gebhart/patrepeval huggingface dataset:
Changes in levels of cellular retinol- and retinoic-acid-binding proteins of liver and lung during perinatal development of rat. (1976)

Cellular retinol-binding protein and cellular retinoic-acid-binding protein, canditates for mediating the action of vitamin A, were found to be present in tissues of the fetal rat. Cellular retinol-binding proteins were still present in most tissues of the adult, but the retinoic-acid-binding protein was not detected in some, including lung, liver, intestine, and kidney. During perinatal development of lung the level of cellular retinol-binding protein remained relatively constant while the level of the cellular retinoic-acid-binding protein peaked at 10 days postnatally, then declined. It was not detectable in lung tissue from 21-day-old rats. In liver, however, the retinoic-acid-binding protein was not detectable later than 5 days postnatally, while the level of the cellular retinol-binding proteinrose sharply near birth, declining only after 21 days to the lower adult levels. The variations observed in the levels of the two binding proteins suggest different and changing requirements for retinol and retinoic acid in organ development and maturation.
A Multicenter Phase II Study of Ganetespib Monotherapy in Patients with Genotypically Defined Advanced Non–Small Cell Lung Cancer (2013)

Ganetespib monotherapy showed a manageable side effect profile as well as clinical activity in heavily pretreated patients with advanced NSCLCs, particularly in patients with tumors harboring ALK gene rearrangement.
Enhanced animal growth via ligand regulated GHRH myogenic injectable vectors (2002)

Regulated animal growth occurred following a single electroporated injection of a mixture of two plasmids (10 microg of DNA), one expressing the GeneSwitch regulator protein, the other an inducible growth hormone releasing hormone (GHRH) gene, into the tibialis anterior muscles of adult SCID mice. Administration of the ligand mifepristone (MFP) up-regulated GHRH expression, as shown by elevations of IGF-I levels, and when MFP dosing was withdrawn, IGF-I returned to baseline levels. Five cycles of IGF-I induction were observed during a five-month period. Chronic MFP dosing for 25 days increased lean body mass, weight gain, and bone mineral density significantly compared with non-MFP treated controls. In summary, long-term drug-regulated GHRH expression was achieved following plasmid-based gene therapy, and chronic induction of GHRH expression in adult animals led to improvements in weight gain and body composition.
Antiretroviral Therapy in Adults (2000)

The availability of new antiretroviral drugs has expanded treatment choices. The importance of adherence, emerging long-term complications of therapy, recognition and management of antiretroviral failure, and new monitoring tools are addressed. Optimal care requires individualized management and ongoing attention to relevant scientific and clinical information in the field.
Identification of a New Family of Tissue-Specific Basic Helix-Loop-Helix Proteins with a Two-Hybrid System (1995)

With modified two-hybrid technology, we have isolated a member of a new family of basic helix-loop-helix (bHLH) transcription factors. Thing1 (Th1) was identified in a screen of a mouse embryo cDNA library as a partner for the Drosophila E protein daughterless. RNA in situ hybridization and reverse transcriptase-PCR demonstrate a stage- and tissue-specific distribution for the expression of Th1. Although tissue specific, the expression pattern of Th1 is fairly complex. During development, Th1 mRNA is widely expressed in extraembryonic tissues, portions of the heart, autonomic ganglia, the gut, and pharyngeal arches. At embryonic day 7.5 (E7.5), extraembryonic derivatives show robust Th1 expression. By E8.5, expression in the embryonic heart becomes detectable. During the next 2 days of development, the signal also includes gut and pharyngeal arches. Predominant expression at E13.5 is in neural crest derivatives, especially the autonomic nervous system and adrenal medulla. Expression of Th1 persists in the adult, in which it is localized to the smooth muscle cells of the gut. In vitro, Th1 protein recognizes a set of DNA sites that are more degenerate than has been determined for other bHLH factors, indicating a reduced binding specificity. Transient transfection of NIH 3T3 cells with GAL4-Th1 fusions reveals a repression activity mediated by the Th1 bHLH domain. In combination, these properties define Th1 as a new bHLH protein with a unique set of properties.
Information retrieval from hypertext using dynamically planned guided tours (1993)

