gebhart/patrepeval huggingface dataset:
A test of the model to predict unusually stable RNA hairpin loop stability (2000)

To investigate the accuracy of a model [Giese et al., 1998, Biochemistry37:1094-1100 and Mathews et al., 1999, JMol Biol 288:911-940] that predicts the stability of RNA hairpin loops, optical melting studies were conducted on sets of hairpins previously determined to have unusually stable thermodynamic parameters. Included were the tetraloops GNRA and UNCG (where N is any nucleotide and R is a purine), hexaloops with UU first mismatches, and the hairpin loop of the iron responsive element, CAGUGC. The experimental values for the GNRA loops are in excellent agreement (deltaG degrees 37 within 0.2 kcal/mol and melting temperature (TM) within 4 degrees C) with the values predicted by the model. When the UNCG hairpin loops are treated as tetraloops, and a bonus of 0.8 kcal/mol included in the prediction to account for the extra stable first mismatch (UG), the measured and predicted values are also in good agreement (deltaG degrees 37 within 0.7 kcal/mol and TM within 3 degrees C). Six hairpins with unusually stable UU first mismatches also gave good agreement with the predictions (deltaG degrees 37 within 0.5 kcal/mol and TM within 8 degrees C), except for hairpins closed by wobble base pairs. For these hairpins, exclusion of the additional stabilization term for UU first mismatches improved the prediction (AG degrees 37 within 0.1 kcal/mol and TM within 3 degrees C). Hairpins with the iron-responsive element loop were not predicted well by the model, as measured deltaG degrees 37 values were at least 1 kcal/mol greater than predicted.
Cyclic nucleotides and phosphodiesterases and airway function (1995)

The cyclic nucleotides, cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP) play an important role in the regulation of airway smooth muscle tone and activation of inflammatory cells. Intracellular concentrations of these nucleotides are tightly regulated by phosphodiesterases (PDEs). Several families of PDEs are now recognized and, within each isoenzyme family, molecular cloning has revealed multiple members. PDE III and IV are important in the breakdown of cAMP; PDE III is involved in the regulation of airway smooth muscle tone, whereas PDE IV is more important in inflammatory cells, including mast cells, macrophages, eosinophils, T-lymphocytes and epithelial cells. PDE V is involved in the breakdown of cGMP in airway and vascular smooth muscle. Regulation of PDE expression in health and disease is now under investigation. Several selective PDE inhibitors have recently been developed, and experimental studies indicate that PDE IV inhibitors may be useful as anti-inflammatory treatments in asthma. Clinical trials in asthma are now in progress.
The Oral Dipeptidyl Peptidase-4 Inhibitor Sitagliptin Increases Circulating Endothelial Progenitor Cells in Patients With Type 2 Diabetes (2010)

Sitagliptin increases circulating EPCs in type 2 diabetic patients with concomitant upregulation of SDF-1alpha. This ancillary effect of DPP-4 inhibition might have potential favorable cardiovascular implications.
Botulinum-A Toxin as a Treatment of Detruosor-Sphincter Dyssynergia: A Prospective Study in 24 Spinal Cord Injury Patients (1996)

Although costly, botulinum-A toxin injections, which aim at suppressing detrusor-sphincter dyssynergia but not bladder neck dyssynergia, appear to be a valid alternative for patients who do not desire surgery or are unable to perform self-catheterization.
Selective induction of endothelial cell tissue factor in the presence of a tumour‐derived mediator: A potential mechanism of flavone acetic acid action in tumour vasculature (1991)

