gebhart/patrepeval huggingface dataset:
Sequestration of DROSHA and DGCR8 by Expanded CGG RNA Repeats Alters MicroRNA Processing in Fragile X-Associated Tremor/Ataxia Syndrome (2013)

Fragile X-associated tremor/ataxia syndrome (FXTAS) is an inherited neurodegenerative disorder caused by the expansion of 55-200 CGG repeats in the 5' UTR of FMR1. These expanded CGG repeats are transcribed and accumulate in nuclear RNA aggregates that sequester one or more RNA-binding proteins, thus impairing their functions. Here, we have identified that the double-stranded RNA-binding protein DGCR8 binds to expanded CGG repeats, resulting in the partial sequestration of DGCR8 and its partner, DROSHA, within CGG RNA aggregates. Consequently, the processing of microRNAs (miRNAs) is reduced, resulting in decreased levels of mature miRNAs in neuronal cells expressing expanded CGG repeats and in brain tissue from patients with FXTAS. Finally, overexpression of DGCR8 rescues the neuronal cell death induced by expression of expanded CGG repeats. These results support a model in which a human neurodegenerative disease originates from the alteration, in trans, of the miRNA-processing machinery.
Creatine and phosphocreatine analogs: anticancer activity and enzymatic analysis. (1996)

The brain isoform of creatine kinase has been implicated in cellular transformation processes. Cyclocreatine, a creatine kinase substrate analog, was previously shown to be cytotoxic to a broad spectrum of solid tumors. We have synthesized, enzymatically characterized, and evaluated the antitumor activity of a series of substrate analogs of creatine kinase. Using in vitro assays, we demonstrate that several of these analogs are cytotoxic to the human ME-180 cervical carcinoma, the MCF-7 breast adenocarcinoma and the HT-29 colon adenocarcinoma cell lines at low mM concentrations. Analogs that were active in vitro delayed the growth of a subcutaneously implanted rat 13,762 mammary adenocarcinoma. Tumor growth delays of 6-8 days were achieved, which is comparable to effects seen with standard regimens of currently used anticancer drugs. These studies further establish the creatine kinase system as a promising and novel target for anticancer chemotherapy drug design.
Regulated globin mRNA decay is a cytoplasmic event proceeding through 3′-to-5′ exosome-dependent decapping (2002)

The α-globin mRNA contains a C-rich stability element (CRE) in its 3′ untranslated region (3′ UTR) which is critical for the stability of this long-lived mRNA. A protein complex, termed the α-complex, forms on the CRE and has been shown to contribute to stabilization of the mRNA by at least two mechanisms, first by interacting with the poly(A)-binding protein (PABP) to prevent deadenylation, and second by protecting the mRNA from attack by an erythroid endoribonuclease. In this report, we demonstrate that the α-globin 3′ UTR can confer stability on a heterologous mRNA in cells, and this stability is dependent on the α-complex. Moreover, the stability was exclusively detected with cytoplasmic mRNA, suggesting that the regulation of α-globin mRNA stability is a cytoplasmic event. An additional mechanism by which the α-complex can confer stability on an RNA in vitro was also identified and shown to involve inhibition of 3′ to 5′ exonucleolytic degradation. Furthermore, using an in vitro mRNA decay system, we were able to follow the demise of the α-globin RNA and demonstrate that the decay was initiated by deadenylation followed by 3′-to-5′ decay carried out by the exosome and ultimately hydrolysis of the residual cap structure.
Phase I Clinical Study With Multiple Peptide Vaccines in Combination With Tetanus Toxoid and GM-CSF in Advanced-stage HLA-A*0201-positive Melanoma Patients (2007)

