gebhart/patrepeval huggingface dataset:
Maximizing gene expression from plasmid vectors containing the lambda PL promoter: strategies for overproducing transcription termination factor rho. (1985)

We have constructed two plasmids in which transcription of the rho gene from Escherichia coli K-12 is under the control of the lambda phage PL promoter. In p31-356, the normal rho promoter is deleted, but the remainder of the rho leader region, including the ribosome binding site, is present. In p39-AS, the rho leader is completely absent, and the lambda cII ribosome binding site replaces that of rho. Under noninducing conditions, expression of rho protein from these plasmids is repressed by the lambda cI protein in hosts carrying lambda cryptic prophage. Induction using mitomycin C or nalidixic acid in a cryptic lysogen carrying the cI+ repressor resulted in the overproduction of rho protein to levels of 3%-5% of the total cellular protein with p31-356, and to levels of approximately equal to 40% with p39-AS. The overproduced protein is functionally indistinguishable from the rho protein isolated from the K-12 strain W3110, and it can be obtained from cells harboring p39-AS in yields of up to 25 mg of rho per g of cells. In contrast to chemical induction, heat induction in four cryptic lambda lysogens carrying the thermolabile cI857 repressor failed to yield the same high levels of rho protein (with either plasmid). Our results show that chemical induction of PL-containing plasmid expression vectors can serve as a convenient and useful alternative to the commonly used method of heat induction.
Phase I/II trial combining the HDAC inhibitor, valproic acid (VPA) and FEC100 (5-fluorouracil, epirubicin and cyclophosphamide) in locally advanced/metastatic breast cancer (2007)

1065 Background: Cell culture and xenograft studies suggest a synergistic interaction between histone deacetylase inhibitors (HDACi) and topoisomerase (topo) inhibitors, as well as other DNA targeting agents. Methods: In this phase I/II study, we determined the effects of escalating doses of VPA on the clinical efficacy and tolerability of epirubicin. The phase I part was open to patients will all solid tumors. A limited phase II part at the maximum tolerated dose (MTD) of VPA enrolled 10 breast cancer patients and incorporated the breast cancer regimen FEC100 (5-fluorouracil, epirubicin, cyclophosphamide (600/100/600 mg/m 2 )). VPA was given on days 1–3 prior to epirubicin/FEC100 in 3-week cycles. HDAC expression, histone acetylation and topo II expression were evaluated in pre-and post-VPA peripheral blood mononuclear cells and tumor samples. Results: Fifty-four (44 in phase I and 10 in phase II) patients [median age 55 (39–78)] received VPA (mg/kg/day): 15, 30, 45, 60, 75, 90, 100, 120, 140 and 160. Tumor types included: breast (10+10), melanoma (11), lung (6), sarcoma (2), GYN (2), GI (5) and others (8). Dose-limiting toxicities included somnolence, confusion and febrile neutropenia. No exacerbation of FEC100/epirubicin-related toxicities was observed. Objective responses in the phase I part 9/41 (22%) were seen across different tumor types despite a median number of 3 (0–6) prior regimens with stable disease/minor response in 16/41 (39%). In the breast-specific phase II part, partial responses to date were seen in 4/8 (50%) and stable disease in 2/8 (25%), progression in 1/8 (12.5%), 1/8 (12.5%) patients withdrew consent. All breast cancer patients with a response/stable disease received the maximal number of seven cycles. VPA plasma concentrations correlated with VPA dose. There was a positive correlation between histone acetylation and VPA dose as well as plasma levels in PBMC and further correlated with those in tumors. Conclusion: A sequence-specific combination of VPA and FEC100 in breast cancer is highly active without exacerbation of chemotherapy-induced toxicities. A neoadjuvant phase II trial using VPA (120 mg/kg) -&gt; FEC100 in patients with early stage breast cancer is ongoing. [Table: see text]
Breast cancer surgery: understanding the story. (1992)

1. Research has shown that mastectomy, with or without reconstruction, is no more effective in the long run than breast conservation and irradiation. Therefore, the important factor seems to be choice. 2. A Halsted radical mastectomy involves the removal of the whole breast along with the pectoralis major and minor muscles and a complete axillary dissection. A modified radical mastectomy involves removal of the whole breast and most or all of the axillary lymph nodes, but preserves the pectoralis major muscle. 3. Breast preserving strategies remove the malignant cells and minimal surrounding tissue. These segmental resections include lumpectomy, quadranectomy, and wedge resection along with axillary node dissection.
Blood biomarkers for the non-invasive diagnosis of endometriosis (2016)

