gebhart/patrepeval huggingface dataset:
Identification of proteins responsible for adriamycin resistance in breast cancer cells using proteomics analysis (2015)

Chemoresistance is a poor prognostic factor in breast cancer and is a major obstacle to the successful treatment of patients receiving chemotherapy. However, the precise mechanism of resistance remains unclear. In this study, a pair of breast cancer cell lines, MCF-7 and its adriamycin-resistant counterpart MCF-7/ADR was used to examine resistance-dependent cellular responses and to identify potential therapeutic targets. We applied nanoflow liquid chromatography (nLC) and tandem mass tags (TmT) quantitative mass spectrometry to distinguish the differentially expressed proteins (DEPs) between the two cell lines. Bioinformatics analyses were used to identify functionally active proteins and networks. 80 DEPs were identified with either up- or down-regulation. Basing on the human protein-protein interactions (PPI), we have retrieved the associated functional interaction networks for the DEPs and analyzed the biological functions. Six different signaling pathways and most of the DEPs strongly linked to chemoresistance, invasion, metastasis development, proliferation, and apoptosis. The identified proteins in biological networks served to resistant drug and to select critical candidates for validation analyses by western blot. The glucose-6-phosphate dehydrogenase (G6PD), gamma-glutamyl cyclotransferase (GGCT), isocitrate dehydrogenase 1 (NADP+,soluble)(IDH1), isocitrate dehydrogenase 2 (NADP+,mitochondrial) (IDH2) and glutathione S-transferase pi 1(GSTP1), five of the critical components of GSH pathway, contribute to chemoresistance.
Second-Generation Difluorinated Cyclooctynes for Copper-Free Click Chemistry (2008)

The 1,3-dipolar cycloaddition of azides and activated alkynes has been used for site-selective labeling of biomolecules in vitro and in vivo. While copper catalysis has been widely employed to activate terminal alkynes for [3 + 2] cycloaddition, this method, often termed "click chemistry", is currently incompatible with living systems because of the toxicity of the metal. We recently reported a difluorinated cyclooctyne (DIFO) reagent that rapidly reacts with azides in living cells without the need for copper catalysis. Here we report a novel class of DIFO reagents for copper-free click chemistry that are considerably more synthetically tractable. The new analogues maintained the same elevated rates of [3 + 2] cycloaddition as the parent compound and were used for imaging glycans on live cells. These second-generation DIFO reagents should expand the use of copper-free click chemistry in the hands of biologists.
ON-BOARD ADVANCED TRAVELER INFORMATION SYSTEMS (2002)

Advanced Traveler Information Systems (ATIS) acquire, analyze, communicate, and present information to assist travelers to have a safer, more reliable and more enjoyable travel experience. Two major types of ATIS are available: (1) Real-time network information, including traffic and transit information and (2) Traveler information such as pre-trip or on-route route guidance or destination information. This information can be provided in a variety of ways: at kiosks, on websites, using mobile phones enabled by wireless application protocol (WAP); through hand-held computers or "personal digital assistants" (PDA); or via on-board (in-vehicle) computers and displays.
Fallout (1992)

