gebhart/patrepeval huggingface dataset:
RASSF4/AD037 Is a Potential Ras Effector/Tumor Suppressor of the RASSF Family (2004)

Activated Ras proteins interact with a broad range of effector proteins to induce a diverse series of biological consequences. Although typically associated with enhanced growth and transformation, activated Ras may also induce growth antagonistic effects such as senescence or apoptosis. It is now apparent that some of the growth-inhibitory properties of Ras are mediated via the RASSF family of Ras effector/tumor suppressors. To date, four members of this family have been identified (Nore1, RASSF1, RASSF2, and RASSF3). We now identify a fifth member of this group, RASSF4 (AD037). RASSF4 shows approximately 25% identity with RASSF1A and 60% identity with RASSF2. RASSF4 binds directly to activated K-Ras in a GTP-dependent manner via the effector domain, thus exhibiting the basic properties of a Ras effector. Overexpression of RASSF4 induces Ras-dependent apoptosis in 293-T cells and inhibits the growth of human tumor cell lines. Although broadly expressed in normal tissue, RASSF4 is frequently down-regulated by promoter methylation in human tumor cells. Thus, RASSF4 appears to be a new member of the RASSF family of potential Ras effector/tumor suppressors.
Query by image content using multiple objects and multiple features: user interface issues (2002)

On-line collections of images are growing larger and more common, and tools are needed to efficiently manage, organize, and navigate through them. The authors have developed a prototype system called QBIC which allows complex multi-object and multi-feature queries of large image databases. The queries are based on image content-the colors, textures, shapes, and positions of images and the objects/regions they contain. The system computes numeric features to represent the image properties and uses similarity measures based on these features for image retrieval. The focus of the paper is its user interface which allows a user to graphically pose and refine queries based on multiple visual properties of images and their objects.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Lung sound pattern analysis for anesthesia monitoring (2005)

This paper introduces a set of characterizing parameters for identifying patterns in lung sounds. Stochastic analysis is performed to extract sound patterns and understand the impact of noise artifacts on sound pattern recognition and diagnosis.
Graphene based widely-tunable and singly-polarized pulse generation with random fiber lasers (2015)

Pulse generation often requires a stabilized cavity and its corresponding mode structure for initial phase-locking. Contrastingly, modeless cavity-free random lasers provide new possibilities for high quantum efficiency lasing that could potentially be widely tunable spectrally and temporally. Pulse generation in random lasers, however, has remained elusive since the discovery of modeless gain lasing. Here we report coherent pulse generation with modeless random lasers based on the unique polarization selectivity and broadband saturable absorption of monolayer graphene. Simultaneous temporal compression of cavity-free pulses are observed with such a polarization modulation, along with a broadly-tunable pulsewidth across two orders of magnitude down to 900 ps, a broadly-tunable repetition rate across three orders of magnitude up to 3 MHz, and a singly-polarized pulse train at 41 dB extinction ratio, about an order of magnitude larger than conventional pulsed fiber lasers. Moreover, our graphene-based pulse formation also demonstrates robust pulse-to-pulse stability and wide-wavelength operation due to the cavity-less feature. Such a graphene-based architecture not only provides a tunable pulsed random laser for fiber-optic sensing, speckle-free imaging, and laser-material processing, but also a new way for the non-random CW fiber lasers to generate widely tunable and singly-polarized pulses.
Movement-related change of electrocorticographic activity in human supplementary motor area proper (2000)

