gebhart/patrepeval huggingface dataset:
Distinct roles of the homeotic genes Ubx and abd-A in beetle embryonic abdominal appendage development (2000)

Insects are easily distinguishable by the absence of legs on the adult abdomen. Studies performed on the Dipteran, Drosophila melanogaster, indicate that this is because of the repressive effects of the homeotic genes Ultrabithorax (Ubx) and abdominal-A (abd-A) on the limb promoting gene Distal-less (Dll) during embryonic development. However, in many species appendage-like structures are present on abdominal segments in embryonic and juvenile stages. Here, by using classical genetics and double-stranded RNA-mediated gene silencing in the red flour beetle, Tribolium castaneum, a species that develops an appendage on the first abdominal segment, we investigate the roles of Ubx and Abd-A in abdominal limb development. We find that in Tribolium, Abd-A, but not Ubx, represses early expression of Dll in the embryonic abdomen. Ubx appears to modify the A1 appendage. This difference in the activities of Abd-A and Ubx is critical for proper development of this appendage. We suggest that an ancestral role of Abd-A in insect abdominal appendage development was in the repression of Dll initiation and that of Ubx was in modulation of abdominal appendage morphology.
Biosynthesis of the 7-mercaptoheptanoic acid subunit of component B [(7-mercaptoheptanoyl)threonine phosphate] of methanogenic bacteria (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBiosynthesis of the 7-mercaptoheptanoic acid subunit of component B [(7-mercaptoheptanoyl)threonine phosphate] of methanogenic bacteriaRobert H. WhiteCite this: Biochemistry 1989, 28, 2, 860–865Publication Date (Print):January 24, 1989Publication History Published online1 May 2002Published inissue 24 January 1989https://pubs.acs.org/doi/10.1021/bi00428a068https://doi.org/10.1021/bi00428a068research-articleACS PublicationsRequest reuse permissionsArticle Views51Altmetric-Citations16LEARN 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
Premigration deghosting for marine towed streamer data using a bootstrap approach (2012)

Removing the receiver ghost before migration provides better low and high frequency response as well as a higher signal-to-noise ratio for preprocessing steps such as multiple suppression and velocity analysis. We propose a bootstrap approach that self-determines its own parameters for receiver deghosting. The recorded data in shot domain are first used to create mirror data through a 1D ray tracing based normal moveout correction method; then both the recorded and mirror data are used to jointly invert for the receiver-ghost-free data. We demonstrate with both synthetics and real data that our deghosting method can, in many situations, reliably remove the receiver ghost for marine towed streamer data in the premigration stage. Here, this technique is used to partially improve the bandwidth of conventional streamer data but for optimal broadband seismic, a full broadband system (like BroadSeis) is necessary.
A Phase I First-in-Human Study of TRC105 (Anti-Endoglin Antibody) in Patients with Advanced Cancer (2012)

TRC105 was tolerated at 10 mg/kg every week and 15 mg/kg every 2 weeks, with a safety profile that was distinct from that of VEGF inhibitors. Evidence of clinical activity was seen in a refractory patient population. Ongoing clinical trials are testing TRC105 in combination with chemotherapy and VEGF inhibitors and as a single agent in prostate, ovarian, bladder, breast, and hepatocellular cancer.
Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria Desulfotalea psychrophila, Flavobacterium psychrophilum, Psychrobacter arcticus, Psychrobacter cryohalolentis, Psychromonas ingrahamii, Psychroflexus torquis, and Photobacterium profundum (2014)

The results showed that SSB proteins from psychrophilic microorganisms are typical bacterial SSBs and possess relatively high thermostability, offering an attractive alternative to other thermostable SSBs in molecular biology applications.
Incidence of White Mold and Yield of Upright Bean Grown in Different Planting Patterns (1993)

Abstract The commercial dry bean ( Phaseolus vulgaris L) production system in Alberta requires irrigation and the viny cultivars currently used in this production system are prone to outbreaks of white mold caused by Sclerotinia sderotiorum (Lib.) de Bary. The use of beans with an upright growth habit has potential for alleviating the disease problem, but the narrow profile of the upright beans may warrant a different planting pattern to achieve high yield. A study was undertaken to determine the effect of between‐ and within‐row spacings on the occurrence of white mold and seed yield of upright beans. An experimental navy bean composite with upright growth habit, and a susceptible control Red Mexican, UI 37, were evaluated using three between‐row (BR) and three within‐row (WR) spacings in presence or absence of white mold during a 2‐year period. The BR and WR spacings had no effect (P &gt; 0. 05) on disease occurrence in the inoculated upright composite or in the viny control. Regardless of BR and WR spacings, the upright composite had less (P &lt; 0. 01) disease than the control in both years. In general, large differences (P &lt; 0. 05) were found between the upright composite and control spacing treatments in the presence or absence of white mold. BR spacing had a significant effect on seed yield, but WR spacing did not. In most cases, increasing plant density by reducing BR spacings resulted in higher seed yields. These findings suggest that producers may gain in seed yield without increasing risks for white mold occurrence by changing from viny to upright beans and planting in narrower rows.
Coinduction of MDR-1 Multidrug-Resistance and Cytochrome P-450 Genes in Rat Liver by Xenobiotics (1988)