Flavone acetic acid (FAA) is a potentially useful anti-tumour agent which has been reported to induce changes in tumour vasculature, in particular loss of bloodflow. This led us to examine whether endothelium could be a cellular target of FAA action, with resultant modulation of cell-surface coagulant properties leading to activation of coagulation and blockade of tumour blood flow. Incubation of endothelium with FAA led to the expression of functional tissue factor on the cell surface, in a time-dependent and dose-dependent (half-maximal at 0.6-0.7 mg/ml) manner. Induction of tissue-factor activity resulted from de novo translation of the tissue factor message. To explain the selectivity of FAA's action on tumour vasculature in vivo, we considered its interaction with tumour-derived factors. Starting with serum-free FO-I-melanoma cell-conditioned medium, a co-factor enhancing FAA-mediated induction of endothelial tissue factor (FO-I factor) was partially purified by sequential ion exchange and reverse phase chromatography, followed by preparative SDS-PAGE. The FO-I factor migrates with an apparent Mr of approx. 20 to 25,000 on non-reduced SDS-PAGE, is sensitive to protease K, and augments the effect of FAA on endothelial-cell-tissue factor. This activity is not found in supernatants from non-neoplastically transformed cell lines. These data lead us to hypothesize that FAA exerts its action, at least in part, by promoting activation of coagulation on the endothelial surface, and this effect is selective for the tumour bed by virtue of its interaction with a tumour-derived factor. The interaction of FAA with host factors may be important for optimizing its therapeutic efficacy for a particular tumour.
Oncogenic KRAS‐induced interleukin‐8 overexpression promotes cell growth and migration and contributes to aggressive phenotypes of non‐small cell lung cancer (2011)

The CXC chemokine interleukin-8 (IL-8) is an angiogenic growth factor that is overexpressed in various cancers, including non-small cell lung cancer (NSCLC). Previously, IL-8 was shown as a transcriptional target of RAS signaling, raising the possibility of its role in oncogenic KRAS-driven NSCLC. Using microarray analysis, we identified IL-8 as the most downregulated gene by shRNA-mediated KRAS knockdown in NCI-H1792 NSCLC cells where IL-8 is overexpressed. NSCLC cell lines harboring KRAS or EGFR mutations overexpressed IL-8, while IL-8 levels were more prominent in KRAS mutants compared to EGFR mutants. IL-8 expression was downregulated by shRNA-mediated KRAS knockdown in KRAS mutants or by treatment with EGFR tyrosine kinase inhibitors and EGFR siRNAs in EGFR mutants. In our analysis of the relationship of IL-8 expression with clinical parameters and mutation status of KRAS or EGFR in 89 NSCLC surgical specimens, IL-8 expression was shown to be significantly higher in NSCLCs of males, smokers, and elderly patients and those with pleural involvement and KRAS mutated adenocarcinomas. In KRAS mutant cells, the MEK inhibitor markedly decreased IL-8 expression, while the p38 inhibitor increased IL-8 expression. Attenuation of IL-8 function by siRNAs or a neutralizing antibody inhibited cell proliferation and migration of KRAS mutant/IL-8 overexpressing NSCLC cells. These results indicate that activating mutations of KRAS or EGFR upregulate IL-8 expression in NSCLC; IL-8 is highly expressed in NSCLCs from males, smokers, elderly patients, NSCLCs with pleural involvement, and KRAS-mutated adenocarcinomas; and IL-8 plays a role in cell growth and migration in oncogenic KRAS-driven NSCLC.
Protein N-Terminal Processing: Substrate Specificity of Escherichia coli and Human Methionine Aminopeptidases (2010)

Methionine aminopeptidase (MetAP) catalyzes the hydrolytic cleavage of the N-terminal methionine from newly synthesized polypeptides. The extent of removal of methionyl from a protein is dictated by its N-terminal peptide sequence. Earlier studies revealed that MetAPs require amino acids containing small side chains (e.g., Gly, Ala, Ser, Cys, Pro, Thr, and Val) as the P1' residue, but their specificity at positions P2' and beyond remains incompletely defined. In this work, the substrate specificities of Escherichia coli MetAP1, human MetAP1, and human MetAP2 were systematically profiled by screening against a combinatorial peptide library and kinetic analysis of individually synthesized peptide substrates. Our results show that although all three enzymes require small residues at the P1' position, they have differential tolerance for Val and Thr at this position. The catalytic activity of human MetAP2 toward Met-Val peptides is consistently 2 orders of magnitude higher than that of MetAP1, suggesting that MetAP2 is responsible for processing proteins containing N-terminal Met-Val and Met-Thr sequences in vivo. At positions P2'-P5', all three MetAPs have broad specificity but are poorly active toward peptides containing a proline at the P2' position. In addition, the human MetAPs disfavor acidic residues at the P2'-P5' positions. The specificity data have allowed us to formulate a simple set of rules that can reliably predict the N-terminal processing of E. coli and human proteins.
The Expression Patterns of ER, PR, HER2, CK5/6, EGFR, Ki-67 and AR by Immunohistochemical Analysis in Breast Cancer Cell Lines (2010)