Successful induction of functional tumor-specific T cells by peptide vaccination in animal models has resulted in many clinical trials to test this approach in advanced-stage melanoma patients. In this phase I clinical trial, 11 end-stage melanoma patients were vaccinated intradermally with 3 peptides: MART-1(26-35) E27L (ELAGIGILTV), tyrosinase(368-376) N375Q (YMDGTMSQV), and gp100(209-217) T210M (IMQVPFSV), admixed with tetanus toxoid and granulocyte-monocyte colony stimulating factor. The peptide vaccine was well tolerated at all tested doses, and led to grade 1-2 toxicity only. Although all patients did show a rise in antitetanus IgG titers, in only 3 patients peptide-specific CD8 T-cells were induced. In 2 cases, the response was directed against MART-1(26-35) and consisted of 0.2% and 3.3% of the CD8 population; however, in both instances these cells did not produce interferon-gamma on stimulation with the unmodified peptide. The third patient mounted a small (0.1%) response against gp100. In a fourth patient, a nonfunctional tyrosinase-specific response (0.6%) was found that was present before vaccination, but was not affected in size nor in function by the vaccine. None of the 11 patients responded clinically according to response evaluation criteria in solid tumors criteria. Although this study is a small scale phase I clinical trial, the efficacy that was observed was disappointingly low. In accordance with previously published peptide vaccination studies, these results add to the increasing evidence that peptide vaccination in itself is not potent enough as an effective melanoma immunotherapy in advanced-stage patients.
Effectiveness of Low-Level Laser Therapy in Temporomandibular Joint Disorders: A Placebo-Controlled Study (2007)

The results suggest that LLLT (application of 10 J/cm(2) and 15 J/cm(2)) can be considered as a useful method for the treatment of TMD-related pain, especially long lasting pain.
LIGAND database for enzymes, compounds and reactions (1999)

LIGAND is a composite database consisting of three sections and containing the information of chemical substances, chemical reactions and enzymes that catalyze reactions. The COMPOUND section is a collection of metabolic compounds, as well as macromolecules, chemical elements and other chemical substances in a living cell. The ENZYME section is a collection of all known enzymatic reactions, together with the information of enzyme molecules, classified according to the EC (Enzyme Commission) numbers. The REACTION section is a new addition to the database containing metabolic reactions that appear in the pathway diagrams of the KEGG/PATHWAY database and/or in the ENZYME section. The LIGAND database can be accessed through the WWW (http://www.genome.ad.jp/dbget/ligand.html) or may be downloaded by anonymous FTP (ftp://kegg.genome.ad. jp/molecules/ligand).
Micellization of mixed nonionic surface active agents (1975)

A theory is developed for micellization in systems of mixed nonionic surfactants. Assumptions of ideal mixing in the micellel and of a simple phase separation model enable the concentration of each monomeric species and hence the micellar composition to be calculated as a function of total concentration (c). For mixtures of homologous surfactants the surface tension (γ) at the air-water interface is calculated by assuming the mixed monolayer to be in equilibrium with the monomers in solution. The γ against log c curve in such a system is predicted to have a minimum. Comparison with γ against log c curves obtained experimentally shows excellent agreement with theory over the whole concentration range both below and above the c.m.c.
Synthesis and fungitoxicity of rationally designed thiazolo-1,3-dithiins, -thiazines, and -oxathiins (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and fungitoxicity of rationally designed thiazolo-1,3-dithiins, -thiazines, and -oxathiinsLal Dhar S. Yadav, Sangeeta. Sharma, and Anjum. VaishCite this: J. Agric. Food Chem. 1992, 40, 7, 1214–1216Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://pubs.acs.org/doi/10.1021/jf00019a028https://doi.org/10.1021/jf00019a028research-articleACS PublicationsRequest reuse permissionsArticle Views71Altmetric-Citations-LEARN 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-Alertsclose Get e-Alerts
Development of image mappers for hyperspectral biomedical imaging applications (2010)

A new design and fabrication method is presented for creating large-format (>100 mirror facets) image mappers for a snapshot hyperspectral biomedical imaging system called an image mapping spectrometer (IMS). To verify this approach a 250 facet image mapper with 25 multiple-tilt angles is designed for a compact IMS that groups the 25 subpupils in a 5 x 5 matrix residing within a single collecting objective's pupil. The image mapper is fabricated by precision diamond raster fly cutting using surface-shaped tools. The individual mirror facets have minimal edge eating, tilt errors of <1 mrad, and an average roughness of 5.4 nm.
Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure (2006)