We investigated movement-related change in the cortical EEG signal by simultaneous recording from the primary sensorimotor area (S1-M1) and the supplementary motor area proper (SMA proper) in four patients with intractable partial epilepsy. By the use of temporal spectral evolution (TSE) analysis, the change in background cortical activity in relation to self-paced finger/wrist extension was compared among the SMA proper, S1 and M1. All three areas showed a decrease in the amount of activity for the frequency range between 10 and 40 Hz before the onset of movement [event-related desynchronization (ERD)]. The SMA proper showed earlier onset of ERD for 18-22 Hz activity (-3.4 +/- 0.5 s, mean +/- standard deviation) than M1 (-1.7 +/- 0.7 s) and S1 (-1.4 +/- 0.5 s). The degree of ERD in S1 was greatest for 10-14 Hz and that in M1 for 18-22 Hz, whereas in the SMA proper ERD was observed throughout the frequency bands from 10 to 40 Hz. Neither the degree nor the onset time of ERD in the SMA proper was lateralized to either the ipsilateral or the contralateral side with respect to the movement. A transient increase in activity after movement [event-related synchronization (ERS)] was observed in all three areas. In the SMA proper, two out of four subjects showed ERS for frequency bands below 40 Hz with both ipsilateral and contralateral movements. By contrast, in S1 and M1, ERS was recorded for frequency bands between 20 and 90 Hz, and was predominantly associated with the contralateral movement. The present study suggests that the background cortical activity in the SMA proper has a specific temporal pattern with respect to self-paced movement, and that the SMA proper is involved in motor preparation earlier than S1-M1 in a bilaterally organized manner.
Potential clinical applications of halichondrins in breast cancer and other neoplasms (2012)

Halichondrin B is a large polyether macrolide found in a rare Japanese sponge, Halichondria okadai and has been shown to have anticancer activity. Eribulin mesylate is a completely synthetic analog of halichondrin B with a unique mechanism of action relative to other antimicrotubule agents. This new agent has demonstrated activity in preclinical studies, and it is being developed for the treatment of different tumor types. Eribulin has been approved by the United States Food and Drug Administration and the European Medicines Agency as late-line therapy for metastatic breast cancer patients previously treated with an anthracycline and a taxane. It has demonstrated superiority over other treatments in overall survival (OS) (hazard ratio: 0.81, P = 0.041), leading to its regulatory approbation for clinical practice use. Median OS for the eribulin-treated group was 13.1 months versus 10.6 months in the physician's treatment-of-choice group. Eribulin demonstrated a manageable toxicity profile. Most common adverse events associated with treatment were mild neutropenia and fatigue, mainly of grade 1 or 2. In contrast to other antimicrotubule agents, eribulin has a relatively low incidence of peripheral neuropathy and alopecia. Eribulin has been extensively studied in breast cancer and is currently being developed for treatment of other cancer types. Eribulin has demonstrated activity in Phase II trials in non-small cell lung cancer, pancreatic cancer, urothelial tract cancer, and sarcomas. Further studies in these cancers are ongoing. This article reviews pharmacology, mechanism of action, pharmacokinetics and efficacy of eribulin in breast cancer and other neoplasms.
The digital news system at EDUCOM (1991)

article Free Access Share on The digital news system at EDUCOM: a convergence of interactive computing, newspapers, television and high-speed networks Authors: Eric M. Hoffert Apple Computers, Inc., Cupertino, CA Apple Computers, Inc., Cupertino, CAView Profile , Greg Gretsch Apple Computers, Inc., Cupertino, CA Apple Computers, Inc., Cupertino, CAView Profile Authors Info & Claims Communications of the ACMVolume 34Issue 4April 1991 pp 113–116https://doi.org/10.1145/103085.103096Online:01 April 1991Publication History 23citation439DownloadsMetricsTotal Citations23Total Downloads439Last 12 Months23Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Activation of mammalian ribosomal gene transcription requires phosphorylation of the nucleolar transcription requires phosphorylation of the nucleolar trasnscription factor UBF (1995)

The nucleolar factor UBF is phosphorylated by casein kinase II (CKII) at serine residues within the C-terminal acidic domain which is required for transcription activation. To investigate the biological significance of UBF modification, we have compared the trans-activating properties of cellular UBF and recombinant UBF expressed in Escherichia coli. Using a variety of assays we demonstrate that unphosphorylated UBF is transcriptionally inactive and has to be phosphorylated at multiple sites to stimulate transcription. Examination of cDNA mutants in which the serine residues within the C-terminal domain were altered by site-directed mutagenesis demonstrates that CKII-mediated phosphorylations of UBF contribute to, but are not sufficient for, transcriptional activation. Besides CKII, other cellular protein kinases phosphorylate UBF at distinct sites in a growth-dependent manner. The marked differences in the tryptic peptide maps of UBF from growing and serum-starved cells suggest that alterations in the degree of UBF phosphorylation may modulate rRNA synthetic activity in response to extracellular signals.
Functional Characterization of the Two Alcohol Oxidase Genes from the Yeast Pichia pastoris (1989)

