gebhart/patrepeval huggingface dataset:
Clostridium difficileand inflammatory bowel disease: Role in pathogenesis and implications in treatment (2013)

Clostridium difficile (C. difficile) is the leading cause of antibiotic associated colitis and nosocomial diarrhea. Patients with inflammatory bowel disease (IBD) are at increased risk of developing C. difficile infection (CDI), have worse outcomes of CDI-including higher rates of colectomy and death, and experience higher rates of recurrence. However, it is still not clear whether C. difficile is a cause of IBD or a consequence of the inflammatory state in the intestinal environment. The burden of CDI has increased dramatically over the past decade, with severe outbreaks described in many countries, which have been attributed to a new and more virulent strain. A parallel rise in the incidence of CDI has been noted in patients with IBD. IBD patients with CDI tend be younger, have less prior antibiotic exposure, and most cases of CDI in these patients represent outpatient acquired infections. The clinical presentation of CDI in these patients can be unique-including diversion colitis, enteritis and pouchitis, and typical findings on colonoscopy are often absent. Due to the high prevalence of CDI in patients hospitalized with an IBD exacerbation, and the prognostic implications of CDI in these patients, it is recommended to test all IBD patients hospitalized with a disease flare for C. difficile. Treatment includes general measures such as supportive care and infection control measures. Antibiotic therapy with either oral metronidazole, vancomycin, or the novel antibiotic-fidaxomicin, should be initiated as soon as possible. Fecal macrobiota transplantation constitutes another optional treatment for severe/recurrent CDI. The aim of this paper is to review recent data on CDI in IBD: role in pathogenesis, diagnostic methods, optional treatments, and outcomes of these patients.
Identification and characterization of a second butyrate kinase from Clostridium acetobutylicum ATCC 824. (2000)

A gene encoding a new butyrate kinase isozyme (BKII) was identified from the C. acetobutylicum ATCC 824 DNA database. The enzyme was expressed in Escherichia coli, purified, and characterized. The purified enzyme exhibited a subunit molecular mass of 43 kDa by SDS-PAGE, and a native molecular mass of 80 kDa by gel filtration suggesting it functions as a dimer. In the butyryl phosphate-forming direction the optimal pH of BKII was 8.5. The enzyme had a Km of 0.62 M and a turn over rate of 2.2 x 10(5)/sec (Vmax of 165 units/mg). The presence of a mRNA encoding the BKII was demonstrated using a reverse transcription PCR reaction. The expression of the BKII in Clostridium acetobutylicum ATCC 824 was further examined by Western blot analysis using a polyclonal antibody prepared against recombinant BKII.
Mice with Spontaneous Pancreatic Cancer Naturally Develop MUC-1-Specific CTLs That Eradicate Tumors When Adoptively Transferred (2000)

Pancreatic cancer is a highly aggressive, treatment refractory cancer and is the fourth leading cause of death in the United States. In humans, 90% of pancreatic adenocarcinomas overexpress altered forms of a tumor-specific Ag, mucin 1 (MUC1; an epithelial mucin glycoprotein), which is a potential target for immunotherapy. We have established a clinically relevant animal model for pancreatic cancer by developing a double transgenic mouse model (called MET) that expresses human MUC1 as self molecule and develops spontaneous tumors of the pancreas. These mice exhibit acinar cell dysplasia at birth, which progresses to microadenomas and acinar cell carcinomas. The tumors express large amounts of underglycosylated MUC1 similar to humans. Tumor-bearing MET mice develop low affinity MUC1-specific CTLs that have no effect on the spontaneously occurring pancreatic tumors in vivo. However, adoptive transfer of these CTLs was able to completely eradicate MUC1-expressing injectable tumors in MUC1 transgenic mice, and these mice developed long-term immunity. These CTLs were MHC class I restricted and recognized peptide epitopes in the immunodominant tandem repeat region of MUC1. The MET mice appropriately mimic the human condition and are an excellent model with which to elucidate the native immune responses that develop during tumor progression and to develop effective antitumor vaccine strategies.
Synthesis and Characterization of Highly Efficient, Chemically and Thermally Stable Chromophores with Chromone-Containing Electron Acceptors for NLO Applications (1999)

