patrepeval huggingface dataset:
The Mammalian Gene Collection (1999)

The Mammalian Gene Collection (MGC) project is a new effort by the NIH to generate full-length complementary DNA (cDNA) resources. This project will provide publicly accessible resources to the full research community. The MGC project entails the production of libraries, sequencing, and database and repository development, as well as the support of library construction, sequencing, and analytic technologies dedicated to the goal of obtaining a full set of human and other mammalian full-length (open reading frame) sequences and clones of expressed genes.
Costimulation through CD28 enhances T cell-dependent B cell activation via CD40-CD40L interaction. (1994)

Changes in T cell helper function were analyzed when anti-CD3-activated T cells were costimulated with mAbs to the CD28 receptor (anti-CD28). T cell-dependent B cell growth and differentiation were consistently augmented if anti-CD3 stimulated-T cells were simultaneously activated with anti-CD28. Although anti-CD28 enhanced IL-2 and IL-4 production, it did not increase B cell responses solely by augmenting production of soluble lymphokines. Anti-CD28 costimulation induced increases on T cells of CD40 ligand (CD40L), known to promote B cell proliferation and Ig secretion. Because anti-CD28 promoted T cell helper functions and expression of CD40L, we examined the dependence for CD40L during T cell-dependent B cell responses. Although soluble CD40 fusion proteins only partially inhibited T cell-dependent B cell activation, we found a strict requirement for CD40L expression at initiating B cell responses. Both CD40L expression and T cell help were blocked by cyclosporin A after TCR cross-linking, and, unlike T cell proliferation, both remained cyclosporin A sensitive during CD28 costimulation. In addition, anti-CD28 could not compensate for the T cell helper deficiency of hyper IgM syndrome patients who lack functional CD40L. Thus, anti-CD28-induced T cell help is delivered via a CD40L-dependent process. The fact that cross-linking CD40 on B cells promotes expression of the B7/BB-1 ligand for CD28 suggest T and B interactions may have a reciprocal amplification mechanism.
A Similarity Between Viral Defense and Gene Silencing in Plants (1997)

Gene silencing in plants, in which an endogenous gene is suppressed by introduction of a related transgene, has been used for crop improvement. Observations that viruses are potentially both initiators and targets of gene silencing suggested that this phenomenon may be related to natural defense against viruses. Supporting this idea, it was found that nepovirus infection of nontransgenic plants induces a resistance mechanism that is similar to transgene-induced gene silencing.
Wnt11 gene therapy with adeno-associated virus 9 improves the survival of mice with myocarditis induced by coxsackievirus B3 through the suppression of the inflammatory reaction (2015)

The wnt signaling pathway plays important roles in development and in many diseases. Recently several reports suggest that non-canonical Wnt proteins contribute to the inflammatory response in adult animals. However, the effects of Wnt proteins on virus-induced myocarditis have not been explored. Here, we investigated the effect of Wnt11 protein in a model of myocarditis induced by coxsackievirus B3 (CVB3) using recombinant adeno-associated virus 9 (rAAV9). The effect of Wnt11 gene therapy on a CVB3-induced myocarditis model was examined using male BALB/c mice. Mice received a single intravenous injection of either rAAV9-Wnt11 or rAAV9-LacZ 2 weeks before intraperitoneal administration of CVB3. Intravenous injection of the rAAV9 vector resulted in efficient, durable, and relatively cardiac-specific transgene expression. Survival was significantly greater among rAAV9-Wnt11 treated mice than among mice treated with rAAV9-LacZ (87.5% vs. 54.1%, P < 0.05). Wnt11 expression also reduced the infiltration of inflammatory cells, necrosis of the myocardium, and suppressed the mRNA expression of inflammatory cytokines. This is the first report to show that Wnt11 expression improves the survival of mice with CVB3-induced myocarditis. AAV9-mediated Wnt11 gene therapy produces beneficial effects on cardiac function and increases the survival of mice with CVB3-induced myocarditis through the suppression of both infiltration of inflammatory cells and gene expression of inflammatory cytokines.
Bacterial translocation from the gut: a mechanism of infection. (1988)