FALLOUT IKyoko Mori i. from FukuoL· to Kagoshima Bottom to top, blue fills the windowpane across the aisle as though our train rode on water. Where narrow strips of land interpose between the tracks and the sea, carp tails rise out of roof slates, turn into dragons or phoenixes. In our window, small houses crowd against the steep mountainside, stopping all that green from cascading down to sea in one sweep of eloquence. ii. Kagoshima Sakurajima stretches across the panelled windows of the restaurant, large as a close-up at an outdoor flick, a desperado with a smoking gun. While the young sip coffee on this fifth floor, eye-level to volcanic disaster, grandmothers walk past store displays below with umbrellas open to the mid-day sun. At their feet, white dust accumulates: witness to the dangers they've known. All week, ashes fall like memory on the statue of Saigo Takamori, a hero of sweet failures. 24 · The Missouri Review iti. Hiroshima In the Peace Memorial Park, umbrellas of school children blossom yellow, identical among rain-washed statues, thousand cranes gleaming like wet gladioli. Inside the museum, singed blouses guard the numerous shelves of displayable pain: glass pulled from burnt skin, yellowed toenails curved to the tip, watches precise on the fatal moment. Around the diorama of the city intact before the bomb, children point out the buildings that still remain near their houses. At eight or nine, how could they know that whole forests and villages have burnt since? Six hundred meters below the epicenter, the words engraved in stone promise that the mistake shall not be repeated but fail to say whether the mistake is the bomb or the War, or all war. Though we ask the dead to rest in peace, we gloss over the core of their tragedy: they have died for the wrong cause. We prefer to Kyoko Mori The Missouri Review · 25 see them like the rock turned partially to glass by the flash and made sadly beautiful— another sweet failure to mourn. The peace goddess is sick with mutation, her arms freeze in a bodhisattva greeting while her angel wings beat beneath the Hindu head-dress. God help us, someone's written in the museum guest book before me. What god can help us if we ride the waters of easy pain while the houses holding up the mountainside turn solemn under their burden? Kyoko Mori was born in Japan and is currently an associate professor at St. Norbert College in Wisconsin. She has published work in The Denver Quarterly, Kenyan Review and elsewhere. 26 · The Missouri Review Kyoko Mori ...
Wound Healing of Autologous Implants in the Nasal Septal Cartilage (1991)

The cartilaginous nasal septum of the child is often involved in trauma or congenital deformation. In perspective of its role in postnatal growth of the midface, the wound healing of septal cartilage in reaction to various surgical procedures was studied in young rabbits. It was concluded that (1) elevation of mucoperichondrium does not induce significant histologic reactions in the septal cartilage and (2) the wound reaction of cut edges includes only a ± 0.8-mm-deep zone and lasts no longer than 2 weeks, resulting in a stump, encapsulated by fibrous tissue. Reconnection of separated parts occurs 2 weeks after surgery, mostly by merging of the perichondrial layers. Reimplantation of resected cartilage does not lead to normalisation of septal growth. This is not caused by extensive necrosis, loss of morphological organisation or decreased growth potential of the reimplanted cartilage. The essential factor seems to be dislocation (duplication, angulation) of the implant versus the non-mobilised parts of the septum preventing the growth of the implant to contribute fully to the lengthening of the total septum.
A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning (2003)

A new approach to analyzing macromolecular single-crystal X-ray diffraction intensity statistics is presented. Instead of considering reflections in resolution shells, differences between local pairs of reflection intensities are taken and normalized separately. When the two reflections to be compared (having intensities I(1) and I(2), respectively) are chosen appropriately, the behavior of the parameter L = (I(1) - I(2))/(I(1) + I(2)) is insensitive to phenomena that tend to confound traditional intensity statistics, such as anisotropic diffraction and pseudo-centering. The distributions and expected values for L take simple forms when the intensity data are from ordinary crystals or from perfectly twinned specimens. The robustness of the approach is demonstrated with examples using real proteins whose diffraction data appear aberrant by other methods of intensity analysis. The new statistic is better suited than other available methods for diagnosing perfect hemihedral twinning.
Optimizing Bone Screw Pullout Force (1990)

Stability of internal fixation by plate and screw depends on the interface of bone and screw threads. Bone-screw thread design was tested in a synthetic bone model to determine maximum bone-screw pullout force. The model was confirmed to provide reproducible results in a clinically relevant range. Consistent material properties were reflected in the relatively small standard deviations in pullout force, which were less than 10% of mean values. As expected, major diameter was an important determinant of pullout force in a roughly linear manner. Pitch was important with a finer thread giving greater purchase. Minor diameter and the ratio of major to minor diameter had a small but significant effect on pullout force. This study was significant for establishing a good bone-screw testing model and suggesting important thread parameters in selecting or manufacturing a bone screw to optimize its holding power.
Regulated surface expression and shedding support a dual role for semaphorin 4D in platelet responses to vascular injury (2007)