The levels of mRNA for multidrug-resistance (MDR-1) and selective cytochrome P-450 genes were determined in adult rat liver following administration of various natural and synthetic xenobiotics. MDR-1 (also known as PGY1) was induced following administration of aflatoxin B1, 2-(acetylamino)fluorene (AAF), N-hydroxy-2-(acetylamino)fluorene, isosafrole, phenothiazine, and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), but not after phenobarbital or 7-hydroxy-2-(acetylamino)fluorene treatment. Cytochrome P-450 isoform d was induced by TCDD, isosafrole, phenothiazine, and AAF, while cytochrome P-450 isoform b was induced by phenobarbital, and to a lesser extent by isosafrole. These observations suggest that both MDR and cytochrome P-450 gene families are evolutionarily selected by the capacity of various xenobiotics to induce their own detoxification either through metabolism to hydrophilic derivatives by the cytochrome P-450 system or direct excretion from the cell by the MDR gene family. Furthermore, the data indicate that induction of selective members of the MDR and the cytochrome P-450 gene families may depend on overlapping regulatory elements.
[The effect of a combination of immune and bacterial preparations on the microbial ecology of pregnant women in a risk group]. (1993)

Clinical and microbiologic examinations of 200 pregnant women with perinatal risk factors helped single out a group at high risk of intestinal dysbacteriosis (abnormal microflora) in their babies. The preparation of these women to labor included correction of the bacterial ecology of the vagina and intestine with a complex of immunologic and bacterial drugs. Administration of this drug complex favorably influenced the course of pregnancy, labor and the postpartum period, as well as the bacterial ecologic status of the mother and child, resulting in a reduced incidence of infectious complications in the newborns.
Collagenase Lot Selection and Purification for Adipose Tissue Digestion (1995)

Crude Clostridial collagenase (CCC) remains the most widely used enzyme for the digestion of tissues prior to cell isolation and culture. CCC contains numerous components in addition to specific collagenases and proteases. A chronic problem associated with CCC is significant lot variability which occurs with respect to the ability of different lots of CCC to digest tissue. We have evaluated numerous commercially available samples of CCC for their ability to digest human liposuction-derived SC fat. Digestion capacity was evaluated as the ability to release endothelial cells from fat as well as the ability of isolated cells to adhere to tissue culture plastic. A significant variation in digestion efficacy between lots of collagenase was observed. We subsequently purified CCC using a partial purification method with dialysis and centrifugation as well as a complete purification, using liquid chromatography, to remove all nonspecific proteases. While partially purified collagenase retained digestion capacity, pure collagenase exhibited reduced digestion capacity. Maximum digestion was achieved with pure collagenase when trypsin was added. The use of completely purified collagenase with trypsin is advantageous where all components in the enzyme digestion mixture must be known.
The Agonists of Formyl Peptide Receptors Prevent Development of Severe Sepsis after Microbial Infection (2010)

Severe sepsis, a principal cause of death in intensive care units, occurs when host immune defenses fail to combat invading microbes. In this paper, we report that the administration of peptide agonists of formyl peptide receptors, including Trp-Lys-Tyr-Met-Val-D-Met (WKYMVm), protected against death by enhanced bactericidal activity and inhibition of vital organ inflammation and immune cell apoptosis in a cecal ligation and puncture (CLP) sepsis mouse model. The administration of WKYMVm also enhanced the production of type 1 (IFN-γ and IL-12) and type 17 (IL-17 and TGF-β) cytokines in CLP mice. In contrast, the administration of WKYMVm inhibited the production of proinflammatory cytokines (TNF-α, IL-1β, and IL-6) in the CLP mice. The therapeutic and bactericidal effects of WKYMVm were partly reversed in IFN-γ-deficient mice, whereas target organ inflammation was not. Meanwhile, the therapeutic and anti-inflammatory effects of WKYMVm were partly reversed in IL-17-deficient mice. In addition, the administration of WKYMVm also enhanced type 1 and type 17 Th cell responses in mice sensitized with LPS plus Ags. These results suggest that the agonists of formyl peptide receptors effectively prevent development of severe sepsis following microbial infection partly via augmentation of type 1 and type 17 immune responses.
Cellodextrin Transport in Yeast for Improved Biofuel Production (2010)