In using any hypertext system a user will encounter many technical problems which have been well-documented in the literature.
Synthesis, Characterization, and Ethylene Oligomerization Action of [(C6H5)2PC6H4C(O-B(C6F5)3)O-κ2P,O]Ni(η3-CH2C6H5) (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSynthesis, Characterization, and Ethylene Oligomerization Action of [(C6H5)2PC6H4C(O-B(C6F5)3)O-κ2P,O]Ni(η3-CH2C6H5)Zachary J. A. Komon, Xianhui Bu, and Guillermo C. BazanView Author Information Departments of Chemistry and Materials University of California, Santa Barbara, California 93106 Cite this: J. Am. Chem. Soc. 2000, 122, 49, 12379–12380Publication Date (Web):November 23, 2000Publication History Received8 June 2000Published online23 November 2000Published inissue 1 December 2000https://pubs.acs.org/doi/10.1021/ja002042thttps://doi.org/10.1021/ja002042trapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views1083Altmetric-Citations119LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Catalysts,Hydrocarbons,Kinetic parameters,Oligomerization,Pharmaceuticals Get e-Alerts
Enhanced B-1 Cell Development, But Impaired IgG Antibody Responses in Mice Deficient in Secreted IgM (1998)

The role of endogenous natural IgM in promoting the adaptive Ab response was investigated in newly constructed mutant mice in which B cells do not secrete IgM but still express surface IgM and IgD and undergo class switching to express other Ig isotypes. While the mutant mice had relatively normal numbers of conventional B (B-2) cells in all tissues examined, unexpectedly, B-1 cells in the peritoneum and spleen were approximately threefold more abundant. The elevated levels of B-1 cells were already detectable at 4 wk of age and were stably maintained throughout life. The levels of serum IgG2a, IgG3, and IgA were also elevated in the mutant mice at an early age. IgG2a response to a T cell-independent Ag was augmented, whereas IgG Ab responses to suboptimal doses of a T cell-dependent Ag were impaired. The latter defect was associated with fewer splenic germinal centers, impaired Ab affinity maturation, and less Ag trapping on follicular dendritic cells. Together, these findings demonstrate a physiologic role of natural IgM in the feedback regulation of B-1 cell development, the regulation of IgG2a production, and the promotion of efficient B-2 cell Ab responses.
Cytotoxic activity of chimeric toxins containing the epidermal growth factor-like domain of heregulins fused to PE38KDEL, a truncated recombinant form of Pseudomonas exotoxin. (1995)

The EGF-like domains of heregulin alpha, beta 1, beta 2, and beta 3 were fused to a truncated form of Pseudomonas exotoxin (PE38KDEL), which contains a modified carboxyl-terminal sequence, KDEL, that increases that toxin activity. The resulting chimeric toxins were produced in Escherichia coli, purified to near homogeneity, and shown to be cytotoxic to target cells with very high activity on HTB20, N-87 MCF-7, and HepG2 cells; high activity on A431 and MDA-MB468 cells; and low activity toward SK-OV3, L929, and KB cells. The fact that cytotoxicity did not correlate with the levels of erbB2 expression indicated that another receptor in the erb family might be involved. Accordingly, cytotoxicity assays were performed on NIH/3T3 cell lines transfected with EGFR, ErbB2, ErbB3, or ErbB4. The results indicate that the heregulin toxins target ErbB4 or possibly ErbB3 but not ErbB2.
Some remarks on the theory of graphs (1947)

Recently very much more general theorems have been proved by Grnwald and Milgram. 3 They in fact proved (among others) that the condition that G' contains no closed directed path is superfluous.
Passive and Electrically Actuated Solid-State Nanopores for Sensing and Manipulating DNA (2012)

Solid-state nanopores have emerged as powerful new tools for electrically characterizing single DNA molecules. When DNA molecules are made to rapidly translocate a nanopore by electrophoresis, the resulting ionic current blockage provides information about the molecular length and folding conformation. A solid-state nanopore can also be integrated with nanofabricated actuators and sensors, such as an embedded gate electrode or transverse tunneling electrodes, to enhance its functionality. Here we describe detailed methods for fabricating passive solid-state nanopores and using them to detect DNA translocations. We also describe procedures for integrating electrodes into the nanopore membrane in order to create an electrically active structure. Finally, we describe how to modulate the ionic conductance through a pore whose inner surface is surrounded by an embedded annular gate electrode.
Approximate pattern matching and its applications (1992)

