gebhart/patrepeval huggingface dataset:
The transcription factor lymphoid enhancer factor 1 controls invariant natural killer T cell expansion and Th2-type effector differentiation (2015)

Invariant natural killer T cells (iNKT cells) are innate-like T cells that rapidly produce cytokines that impact antimicrobial immune responses, asthma, and autoimmunity. These cells acquire multiple effector fates during their thymic development that parallel those of CD4(+) T helper cells. The number of Th2-type effector iNKT cells is variable in different strains of mice, and their number impacts CD8 T, dendritic, and B cell function. Here we demonstrate a unique function for the transcription factor lymphoid enhancer factor 1 (LEF1) in the postselection expansion of iNKT cells through a direct induction of the CD127 component of the receptor for interleukin-7 (IL-7) and the transcription factor c-myc. LEF1 also directly augments expression of the effector fate-specifying transcription factor GATA3, thus promoting the development of Th2-like effector iNKT cells that produce IL-4, including those that also produce interferon-γ. Our data reveal LEF1 as a central regulator of iNKT cell number and Th2-type effector differentiation.
Identification of candidate mitochondrial RNA editing ligases from Trypanosoma brucei (2001)

Most mitochondrial genes of Trypanosoma brucei do not contain the necessary information to make translatable mRNAs. These transcripts must undergo RNA editing, a posttranscriptional process by which uridine residues are added and deleted from mitochondrial mRNAs. RNA editing is believed to be catalyzed by a ribonucleoprotein complex containing endonucleolytic, terminal uridylyl transferase (TUTase), 3' uridine-specific exonucleolytic (U-exo), and ligase activities. None of the catalytic enzymes for RNA editing have been identified. Here we describe the identification of two candidate RNA ligases (48 and 52 kDa) that are core catalytic components of the T. brucei ribonucleoprotein editing complex. Both enzymes share homology to the covalent nucleotidyl transferase superfamily and contain five key signature motifs, including the active site KXXG. In this report, we present data on the proposed 48 kDa RNA editing ligase. We have prepared polyclonal antibodies against recombinant 48 kDa ligase that specifically recognize the trypanosome enzyme. When expressed in trypanosomes as an epitope-tagged fusion protein, the recombinant ligase localizes to the mitochondrion, associates with RNA editing complexes, and adenylates with ATP. These findings provide strong support for the enzymatic cascade model for kinetoplastid RNA editing.
Tristetraprolin inhibits gastric cancer progression through suppression of IL-33 (2016)

Tristetraprolin (TTP) is an adenine/uridine (AU)-rich element (ARE)-binding protein that can induce degradation of mRNAs. In this study, we report that TTP suppresses the expression of interleukin-33 (IL-33), a tumor-promoting inflammatory cytokine, and thereby inhibits the progression of gastric cancer (GC). Overexpression of TTP decreased the level of IL-33, whereas knockdown of TTP increased IL-33 levels. We also discovered that TTP inhibited the proliferation, migration, and invasion of GC cell lines through regulation of IL-33. Furthermore, TTP RNA and protein levels were remarkably reduced in GC and inversely correlated with IL-33 level, and they were also closely associated with depth of invasion, lymph node metastasis, advanced TNM stage, as well as survival rate. Taken together, these findings identified TTP as a downregulator of IL-33, and further suggest that TTP can serve as a novel biomarker for the diagnosis of GC and as a potential therapeutic target for GC treatment.
A Phase II Study of Allogeneic GM-CSF–Transfected Pancreatic Tumor Vaccine (GVAX) with Ipilimumab as Maintenance Treatment for Metastatic Pancreatic Cancer (2020)

GVAX and ipilimumab maintenance therapy did not improve OS over continuation of chemotherapy and resulted in a numerically inferior survival in metastatic PDA. However, clinical responses and biological effects on immune cells were observed. Further study of novel combinations in the maintenance treatment of metastatic PDA is feasible.
Structural similarity between the lepidoptera- and diptera-specific insecticidal endotoxin genes of Bacillus thuringiensis subsp. "kurstaki" and "israelensis" (1986)