In Pichia pastoris, alcohol oxidase (AOX) is the first enzyme in the methanol utilization pathway and is encoded by two genes, AOX1 and AOX2. The DNA and predicted amino acid sequences of the protein-coding portions of the genes are closely homologous, whereas flanking sequences share no homology. The functional roles of AOX1 and AOX2 in the metabolism of methanol were examined. Studies of strains with disrupted AOX genes revealed that AOX1 was the major source of methanol-oxidizing activity in methanol-grown P. pastoris. The results of two types of experiments each suggested that the difference in AOX activity contributed by the two genes was a consequence of sequences located 5' of the protein-coding portions of the genes. First, the coding portion of AOX2 was able to functionally substitute for that of AOX1 when placed under the control of AOX1 regulatory sequences. Second, when labeled oligonucleotide probes specific for the 5' nontranslated region of each gene were used, it was apparent that the steady-state level of AOX1 mRNA was much higher than that of AOX2. Except for the difference in the amount of mRNA present, the two genes appeared to be regulated in the same manner. A physiological reason for the existence of AOX2 was sought but was not apparent.
Carbon Dioxide Capture: Prospects for New Materials (2010)

The escalating level of atmospheric carbon dioxide is one of the most pressing environmental concerns of our age. Carbon capture and storage (CCS) from large point sources such as power plants is one option for reducing anthropogenic CO(2) emissions; however, currently the capture alone will increase the energy requirements of a plant by 25-40%. This Review highlights the challenges for capture technologies which have the greatest likelihood of reducing CO(2) emissions to the atmosphere, namely postcombustion (predominantly CO(2)/N(2) separation), precombustion (CO(2)/H(2)) capture, and natural gas sweetening (CO(2)/CH(4)). The key factor which underlies significant advancements lies in improved materials that perform the separations. In this regard, the most recent developments and emerging concepts in CO(2) separations by solvent absorption, chemical and physical adsorption, and membranes, amongst others, will be discussed, with particular attention on progress in the burgeoning field of metal-organic frameworks.
Frequency of nursing, physician and hospital interventions in women at risk for preterm delivery (2004)

Objective: To determine the frequency of nursing intervention, physician treatment and hospital evaluation for women receiving outpatient management services for preterm labor. Methods: Outpatient services included: patient education; daily and as-needed nursing assessment of monitored uterine activity (MUA) and patient symptoms; treatment compliance; and physician notification for values exceeding established limits. We analyzed service data from women with singleton gestations at 20.0-34.9 weeks. Results: Overall, 307 249 days of data from 10 660 women were reviewed, and 634 983 hours of MUA was assessed. On 53 665 (17.5%) of monitored days, patients exhibited increased MUA and/or symptoms of preterm labor with nursing intervention and reassessment. Physician notification/intervention was required 7316 (13.6%) times, and hospital admission was needed for 3163 (43.2%) of these patients. In the hospital 1400 (44.3%) patients received tocolysis. The mean ( ± standard deviation) length of hospital stay was 3.2 ± 7.2 days, and 428 (13.5%) of women remained hospitalized until delivery, with 324 (10.2%) delivering within 48 h. Conclusion: In this population of women receiving outpatient preterm-labor management services, 95.1% of excessive MUA or patient-reported symptoms of preterm labor were managed on an outpatient basis. Outpatient management allowed for appropriate identification and triage of women requiring hospital admission.
Direct writing in three dimensions (2004)