Of the biomarkers that were subjected to meta-analysis, none consistently met the criteria for a replacement or triage diagnostic test. A subset of blood biomarkers could prove useful either for detecting pelvic endometriosis or for differentiating ovarian endometrioma from other benign ovarian masses, but there was insufficient evidence to draw meaningful conclusions. Overall, none of the biomarkers displayed enough accuracy to be used clinically outside a research setting. We also identified blood biomarkers that demonstrated no diagnostic value in endometriosis and recommend focusing research resources on evaluating other more clinically useful biomarkers.
Trifluoromethyl Fluorocoxib A Detects Cyclooxygenase-2 Expression in Inflammatory Tissues and Human Tumor Xenografts (2014)

Fluorocoxib A is an effective COX-2-targeted optical imaging agent, used for in vivo detection of inflammatory tissues and premalignant and malignant tumors that express elevated levels of COX-2 (Uddin et al. Cancer Res. 2010, 70, 3618-3627). In an effort to discover novel optical probes for COX-2, a trifluoromethyl analogue of fluorocoxib A (CF3-fluorocoxib A) was synthesized and evaluated for its ability to inhibit COX-2 in vitro purified enzyme and human cancer cell lines. Kinetic analysis revealed that CF3-fluorocoxib A is a slow, tight binding inhibitor of COX-2 that exhibits low nanomolar inhibitory potency. While CF3-fluorocoxib A and fluorocoxib A are similar in structure, CF3-fluorocoxib A shows improved potency in inhibition of wtCOX-2 and with a series of site-directed COX-2 mutants. After intraperitoneal injection, selective uptake of CF3-fluorocoxib A is detected in inflamed mouse paws compared to noninflamed contralateral paws by optical imaging, and uptake is blocked by pretreatment with the COX-2 inhibitor, celecoxib. Selective uptake is also detected in the COX-2-positive human tumor xenografts (1483 HNSCC) as compared with the COX-2-negative tumor xenografts (HCT116) in an in vivo nude mouse tumor model. These in vitro and in vivo studies suggest that binding to COX-2 is the major determinant of uptake of CF3-fluorocoxib A into the inflamed tissues and tumor xenografts. Thus, this new COX-2-targeted imaging probe should find utility in the detection and evaluation of COX-2 status in naturally occurring malignancies.
Transient dominant selection of recombinant vaccinia viruses (1990)

A general method for constructing and selecting recombinant vaccinia viruses with insertions, deletions, or mutations in any gene that is similar in principle to one originally devised for Saccharomyces cerevisiae (S. Scherer and R. W. Davis, Proc. Natl. Acad. Sci. USA 76:4951-4955, 1979) is described. The selectable marker used, Escherichia coli guanine phosphoribosyltransferase, is not retained within the final recombinant virus, and hence, this procedure may be used serially to introduce several foreign genes or to make multiple site-directed mutations.
A 62 mV 0.13 $\mu$m CMOS Standard-Cell-Based Design Technique Using Schmitt-Trigger Logic (2011)

Supply voltage reduction beyond the minimum energy per operation point is advantageous for supply voltage constrained applications, but is limited by the degradation of on-to-off current ratios with decreasing supply. In this work, we show that the effective on-to-off ratio can be considerably improved by the use of Schmitt Trigger structures, which effectively reduce the leakage from the gate output node and thereby stabilize the output level. A method for applying this concept to general logic is presented. Design rules concerning transistor sizing, gate selection and layout necessary to further minimize the required supply voltage are outlined and applied to the design of a chip implementing 8 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\,\times\,$</tex> </formula> 8 bit multipliers as test structures. The only custom design step is the creation of the Schmitt Trigger standard-cell library, otherwise a regular digital tool chain is used. The multipliers exhibit full functionality down to supply voltages of 84 mV–62 mV, depending on the area overhead invested. No process or post-silicon tuning like body biasing is used. At the minimum possible supply voltage of 62 mV, a power consumption of 17.9 nW at an operation frequency of 5.2 kHz is measured for an 8 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">$\,\times\,$</tex></formula> 8 bit multiplier.
Twenty-Four-Hour Induction of Freezing and Drought Tolerance in Plumules of Winter Rye Seedlings by Desiccation Stress at Room Temperature in the Dark (1982)