The molecular classification for breast carcinomas has been used in clinical studies with a simple surrogate panel of immunohistochemistry (IHC) markers. The objective of this current project was to study the molecular classification of commonly used breast cancer cell lines by IHC analysis. Seventeen breast cancer cell lines were harvested, fixed in formalin and made into cell blocks. IHC analyses were performed on each cell block with antibodies to estrogen receptor (ER), progesterone receptor (PR), HER2, EGFR, CK5/6, Ki-67 and androgen receptor (AR). Among the 17 cell lines, MCF-7 and ZR-75-1 fell to Luminal A subtype; BT-474 to Luminal B subtype; SKBR-3, MDA-MD-435 and AU 565 to HER2 over-expression subtype; MDA-MB-231, MCF-12A, HBL 101, HS 598 T, MCF-10A, MCF-10F, BT-20, 468 and BT-483 to basal subtype. MDA-MB-453 belonged to Unclassified subtype. Since each subtype defined by this IHC-based molecular classification does show a distinct clinical outcome, attention should be paid when choosing a cell line for any study.
Increased levels of serum IL‐31 in chronic spontaneous urticaria* (2010)

IL-31 represents a novel cytokine involved in pruritic skin diseases including atopic dermatitis (AD). We, therefore, aimed at investigating IL-31 levels in chronic spontaneous urticaria (CU). We included 46 patients with CU, 26 non-atopic skin healthy subjects as negative and 28 patients with AD as positive controls. IL-31 serum levels were analysed using commercial ELISA kit. IL-31 serum levels were higher in patients with CU compared to healthy controls (P < 0.001), but lower compared to patients with AD (P < 0.001). There was no difference in IL-31 serum levels in autologous serum skin test positive or negative CU patients and patients with infectious trigger factors including helicobacter pylori infection. IL-31 serum levels may play a role in the pathophysiology of CU. This is supported by the finding that not all patients with CU respond to antihistamine treatment but to the treatment with immunosuppressive drugs.
Inhibition of Tau Filament Formation by Conformational Modulation (2013)

Antiaggregation drugs play an important role in therapeutic approaches for Alzheimer's disease. Although a large number of small molecules that inhibit the aggregation of the tau protein have been identified, little is known about their mode of action. Here, we reveal the mechanism and the nature of tau species that are generated by interaction of tau with the organic compound pthalocyanine tetrasulfonate (PcTS). We demonstrate that PcTS interferes with tau filament formation by targeting the protein into soluble oligomers. A combination of NMR spectroscopy, electron paramagnetic resonance, and small-angle X-ray scattering reveals that the soluble tau oligomers contain a dynamic, noncooperatively stabilized core with a diameter of 30-40 nm that is distinct from the core of tau filaments. Our results suggest that specific modulation of the conformation of tau is a viable strategy for reduction of pathogenic tau deposits.
A shallow model of backchannel continuers in spoken dialogue (2003)

Spoken dialogue systems would be more acceptable if they were able to produce backchannel continuers such as mm-hmm in naturalistic locations during the user's utterances. Using the HCRC Map Task Corpus as our data source, we describe models for predicting these locations using only limited processing and features of the user's speech that are commonly available, and which therefore could be used as a low-cost improvement for current systems. The baseline model inserts continuers after a predetermined number of words. One further model correlates back-channel continuers with pause duration, while a second predicts their occurrence using trigram POS frequencies. Combining these two models gives the best results.
Massively parallel digital transcriptional profiling of single cells (2017)

Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3' mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system's technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. We profiled 68k peripheral blood mononuclear cells to demonstrate the system's ability to characterize large immune populations. Finally, we used sequence variation in the transcriptome data to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients.
Integrated Human Papillomavirus Type 16 Is Frequently Found in Cervical Cancer Precursors as Demonstrated by a Novel Quantitative Real-Time PCR Technique (2002)