Donor–acceptor substituted nonlinear optical (NLO) chromophores possessing large molecular hyperpolarizabilities and chemical and thermal stabilities are of interest because of their potential applications in high-speed electro-optic devices. Here, a series of chromophores is presented with a diethylamino group as donor and a variety of strong electron withdrawing groups on the chromone moiety. Incorporation of these chromophores into a polyimide gives a material with high E-O coefficients, low optical loss, and good thermal stability.
New tetramethylthiepinium (TMTI) for copper-free click chemistry (2012)

A new derivative of the strained 3,3,6,6-tetramethylthiacycloheptyne (TMTH) bearing a functional handle is reported. Following an optimized synthesis, the handle was introduced by mild alkylation of the sulphur atom. The resulting functionalized strained 4,5-didehydro-3,3,6,6-tetramethyl-2,3,6,7-tetrahydrothiepinium (TMTI) proved to be stable and underwent extremely fast [3+2] cycloaddition reaction with benzyl azide in both organic and aqueous solvents. The reaction was equally efficient in cell lysate and serum and therefore opens interesting prospects for chemical-biology applications.
The Interpretation of Permeability Changes During Acid Injection In Carbonates: A New Integrated Methodology (2015)

Abstract Monitoring and predicting the behavior induced by the injection of reactive fluids in carbonates is a common challenge for different applications. More particularly, acid is routinely injected in producers and injector wells within carbonate reservoirs to improve the permeability near the wellbore area. During a typical acid stimulation operation, two parameters are mainly monitored; these are the Bottom Hole Pressure (BHP) and the pumping rate. The objective of this paper is to highlight the importance of local changes on the overall pressure evolution and to provide a new methodology providing better interpretation of pressure-time evolution curves during acid stimulation operations. First, a series of elevated temperature and pressure acid injection core flooding experiments were conducted. The overall pressure drop across the core samples was monitored classically using two pressure transducers at the inlet and outlet of the samples. In addition five pressure taps were recorded along the samples to be able to monitor the pressure evolution along the cores. Permeability time-evolution was then obtained for different flow rates, acid types and carbonate cores. The carbonate cores were characterized using high resolution pore-scale imaging, MICP and XRD measurements. Then, we complemented our core flooding measurements with values of permeability-changes induced by acid injection found in the literature. A database was formed and was subsequently analyzed. We show that local changes in permeability can take place without impacting the overall pressure response. The measured permeability change depends on the scale of observation. We identified three main regimes of time-evolution permeability changes. We showed that the permeability is not directly proportional to the wormhole penetration. There is a certain time needed before starting to notice permeability increase. The wormhole breakthrough is characterized by a sharp increase in permeability. A new correlation factor that takes into account the pore size and the injection flow rate was obtained in order to correct for the time evolution permeability readings and take into account the impact of the scale of observations. This correlation was validated on the measurements from literature and from our laboratories. The next step will be to implement this correlation on a field case during acid stimulation operations. Insights and results of this methodology can be applicable to better monitor other injections of reactive fluids in the areas of EOR and CCS.
Solvent isotope effect in H2O-D2O mixtures (1964)

Abstract
Über pflanzliche Herzgifte, XXVI. Mitteil.: Die Cardenolid‐Glykoside der Blätter von Convallaria majalis (1954)

Abstract Herrn Prof. Dr. H. H. Schlubach zum 65. Geburtstag gewidmet Aus den Blättern des Maiglöckchens, Convallaria majalis L., wurden in kristallisierter Form, neben dem schon bekannten Convallatoxin, auch Convallatoxol und Convallosid isoliert. Ferner wurden zwei kristallisierte Glykoside gewonnen, deren Aglykon auf Grund des UV‐Spektrums keine Aldehydgruppe, sondern vermutlich eine Ketogruppe enthält; sie erhielten die Bezeichnung Vallarotoxin und Majalosid. Ihre Zucker sind Rhamnose bzw. Rhamnose und Glucose. Es wurde weiter das Vorkommen von Convallatoxolosid und Gluco‐convallosid wahrscheinlich gemacht. Daneben finden sich noch zwei Glykoside vor, in deren Aglykonen keine Oxogruppe vorkommt; sie konnten aber noch nicht kristallisiert erhalten werden.
Paragraph-level Neural Question Generation with Maxout Pointer and Gated Self-attention Networks (2018)