A gene from Bacillus thuringiensis subsp. "israelensis" was cloned from the large plasmids of this subspecies and was shown to code for a mosquitocidal polypeptide. The gene could be expressed in either Escherichia coli, Bacillus subtilis, or B. thuringiensis subsp. "israelensis" to produce the larvicidal activity. Similarly, a Lepidoptera-specific toxin gene from B. thuringiensis subsp. "kurstaki" was also cloned and expressed in E. coli and B. subtilis. Both cloned genes were sequenced and subjected to computer analysis. A long open translational reading frame coded for the B. thuringiensis subsp. "kurstaki" gene product. However, the B. thuringiensis subsp. "israelensis" clone was composed of two adjacent open reading frames oriented as if they were in a transcriptional operon. The products of the cloned genes retained their specificity for either Lepidoptera or Diptera. The control regions immediately preceding the toxin genes of both B. thuringiensis subspecies showed considerable DNA homology, most likely because both toxins are expressed only during sporulation. In addition, the deduced amino acid sequences from the two contiguous B. thuringiensis subsp. "israelensis" genes bore a striking resemblance to the deduced amino acid sequence from the single larger B. thuringiensis subsp. "kurstaki" gene, as if these two arrangements were evolutionarily related.
Regulation of Fracture Repair by Growth Factors (1992)

Fractured bones heal by a cascade of cellular events in which mesenchymal cells respond to unknown regulators by proliferating, differentiating, and synthesizing extracellular matrix. Current concepts suggest that growth factors may regulate different steps in this cascade (10). Recent studies suggest regulatory roles for PDGF, aFGF, bFGF, and TGF-beta in the initiation and the development of the fracture callus. Fracture healing begins immediately following injury, when growth factors, including TGF-beta 1 and PDGF, are released into the fracture hematoma by platelets and inflammatory cells. TGF-beta 1 and FGF are synthesized by osteoblasts and chondrocytes throughout the healing process. TGF-beta 1 and PDGF appear to have an influence on the initiation of fracture repair and the formation of cartilage and intramembranous bone in the initiation of callus formation. Acidic FGF is synthesized by chondrocytes, chondrocyte precursors, and macrophages. It appears to stimulate the proliferation of immature chondrocytes or precursors, and indirectly regulates chondrocyte maturation and the expression of the cartilage matrix. Presumably, growth factors in the callus at later times regulate additional steps in repair of the bone after fracture. These studies suggest that growth factors are central regulators of cellular proliferation, differentiation, and extracellular matrix synthesis during fracture repair. Abnormal growth factor expression has been implicated as causing impaired or abnormal healing in other tissues, suggesting that altered growth factor expression also may be responsible for abnormal or delayed fracture repair. As a complete understanding of fracture-healing regulation evolves, we expect new insights into the etiology of abnormal or delayed fracture healing, and possibly new therapies for these difficult clinical problems.
Phase I trial: safety and feasibility of intracranial electroencephalography using hybrid subdural electrodes containing macro- and microelectrode arrays (2008)

The authors demonstrate the use of hybrid subdural strip and grid electrodes containing high-density microwire arrays and standard clinical macroelectrodes. Hybrid electrodes provide high spatial resolution electrophysiology of the neocortex that is impossible with standard clinical iEEG. In this initial study in 24 patients, the complication rate is acceptable, and there does not appear to be increased risk associated with the use of hybrid electrodes compared with standard subdural and depth iEEG electrodes. More research is required to show whether hybrid electrode recordings will improve localization of epileptic foci and tracking the generation of neocortical seizures.
Human papillomavirus 16 DNA in NIH3T3 cells transformed by colonic cancer cellular DNA. (1993)

Human papillomavirus (HPV) 16 DNA is closely associated with human cancers. It has been identified as an aetiological agent in cervical cancers and, recently, in colonic neoplasms. To further understand the role of HPV 16 DNA in colorectal carcinogenesis, NIH3T3 cells were transformed with high molecular weight DNA from colonic cancer cells and the expression of HPV 16 DNA detected. Both human Alu and HPV 16 DNA sequences were found in the type II foci of CC-M2T cells by Southern blot hybridisation. Additionally, 100% tumorigenicity in nude mice was seen. This study shows the transfection of HPV DNA from colonic cancers into NIH3T3 mouse cells and suggests that HPV type 16 might be associated with the malignant transformation of colonic cells.
Genetic delivery of enzymes for cancer therapy. (1995)