Human and mouse genome sequences contain roughly 100,000 regions that are unalignable in primary sequence and neighbor corresponding alignable regions between both organisms. These pairs are generally assumed to be nonconserved, although the level of structural conservation between these has never been investigated. Owing to the limitations in computational methods, comparative genomics has been lacking the ability to compare such nonconserved sequence regions for conserved structural RNA elements. We have investigated the presence of structural RNA elements by conducting a local structural alignment, using FOLDALIGN, on a subset of these 100,000 corresponding regions and estimate that 1800 contain common RNA structures. Comparing our results with the recent mapping of transcribed fragments (transfrags) in human, we find that high-scoring candidates are twice as likely to be found in regions overlapped by transfrags than regions that are not overlapped by transfrags. To verify the coexpression between predicted candidates in human and mouse, we conducted expression studies by RT-PCR and Northern blotting on mouse candidates, which overlap with transfrags on human chromosome 20. RT-PCR results confirmed expression of 32 out of 36 candidates, whereas Northern blots confirmed four out of 12 candidates. Furthermore, many RT-PCR results indicate differential expression in different tissues. Hence, our findings suggest that there are corresponding regions between human and mouse, which contain expressed non-coding RNA sequences not alignable in primary sequence.
Thermally Induced Structural Transformation of Bisphenol‐1,2,3‐triazole Polymers: Smart, Self‐Extinguishing Materials (2010)

Safer plastics: A novel class of polymers, termed bisphenol-1,2,3-triazole (BPT) polyarylates, was prepared by polycondensation chemistry. They exhibit high-performance and self-extinguishing properties as a result of their heterocyclic nature and a thermally induced structural transformation (see picture). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
ALZHEIMER'S DISEASE: PAIRED HELICAL FILAMENTS AND CYTOMEMBRANES (1987)

Observations were made with the electron microscope on biopsies from the frontal cerebral cortex of four patients showing the clinical symptoms of advanced Alzheimer's disease (AD). Sections from all four biopsies showed neuronal dendrites, and to a lesser extent, perikarya, packed with paired helical filaments (PHFs) and a correlated complete loss of the normal content of microtubules. It was usually impossible to visualize the beginning and end of the PHF since it passed out of the plane of section. However, not infrequently, PHFs could be seen apparently arising at or from the surfaces of cytomembranes. Such membranes (in perikarya or dendrite) often formed irregular stacks or lamellated bodies. These membranes were invariably agranular (i.e. not studded with ribosomes) and so might be considered as pathological forms of smooth endoplasmic reticulum (SER). A correlation is established between the known biochemical nature of PHFs and their postulated membrane origin.
Comparison between Calcitriol and Calcitriol Plus Low-Dose Cinacalcet for the Treatment of Moderate to Severe Secondary Hyperparathyroidism in Chronic Dialysis Patients (2013)

We conclude that combination therapy of low-dose cinacalcet and calcitriol is more effective than calcitriol alone as a treatment for moderate and severe UHPT in chronic dialysis patients. Furthermore, this therapy is associated with improvement in hyperphosphatemia and hypercalcemia.
Combined status of MUC1 mucin and surfactant apoprotein A expression can predict the outcome of patients with small‐size lung adenocarcinoma (2004)

A high MUC1/SP-A ratio is strongly associated with a poor outcome in patients with small-size lung adenocarcinoma.
Elevated levels of circulating microRNA-200 family members correlate with serous epithelial ovarian cancer (2012)

We identified serum microRNAs able to discriminate patients with high grade SEOC from age-matched healthy controls. The addition of these microRNAs to current testing regimes may improve diagnosis for women with SEOC.
The effect of cyclization on the enzymatic degradation of herpes simplex virus glycoprotein D derived epitope peptide (2005)