Question generation, the task of automatically creating questions that can be answered by a certain span of text within a given passage, is important for question-answering and conversational systems in digital assistants such as Alexa, Cortana, Google Assistant and Siri. Recent sequence to sequence neural models have outperformed previous rule-based systems. Existing models mainly focused on using one or two sentences as the input. Long text has posed challenges for sequence to sequence neural models in question generation -worse performances were reported if using the whole paragraph (with multiple sentences) as the input. In reality, however, it often requires the whole paragraph as context in order to generate high quality questions. In this paper, we propose a maxout pointer mechanism with gated self-attention encoder to address the challenges of processing long text inputs for question generation. With sentence-level inputs, our model outperforms previous approaches with either sentence-level or paragraph-level inputs. Furthermore, our model can effectively utilize paragraphs as inputs, pushing the state-of-the-art result from 13.9 to 16.3 (BLEU 4).
Alternatively Spliced Genes as Biomarkers for Schizophrenia, Bipolar Disorder and Psychosis: A Blood-Based Spliceome-Profiling Exploratory Study (Supplementry Table) (2009)

OBJECTIVE: Transcriptomic biomarkers of psychiatric diseases obtained from a query of peripheral tissues that are clinically accessible (e.g., blood cells instead of post-mortem brain tissue) have substantial practical appeal to discern the molecular subtypes of common complex diseases such as major psychosis. To this end, spliceome-profiling is a new methodological approach that has considerable conceptual relevance for discovery and clinical translation of novel biomarkers for psychiatric illnesses. Advances in microarray technology now allow for improved sensitivity in measuring the transcriptome while simultaneously querying the "exome" (all exons) and "spliceome" (all alternatively spliced variants). The present study aimed to evaluate the feasibility of spliceome-profiling to discern transcriptomic biomarkers of psychosis. METHODS: We measured exome and spliceome expression in peripheral blood mononuclear cells from 13 schizophrenia patients, nine bipolar disorder patients, and eight healthy control subjects. Each diagnostic group was compared to each other, and the combined group of bipolar disorder and schizophrenia patients was also compared to the control group. Furthermore, we compared subjects with a history of psychosis to subjects without such history. RESULTS: After applying Bonferroni corrections for the 21,866 full-length gene transcripts analyzed, we found significant interactions between diagnostic group and exon identity, consistent with group differences in rates or types of alternative splicing. Relative to the control group, 18 genes in the bipolar disorder group, eight genes in the schizophrenia group, and 15 genes in the combined bipolar disorder and schizophrenia group appeared differentially spliced. Importantly, thirty-three genes showed differential splicing patterns between the bipolar disorder and schizophrenia groups. More frequent exon inclusion and/or over-expression was observed in psychosis. Finally, these observations are reconciled with an analysis of the ontologies, the pathways and the protein domains significantly over-represented among the alternatively spliced genes, several of which support prior discoveries. CONCLUSIONS: To our knowledge, this is the first blood-based spliceome-profiling study of schizophrenia and bipolar disorder to be reported. The battery of alternatively spliced genes and exons identified in this discovery-oriented exploratory study, if replicated, may have potential utility to discern the molecular subtypes of psychosis. Spliceome-profiling, as a new methodological approach in transcriptomics, warrants further work to evaluate its utility in personalized medicine. Potentially, this approach could also permit the future development of tissue-sampling methodologies in a form that is more acceptable to patients and thereby allow monitoring of dynamic and time-dependent plasticity in disease severity and response to therapeutic interventions in clinical psychiatry.
High Luminous Efficiency Blue Organic Light-Emitting Devices Using High Triplet Excited Energy Materials (2007)

We succeeded to fabricate highly efficient blue organic light-emitting devices (OLEDs) by using a phosphorescent emitter, iridium(III) bis[(4,6-di-fluorophenyl)-pyridinate-N,C2']picolinate, and high triplet energy materials as the host and the carrier transport materials. A high power efficiency of 39 lm/W and external quantum efficiency of 21% were obtained at 100 cd/m2.
Levels of antibody to defined antigens of Mycobacterium tuberculosis in tuberculous meningitis (1989)