The ability to pattern materials in three dimensions is critical for several emerging technologies, including photonics, microfluidics, microelectromechanical systems, and biomaterials. Direct-write assembly allows one to design and rapidly fabricate materials in complex three-dimensional shapes without the need for expensive tooling, dies, or lithographic masks. Here, recent advances in ink and laser writing techniques are reviewed with an emphasis on the push toward finer feature sizes. Opportunities and challenges associated with direct-write assembly are also highlighted.
Antigenic structure of soluble herpes simplex virus (HSV) glycoprotein D correlates with inhibition of HSV infection (1997)

Soluble forms of herpes simplex virus (HSV) glycoprotein D (gD) block viral penetration. Likewise, most HSV strains are sensitive to gD-mediated interference by cells expressing gD. The mechanism of both forms of gD-mediated inhibition is thought to be at the receptor level. We analyzed the ability of different forms of soluble, truncated gD (gDt) to inhibit infection by different strains of HSV-1 and HSV-2. Strains that were resistant to gD-mediated interference were also resistant to inhibition by gDt, thereby suggesting a link between these two phenomena. Virion gD was the major viral determinant for resistance to inhibition by gDt. An insertion-deletion mutant, gD-1(delta 290-299t), had an enhanced inhibitory activity against most strains tested. The structure and function of gDt proteins derived from the inhibition-resistant viruses rid1 and ANG were analyzed. gD-1(ridlt) and gD-1(ANGt) had a potent inhibitory effect on plaque formation by wild-type strains of HSV but, surprisingly, little or no effect on their parental strains. As measured by quantitative enzyme-linked immunosorbent assay with a diverse panel of monoclonal antibodies, the antigenic structures of gD-1(rid1t) and gD-1(ANGt) were divergent from that of the wild type yet were similar to each other and to that of gD-1 (delta 290-299t). Thus, three different forms of gD have common antigenic changes that correlate with enhanced inhibitory activity against HSV. We conclude that inhibition of HSV infectivity by soluble gD is influenced by the antigenic conformation of the blocking gDt as well as the form of gD in the target virus.
Human T-Cell Clones from Autoimmune Thyroid Glands: Specific Recognition of Autologous Thyroid Cells (1985)

The thyroid glands of patients with autoimmune diseases such as Graves' disease and certain forms of goiter contain infiltrating activated T lymphocytes and, unlike cells of normal glands, the epithelial follicular cells strongly express histocompatibility antigens of the HLA-DR type. In a study of such autoimmune disorders, the infiltrating T cells from the thyroid glands of two patients with Graves' disease were cloned in mitogen-free interleukin-2 (T-cell growth factor). The clones were expanded and their specificity was tested. Three types of clones were found. One group, of T4 phenotype, specifically recognized autologous thyroid cells. Another, also of T4 phenotype, recognized autologous thyroid or blood cells and thus responded positively in the autologous mixed lymphocyte reaction. Other clones derived from cells that were activated in vivo were of no known specificity. These clones provide a model of a human autoimmune disease and their analysis should clarify mechanisms of pathogenesis and provide clues to abrogating these undesirable immune responses.
Invertibility of a room impulse response (1979)

When a conversation takes place inside a room, the acoustic speech signal is distorted by wall reflections. The room’s effect on this signal can be characterized by a room impulse response. If the impulse response happens to be minimum phase, it can easily be inverted. Synthetic room impulse responses were generated using a point image method to solve for wall reflections. A Nyquist plot was used to determine whether a given impulse response was minimum phase. Certain synthetic room impulse responses were found to be minimum phase when the initial delay was removed. A minimum phase inverse filter was successfully used to remove the effect of a room impulse response on a speech signal.
Fast and accurate short read alignment with Burrows–Wheeler transform (2009)

http://bio-bwa.sourceforge.net
The RNA binding protein Zfp36l1 is required for normal vascularisation and post‐transcriptionally regulates VEGF expression (2006)