Semaphorin 4D (sema4D; CD100) is an integral membrane protein and the ligand for two receptors, CD72 and plexin-B1. Soluble sema4D has been shown to evoke angiogenic responses from endothelial cells and impair monocyte migration, but the origin of soluble sema4D, particularly at sites of vascular injury, has been unclear. Here we show that platelets express sema4D and both of its receptors and provide evidence that these molecules promote thrombus formation. We also show that the surface expression of sema4D and CD72 increases during platelet activation, followed by the gradual shedding of the sema4D extracellular domain. Shedding is blocked by metalloprotease inhibitors and abolished in mouse platelets that lack the metalloprotease ADAM17 (TACE). Mice that lack sema4D exhibit delayed arterial occlusion after vascular injury in vivo, and their platelets show impaired collagen responses in vitro. In resting platelets, as in B lymphocytes, CD72 is associated with the protein tyrosine phosphatase SHP-1. Platelet activation causes dissociation of the complex, as does the addition of soluble sema4D. These findings suggest a dual role for sema4D in vascular responses to injury. As thrombus formation begins, platelet-associated sema4D can bind to its receptors on nearby platelets, promoting thrombus formation. As thrombus formation continues, sema4D is shed from the platelet surface and becomes available to interact with receptors on endothelial cells and monocytes, as well as continuing to interact with platelets.
Multi-label learning by exploiting label dependency (2010)

In multi-label learning, each training example is associated with a set of labels and the task is to predict the proper label set for the unseen example. Due to the tremendous (exponential) number of possible label sets, the task of learning from multi-label examples is rather challenging. Therefore, the key to successful multi-label learning is how to effectively exploit correlations between different labels to facilitate the learning process. In this paper, we propose to use a Bayesian network structure to efficiently encode the conditional dependencies of the labels as well as the feature set, with the feature set as the common parent of all labels. To make it practical, we give an approximate yet efficient procedure to find such a network structure. With the help of this network, multi-label learning is decomposed into a series of single-label classification problems, where a classifier is constructed for each label by incorporating its parental labels as additional features. Label sets of unseen examples are predicted recursively according to the label ordering given by the network. Extensive experiments on a broad range of data sets validate the effectiveness of our approach against other well-established methods.
unc-93(e1500): A BEHAVIORAL MUTANT OF CAENORHABDITIS ELEGANS THAT DEFINES A GENE WITH A WILD-TYPE NULL PHENOTYPE (1980)

The uncoordinated, egg-laying-defective mutation, unc-93(e1500) III, of the nematode Caenorhabditis elegans spontaneously reverts to a wild-type phenotype. We describe 102 spontaneous and mutagen-induced revertants that define three loci, two extragenic (sup-9 II and sup-10 X) and one intragenic. Genetic analysis suggests that e1500 is a rare visible allele that generates a toxic product and that intragenic reversion, resulting from the generation of null alleles of the unc-93 gene, eliminates the toxic product. We propose that the genetic properties of the unc-93 locus, including the spontaneous reversion of the e1500 mutation, indicate that unc-93 may be a member of a multigene family. The extragenic suppressors also appear to arise as the result of elimination of gene activity; these genes may encode regulatory functions or products that interact with the unc-93 gene product. Genes such as unc-93, sup-9 and sup-10 may be useful for genetic manipulations, including the generation of deficiencies and mutagen testing.
Tumor-infiltrating lymphocytes derived from select B-cell lymphomas secrete granulocyte-macrophage colony-stimulating factor and tumor necrosis factor-alpha in response to autologous tumor stimulation (1993)