Exposure of seedlings of winter rye (Secale cereale L., cv. Puma) for 2 weeks or 24 hours to desiccation stress (40% relative humidity) at room temperature (21 degrees C) in the dark induced degrees of freezing and drought tolerance in the plumules comparable to those produced by cold conditioning for 2 weeks at 3 degrees C. The induction was associated with repression of growth and could not be produced in plumules excised from the seedlings indicating a requirement for translocation of nutrients from the endosperm. Rapid increase in osmotic pressure, soluble proteins, and phospholipids in plumules in association with the development of freezing and drought tolerance and the requirement of endosperm suggested diversion of nutrient from use in extension growth, to use in augmentation of protoplasm in plumule cells. Since cold acclimation slowed or arrested growth and is associated with augmentation of protoplasm, it is suggested that the common element in the induction of freezing tolerance by cold and drought is the necessity for producing a condition of augmented protoplasm and membranes in cells thus reinforcing a similar conclusion reached from seasonal studies on woody plants.
Interleukin-8 Is a Major Neutrophil Chemotactic Factor in Pleural Liquid of Patients with Empyema (1992)

Interleukin-8 (IL-8), a potent neutrophil chemotactic peptide, has been found in association with human disease, but its contribution to chemotactic activity in humans is not yet known. We asked whether IL-8 is present in inflammatory human pleural effusions, and to what extent it contributes to pleural liquid neutrophil chemotactic activity. Because tumor necrosis factor alpha (TNF-alpha) is a strong inducer of IL-8, we also asked whether TNF-alpha was present. For this prospective study, we collected pleural liquid from 51 patients (empyema, 14; parapneumonic, four; tuberculous, eight; malignant, nine; miscellaneous exudative, seven; and transudative, nine), counted pleural neutrophils, and measured IL-8 and TNF-alpha concentrations in the supernatant. To determine the contribution of IL-8 to chemotactic activity in empyema, we measured the neutrophil migration induced by empyemic liquids before and after addition of anti-IL-8 F(ab')2 antibody fragments or control anti-IL-6 F(ab')2. We found that IL-8 concentrations were higher in empyema (61.3 +/- 21.0 ng/ml [SEM]) than in all other effusions (1.1 +/- 0.5 ng/ml) (p = 0.0001). All empyema liquids had IL-8 concentrations above 2.5 ng/ml, which was true for only three of the other 37 effusions (two parapneumonic, one tuberculous). IL-8 levels correlated with the pleural neutrophil count (r = 0.46; p = 0.007) and the neutrophil chemotactic activity of pleural liquid (r = 0.43; p = 0.008). Anti-IL-8 antibodies decreased chemotactic activity in empyema liquids by 65 +/- 5%, whereas the control antibody had no effect (0 +/- 5% decrease) (p = 0.0005).(ABSTRACT TRUNCATED AT 250 WORDS)
Multiple Ras Downstream Pathways Mediate Functional Repression of the Homeobox Gene Product TTF-1 (2000)

Expression of oncogenic Ras in thyroid cells results in loss of expression of several thyroid-specific genes and inactivation of TTF-1, a homeodomain-containing transcription factor required for normal development of the thyroid gland. In an effort to understand how signal transduction pathways downstream of Ras may be involved in suppression of the differentiated phenotype, we have tested mutants of the Ras effector region for their ability to affect TTF-1 transcriptional activity in a transient-transfection assay. We find that V12S35 Ras, a mutant known to interact specifically with Raf but not with RalGDS or phosphatidylinositol 3-kinase (PI3 kinase) inhibits TTF-1 activity. Expression of an activated form of Raf (Raf-BXB) also inhibits TTF-1 function to a similar extent, while the MEK inhibitors U0126 and PD98059 partially relieve Ras-mediated inactivation of TTF-1, suggesting that the extracellular signal-regulated kinase (ERK) pathway is involved in this process. Indeed, ERK directly phosphorylates TTF-1 at three serine residues, and concomitant mutation of these serines to alanines completely abolishes ERK-mediated phosphorylation both in vitro and in vivo. Since activation of the Raf/MEK/ERK pathway accounts for only part of the activity elicited by oncogenic Ras on TTF-1, other downstream pathways are likely to be involved in this process. We find that activation of PI3 kinase, Rho, Rac, and RalGDS has no effect on TTF-1 transcriptional activity. However, a poorly characterized Ras mutant, V12N38 Ras, can partially repress TTF-1 transcriptional activity through an ERK-independent pathway. Importantly, concomitant expression of constitutive activated Raf and V12N38 Ras results in almost complete loss of TTF-1 activity. Our data indicate that the Raf/MEK/ERK cascade may act in concert with an as-yet-uncharacterized signaling pathway activated by V12N38 Ras to repress TTF-1 function and ultimately to inhibit thyroid cell differentiation.
Covalently bonded single-molecule junctions with stable and reversible photoswitched conductivity (2016)