One linear and three cyclic peptides corresponding to the 278-287 ((278)LLEDPVGTVA(287)) sequence of glycoprotein D (gD-1) of herpes simplex virus were synthesized for the analysis of the effect of cyclization on protection against enzymatic degradation. In this design, the turn-forming motif ((281)DPVG(284)) was positioned in the central part of the peptide and elongated by three amino acids at both termini. Cyclopeptide formation was achieved by the introduction of a peptide bond, a disulfide bridge or a thioether link. The stability of these peptides was compared in human serum and also in rat lysosomal preparations. The data obtained in 10% and 50% human serum show that all three types of cyclization enhanced the stability, but at different levels. Complete stability was only achieved by the introduction of a thioether link, while the presence of a disulfide or peptide bond resulted in improved, but partial resistance against hydrolytic decomposition. In lysosomal preparations the presence of cyclic primary structure provided full protection against enzymatic hydrolysis. Taken together, these findings indicate that by appropriate structural modification it is feasible to construct a synthetic antigen with high stability against enzymatic degradation in complex biological fluids. Further studies are in progress to identify enzymes responsible for degradation in diluted human sera as well as in the lysosomal preparations and to gain more detailed information on the mechanism of action.
Contact glow-discharge electrolysis (1964)

A. Hickling and M. D. Ingram, Trans. Faraday Soc., 1964, 60, 783 DOI: 10.1039/TF9646000783
Time-dependent heart period and contractility responses to successive brief vagal stimuli (1980)

The vagosympathetic trunks of anesthetized propranolized dogs were stimulated with brief electrical bursts, and heart period (P-P interval), atrioventricular conduction (P-R interval), and pressure generated on a balloon anchored in the atrium (AP) were measured. Two vagal stimulus bursts were given separated by an integral number of cardiac cycles but with each placed at the same relative time in the cardiac cycle. The time between stimulus bursts (T) varied from 2 to 60 s. For all cardiac variables over this time span, the peak response to the second stimulus (P2) was less than that of the first (P1) i.e., the ratio P2/P1 was less than unity. The maximum depression of P2/P1 for all variables occurred at a T of about 5 s. The effect of changing the time in the cardiac cycle at which the stimulus was given, and the effect of stimulus intensity on the P2/P1 ratio was also measured. Previous experiments observing the P-R interval alone suggested that synthesis and release of acetylcholine were not involved in the time dependent P2/P1 effect. The present results suggest that neuroeffector mechanisms at the target cellular level are also not involved in the depression of P2/P1. A time-dependent increase in acetylcholine inactivation is consistent with the present results, but an antagonism between primary and secondary inhibitory effects also cannot be ruled out.
Design, Synthesis, and Validation of a Branched Flexible Linker for Bioactive Peptides (2007)

A branched flexible linker that incorporates a fluorescent dansyl moiety was synthesized and used to connect two high affinity NDP-alpha-MSH ligands or two low affinity MSH(4) ligands. The linker was incorporated into the conjugate by solid-phase synthesis. In vitro biological evaluations showed that potency of binding to the human melanocortin 4 receptor was not diminished for linker-ligand combinations relative to the corresponding ligand alone.
Class II Histone Deacetylases Are Directly Recruited by BCL6 Transcriptional Repressor (2002)

BCL6 is a member of the POZ/zinc finger (POK) family involved in survival and/or differentiation of a number of cell types and in B cell lymphoma upon chromosomal alteration. Transcriptional repression by BCL6 is thought to be achieved in part by recruiting a repressor complex containing two class I histone deacetylases (HDACs). In this study we investigated whether BCL6 could also target members of class II HDACs. Our results indicate that three related class II deacetylases, HDAC4, HDAC5, and HDAC7 can associate with BCL6 in vivo and in vitro. Using electron microscopy, we found that endogenous BCL6 and class II HDACs partially co-localize in the nucleus. Overexpression experiments showed that BCL6 and HDAC4, -5, or -7 are intermingled onto common nuclear substructures and form stable complexes. A highly conserved domain in the N-terminal region of HDAC5 and HDAC7 as well as the zinc finger region of BCL6 were found necessary for the complex formation in vivo and in vitro. Moreover, our data point to the zinc finger region of BCL6 as a multifunctional domain which, beside its known capacity to bind DNA, is involved in the nuclear targeting of the protein and in the recruitment of the class II HDACs, and hence constitutes an autonomous repressor domain. Since PLZF, a BCL6 relative, could also interact with HDAC4, -5, and 7, we suggest that class II HDACs are largely involved in the control of the POK transcription factors activity.
Vapourisation of ionic liquids (2007)