Tumor infiltrating lymphocytes (TIL) were cultured from 17 B-cell lymphoma specimens derived from patients with predominantly low-grade malignancies. Specimens included 15 lymph-node biopsies, 1 malignant pleural effusion, and PBL from 1 patient with circulating lymphoma cells. The phenotypic and proliferative characteristics of TIL cultured in interleukin-2 (IL-2) were studied, as well as cytolysis and cytokine secretion in response to autologous tumor. Flow cytometry of fresh tumor suspensions showed that 50% of cells (median) were malignant B cells and 36% were infiltrating T lymphocytes. After culture for approximately 1 month, TIL were 75% +/- 8% CD3+ (mean +/- SEM), 47% +/- 8% CD4+ and 35% +/- 7% CD8+. TIL proliferation was modest in most cases: the median maximum expansion was 32-fold in 25 days. Lysis of autologous tumor in 4-hour 51Cr release assays was mediated by 2 of 12 TIL studied, but was nonspecific. However, these same two TIL, when cocultured with various tumor stimulators, preferentially secreted tumor necrosis factor-alpha and granulocyte-macrophage colony- stimulating factor after autologous tumor stimulation; unstimulated TIL secreted undetectable or barely detectable levels of these cytokines. In one TIL culture, cytokines were secreted by purified CD4+ TIL but not by CD8+ cells, and secretion was completely abrogated by the anti- major histocompatibility complex (MHC) class II antibody IVA12. Thus, although specific cytokine secretion by lymphoma TIL in response to autologous tumor was observed, it occurred in fewer than 20% of patients studied.
Lithographic and letterpress ink vehicles from vegetable oils (1991)

Abstract Our objectives for this study were to produce vegetable oil‐based printing ink vehicles that did not require any petroleum components, which meet or exceed industry standards for rub‐off resistance, viscosity and tackiness for a variety of printing applications. These objectives were satisfactorily met. Vehicles were completely compatible with carbon black, making them suitable for black ink formulations. In addition, the resulting vehicles had exceptionally light colors, and permitted formulations of colored inks that had substantially reduced pigment levels compared to industry standards.
Re-programming of newt cardiomyocytes is induced by tissue regeneration (2006)

Newt hearts are able to repair substantial cardiac injuries without functional impairment, whereas mammalian hearts cannot regenerate. The cellular and molecular mechanisms that control the regenerative capacity of the newt heart are unknown. Here, we show that the ability of newt cardiomyocytes to regenerate cardiac injuries correlates with their ability to transdifferentiate into different cell types. Mechanical injury of the heart led to a severe reduction of sarcomeric proteins in the myocardium, indicating a partial de-differentiation of adult newt cardiomyocytes during regeneration. Newt cardiomyocytes implanted into regenerating limbs lost their cardiac phenotype and acquired skeletal muscle or chondrocyte fates. Reprogramming of cardiomyocytes depended on contact with the limb blastema because cardiomyocytes implanted into intact, non-regenerating limbs or cultured in vitro retained their original identity. We reason that signals from the limb blastema led to de-differentiation of cardiomyocytes, cell proliferation and re-differentiation into specialized cells and propose that the ability of cardiomyocytes to transdifferentiate into different cell types reflects the cellular program that enables heart regeneration.
Danazol for treatment of refractory autoimmune hemolytic anaemia. (1989)

Autoimmune hemolytic anemia (AHA) is uncommon in childhood. A female child presented with severe and chronic clinical course. She was refractory to steroid and the response to splenectomy was poor. She showed excellent remission of hematological condition with Danazol. Danazol may be the drug of choice for refractory autoimmune hemolytic anemia.
Chemical synthesis of a very long oligoribonucleotide with 2-cyanoethoxymethyl (CEM) as the 2′-O-protecting group: structural identification and biological activity of a synthetic 110mer precursor-microRNA candidate (2007)

A long RNA oligomer, a 110mer with the sequence of a precursor-microRNA candidate, has been chemically synthesized in a single synthesizer run by means of standard automated phosphoramidite chemistry. The synthetic method involved the use of 2-cyanoethoxymethyl (CEM), a 2'-hydroxyl protecting group recently developed in our laboratory. We improved the methodology, introducing better coupling and capping conditions. The overall isolated yield of highly pure 110mer was 5.5%. Such a yield on a 1-mumol scale corresponds to 1 mg of product and emphasizes the practicality of the CEM method for synthesizing oligomers of more than 100 nt in sufficient quantity for biological research. We confirmed the identity of the 110mer by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, as well as HPLC, electrophoretic methods, and RNase-digestion experiments. The 110mer also showed sense-selective specific gene-silencing activity. As far as we know, this is the longest chemically synthesized RNA oligomer reported to date. Furthermore, the identity of the 110mer was confirmed by both physicochemical and biological methods.
Aberrant Epidermal Growth Factor Receptor Signaling and Enhanced Sensitivity to EGFR Inhibitors in Lung Cancer (2005)