For many years, antibodies have been examined as means to deliver cytotoxic proteins to kill target cells (immunotoxins). More recently, there have been studies on enzymes that convert prodrugs to active drugs to kill target cells. The advances in gene therapy strategies now allow one to deliver the gene for the protein or enzyme as an alternative. This technique, although in its infancy, promises to overcome some of the problems associated with antibody-mediated delivery. Thymidine kinase and cytosine deaminase are some of the enzymes currently being exploited in this way, but more are on the horizon. However, more research is still needed to enable full exploitation of the transcriptional differences between tumour and normal cells so that more existing cancers can be treated in this way.
Optimizing query rewrites for keyword-based advertising (2008)

We consider the problem of query rewrites in the context of pay-per-click search advertising. Given a three-layer graph consisting of queries, query rewrites, and the corresponding ads that can be served for the rewrites, we formulate a family of graph covering problems whose goals are to suggest a subset of ads with the maximum benefit by suggesting rewrites for a given query. We obtain constant-factor approximation algorithms for these covering problems, under two versions of constraints and a realistic notion of ad benefit. We perform experiments on real data and show that our algorithms are capable of outperforming a competitive baseline algorithm in terms of the benefit of the rewrites.
Identification of a fibronectin-binding protein (GfbA) in pathogenic group G streptococci (1996)

Attachment to eukaryotic cell surfaces is an essential step in the establishment of colonization and infection by bacterial pathogens. This report examines the adherence capabilities of pathogenic group G streptococci and demonstrates that certain group G streptococcal clinical isolates express a fibronectin-binding protein. This protein, termed GfbA for group G streptococcal fibronectin-binding protein, mediates adherence to human skin fibroblasts (HSF). The gene encoding this protein, gfbA, was isolated, and the complete DNA sequence of gfbA was determined. From this sequence GfbA was predicted to be a 580-amino-acid protein (molecular weight = 64,979) with significant amino acid identity to the group A streptococcal fibronectin-binding proteins SfbI and protein F (PrtF) (76 and 78% identity, respectively). GfbA contains regions with notable identity to the fibronectin-binding repeat domains of PrtF. gfbA(+) strains were able to bind to HSF, and preincubation of the gfbA(+) strains with fibronectin blocked this adherence. In addition, gfbA(+) strains were able to bind radiolabeled fibronectin, and this binding was inhibited with addition of excess unlabeled fibronectin. gfbA-negative strains were not able to bind either the HSF or radiolabeled fibronectin. DNA homologous to gfbA was found in 36% of the group G streptococcal isolates examined. Since not all group G streptococcal strains examined contained gfbA, this suggests there might be other tissue-specific adherence molecules expressed by these pathogenic strains.
American Society of Clinical Oncology - 36th Annual Meeting. (2000)

The American Society of Clinical Oncology (ASCO) 36th Annual Meeting, which took place from 20-23 May 2000 in New Orleans, was, as usual, a large, well-attended, internationally-represented meeting of cancer specialists. Both clinical trials of well established drugs for the treatment of cancer, as well as novel agents under development were presented in poster sessions, poster discussion sessions and large oral sessions. The prominent areas of new drug development presented were anti-angiogenic agents, tyrosine kinase inhibitors, immunotherapeutics and agents that modify the pharmacology or pharmacodynamics of chemotherapeutic agents. Sessions highlighting the translational development of several compounds with other mechanisms of action were also well attended. While there were no agents with unexpectedly dramatic clinical benefit, there were a number of promising developments.
A structural and electrical comparison of thin SiO2 films grown on silicon by plasma anodization and rapid thermal processing to furnace oxidation (1988)