Through molecular engineering, single diarylethenes were covalently sandwiched between graphene electrodes to form stable molecular conduction junctions. Our experimental and theoretical studies of these junctions consistently show and interpret reversible conductance photoswitching at room temperature and stochastic switching between different conductive states at low temperature at a single-molecule level. We demonstrate a fully reversible, two-mode, single-molecule electrical switch with unprecedented levels of accuracy (on/off ratio of ~100), stability (over a year), and reproducibility (46 devices with more than 100 cycles for photoswitching and ~10(5) to 10(6) cycles for stochastic switching).
Oleanane Triterpenoid CDDO‐Me inhibits growth and induces apoptosis in prostate cancer cells by independently targeting pro‐survival Akt and mTOR (2009)

This study demonstrated potent antitumor activity of CDDO-Me against prostate cancer cells both in vitro and in vivo. Data also identified Akt and mTOR as molecular targets of CDDO-Me in prostate cancer cells.
IN VIVO SOMATIC MUTATIONS IN HUMANS: MEASUREMENT AND ANALYSIS (1990)

Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A ...Read More
Vesicular Stomatitis Virus as an Oncolytic Vector (2004)

Recent data has shown that viruses such as vesicular stomatitis virus (VSV), a relatively non-pathogenic, negative-stranded RNA virus, can preferentially replicate in malignant cells and less so in normal cells. VSV appears able to carry out this function in transformed cells since these hosts exhibit the hallmarks of flawed host defense, probably involving the interferon system, which is essential for preventing virus replication. The simple genetic constitution of VSV, lack of any known transforming, integrating or reassortment properties, extensive knowledge relating to its interaction with the immune system and the ability to genetically manipulate this agent affords an ideal opportunity to exploit the oncolytic and gene targeting potential of this innocuous virus. Thus, aside from preferentially targeting malignant cells VSV recombinants could be generated that could increase a tumor's susceptibility to chemotherapeutic agents and/ or importantly, the host immune response. Collectively, our data and others demonstrate that VSV as well as other RNA viruses could provide a promising and exciting approach to cancer therapy.
Rift Valley Fever Virus NSs mRNA Is Transcribed from an Incoming Anti-Viral-Sense S RNA Segment (2005)

Analysis of purified Rift Valley fever virus (RVFV) particles demonstrated the presence of three negative-sense RNA genomes, plus three anti-viral-sense RNA segments. The virion-associated anti-viral-sense S segment served as a template for the synthesis of NSs mRNA immediately after infection. NSs protein synthesis also occurred early in infection, suggesting that NSs protein produced early in infection probably has biologically significant roles in virus replication and/or survival in the host. Translation inhibitor treatment of mammalian cells infected with viruses belonging to the Bunyaviridae family generally inhibits viral mRNA synthesis. However, RVFV NSs mRNA synthesis, but not N mRNA synthesis, was resistant to puromycin treatment during primary transcription, pointing to the uniqueness of RVFV NSs mRNA synthesis.
Streptavidin bead pulldown assay to determine homooligomerization (2017)

Pulldown assay is a conventional method to determine protein-protein interactions <i>in vitro</i>. Expressing a protein of interest with two different tags allows testing whether both versions can be captured via one of the two tags as homooligomeric complex. This protocol is based on streptavidin bead capture of a biotinylated protein and co-associated Flag-tagged protein using Streptavidin MagBeads.
Stereotactic Surgery with Image Processing of Computerized Tomographic Scans (1978)

The three-dimensional information from computerized tomographic scans has been transformed by image processing for use in stereotactic surgery. A lateral image of the target and calvarium can be superimposed on the lateral x-ray film taken at operation. Computer processing also eliminates extraneous data on the scan and gives the precise distance of the target from the midline. Testing the technique on a phantom shows it to be accurate to better than 0.5 cm. Application of the method for the stereotactic biopsy of a deep tumor is illustrated.
THE BIOCHEMISTRY AND GENETICS OF CAPSULAR POLYSACCHARIDE PRODUCTION IN BACTERIA (1996)