In contrast to cervical cancer, integration of human papillomavirus (HPV) DNA into the host genome has been considered a rare event in cancer precursor lesions (cervical intraepithelial neoplasia [CIN]). With our new real-time PCR method, we demonstrated that integrated HPV type 16 (HPV16) is already present in CIN lesions. The physical state of HPV16 and the viral load were simultaneously detected. A unique region of the E2 open reading frame (ORF) that is most often deleted during HPV16 integration is targeted by one set of PCR primers and a probe, and another set targets the E6 ORF. In episomal form, both targets should be equivalent, while in integrated form, the copy numbers of E2 would be less than those of E6. The method was tested with DNAs from 31 cervical lesions (non-CIN to CINIII) from 24 women prospectively followed up for 10 years. This report presents viral load and integration results from the largest series of CIN lesions described to date. Only one sample contained exclusively episomal HPV16 DNA, and this lesion regressed spontaneously. Samples from another patient, with only integrated HPV16, rapidly progressed from CINI to CINIII in 2 years. In all other patients, episomal and integrated forms of HPV16 DNA were found to coexist. Rapid progression of the CIN lesions was closely associated with a heavy load of integrated HPV16. Thus, the method described here is a very sensitive tool with which to assess the physical state of HPV, which is useful in predicting disease progression.
In Defense of Irreligious Bioethics (2012)

Some commentators have criticized bioethics as failing to engage religion both as a matter of theory and practice. Bioethics should work toward understanding the influence of religion as it represents people's beliefs and practices, but bioethics should nevertheless observe limits in regard to religion as it does its normative work. Irreligious skepticism toward religious views about health, healthcare practices and institutions, and responses to biomedical innovations can yield important benefits to the field. Irreligious skepticism makes it possible to raise questions that otherwise go unasked and to protect against the overreach of religion. In this sense, bioethics needs a vigorous irreligious outlook every bit as much as it needs descriptive understandings of religion.
Fast and Efficient Skinning of Animated Meshes (2010)

Abstract Skinning is a simple yet popular deformation technique combining compact storage with efficient hardware accelerated rendering. While skinned meshes (such as virtual characters) are traditionally created by artists, previous work proposes algorithms to construct skinning automatically from a given vertex animation. However, these methods typically perform well only for a certain class of input sequences and often require long pre‐processing times. We present an algorithm based on iterative coordinate descent optimization which handles arbitrary animations and produces more accurate approximations than previous techniques, while using only standard linear skinning without any modifications or extensions. To overcome the computational complexity associated with the iterative optimization, we work in a suitable linear subspace (obtained by quick approximate dimensionality reduction) and take advantage of the typically very sparse vertex weights. As a result, our method requires about one or two orders of magnitude less pre‐processing time than previous methods.
The Immunoproteasome: An Emerging Therapeutic Target (2011)

The proteasome, a large multisubunit protease complex, has been extensively investigated over the years, greatly enhancing our understanding of critical roles that the proteasome plays in cells. The FDA approval of bortezomib for the treatment of multiple myeloma and mantle cell lymphoma has validated the proteasome as an anticancer target. However, the undesirable toxicities of these agents limit their broad utility. The immunoproteasome, an alternative form of the constitutive proteasome, has recently been explored as a therapeutic target. While the immunoproteasome, normally expressed in cells of hematopoietic origin, has been shown to be associated with various types of cancer and inflammatory diseases, its multifaceted function is not fully understood due to the lack of appropriate molecular probes. In this review, recent advances in the immunoproteasome field are covered, including potential implications in disease states. In particular, recent developments in immunoproteasome-specific inhibitors are emphasized.
RXR alpha mutant mice establish a genetic basis for vitamin A signaling in heart morphogenesis. (1994)

We have established a targeted loss-of-function mutation in the RXR alpha gene in the mouse germ line that results in embryonic lethality between E13.5 and E16.5 when bred to homozygosity. The major defect responsible for lethality is hypoplastic development of the ventricular chambers of the heart, which is manifest as a grossly thinned ventricular wall with concurrent defects in ventricular septation. This phenotype is identical to a subset of the effects of embryonic vitamin A deficiency and, therefore, establishes RXR alpha as a genetic component of the vitamin A signaling pathway in cardiac morphogenesis. The cardiac outflow tracts and associated vessels, which are populated by derivatives of the neural crest and which are also sensitive to vitamin A deficiency, are normal in homozygous embryos, indicating the genetic independence of ventricular chamber development. Hepatic differentiation was dramatically but transiently retarded yet is histologically and morphologically normal. These results ascribe an essential function for the RXR alpha gene in embryonic development and provide the first evidence of a requirement for RXR in one of its predicted hormone response pathways.
Depolymerized Products of λ-Carrageenan as a Potent Angiogenesis Inhibitor (2007)