Bacterial infection is a common and serious problem in burn victims who survive the shock phase of thermal injury. Our experimental work, plus the clinical studies of others, suggests that the gut can serve as a reservoir for systemic infections caused by bacteria that cross (translocate) the gastrointestinal (GI) epithelium. Bacterial translocation from the GI tract does not normally occur in the healthy animal owing to (1) the presence of an indigenous GI microflora preventing bacterial overgrowth, (2) an intact intestinal epithelial barrier, and (3) normal host immune defenses. However, a thermal injury, as well as other stressors, can result in the disruption or impairment of any of these protective mechanisms, potentially leading to lethal systemic infections with bacteria colonizing the gut.
Knockout of the regulatory site of 3‐ketoacyl‐ACP synthase III enhances short‐ and medium‐chain acyl‐ACP synthesis (2000)

3-ketoacyl-acyl carrier protein synthase (KAS) III catalyses the first condensing step of the fatty acid synthase (FAS) type II reaction in plants and bacteria, using acetyl CoA and malonyl-acyl carrier protein (ACP) as substrates. Enzymatic characterization of recombinant KAS III from Cuphea wrightii embryo shows that this enzyme is strongly inhibited by medium-chain acyl-ACP end products of the FAS reaction, i.e. inhibition by lauroyl-ACP was uncompetitive towards acetyl CoA and non-competitive with regard to malonyl-ACP. This indicated a distinct attachment site for regulatory acyl-ACPs. Based on alignment of primary structures of various KAS IIIs and 3-ketoacyl CoA synthases, we suspected the motif G290NTSAAS296 to be responsible for binding of regulatory acyl-ACPs. Deletion of the tetrapeptide G290NTS293 led to a change of secondary structure and complete loss of KAS III condensing activity. Exchange of asparagine291 to aspartate, alanine294 to serine and alanine295 to proline, however, produced mutant enzymes with slightly reduced condensing activity, yet with insensitivity towards acyl-ACPs. To assess the potential of unregulated KAS III as tool in oil production, we designed in vitro experiments employing FAS preparations from medium-chain fatty acid-producing Cuphea lanceolata seeds and long-chain fatty acid-producing rape seeds, each supplemented with a fivefold excess of the N291D KAS III mutant. High amounts of short-chain acyl-ACPs in the case of C. lanceolata, and of medium-chain acyl-ACPs in the case of rape seed preparations, were obtained. This approach targets regulation and offers new possibilities to derive transgenic or non-transgenic plants for production of seed oils with new qualities.
Inhibition of memory consolidation by antibodies against cell adhesion molecules after active avoidance conditioning in zebrafish (1999)

Cell adhesion molecules are expected to play an important role in long-term storage of information in the central nervous system. Several of these glycoproteins, such as NCAM, L1, and the ependymins, express the HNK-1 carbohydrate structure, which is known to be involved in cell-cell and cell-matrix interactions. To investigate the contribution of the HNK-1 epitope and the secretory glycoproteins ependymins to memory formation in zebrafish (Brachydanio rerio), we developed an active avoidance conditioning paradigm. Zebrafish were trained in a shuttle-box to cross a hurdle, to avoid mild electric shocks following a conditioning light signal. One hour after acquisition of the task, zebrafish were injected intracerebroventricularly with monoclonal antibodies against the HNK-1 epitope or polyclonal antibodies against ependymins. Control fish received immunoglobulins G (IgGs) from nonimmune rat serum or the monoclonal antibody C183 against an unrelated cell-surface protein of the cyprinid brain. Two days later, injected zebrafish were tested for recall, and for quantitative evaluation a retention score (RS), ranging from 1.0 for immediate recall to 0.0, indicating no saving, was calculated. The average RS of anti-HNK-1-injected fish (RS = 0.30) and anti-ependymin-injected fish (0.24) were significantly different from the RS of uninjected fish (0.77), of controls injected with nonimmune serum IgGs (0.68), of C183-injected controls (0.78), and of overtrained fish injected with anti-HNK-1 antibodies (0.81). Anti-HNK-1 and anti-ependymin antibodies were characterized by Western blot analyses of subcellular brain fractions and immunohistochemical staining of the zebrafish optic tectum. Our data suggest that the antibodies influence cell recognition events at synaptic membranes and/or associated intracellular signaling cascades, and thereby block memory consolidation.
Calcium-Ion–Sensing Cell-Surface Receptors (1995)

Calcium ions are essential for a wide variety of biologic functions, including vital extracellular processes, such as blood clotting, intercellular adhesion, and skeletal integrity, as well as intracellular processes, such as the regulation of hormonal secretion, cell division, and cell motility.14 Complex, free-living terrestrial organisms must maintain a near-constant concentration of extracellular calcium. How the body maintains and regulates extracellular calcium levels is a complex puzzle that has intrigued researchers for decades.35 One large piece of this puzzle that is falling into place concerns a cell-surface receptor that responds to, or “senses,” extracellular calcium-ion concentrations in parathyroid, kidney, . . .
Enhancing the GLP‐1 receptor signaling pathway leads to proliferation and neuroprotection in human neuroblastoma cells (2010)