Bacterial polysaccharides are usually associated with the outer surface of the bacterium. They can form an amorphous layer of extracellular polysaccharide (EPS) surrounding the cell that may be further organized into a distinct structure termed a capsule. Additional polysaccharide molecules such as lipopolysaccharide (LPS) or lipooligosaccharide (LOS) may also decorate the cell surface. Polysaccharide capsules may mediate a number of biological processes, including invasive infections of human beings. Discussed here are the genetics and biochemistry of selected bacterial capsular polysaccharides and the basis of capsule diversity but not the genetics and biochemistry of LPS biosynthesis (for reviews see 100, 140).
Human β-Cell Glucokinase (1995)

Glucokinase is distinguished from yeast hexokinase and low Km mammalian hexokinases by its low affinity for glucose and its cooperative behavior, even though glucose binding residues and catalytic residues are highly conserved in all of these forms of hexokinase. The roles of Ser-151 and Asn-166 as determinants of hexose affinity and cooperative behavior of human glucokinase have been evaluated by site-directed mutagenesis, expression and purification of the wild-type and mutant enzymes, and steady-state kinetic analysis. Mutation of Asn-166 to arginine increased apparent affinity for both glucose and ATP by a factor of 3. Mutation of Ser-151 to cysteine, alanine, or glycine lowered the Km for glucose by factors of 2-, 26-, and 40-fold, respectively, decreased Vmax, abolished cooperativity for glucose, and also decreased Km for mannose and fructose. The Ser-151 mutants had hexose Km values similar to those of yeast hexokinase, hexokinase I, and the recombinantly expressed COOH-terminal half of hexokinase I. However, the Ki values for the competitive inhibitors, N-acetylglucosamine and glucose-6-P, were unchanged, suggesting that Ser-151 is not important for inhibitor binding. Mutation of Ser-151 also increased the Km for ATP about 5-fold and abolished the enzyme's low ATPase activity, which indicates it is essential for ATP hydrolysis. The substrate-induced change in intrinsic fluorescence of S151A occurred at a much lower glucose concentration than that for wild-type enzyme. The results implicate a dual role for Ser-151 as a determinant of hexose affinity and catalysis, exclusive of the glucose-induced conformational change, and suggest that the low hexose affinity of glucokinase is dependent on interaction of Ser-151 with other regions of the protein.
Reconstitution of functional L-selectin ligands on a cultured human endothelial cell line by cotransfection of α1→3 fucosyltransferase VII and newly cloned GlcNAcβ:6-sulfotransferase cDNA (1999)

Recently, we proposed sialyl 6-sulfo Lewis X as a major carbohydrate-capping group of the L-selectin ligands on high endothelial venules in human lymph nodes. In this study we succeeded in reconstituting functional L-selectin ligands on a cultured human endothelial cell line, ECV304, by transfecting the alpha1-->3fucosyltranseferase VII (Fuc-T VII) and newly cloned GlcNAcbeta:6-sulfotransferase (6-Sul-T) cDNAs. The ECV304 cells transfected with Fuc-T VII cDNA expressed conventional sialyl Lewis X detected with specific antibodies including 2H5, whereas the cells transfected with 6-Sul-T cDNA expressed sialyl 6-sulfo lactosamine as well as MECA-79-defined carbohydrate determinants, but these singly transfected cells failed to express sialyl 6-sulfo Lewis X, as detected with the antisialyl 6-sulfo Lewis X mAb G152. Sialyl 6-sulfo Lewis X appeared only on the cells that were cotransfected with both 6-Sul-T and Fuc-T VII cDNAs. Significant adhesion of L-selectin-expressing cells was seen only to the doubly transfected ECV304 cells and was inhibited by G152. No adhesion was observed to the cells transfected either with 6-Sul-T or with Fuc-T VII cDNA alone. The mRNAs of the two enzymes were expressed or were inducible upon interleukin 1 stimulation in human endothelial cells. These results indicate that a set of carbohydrate determinants synthesized by the concerted action of the two enzymes, as typically represented by the sialyl 6-sulfo Lewis X-capping group, serves as an essential component of the ligand for L-selectin and that the reagents 2H5 and MECA-79, utilized in earlier studies to detect L-selectin ligand on high endothelial venules, recognize two different aspects of the same set of synthetic products.