Since angiogenesis is involved in initiating and promoting several diseases such as cancer and cardiovascular events, this study was designed to evaluate the anti-angiogenesis of low-molecular-weight (LMW), highly sulfated lambda-carrageenan oligosaccharides (lambda-CO) obtained by carrageenan depolymerization, by CAM (chick chorioallantoic membrane) model and human umbilical vein endothelial cells (HUVECs). Significant inhibition of vessel growth was observed at 200 microg/pellet. A histochemistry assay also revealed a decrease of capillary plexus and connective tissue in lambda-CO treated samples. lambda-CO inhibited the viability of cells at the high concentration of 1 mg/mL, whereas it affected the cell survival slightly (>95%) at a low concentration (<250 microg/mL), and HUVEC is the most sensitive to lambda-CO among three kinds of cells. Furthermore, the inhibitory action of lambda-CO was also observed in the endothelial cell invasion and migration at relatively low concentration (150-300 microg/mL), through down-regulation of intracellular matrix metalloproteinases (MMP-2) expression on endothelial cells. Taken together, these findings demonstrate that lambda-CO is a potential angiogenesis inhibitor with combined effects of inhibiting invasion, migration, and proliferation.
Sensors for Detecting Molecular Hydrogen Based on Pd Metal Alloys (1997)

A simple process using a shadow mask is described to fabricate Pd/Ni resistors for detecting . The performance of the resistive sensors is studied in relation to annealing the devices at different temperatures in 2% in for 2 h. The Pd/Ni film surface morphology is also examined in relation to the resistor response when exposed to . The detailed information learned about the performance of the prototype resistors is used to fabricate wide‐range‐hydrogen microsensors, which combine a Pd/Ni chemiresistor and metal‐oxide semiconductor capacitor along with a thin film metal heater and temperature sensor. These studies provide an important step for improving the reliability of microsensors used to detect over concentrations ranging from 1 mTorr to 700 Torr.
Machine Learning Models for Multiparametric Glioma Grading With Quantitative Result Interpretations (2019)

Gliomas are the most common primary malignant brain tumors in adults. Accurate grading is crucial as therapeutic strategies are often disparate for different grades and may influence patient prognosis. This study aims to provide an automated glioma grading platform on the basis of machine learning models. In this paper, we investigate contributions of multi-parameters from multimodal data including imaging parameters or features from the Whole Slide images (WSI) and the proliferation marker Ki-67 for automated brain tumor grading. For each WSI, we extract both visual parameters such as morphology parameters and sub-visual parameters including first-order and second-order features. On the basis of machine learning models, our platform classifies gliomas into grades II, III, and IV. Furthermore, we quantitatively interpret and reveal the important parameters contributing to grading with the Local Interpretable Model-Agnostic Explanations (LIME) algorithm. The quantitative analysis and explanation may assist clinicians to better understand the disease and accordingly to choose optimal treatments for improving clinical outcomes. The performance of our grading model was evaluated with cross-validation, which randomly divided the patients into non-overlapping training and testing sets and repeatedly validated the model on the different testing sets. The primary results indicated that this modular platform approach achieved the highest grading accuracy of 0.90 ± 0.04 with support vector machine (SVM) algorithm, with grading accuracies of 0.91 ± 0.08, 0.90 ± 0.08, and 0.90 ± 0.07 for grade II, III, and IV gliomas, respectively.
Gliadel (BCNU) wafer plus concomitant temozolomide therapy after primary resection of glioblastoma multiforme (2008)

In this experience, concomitant TMZ therapy in addition to Gliadel wafer implantation was associated with a median survival of nearly 21 months without increased perioperative morbidity. Temozolomide can be safely administered to patients receiving Gliadel wafers after resection of GBM.