Increasing evidence suggests that glucagon-like peptide-1 (GLP-1), an incretin hormone of current interest in type 2 diabetes, is neuroprotective in both cell culture and animal models. To characterize the neuroprotective properties of GLP-1 and associated underlying mechanisms, we over-expressed the GLP-1 receptor (GLP-1R) on human neuroblastoma SH-SY5Y cells to generate a neuronal culture system featuring enhanced GLP-1R signaling. In GLP-1R over-expressing SH-SY5Y (SH-hGLP-1R#9) cells, GLP-1 and the long-acting agonist exendin-4 stimulated cell proliferation and increased cell viability by 2-fold at 24 h at physiologically relevant concentrations. This GLP-1R-dependent action was mediated via the protein kinase A and phosphoinositide 3-kinase signaling pathways, with the MAPK pathway playing a minor role. GLP-1 and exendin-4 pretreatment dose-dependently protected SH-hGLP-1R#9 cells from hydrogen peroxide (H(2)O(2))- and 6-hydroxydopamine-induced cell death. This involved amelioration of elevated caspase 3 activity, down-regulation of pro-apoptotic Bax and up-regulation of anti-apoptotic Bcl-2 protein. In the presence of 6-hydroxydopamine, GLP-1's ability to lower caspase-3 activity was abolished with the phosphoinositide 3-kinase inhibitor, LY2940002, and partly reduced with the protein kinase A inhibitor, H89. Hence, GLP-1R mediated neurotrophic and anti-apoptotic actions co-contribute to the neuroprotective property of GLP-1 in neuronal cell cultures, and reinforce the potential therapeutic value of GLP-1R agonists in neurodegenerative disorders involving oxidative stress.
Elastin‐like polypeptides: A strategic fusion partner for biologics (2016)

Elastin-like peptides (ELPs) are derivatives of tropoelastin with a unique property that allows them to stay soluble below a certain critical temperature but reversibly form aggregates above that temperature. Since they are derived from tropoelastin, ELPs are biocompatible, non-toxic, and non-immunogenic. The unique properties of ELPs have made them a desirable class of fusion tags used in several biomedical applications including targeted drug delivery and enhancing the half-life of protein drugs. The most significant property of an ELP is that when fused to other proteins, the phase transition property of the ELP is maintained, and the target protein can be purified using the thermally driven property of the ELP. The ELP tag purification process is simple and inexpensive, and involves cycling the protein above and below the transition temperature of the ELP fusion followed by centrifugation to obtain the desired protein, without any need for chromatography. Consequently, using ELPs as a purification tag should be potentially interesting to biopharmaceutical companies who spend a significant percentage of their manufacturing costs on expensive protein purification techniques such as chromatography and filtration. However, ELP tags have not yet been used for commercial protein purification due to some challenges of translating this technique, which has been demonstrated mostly in academic laboratories, to a biotechnology manufacturing environment. The article first reviews the state-of-the-art in protein "ELPylation," and discusses some applications which have benefitted from using ELP as a fusion tag. Then, the article discusses the main advantages of using ELP as a purification tag, and evaluates the remaining hurdles for its implementation in industrial protein production. Biotechnol. Bioeng. 2016;113: 1617-1627. © 2016 Wiley Periodicals, Inc.
Effects of swainsonine and polyinosinic:polycytidylic acid on murine tumor cell growth and metastasis. (1986)