In this thesis, we study approximate pattern matching problems. Our study is based on the Levenshtein distance model, where errors considered are 'insertions', 'deletions', and 'substitutions'. In general, given a text string, a pattern, and an integer k, we want to find substrings in the text that match the pattern with no more than k errors. The pattern can be a fixed string, a limited expression, or a regular expression. The problem has different variations with different levels of difficulties depending on the types of the pattern as well as the constraint imposed on the matching. We present new results both of theoretical interest and practical value. We present a new algorithm for approximate regular expression matching, which is the first to achieve a subquadratic asymptotic time for this problem. For the practical side, we present new algorithms for approximate pattern matching that are very efficient and flexible. Based on these algorithms, we developed a new software tool called 'agrep', which is the first general purpose approximate pattern matching tool in the UNIX system. 'agrep' is not only usually faster than the UNIX 'grep/egrep/fgrep' family, it also provides many new features such as searching with errors allowed, record-oriented search, AND/OR combined patterns, and mixed exact/approximate matching. 'agrep' has been made publicly available through anonymous ftp from cs.arizona.edu since June 1991.
Sustained Type I interferon signaling as a mechanism of resistance to PD-1 blockade (2019)

PD-1 blockade represents a major therapeutic avenue in anticancer immunotherapy. Delineating mechanisms of secondary resistance to this strategy is increasingly important. Here, we identified the deleterious role of signaling via the type I interferon (IFN) receptor in tumor and antigen presenting cells, that induced the expression of nitric oxide synthase 2 (NOS2), associated with intratumor accumulation of regulatory T cells (Treg) and myeloid cells and acquired resistance to anti-PD-1 monoclonal antibody (mAb). Sustained IFNβ transcription was observed in resistant tumors, in turn inducing PD-L1 and NOS2 expression in both tumor and dendritic cells (DC). Whereas PD-L1 was not involved in secondary resistance to anti-PD-1 mAb, pharmacological or genetic inhibition of NOS2 maintained long-term control of tumors by PD-1 blockade, through reduction of Treg and DC activation. Resistance to immunotherapies, including anti-PD-1 mAb in melanoma patients, was also correlated with the induction of a type I IFN signature. Hence, the role of type I IFN in response to PD-1 blockade should be revisited as sustained type I IFN signaling may contribute to resistance to therapy.
B Cell–attracting Chemokine 1, a Human CXC Chemokine Expressed in Lymphoid Tissues, Selectively Attracts B Lymphocytes via BLR1/CXCR5 (1998)

Although most leukocytes, T lymphocytes in particular, respond to several different chemokines, there is virtually no information on chemokine activities and chemokine receptors in B lymphocytes. A putative chemokine receptor, BLR1, that is expressed in Burkitt's lymphoma cells and B lymphocytes was cloned a few years ago. Deletion of the gene for BLR1 yielded mice with abnormal primary follicles and germinal centers of the spleen and Peyer's patches, reflecting the inability of B lymphocytes to migrate into B cell areas. By screening expressed sequence tag DNA sequences, we have identified a CXC chemokine, termed B cell-attracting chemokine 1 (BCA-1), that is chemotactic for human B lymphocytes. BCA-1 cDNA encodes a protein of 109 amino acids with a leader sequence of 22 residues. The mature protein shares 23-34% identical amino acids with known CXC chemokines and is constitutively expressed in secondary lymphoid organs. BCA-1 was chemically synthesized and tested for activity on murine pre-B cells 300-19 transfected with BLR1 and on human blood B lymphocytes. In transfected cells, BCA-1 induced chemotaxis and Ca2+ mobilization demonstrating that it acts via BLR1. Under the same conditions, no activity was obtained with 10 CXC and 19 CC chemokines, lymphotactin, neurotactin/fractalkine and several other peptide ligands. BCA-1 was also a highly effective attractant for human blood B lymphocytes (which express BLR1), but was inactive on freshly isolated or IL-2-stimulated T lymphocytes, monocytes, and neutrophils. In agreement with the nomenclature rules for chemokine receptors, we propose the term CXCR5 for BLR1. Together with the observed disturbance of B cell colonization in BLR1/ CXCR5-deficient mice, the present results indicate that chemotactic recruitment by locally produced BCA-1 is important for the development of B cell areas of secondary lymphoid tissues.
Galactose Metabolism and Capsule Formation in a Recombinant Strain of Streptococcus thermophilus with a Galactose-Fermenting Phenotype (2007)