The Zfp36l1 gene encodes a zinc finger-containing mRNA binding protein implicated in the posttranscriptional control of gene expression. Mouse embryos homozygous for a targeted mutation in the Zfp36l1 locus died mid-gestation and exhibited extraembryonic and intraembryonic vascular abnormalities and heart defects. In the developing placenta, there was a failure of the extraembryonic mesoderm to invaginate the trophoblast layer. The phenotype was associated with an elevated expression of vascular endothelial growth factor (VEGF)-A in the embryos and in embryonic fibroblasts cultured under conditions of both normoxia and hypoxia. VEGF-A overproduction by embryonic fibroblasts was not a consequence of changes in Vegf-a mRNA stability; instead, we observed enhanced association with polyribosomes, suggesting Zfp36l1 influences translational regulation. These data implicate Zfp36l1as a negative regulator of Vegf-a gene activity during development.
Interleukin-6 inhibitors in the treatment of rheumatoid arthritis (2008)

Recent developments in understanding the immunopathogenesis of rheumatoid arthritis (RA), combined with progress in biopharmaceutical development, have facilitated the introduction of novel immune modulating therapies for this progressive debilitating disorder. Efficacy achieved with certain agents, particularly the TNF inhibitors, has spurred the development of additional biologic agents targeting other components of the dysregulated immune response relevant to the etiology and sustenance of immune driven systemic inflammation characteristic of RA. Among these other potential targets is IL-6, a cytokine with effects on numerous cell types, including those involved in the pathogenesis of RA. Based on its activities, IL-6 appeared to be a viable target for autoimmune disease. Inhibitors of IL-6 were successful in animal models of autoimmune disease paving the way for subsequent studies in humans. The greatest experience to date has been with tocilizumab, a humanized monoclonal antibody specific for the IL-6 receptor (IL-6R). Beginning with open label studies, and progressing through larger and more rigorous controlled trials, tocilizumab has been shown to have significant Efficacy in patients with RA. Additional studies analyzing its effects in varied populations of RA patients, as well as greater detail concerning its longer-term tolerability and safety, will help define the ultimate role of tocilizumab and other future inhibitors of IL-6 activity as potential therapies for RA.
Analysis of Toxoplasma gondii stably transfected with a transmembrane variant of its major surface protein, SAG1 (1998)

We have genetically engineered Toxoplasma gondii so that its major surface antigen SAG1 is anchored by a human transmembrane domain (SAG1-TM) instead of its natural GPI anchor (SAG1-GPI) in order to initiate studies to address the function of this protein anchor in parasitic protozoa as well as to get insights into the functional role of SAG1. Our results show that SAG1-TM is correctly folded (at least as judged by the presence of conformationally dependent epitopes) and targeted to the surface of the parasite, indicating that the GPI anchor does not determine its localization nor overall three-dimensional structure. No significant difference was seen in any aspect of the growth of the SAG1-TM mutant. However, compared to the natural SAG1-GPI, SAG1-TM does not form strong associations with itself and/or other molecules in high molecular weight complexes suggesting that allowing such complexes to form may be one role of the GPI anchor. The in vitro half-life of SAG1-TM of extracellular parasites is significantly lower than that of SAG1-GPI suggesting a stabilizing function of the glycolipid anchor against degradation and/or membrane release. Antibodies to SAG1 are shed from SAG1-TM parasites as they invade, just as they are stripped from SAG1-GPI bearing parasites. The stripping, therefore, is unlikely to be driven by the action of lipases.
The use of a linguistically motivated language model in conversational speech recognition (2004)

Structured language models have recently been shown to give significant improvements in large-vocabulary recognition relative to traditional word N-gram models, but typically imply a heavy computational burden and have not been applied to large training sets or complex recognition systems. Previously, we developed a linguistically motivated and computationally efficient almost-parsing language model, using a data structure derived from constraint dependency grammar parsing, that tightly integrates knowledge of words, lexical features, and syntactic constraints. We show that such a model can be used effectively and efficiently in all stages of a complex, multi-pass conversational telephone speech recognition system. Compared to a state-of-the-art 4-gram interpolated word- and class-based language model, we obtained a 6.2% relative word error reduction (a 1.6% absolute reduction) on a recent NIST evaluation set.