Eight common imidazolium based ionic liquids have been successfully evaporated in ultra-high vacuum, their vapours analysed by line of sight mass spectrometry and their heats (enthalpy) of vapourisation determined. They were found to evaporate as ion pairs, with heats of vapourisation which depend primarily on the coulombic interactions within the liquid phase and the gas phase ion pair. An electrostatic model is presented relating the heats of vapourisation to the molar volumes of the ionic liquids.
Immunotherapy for Childhood Warts (2009)

Treatment-resistant warts are a common and frustrating problem for patients, parents, and providers alike. No wart treatment is uniformly effective. Indeed, well-designed randomized controlled trials are sorely needed to establish the true efficacy of all wart therapies. Treatment should be tailored to each individual patient. Although none of the immunologically-based treatments listed above (see Table, page 377) is FDA-approved for warts, they provide the treating physician with options for patients with warts that are resistant to standard treatments.
Determination of features indicating progression in atypical squamous cells with undetermined significance (2002)

Human papillomavirus typing and DNA content measurements may delineate a distinct group of ASCUS. Our preliminary data suggest that ASCUS cases with high-risk HPV positivity and with rare cells with abnormally high DNA content represent similar biologic features as high-grade SIL and are at elevated risk to develop cancer.
Glial cell line-derived neurotrophic factor but not transforming growth factor beta 3 prevents delayed degeneration of nigral dopaminergic neurons following striatal 6-hydroxydopamine lesion. (1995)

Glial cell line-derived neurotrophic factor (GDNF) and transforming growth factor beta 3 (TGF-beta 3) are members of the TGF-beta superfamily with high neurotrophic activity on cultured nigral dopamine neurons. We investigated the effects of intracerebral administration of GDNF and TGF-beta 3 on the delayed cell death of the dopamine neurons in the rat substantia nigra following 6-hydroxydopamine lesions of dopaminergic terminals in the striatum. Fluorescent retrograde tracer injections and tyrosine hydroxylase immunocytochemistry demonstrated nigral degeneration with an onset 1 week after lesion, leading to extensive death of nigral neurons 4 weeks postlesion. Administration of recombinant human GDNF for 4 weeks over the substantia nigra at a cumulative dose of 140 micrograms, starting on the day of lesion, completely prevented nigral cell death and atrophy, while a single injection of 10 micrograms 1 week postlesion had a partially protective effect. Continuous administration of TGF-beta 3, starting on the day of lesion surgery, did not affect nigral cell death or atrophy. These findings support the notion that GDNF, but not TGF-beta 3, is a potent neurotrophic factor for nigral dopamine neurons in vivo.
Chemotherapy Synergizes with Radioimmunotherapy Targeting La Autoantigen in Tumors (2009)

We report proof-of-concept data supporting a unique form of radioimmunotherapy, which delivers bystander killing to viable cancer cells after targeting the universal cancer antigen, La, created by DNA-damaging treatment in neighboring dead cancer cells. Subsequently we propose that DAB4-targeted ionizing radiation induces additional cycles of tumor cell death, which further augments DAB4 binding to produce a tumor-lethal 'genotoxic chain reaction'. Clinically, this approach may be useful as consolidation treatment after a drug-induced cell death among (small-volume) metastatic deposits, the commonest cause of cancer death. This article is part II of a two-part series providing proof-of-concept for the diagnostic and therapeutic use of the DAB4 clone of the La-specific monoclonal antibody, APOMAB.