The capsule-producing, galactose-negative Streptococcus thermophilus MR-1C strain was first transformed with a low-copy plasmid containing a functional galK gene from Streptococcus salivarius to generate a recombinant galactose-fermenting Strep. thermophilus strain named MR-AAC. Then, we compared the functional properties of Strep. thermophilus MR-AAC with those of the parent MR-1C strain when used as starter for fermented products and cheese. In lactose-supplemented laboratory medium, MR-AAC metabolized galactose, but only when the amount of lactose was less than 0.1% (wt/vol). After 7 h of fermentation, the medium was almost depleted of galactose. The parent strain, MR-1C, showed the same pattern, except that the concentration of galactose decreased by only 25% during the same period. It was found that, during milk fermentation and Mozzarella cheese production, the galactose-fermenting phenotype was not expressed by MR-AAC and this strain expelled galactose into the medium at a level similar to the parent MR-1C strain. In milk and in lactose-supplemented medium, capsular exopolysaccharide production occurred mainly during the late exponential phase and the stationary growth phase with similar kinetics between MR-1C and MR-AAC.
A Four-Kallikrein Panel Predicts Prostate Cancer in Men with Recent Screening: Data from the European Randomized Study of Screening for Prostate Cancer, Rotterdam (2010)

A panel of four kallikreins can help predict the result of initial biopsy in previously screened men with elevated PSA. Use of a statistical model based on the panel would substantially decrease rates of unnecessary biopsy.
Identification of two point mutations and a one base deletion in exon 19 of the dystrophin gene by heteroduplex formation (1993)

Two thirds of the Duchenne muscular dystrophy population have either gene deletions or duplications. The nondeletion/duplication cases are most likely the result of point mutations or small deletions and duplications that cannot be easily identified by current strategies. The major obstacle in identifying small mutations is due to the large size of the dystrophin gene. We selectively screened 5 DMD exons containing CpG dinucleotides in 110 DMD patients without detectable deletions or duplications. Nonsenses mutations are frequently due to a C- to -T transition within a CG dinucleotide pair. To screen for the nonsense mutations, we used the heteroduplex method. Utilizing this approach, we identified 2 different nonsense mutations and a single base deletion all occurring in exon 19. This is the first report of a clustering of small mutations in the dystrophin gene.
Enzymatic Route toward 6‐Methylated Baeocystin and Psilocybin (2019)

Psilocybin and its direct precursor baeocystin are indole alkaloids of psychotropic Psilocybe mushrooms. The pharmaceutical interest in psilocybin as a treatment option against depression and anxiety is currently being investigated in advanced clinical trials. Here, we report a biocatalytic route to synthesize 6-methylated psilocybin and baeocystin from 4-hydroxy-6-methyl-l-tryptophan, which was decarboxylated and phosphorylated by the Psilocybe cubensis biosynthesis enzymes PsiD and PsiK. N-Methylation was catalyzed by PsiM. We further present an in silico structural model of PsiM that revealed a well-conserved SAM-binding core along with peripheral nonconserved elements that likely govern substrate preferences.
Genetically Engineered Mesenchymal Stem Cells: Applications in Spine Therapy (2008)