Fungal degradation of plant biomass may provide insights for improving cellulosic biofuel production. We show that the model cellulolytic fungus Neurospora crassa relies on a high-affinity cellodextrin transport system for rapid growth on cellulose. Reconstitution of the N. crassa cellodextrin transport system in Saccharomyces cerevisiae promotes efficient growth of this yeast on cellodextrins. In simultaneous saccharification and fermentation experiments, the engineered yeast strains more rapidly convert cellulose to ethanol when compared with yeast lacking this system.
Time-dependent cytotoxicity induced by SJG-136 (NSC 694501): influence of the rate of interstrand cross-link formation on DNA damage signaling (2006)

SJG-136 is a new pyrrolobenzodiazepine dimer inducing time-dependent cytotoxicity. HCT 116 cells were exposed to 50 nmol/L of SJG-136 for 1 hour or 1 nmol/L of SJG-136 for 24 hours to achieve similar levels of interstrand cross-links (ICL). The short exposure led to a rapid formation of ICLs (1 hour), early H2AX foci formation (4 hours), prominent S phase arrest, and greater phosphorylation of Nbs1 (on serine 343) and Chk1 (on serine 317) than a 24-hour exposure. The prolonged exposure at low concentrations of SJG-136 induced a gradual formation of ICLs (up to 24 hours) which was associated with a limited S phase arrest and delayed Nbs1 phosphorylation. Prolonged exposure was also associated with a reduced phosphorylation of p53 on serines 15 and 20, a limited and delayed phosphorylation on serine 392, and a less prominent increase in p21 levels. These data suggest that the 24-hour exposure to a low concentration of SJG-136 led to delayed and reduced DNA damage signaling compared with a higher concentration of SJG-136 for 1 hour, resulting in greater cytotoxicity and contributing to the time-dependent cytotoxic effect of SJG-136.
Ionospheric Joule heating, fast flow channels, and magnetic field line topology for IMF By‐dominant conditions: Observations and comparisons with predicted reconnection jet speeds (2012)

When the interplanetary magnetic field (IMF) is dawnward or duskward, magnetic merging between the IMF and the geomagnetic field occurs near the cusp on the dayside flanks of the magnetosphere. While these periods are usually considered “quiet,” they can lead to intense localized energy deposition into the dayside ionosphere. We analyze two intervals during the geomagnetic storm on 24 August 2005: one with steady duskward IMF and one with steady dawnward IMF. Using outputs from the Assimilative Mapping of Ionospheric Electrodynamics (AMIE) and data from the Defense Meteorological Satellite Program, we show that intense Joule heating exists on fast ionospheric flow channels which lie on open field lines. In addition, the flow channels on open field lines have large components in the sunward direction and therefore resist the bulk solar wind and magnetosheath flow. We compare observed velocities with predicted reconnection jet speeds using magnetosheath and cusp parameters from an MHD simulation. Results suggest that the fast ionospheric flow corresponds to portions of the reconnection jet populated by low‐density plasma. The importance of ionospheric conductance in determining the ionospheric flow is also discussed.
To fuse or not to fuse: What is your purpose? (2013)

Since the dawn of time, or at least the dawn of recombinant DNA technology (which for many of today's scientists is the same thing), investigators have been cloning and expressing heterologous proteins in a variety of different cells for a variety of different reasons. These range from cell biological studies looking at protein-protein interactions, post-translational modifications, and regulation, to laboratory-scale production in support of biochemical, biophysical, and structural studies, to large scale production of potential biotherapeutics. In parallel, fusion-tag technology has grown-up to facilitate microscale purification (pull-downs), protein visualization (epitope tags), enhanced expression and solubility (protein partners, e.g., GST, MBP, TRX, and SUMO), and generic purification (e.g., His-tags, streptag, and FLAG™-tag). Frequently, these latter two goals are combined in a single fusion partner. In this review, we examine the most commonly used fusion methodologies from the perspective of the ultimate use of the tagged protein. That is, what are the most commonly used fusion partners for pull-downs, for structural studies, for production of active proteins, or for large-scale purification? What are the advantages and limitations of each? This review is not meant to be exhaustive and the approach undoubtedly reflects the experiences and interests of the authors. For the sake of brevity, we have largely ignored epitope tags although they receive wide use in cell biology for immunopreciptation.
Using sensor pattern noise for camera model identification (2008)

Sensor photo-response non-uniformity (PRNU) was introduced by Lukáš et al. [1] to solve the problem of digital camera sensor identification. The PRNU is the main component of a camera fingerprint that can reliably identify a specific camera. This fingerprint can be estimated from multiple images taken by the camera. In this paper, we demonstrate that the same fingerprint can be used for identification of camera brand and model. This is possible due to the fact that fingerprints estimated from images in the TIFF/JPEG format contain local structure due to various in-camera processing that can be detected by extracting a set of numerical features from the fingerprints and classifying them using pattern classification methods. We estimate and classify fingerprints for more than 4500 digital cameras spanning 8 different brands and 17 models. The average probability of correctly classified camera brand was 90.8%.
Dynamic trafficking and delivery of connexons to the plasma membrane and accretion to gap junctions in living cells (2002)