We have used capacitance-voltage (C-V) techniques and x-ray photoelectron spectroscopy (XPS) to study for the first time the electrical and structural properties of thin SiO2 films grown on silicon by plasma anodization and rapid thermal processes (RTO) and then compared them to furnace oxides. We have compared the SiO4 tetrahedral ring structure and the suboxide content of the ∼3-nm-thick interfacial region of these oxides and have found significant structural differences. By correlating these differences with measured electrical differences, we have identified the structural causes of some of the electrical characteristics of the plasma and RTO oxides. In plasma oxides we see larger amounts of silicon dangling bonds, Pb centers, at the Si-SiO2 interface and have identified these dangling bonds as the source of a localized peak of interface states found at 0.3 eV above the silicon valence band. Low-temperature rapid thermal annealing of the plasma oxides relieves localized compressive interfacial strain, apparently by allowing the completion of oxidation at the interface, and reduces the amount of dangling bonds. However, this strain relief simultaneously increases the average SiO4 ring structure at the interface. A larger interfacial SiO4 ring structure is also seen in rapid thermal oxides and has been attributed to the very rapid cooling which takes place at the end of the rapid thermal process. Post-growth thermal processing has been shown to reduce the average ring structure by relieving localized tensile interfacial stress, but this stress relief is accompanied by the appearance of a peak of interface states at about 0.8 eV above the valence band which is attributed to Si–O bonds broken during the anneal. Long furnace anneals of rapid thermal oxides remove these states and give interface state densities comparable to those of furnace oxides.
Relation Classification via Convolutional Deep Neural Network (2014)

The state-of-the-art methods used for relation classification are primarily based on statistical ma-chine learning, and their performance strongly depends on the quality of the extracted features. The extracted features are often derived from the output of pre-existing natural language process-ing (NLP) systems, which leads to the propagation of the errors in the existing tools and hinders the performance of these systems. In this paper, we exploit a convolutional deep neural network (DNN) to extract lexical and sentence level features. Our method takes all of the word tokens as input without complicated pre-processing. First, the word tokens are transformed to vectors by looking up word embeddings1. Then, lexical level features are extracted according to the given nouns. Meanwhile, sentence level features are learned using a convolutional approach. These two level features are concatenated to form the final extracted feature vector. Finally, the fea-tures are fed into a softmax classifier to predict the relationship between two marked nouns. The experimental results demonstrate that our approach significantly outperforms the state-of-the-art methods. 1
A vector for expressing foreign genes in the brains and hearts of transgenic mice (1996)

An expression plasmid (MoPrP.Xho), for use in transgenic mice, was developed from the promoter, 5′ intronic, and 3′ untranslated sequences of the murine prion protein gene. Analyses of mice harboring the MoPrP.Xho construct with cDNA genes encoding the amyloid precursor protein (APP) and human presenilin 1 demonstrated that this vector provides relatively high levels of transgene-encoded polypeptides in brains and hearts of transgenic mice. The MoPrP.Xho vector should be very useful in strategies designed to overexpress a variety of wild-type and disease related mutant transgenes in the heart and brain.
Cytokines and bullous pemphigoid. (1999)

This report reviews the data presented in the literature concerning the presence and levels of different cytokines in sera, lesional tissue or blister fluids of patients with bullous pemphigoid. The list of cytokines analysed includes 21 molecules: interleukins (IL)-1 => 8, IL-10 => 13, IL-15, granulocyte-monocyte-colony stimulating factor (GM-CSF), interferon-gamma (IFN-gamma), oncostatin-M (OSM), regulated upon activation normal T cell expressed and presumably secreted (RANTES), transforming growth factor-beta 1 (TGF-beta 1), tumor necrosis factor-alpha (TNF-alpha) and vascular endothelial growth factor (VEGF). Basic information regarding the functions of these cytokines and their possible involvement in the pathogenetic steps of the disease, such as autoantigen expression, autoantibody induction, complement activation, local cell recruitment and stimulation, resident cell activation, release of various effector molecules and tissue damage are also reported. A specific function for each cytokine in bullous pemphigoid induction cannot be still defined, however, the literature attributes a major role to IL-1, IL-4, IL-5, IL-6, IL-8 and IFN-gamma. On the basis of significant (direct or inverse) correlations found between disease intensity and the blister fluid/serum levels, the following cytokines IL-7, IL-15, RANTES, VEGF and TNF-alpha, besides those previously mentioned, may also be involved in this disease.
Differentiation of Multiple Sclerosis from Other Inflammatory Disorders and Cerebrovascular Disease: Value of Spinal MR Imaging (2002)