Spine disorders and intervertebral disc degeneration are considered the main causes for the clinical condition commonly known as back pain. Spinal fusion by implanting autologous bone to produce bony bridging between the two vertebrae flanking the degenerated-intervertebral disc is currently the most efficient treatment for relieving the symptoms of back pain. However, donor-site morbidity, complications and the long healing time limit the success of this approach. Novel developments undertaken by regenerative medicine might bring more efficient and available treatments. Here we discuss the pros and cons of utilizing genetically engineered mesenchymal stem cells for inducing spinal fusion. The combination of the stem cells, gene and carrier are crucial elements for achieving optimal spinal fusion in both small and large animal models, which hopefully will lead to the development of clinical applications.
In Vivo Activation of cAMP Signaling Induces Growth Arrest and Differentiation in Acute Promyelocytic Leukemia (2002)

Differentiation therapy for acute myeloid leukemia uses transcriptional modulators to reprogram cancer cells. The most relevant clinical example is acute promyelocytic leukemia (APL), which responds dramatically to either retinoic acid (RA) or arsenic trioxide (As(2)O(3)). In many myeloid leukemia cell lines, cyclic adenosine monophosphate (cAMP) triggers growth arrest, cell death, or differentiation, often in synergy with RA. Nevertheless, the toxicity of cAMP derivatives and lack of suitable models has hampered trials designed to assess the in vivo relevance of theses observations. We show that, in an APL cell line, cAMP analogs blocked cell growth and unraveled As(2)O(3)-triggered differentiation. Similarly, in RA-sensitive or RA-resistant mouse models of APL, continuous infusions of 8-chloro-cyclic adenosine monophosphate (8-Cl-cAMP) triggered major growth arrest, greatly enhanced both spontaneous and RA- or As(2)O(3)-induced differentiation and accelerated the restoration of normal hematopoiesis. Theophylline, a well-tolerated phosphodiesterase inhibitor which stabilizes endogenous cAMP, also impaired APL growth and enhanced spontaneous or As(2)O(3)-triggered cell differentiation in vivo. Accordingly, in an APL patient resistant to combined RA-As(2)O(3) therapy, theophylline induced blast clearance and restored normal hematopoiesis. Taken together, these results demonstrate that in vivo activation of cAMP signaling contributes to APL clearance, independently of its RA-sensitivity, thus raising hopes that other myeloid leukemias may benefit from this therapeutic approach.
Pharmacokinetic Evaluation of Twice‐Daily Extended‐Release Carbamazepine (CBZ) and Four‐Times‐Daily Immediate‐Release CBZ in Patients with Epilepsy (1998)

Our results demonstrate that extended-release CBZ twice daily was bioequivalent to immediate-release CBZ four times daily, with regard to CBZ levels and summation of CBZ and CBZ-E levels, based on the pharmacokinetic parameters evaluated. Substituting one formulation for the other did not cause patients to have a significant change in seizure frequency.
Intelligent Distributed Acoustic Sensing for In-well Monitoring (2014)

Abstract Interval Control Valves ICVs and Inflow Control Devices ICDs can enable optimization of the production and injection profile along the wellbore. The ICV devices are operated to increase the hydrocarbon recovery and prevent unwanted fluid production. The ICDs are selected and positioned to optimize the water flood profile. Although the operations of devices are well understood, the optimization of these devices in-situ is complex. The real-time monitoring of fluid flow along the wellbore can provide valuable information to set the position of the inflow devices and optimize the fluid flow in multilateral zones. The intelligent Distributed Acoustic Sensor (iDAS) uniquely allows the simultaneous recording of acoustic energy along many kilometers of optical fiber deployed along the wellbore. The system uses a novel digital optoelectronics detection technique that captures the amplitude and phase of the acoustic waves generated and propagated along the wellbore over a wide frequency (1mHz – 100kHz) range with a high dynamic range (&amp;gt;120dB). A number of signal processing techniques have been developed for processing a large array of acoustic data that can be recorded along the wellbore for monitoring the inflow at different zones. The iDAS system can be used with single-mode as well as multimode optical fibers. The iDAS system was retrofitted to existing optical fibers that were already installed along several wells in Saudi Arabia. The acoustic noise energy generated across the inflow devices and propagating along the wellbore tubing was recorded. The acoustic noise spectrum can be used to monitor the fluid flow through the inflow devices. Using array processing, the speed of sound can be determined over several sections of the tubing to identify the fluid composition. This paper reports on the results of the field trial carried in 2012 in several wells equipped with inflow devices.