gebhart/patrepeval huggingface dataset:
Future prospects for reconstructive surgery in breast cancer (1996)

Reconstructive surgery has become an integral part of primary breast cancer therapy in patients requiring total mastectomy. State-of-the-art reconstructions with autogenous tissue are transverse rectus abdominis (TRAM) flap procedures. Superior aesthetic results in terms of both appearance and consistency, seem to outweigh the disadvantages of impaired abdominal wall competence and donor site scars. The “free,” microvascular TRAM flap may be the way to minimize abdominal wall weakness, since only a little portion of the rectus abdominis muscle must be sacrificed. Despite all discussions, breast reconstruction using silicone (gel) implants is a safe and reliable method and will be in the future. However, not every patient may be the right candidate for silicone reconstruction. Advantages of using silicone implants include (relatively) simple technique, short operation time, and no donor site morbidity. In patients suffering from breast-conserving therapy failures, plastic surgery has to address skin and parenchymal loss in an irradiated environment. Oncoplastic surgery, such as volume shrinking or volume replacement techniques, are useful for immediate reconstruction in breast-conserving therapy. © 1996 Wiley-Liss, Inc.
A structural and biochemical basis for PAPS-independent sulfuryl transfer by aryl sulfotransferase from uropathogenic Escherichia coli (2008)

Sulfotransferases are a versatile class of enzymes involved in numerous physiological processes. In mammals, adenosine 3'-phosphate-5'-phosphosulfate (PAPS) is the universal sulfuryl donor, and PAPS-dependent sulfurylation of small molecules, including hormones, sugars, and antibiotics, is a critical step in hepatic detoxification and extracellular signaling. In contrast, little is known about sulfotransferases in bacteria, which make use of sulfurylated molecules as mediators of cell-cell interactions and host-pathogen interactions. Bacterial arylsulfate sulfotransferases (also termed aryl sulfotransferases), in contrast to PAPS-dependent sulfotransferases, transfer sulfuryl groups exclusively among phenolic compounds in a PAPS-independent manner. Here, we report the crystal structure of the virulence factor arylsulfate sulfotransferase (ASST) from the prototypic, pyelonephritogenic Escherichia coli strain CFT073 at 2.0-A resolution, and 2 catalytic intermediates, at 2.1-A and 2.4-A resolution, with substrates bound in the active site. ASST is one of the largest periplasmic enzymes and its 3D structure differs fundamentally from all other structurally characterized sulfotransferases. Each 63.8-kDa subunit of the ASST homodimer comprises a 6-bladed beta-propeller domain and a C-terminal beta-sandwich domain. The active sites of the dimer are situated at the center of the channel formed by each beta-propeller and are defined by the side chains of His-252, His-356, Arg-374, and His-436. We show that ASST follows a ping-pong bi-bi reaction mechanism, in which the catalytic residue His-436 undergoes transient sulfurylation, a previously unreported covalent protein modification. The data provide a framework for understanding PAPS-independent sulfotransfer and a basis for drug design targeting this bacterial virulence factor.
Effects of nicotine on human psychomotor performance (1993)

Abstract A comprehensive review was conducted to establish whether there were any grounds to the claim that nicotine can enhance human psychomotor performance. Among relevant studies, many failed to distinguish between absolute improvements due to the administration of nicotine (usually in the form of cigarettes) and the relief of the effects of nicotine abstinence among the preferred subject pool of tobacco smokers. However, a few investigations have avoided this anomaly by examining the effects of nicotine in minimally‐abstinent smokers or non‐smokers. The results of these studies suggest that nicotine has small, specific, positive effects on the central nervous system which may facilitate human attention, memory and sensori‐motor function.
Clinical Responsiveness of Glioblastoma Multiforme to Chemotherapy after Vaccination (2004)

We propose that therapeutic vaccination synergizes with subsequent chemotherapy to elicit tangible clinical benefits for GBM patients.
Cell Separation by Dielectrophoretic Field-flow-fractionation (2000)

Dielectrophoretic field-flow-fractionation (DEP-FFF) was applied to several clinically relevant cell separation problems, including the purging of human breast cancer cells from normal T-lymphocytes and from CD34+ hematopoietic stem cells, the separation of the major leukocyte subpopulations, and the enrichment of leukocytes from blood. Cell separations were achieved in a thin chamber equipped with a microfabricated, interdigitated electrode array on its bottom wall that was energized with AC electric signals. Cells were levitated by the balance between DEP and sedimentation forces to different equilibrium heights and were transported at differing velocities and thereby separated when a velocity profile was established in the chamber. This bulk-separation technique adds cell intrinsic dielectric properties to the catalog of physical characteristics that can be applied to cell discrimination. The separation process and performance can be controlled through electronic means. Cell labeling is unnecessary, and separated cells may be cultured and further analyzed. It can be scaled up for routine laboratory cell separation or implemented on a miniaturized scale.
Comprehensive Study on Vitamin C Equivalent Antioxidant Capacity (VCEAC) of Various Polyphenolics in Scavenging a Free Radical and its Structural Relationship (2004)