In contrast to MS, cord lesions are very uncommon in OND. This finding can help differentiate these disorders.
Relationship Between Final Height and Health Outcomes in Adults With Congenital Adrenal Hyperplasia: United Kingdom Congenital Adrenal Hyperplasia Adult Study Executive (CaHASE) (2014)

Adult CAH patients remain short, although height prognosis has improved over time. The shortest adults are those diagnosed late with moderate severity CAH and are at increased risk of adult hypertension; we hypothesize that these patients are exposed in childhood to high androgens and/or excessive glucocorticoids with potential programming of hypertension. Another possibility is inadequate mineralocorticoid treatment early in life in the late-diagnosed patient group. Prospective studies are now required to examine these hypotheses.
Acetaminophen toxicity: suicidal vs accidental (2002)

We recommend that the patients with suicidal acetaminophen overdose, without any concomitant poisoning, can safely managed on the medical floors.
Cytotoxic effects of the lipophilic iron chelator omadine (1986)

Cytotoxic effects were observed following 4 h incubation of human leukaemic cells with the iron chelator 1-hydroxypyridine-2-thione (omadine). Its cytotoxic activity was comparable to that of the cytotoxic drug doxorubicin. At the same concentration two other effective iron chelators, desferrioxamine and 1,2-dimethyl-3-hydroxypyrid-4-one, were not cytotoxic. Addition of iron augmented the effect of omadine. It is suggested that the lipophilic properties of omadine and of its iron complex cause their intracellular accumulation and potent cytotoxic activity.
3-tert-Butyldimethylsilyloxymethyl-2-lithio-2-phenylsulfonyloxirane as a glycidyl anion equivalent; preparation of terminal epoxy ketones (1992)

3-tert-Butyldimethylsilyloxymethyl-2-phenylsulfonyloxirane 2 is efficiently substituted at the 2-position by deprotonation followed by quenching with electrophiles to give 2-substituted 2-phenylsulfonyloxiranes 4. These adducts may be converted in a three-step process into epoxy ketones 1 by ring-opening with magnesium bromide to give the α-bromo ketones 9, desilylation with boron trifluoride–diethyl ether to give the bromohydrins 11 and ring-closure with triethylamine to give the epoxy ketones 1. Alternatively, treatment of the α-bromo ketones 9 with tetrabutylammonium fluoride gives the epoxy ketones 1 in a single step. The ring-opening reaction with magnesium bromide and the ring-closure reaction with tetrabutylammonium fluoride may be carried out in a one-pot process. 2-Acylated 2-phenylsulfonyloxiranes are able act as acyl transfer agents both in an inter- and an intra-molecular sense.
Genetics and cytology of the ms3 male-sterile soybean (1980)

Journal Article Genetics and cytology of the ms3 male-sterile soybean Get access REID G. PALMER, REID G. PALMER SEA-AR, USDA, Iowa State University, Ames, IA 50011; graduate research assistant, Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843; and graduate student, Department of Botany, University of Wisconsin, Madison, WI 53706 Search for other works by this author on: Oxford Academic PubMed Google Scholar CAROL WINGER JOHNS, CAROL WINGER JOHNS SEA-AR, USDA, Iowa State University, Ames, IA 50011; graduate research assistant, Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843; and graduate student, Department of Botany, University of Wisconsin, Madison, WI 53706 Search for other works by this author on: Oxford Academic PubMed Google Scholar PATRICIA S. MUIR PATRICIA S. MUIR SEA-AR, USDA, Iowa State University, Ames, IA 50011; graduate research assistant, Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843; and graduate student, Department of Botany, University of Wisconsin, Madison, WI 53706 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Heredity, Volume 71, Issue 5, September 1980, Pages 343–348, https://doi.org/10.1093/oxfordjournals.jhered.a109383 Published: 01 September 1980
An overview of UNP (1989)

The paper gives a brief introduction to UNP: the Universal Naming Protocol. UNP specifies a generic attribute-based name server upon which a variety of high-level naming services---including white- and yellow-page services---can be built.