Increased sialylation and branching of asparagine-linked oligosaccharides have recently been associated with both neoplastic transformation and the metastatic phenotype. Swainsonine, an inhibitor of Golgi alpha-mannosidase II blocks the synthesis of sialylated tri- and tetraantennary asparagine-linked oligosaccharides and results in the expression of hybrid-type oligosaccharides at the cell surface. Both the lymphoid tumor line MDAY-D2 and B16F10 melanoma cells were less metastatic when grown in swainsonine (0.3 micrograms/ml) for 48 h prior to injection of the cells into the lateral tail veins of mice. The addition of swainsonine (2.5 micrograms/ml) to the drinking water of the mice further reduced the incidence of lung colonization by B16F10 melanoma cells. MDAY-D2 tumors removed from mice on swainsonine-supplemented drinking water showed a loss of leukoagglutinin-binding complex-type oligosaccharides similar to that of tumor cells cultured in medium containing swainsonine. The growth rate of s.c. MDAY-D2 tumors was not reduced by the addition of swainsonine to the drinking water of the host; however, when mice were given two i.p. injections of the interferon-inducing agent polyinosinic:polycytidylic acid in addition to swainsonine, the primary tumor grew at a reduced rate compared to either treatment alone. Swainsonine alone did not inhibit tumor cell growth in vitro; however, the drug enhanced the antiproliferative effect of interferon. The survival time of mice bearing established MDAY-D2 metastases was extended by treating the animals with swainsonine and polyinosinic:polycytidylic acid; however, the number of long-term survival was unchanged. Swainsonine-treated tumor cells appeared to be compromised in two ways: reduced organ colonization potential; and drug-treated MDAY-D2 cells were more sensitive to the antiproliferative effects of interferon in vitro and in vivo.
Fibronectin Expression on Surgical Specimens Correlated with the Response to Intravesical Bacillus Calmette-Guerin Therapy (1993)

Attachment of bacillus Calmette-Guerin (BCG) organisms to the bladder during intravesical therapy is thought to be mediated exclusively by the glycoprotein fibronectin, which is expressed variably on epithelial surfaces and on basement membranes. We examined the relationship between the degree of fibronectin expressed on surgical specimens obtained from 50 candidates for BCG therapy and the subsequent clinical response. Immunoperoxidase staining for fibronectin was performed on tumor, nonadjacent normal mucosa and basement membrane tissues, and the intensity of the staining was scored on a scale of 0 to 3+ (control 2+). In the absence of recurrence at quarterly surveillance cystoscopy, a course of Tice BCG therapy consisted of 6 weekly and 12 monthly instillations. Recurrence of noninvasive tumor prompted a second BCG course. Followup ranged from 24 to 66 months (median 40 months). Of the 50 patients (11 with carcinoma in situ) disease progression occurred in 9 (none with carcinoma in situ). Compared to the results for tumors or for basement membranes, the degree of fibronectin expression on normal mucosa was well correlated with the clinical response (r = 0.59, p < 0.001 by Kendall Tau B). Routine assessment of fibronectin expression on the normal mucosa associated with superficial bladder cancer may be useful for predicting the clinical response to BCG therapy.
Chromatin Remodeling and Control of Cell Proliferation by Progestins via Cross Talk of Progesterone Receptor with the Estrogen Receptors and Kinase Signaling Pathways (2006)

Transcription from the mouse mammary tumor virus (MMTV) promoter can be induced by glucocorticoids or progestins. Progesterone treatment of cultured cells carrying an integrated single copy of an MMTV transgene leads to recruitment of progesterone receptor (PR), SWI/SNF, and SNF2h-related complexes to MMTV promoter. Recruitment is accompanied by selective displacement of histones H2A and H2B from the nucleosome B. In nucleosomes assembled on promoter sequences, SWI/SNF displaces histones H2A and H2B from MMTV nucleosome B, but not from other MMTV nucleosomes or from an rDNA promoter nucleosome. Thus, the outcome of nucleosome remodeling by purified SWI/SNF depends on the DNA sequence. On the other hand, 5 min after hormone treatment, the cytoplasmic signaling cascade Src/Ras/Erk is activated via an interaction of PR with the estrogen receptor, which activates Src. As a consequence of Erk activation PR is phosphorylated, Msk1 is activated, and a ternary complex PR-Erk-Msk1 is recruited to MMTV nucleosome B. Msk1 phosphorylates H3 at serine 10, which is followed by acetylation at lysine 14, displacement of HP1gamma, and recruitment of Brg1, PCAF, and RNA polymerase II. Blocking Erk activation or Msk1 activity prevents induction of the MMTV transgene. Thus, the rapid nongenomic effects of progestins are essential for their transcriptional effects on certain progestin target genes. In rat endometrial stromal cells, picomolar concentrations of progestins trigger the cross talk of PR with ERbeta that activates the Erk and Akt kinase pathways leading to cell proliferation in the absence of direct transcriptional effects of the ligand-activated PR. Thus, depending on the cellular context rapid kinase activation and transcriptional effect play different roles in the physiological response to progestins.
Angiopoietin-1 Inhibits Irradiation- and Mannitol-Induced Apoptosis in Endothelial Cells (2000)