The aim of the study was to develop an antibody immunoassay for tuberculous meningitis with a sensitivity greater than that of the initial bacterial smear while maintaining a 100% specificity. Antibody titers to five purified antigens of Mycobacterium tuberculosis were measured in cerebrospinal fluid by using an enzyme-linked immunosorbent assay technique. Seventy-four patients with tuberculous meningitis (26 culture positive) were compared with 26 patients with purulent meningitis, 69 patients with suspected but excluded tuberculous meningitis, and 29 patients with other neurological diseases. Antibody responses to both the 14-kilodalton (kDa) antigen and lipoarabinomannan were immunodominant, accounting for 74% of those with any antibody titer to a soluble extract of M. tuberculosis. A sensitivity of 61% was achieved (77% for the culture-positive samples) by using immunoglobulin G titers to lipoarabinomannan and the 14-, 19-, and 38-kDa antigens. Thus, estimation of levels of antibody in cerebrospinal fluid to selected mycobacterial antigens would be valuable in the diagnosis of tuberculous meningitis. The possible reasons for the immunodominance of the 14-kDa antigen and lipoarabinomannan in the pathogenesis of tuberculous meningitis are discussed.
Interleukin 1 regulates human metallothionein gene expression. (1985)

Incubation of cultured human cells with interleukin 1 leads to increased expression of the human metallothionein-IIA gene. Recently, metallothionein has been shown to be an efficient free radical scavenger, and induction by interleukin 1 may be part of a protective response to minimize damage by hydroxyl radicals.
Significance of integrin alpha5 gene expression as a prognostic factor in node-negative non-small cell lung cancer. (2000)

The integrin family plays a major role in complex biological events such as differentiation, development, wound healing, and the altered adhesive and invasive properties of tumor cells. Integrin (alpha5beta1 is a classical fibronectin receptor, and it has been known as a tumor suppressor gene because tumor cells overexpressing alpha5beta1 are less tumorigenic than their parent cells. However, this finding conflicts with some recent data that suggests that the emergence of alpha5beta1 expression correlates with the tumor progression. We, therefore, investigated the expression of alpha5beta1 integrin in 20 lung cancer cell lines by flow cytometric analysis and in 88 node-negative non-small cell lung cancers (NSCLCs) by RT-PCR and immunohistochemical assays to determine the significance of this prognostic factor. In the 20 lung cancer cell lines, 8 (40.0%) cell lines strongly expressed integrin alpha5, 3 (15.0%) cell lines had moderate or weak alpha5 expression, and the remaining 9 (45.0%) cell lines expressed no integrin alpha5. In the 88 node-negative NSCLC patients, 44 samples (50.0%) were evaluated as having integrin alpha5 overexpression, and the integrin alpha5 expression was significantly associated with the status of differentiation and the age of the patients (P = 0.0379 and 0.0312, respectively). In the node-negative patients, the overall survival rate for patients with integrin alpha5 overexpressed tumors was significantly worse than for those individuals whose tumors had normal integrin alpha5 expression (P = 0.016).
A Simple Two-Step Approach for Introducing a Protected Diaminedithiol Chelator during Solid-Phase Assembly of Peptides (2002)

A simple synthetic strategy is described to incorporate a protected diaminedithiol (N(2)S(2)) chelator during Fmoc solid-phase synthesis of short peptides. The resulting constructs could be efficiently labeled with technetium-99m (99mTc). The chelator was assembled at the N-terminus of peptides in a two-step procedure where the deprotected terminal amino group was first reacted with di-Fmoc-diaminopropionic acid (Fmoc-DAP-[Fmoc]-OH). The two protected amino groups were then simultaneously deprotected and subsequently reacted with S-benzoylthiolglycolic acid (TGA) to generate a protected N(2)S(2) chelator. This metal binding site was introduced into di- and tripeptides. Each peptide construct was composed of a C-terminal lysine residue and an N-terminal diaminopropionic moiety modified to create the chelator site. The epsilon-amino group at the C-terminal lysine was further derivatized with a nitroimidazole group to facilitate cellular retention. The resulting constructs were then cleaved from the resin support, purified, and labeled with [99mTc]pertechnetate. Six constructs were prepared differing by a single amino acid inserted between the diaminopropionic acid and lysine residues. Optimal labeling yields of >70% were achieved around neutral pH and heating at 75 degrees C for 10 min. Purified 99mTc-labeled constructs were found to accumulate in Chinese hamster ovary (CHO) cells in vitro as a function of charge and hydrophobicity.
Bacterial plasminogen activators and receptors (2001)