Epidermal growth factor receptor (EGFR) is occasionally amplified and/or mutated in non-small cell lung cancer (NSCLC) and can be coexpressed with other members of the HER receptor family to form functional heterodimers. We therefore investigated lung cancer cell lines for alterations in EGFR gene copy number, enhanced expression of EGFR and other HER family members, and EGFR coding sequence mutations and correlated these findings with response to treatment with the EGFR inhibitors and the kinetics of ligand-induced signaling. We show here that somatic deletions in the tyrosine kinase domain of EGFR were associated with increased EGFR gene copy number in NSCLC. Treatment with the specific EGFR tyrosine kinase inhibitors (TKI) gefitinib or erlotinib or the EGFR inhibitory antibody cetuximab induced apoptosis of HCC827, a NSCLC cell line with EGFR gene amplification and an exon 19 deletion. H1819, a NSCLC cell line that expresses high levels of EGFR, ErbB2, and ErbB3 but has wild-type EGFR, showed intermediate sensitivity to TKIs. In both cell lines, ligand-induced receptor tyrosine phosphorylation was delayed and prolonged and AKT was constitutively phosphorylated (but remained inhibitable by EGFR TKI). Thus, in addition to EGFR mutations, other factors in NSCLC cells, such as high expression of ErbB family members, may constitutively activate AKT and sensitize cells to EGFR inhibitors.
Genetic and molecular characterization of suppressors of SIR4 mutations in Saccharomyces cerevisiae. (1989)

In order to learn more about other proteins that may be involved in repression of HML and HMR in Saccharomyces cerevisiae, extragenic suppressor mutations were identified that could restore repression in cells defective in SIR4, a gene required for function of the silencer elements flanking HML and HMR. These suppressor mutations, which define at least three new genes, SAN1, SAN2 and SAN3, arose at the frequency expected for loss-of-function mutations following mutagenesis. All san mutations were recessive. Suppression by san1 was allele-nonspecific, since san1 could suppress two very different alleles of SIR4, and was locus-specific since san1 was unable to suppress a SIR3 mutation or a variety of mutations conferring auxotrophies. The SAN1 gene was cloned, sequenced, and used to construct a null allele. The null allele had the same phenotype as the EMS-induced mutations and exhibited no pleiotropies of its own. Thus, the SAN1 gene was not essential. SAN1-mediated suppression was neither due to compensatory mutations in interacting proteins, nor to translational missense suppression. SAN1 may act posttranslationally to control the stability or activity of the SIR4 protein.
Optical equalization to combat the effects of laser chirp and fiber dispersion (1990)

Optical equalizers capable of combating the effects of laser chirp and fiber chromatic dispersion on high-speed long-haul fiber-optic communication links at 1.5 μm are described. They consist of both reflective and transmissive cavity structures. The equalizers are adaptive in the sense that the position of their periodic frequency responses are optimally adjusted in real time. The equalizers are evaluated by using computer simulation routines based on the rate equations for intensity-modulated lasers. It is shown that, by using equalizers of the type proposed, the receiver data eyes remain open well beyond where they would close without equalization.
Convenient methods for patterning the adhesion of mammalian cells to surfaces using self-assembled monolayers of alkanethiolates on gold (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConvenient methods for patterning the adhesion of mammalian cells to surfaces using self-assembled monolayers of alkanethiolates on goldGabriel P. Lopez, Mark W. Albers, Stuart L. Schreiber, Reed Carroll, Ernest Peralta, and George M. WhitesidesCite this: J. Am. Chem. Soc. 1993, 115, 13, 5877–5878Publication Date (Print):June 1, 1993Publication History Published online1 May 2002Published inissue 1 June 1993https://pubs.acs.org/doi/10.1021/ja00066a087https://doi.org/10.1021/ja00066a087research-articleACS PublicationsRequest reuse permissionsArticle Views742Altmetric-Citations220LEARN 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