Ang1 promotes the survival of endothelial cells in irradiation- and mannitol-induced apoptosis through Tie2 receptor binding and PI3-kinase activation. Pretreatment with Ang1 could be beneficial in maintaining normal endothelial cell integrity during intracoronary irradiation or systemic mannitol therapy.
Selective Detection of Acetone and Hydrogen Sulfide for the Diagnosis of Diabetes and Halitosis Using SnO2 Nanofibers Functionalized with Reduced Graphene Oxide Nanosheets (2014)

Sensitive detection of acetone and hydrogen sulfide levels in exhaled human breath, serving as breath markers for some diseases such as diabetes and halitosis, may offer useful information for early diagnosis of these diseases. Exhaled breath analyzers using semiconductor metal oxide (SMO) gas sensors have attracted much attention because they offer low cost fabrication, miniaturization, and integration into portable devices for noninvasive medical diagnosis. However, SMO gas sensors often display cross sensitivity to interfering species. Therefore, selective real-time detection of specific disease markers is a major challenge that must be overcome to ensure reliable breath analysis. In this work, we report on highly sensitive and selective acetone and hydrogen sulfide detection achieved by sensitizing electrospun SnO2 nanofibers with reduced graphene oxide (RGO) nanosheets. SnO2 nanofibers mixed with a small amount (0.01 wt %) of RGO nanosheets exhibited sensitive response to hydrogen sulfide (Rair/Rgas = 34 at 5 ppm) at 200 °C, whereas sensitive acetone detection (Rair/Rgas = 10 at 5 ppm) was achieved by increasing the RGO loading to 5 wt % and raising the operation temperature to 350 °C. The detection limit of these sensors is predicted to be as low as 1 ppm for hydrogen sulfide and 100 ppb for acetone, respectively. These concentrations are much lower than in the exhaled breath of healthy people. This demonstrates that optimization of the RGO loading and the operation temperature of RGO-SnO2 nanocomposite gas sensors enables highly sensitive and selective detection of breath markers for the diagnosis of diabetes and halitosis.
Determination of the selenium requirement in kittens* (2003)

The purpose of this study was to determine the selenium (Se) requirement in kittens. Thirty-six specific-pathogen-free kittens (9.8 weeks old) were utilized in a randomized complete block design to determine the Se requirement in cats with gender and weight used as blocking criteria. Kittens were fed a low Se (0.02 mg/kg Se) torula yeast-based diet for 5 weeks (pre-test) after which an amino acid-based diet (0.027 mg Se/kg diet) was fed for 8 weeks (experimental period). Six levels of Se (0, 0.05, 0.075, 0.10, 0.20 and 0.30 mg Se/kg diet) as Na2SeO3 were added to the diet and were used to construct a response curve. Response variables included Se concentrations and Se-dependent glutathione peroxidase activities (GSHpx) in plasma and red blood cells (RBC) as well as plasma total T3 (TT3) and total T4 (TT4). No significant changes in food intake, weight gain or clinical signs of Se deficiency were noted. Estimates of the kitten's Se requirement (i.e. breakpoints) were determined for RBC and plasma GSHpx (0.12 and 0.15 mg Se/kg diet, respectively), but no definitive breakpoint was determined for plasma Se. Plasma TT3 increased linearly, whereas plasma TT4 and the ratio of TT4 : TT3 decreased in a quadratic fashion to dietary Se concentration. The requirement estimate determined in this study (0.15 mg Se/kg) for kittens is in close agreement with other species. As pet foods for cats contain a high proportion of animal protein with a Se bioavailability of 30%, it is recommended that commercial diets for cats contain 0.5 mg Se/kg DM.
Optimal IDM-MISO Transmit Strategy with Partial CSI at Transmitter (2006)

In this paper, we treat the analysis and optimization of interleave-division-multiplexing (IDM) MISO systems with partial CSI at the transmitters. In IDM-MISO systems, iterative receivers are employed to achieve parallel cancellation of the cross-antenna interference. We propose a general methodology to evaluate the performance of practical IDM-MISO systems. Specifically, an iterative approach is proposed to fast predict the output SNR of IDM detectors; the methods are developed to analyze the output of the repetition decoder and the LDPC decoder for uncoded and coded systems, respectively. Based on the above approaches, the optimal transmit strategy, i.e., the optimal power set, can be achieved for IDM-MISO systems. The proposed approaches are verified by extensive simulations.