Certain membrane channels including acetylcholine receptors, gap junction (GJ) channels, and aquaporins arrange into large clusters in the plasma membrane (PM). However, how these channels are recruited to the clusters is unknown. To address this question, we have investigated delivery of GJ channel subunits (connexons) assembled from green fluorescent protein (GFP)-tagged connexin 43 (Cx43) to the PM and GJs in living cells. Fluorescence-photobleaching of distinct areas of Cx43-GFP GJs demonstrated that newly synthesized channels were accrued to the outer margins of channel clusters. Time-lapse microscopy further revealed that connexons were delivered in vesicular carriers traveling along microtubules from the Golgi to the PM. Routing and insertion of connexons occurred predominantly into the nonjunctional PM. These PM connexons can move laterally as shown by photo-bleaching and thus, can reach the margins of channel clusters. There, the apposing PMs are close enough to allow connexons to dock into complete GJ channels. When connexon delivery to the PM was inhibited by brefeldin A, or nocodazole pretreatment, the PM pool initially enabled connexon accrual to the clusters but further accrual was inhibited upon depletion. Taken together, our results indicate that GJ channel clusters grow by accretion at their outer margins from connexon subunits that were delivered to the nonjunctional PM, and explain how connexons in the PM can function in intra-/extracellular signaling before GJ channel formation and direct cell-cell communication.
Acute demyelination disrupts the molecular organization of peripheral nervous system nodes (2004)

Intraneurally injected lysolecithin causes both segmental and paranodal demyelination. In demyelinated internodes, axonal components of nodes fragment and disappear, glial and axonal paranodal and juxtaparanodal proteins no longer cluster, and axonal Kv1.1/Kv1.2 K+ channels move from the juxtaparanodal region to appose the remaining heminodes. In paranodal demyelination, a gap separates two distinct heminodes, each of which contains the molecular components of normal nodes; paranodal and juxtaparanodal proteins are properly localized. As in normal nodes, widened nodal regions contain little or no band 4.1B. Lysolecithin also causes "unwinding" of paranodes: The spiral of Schwann cell membrane moves away from the paranodes, but the glial and axonal components of septate-like junctions remain colocalized. Thus, acute demyelination has distinct effects on the molecular organization of the nodal, paranodal, and juxtaparanodal region, reflecting altered axon-Schwann cell interactions.
PAROMOMYCIN. I. PAROMAMINE, A GLYCOSIDE OF D-GLUCOSAMINE1 (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPAROMOMYCIN. I. PAROMAMINE, A GLYCOSIDE OF D-GLUCOSAMINE1Theodore H. Haskell, James C. French, and Quentin R. BartzCite this: J. Am. Chem. Soc. 1959, 81, 13, 3480–3481Publication Date (Print):July 1, 1959Publication History Published online1 May 2002Published inissue 1 July 1959https://pubs.acs.org/doi/10.1021/ja01522a084https://doi.org/10.1021/ja01522a084research-articleACS PublicationsRequest reuse permissionsArticle Views286Altmetric-Citations43LEARN 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
Oncogenic stress sensitizes murine cancers to hypomorphic suppression of ATR (2011)

Oncogenic Ras and p53 loss-of-function mutations are common in many advanced sporadic malignancies and together predict a limited responsiveness to conventional chemotherapy. Notably, studies in cultured cells have indicated that each of these genetic alterations creates a selective sensitivity to ataxia telangiectasia and Rad3-related (ATR) pathway inhibition. Here, we describe a genetic system to conditionally reduce ATR expression to 10% of normal levels in adult mice to compare the impact of this suppression on normal tissues and cancers in vivo. Hypomorphic suppression of ATR minimally affected normal bone marrow and intestinal homeostasis, indicating that this level of ATR expression was sufficient for highly proliferative adult tissues. In contrast, hypomorphic ATR reduction potently inhibited the growth of both p53-deficient fibrosarcomas expressing H-rasG12V and acute myeloid leukemias (AMLs) driven by MLL-ENL and N-rasG12D. Notably, DNA damage increased in a greater-than-additive fashion upon combining ATR suppression with oncogenic stress (H-rasG12V, K-rasG12D, or c-Myc overexpression), indicating that this cooperative genome-destabilizing interaction may contribute to tumor selectivity in vivo. This toxic interaction between ATR suppression and oncogenic stress occurred without regard to p53 status. These studies define a level of ATR pathway inhibition in which the growth of malignancies harboring oncogenic mutations can be suppressed with minimal impact on normal tissue homeostasis, highlighting ATR inhibition as a promising therapeutic strategy.