Invasive bacterial pathogens intervene at various stages and by various mechanisms with the mammalian plasminogen/plasmin system. A vast number of pathogens express plasmin(ogen) receptors that immobilize plasmin(ogen) on the bacterial surface, an event that enhances activation of plasminogen by mammalian plasminogen activators. Bacteria also influence secretion of plasminogen activators and their inhibitors from mammalian cells. The prokaryotic plasminogen activators streptokinase and staphylokinase form a complex with plasmin(ogen) and thus enhance plasminogen activation. The Pla surface protease of Yersinia pestis resembles mammalian activators in function and converts plasminogen to plasmin by limited proteolysis. In essence, plasminogen receptors and activators turn bacteria into proteolytic organisms using a host-derived system. In Gram-negative bacteria, the filamentous surface appendages fimbriae and flagella form a major group of plasminogen receptors. In Gram-positive bacteria, surface-bound enzyme molecules as well as M-protein-related structures have been identified as plasminogen receptors, the former receptor type also occurs on mammalian cells. Plasmin is a broad-spectrum serine protease that degrades fibrin and noncollagenous proteins of extracellular matrices and activates latent procollagenases. Consequently, plasmin generated on or activated by Haemophilus influenzae, Salmonella typhimurium, Streptococcus pneumoniae, Y. pestis, and Borrelia burgdorferi has been shown to degrade mammalian extracellular matrices. In a few instances plasminogen activation has been shown to enhance bacterial metastasis in vitro through reconstituted basement membrane or epithelial cell monolayers. In vivo evidence for a role of plasminogen activation in pathogenesis is limited to Y. pestis, Borrelia, and group A streptococci. Bacterial proteases may also directly activate latent procollagenases or inactivate protease inhibitors of human plasma, and thus contribute to tissue damage and bacterial spread across tissue barriers.
GENETIC AND BIOCHEMICAL STUDIES OF PROTEIN N-MYRISTOYLATION (1994)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Resistance of Escherichia coli to tetracyclines. Changes in permeability to tetracyclines in Escherichia coli bearing transferable resistance factors (1967)

1. When strains of Escherichia coli, bearing transferable factors for resistance to the tetracyclines (R-factors), and previously cultured in the absence of the tetracyclines, are grown for 15-30min. in a low, subinhibitory, concentration (10mug./ml.) of oxytetracycline or tetracycline, there is a rapid and striking increase in resistance to oxytetracycline or tetracycline, this being associated with a marked fall in the absorption of the drug by the cells. 2. Very short preincubation (1min.) with oxytetracycline, followed by growth for 15-30min. in drug-free medium, produces a marked fall in the absorption of the drug by the resistant cells. Preincubation for 30min. with very low concentrations (0.05mug./ml.) of oxytetracycline produces a similar effect. 3. beta-Apo-oxytetracycline, which has very little antibacterial activity, also induces a decreased absorption of oxytetracycline. 4. The ability to exclude oxytetracycline is retained by preincubated resistant cells after growth for 2hr. in drug-free medium. However, after growth for 16hr. in drug-free medium, the cells absorb oxytetracycline freely. 5. Chloramphenicol and proflavine inhibit the adaptive decrease in tetracycline absorption. 5-Fluorouracil has only a slight effect. 6. Spheroplasts prepared from resistant cells show an impaired response to preincubation with tetracycline, compared with intact cells. 7. The relevance of these results to the probable mechanism of tetracycline resistance in R-factor-bearing E. coli is discussed.
The Evolving Role of Immune Checkpoint Inhibitors in Cancer Treatment (2015)

Immunotherapy is an evolving treatment approach based on the role of the immune system in eradicating cancer. An example of an immunotherapeutic is ipilimumab, an antibody that blocks cytotoxic T-lymphocyte antigen-4 (CTLA-4) to augment antitumor immune responses. Ipilimumab is approved for advanced melanoma and induced long-term survival in a proportion of patients. The programmed death-1 (PD-1) checkpoint inhibitors are promising immunotherapies with demonstrated sustained antitumor responses in several tumors. Because they harness the patient's own immune system, immunotherapies have the potential to be a powerful weapon against cancer.