Antioxidant capacity for a wide range of natural or synthetic polyphenolics was comprehensively evaluated by vitamin C equivalent antioxidant capacity (VCEAC) assay using free blue/green ABTS radicals. The polyphenolics tested are grouped into the following categories: vitamins (beta-carotene, alpha-tocopherol, vitamin A, and vitamin C), phenolic acids (benzoic acid, phenylacetic acid, cinnamic acid, and their derivatives), flavonoids (anthocyanidin, flavanol, chalcone, flavanone, flavone, flavonol, isoflavone, and their derivatives), synthetic food additives (BHA, BHT, TBHQ, and PG), and other miscellaneous polyphenolics (ellagic acid, sesamol, eugenol, thymol, etc.). A positive linear relationship between VCEAC and the number of free OH groups around the flavonoid framework was found, whereas, for phenolic acids, the linear relationship was not as good as with the flavonoid aglycones. Groups of chemicals having comparable structures generally showed similar trends. Polyphenolics commonly showed a higher VCEAC compared to monophenolics. Compounds like gallic acid with 3 vicinal hydroxy substitutions on the aromatic ring in phenolic acids or like epigallocatechin with 3 vicinal hydroxy substitutions on the B ring in flavonoids showed the highest antioxidant capcity among the groups. In the flavonoids, 2 characteristic chemical structures were very important, the catechol moiety in the B ring and the 3-OH functional group in a chroman ring. Glycosylated flavonoids showed less potent antioxidant capacity than their aglycone alone. Synthetic antioxidant food additives (BHA, TBHQ, and BHT) conventionally used in the food industry were less effective antioxidants than ascorbic acid. Other naturally occurring polyphenolics tested followed the expected general trends of phenolic acids and flavonoids.
RANK-Fc: A therapeutic antagonist for RANK-L in myeloma (2003)

MM-induced bone destruction requires increased RANK-L expression and is facilitated by a concurrent reduction in OPG, a natural decoy receptor for RANK-L. Administration of the RANK-L antagonist RANK-Fc limits MM-induced osteoclastogenesis, development of bone disease, and MM tumor progression.
Linear amplification using envelope feedback (1971)

An envelope-feedback technique applicable for reducing the distortion of amplitude-modulated signals in transistor amplifiers is described. The basis of the technique is to compare the input and output signals, and to introduce a correction signal into the circuit. An analysis and experimental results are provided.
The Distinctive Nature of HER2-Positive Breast Cancers (2005)

Breast cancer is not a single disease but a group of several important tumor subtypes, each with a different natural history and each requiring a different treatment. Overexpression of HER2 (which derives its name from human epidermal growth factor receptor 2) defines one of these unique subtypes. The HER2/neu gene is a member of a family of genes encoding transmembrane receptors for growth factors, including the epidermal growth factor receptor (EGFR), HER2, HER3, and HER4. The intracellular domain of HER2 has tyrosine kinase activity that regulates important aspects of the physiology, growth, and differentiation of cells.1,2 Extracellular domains of . . .
MAT1-Modulated Cyclin-Dependent Kinase-Activating Kinase Activity Cross-Regulates Neuroblastoma Cell G1 Arrest and Neurite Outgrowth (2004)

Cyclin-dependent kinase-activating kinase (CAK) regulates cell cycle G1 exit, where cells commonly commit either to proliferate or to differentiate. CAK activity in G1 regulation is determined by its assembly factor and targeting subunit, ménage à trois 1 (MAT1). The precise mechanism of how proliferation/differentiation transition is induced from cancer cell G1 arrest remains unknown. We present evidence that in neuroblastoma CHP126 cells, CAK interacts with and phosphorylates retinoblastoma tumor suppressor protein (pRb) and retinoid X receptor alpha (RXRalpha). Retinoic acid (RA)-induced neuroblastoma cell proliferation/differentiation transition is associated with decreased CAK activity, as evidenced by a switch from CAK hyperphosphorylation of pRb and RXRalpha to hypophosphorylation of pRb and RXRalpha. Manipulation of MAT1 abundance shows that MAT1 reduction mimics RA-induced hypophosphorylation of pRb/RXRalpha, proliferation inhibition, and neurite outgrowth, whereas MAT1 overexpression resists these RA actions. Thus, these findings reveal an important mechanism by which MAT1-modulated CAK activity is crucial in the switch from proliferation to differentiation in neuroblastoma cells.
Induction of accelerated feline immunodeficiency virus disease by acute-phase virus passage (1995)

Development of feline immunodeficiency virus (FIV) infection in cats as a small animal model for lentiviral immunodeficiency disease has been hampered by the prolonged and variable disease course following experimental infection. To address this issue, we generated high-titer, unselected FIV stocks by pooling plasma from cats acutely infected with a subgroup C FIV isolate designated CABCpadyOOC (FIV-C-PGammer). Subsequent infection with this virus pool resulted in rapidly progressive, fatal disease in greater than 50% of infected cats. Accelerated FIV disease was characterized by rapid and progressive CD4+ T-cell loss, lymphadenopathy, weight loss, lymphoid depletion, and severe thymic atrophy. Mortality and rate of disease progression were affected by the age of each cat at infection and whether the virus source animal was in the acute or chronic stage of infection. The rapid FIV disease syndrome was consistently associated with systemic lymphoid depletion, clinical disease, and susceptibility to opportunistic infections, analogous to accelerated and/or terminal HIV-1 infection. The results of this study demonstrate that FIV infection is a valid small animal model for lentiviral immunodeficiency disease.
Identification of a Small-Molecule Entry Inhibitor for Filoviruses (2011)

Ebola virus (EBOV) causes severe hemorrhagic fever, for which therapeutic options are not available. Preventing the entry of EBOV into host cells is an attractive antiviral strategy, which has been validated for HIV by the FDA approval of the anti-HIV drug enfuvirtide. To identify inhibitors of EBOV entry, the EBOV envelope glycoprotein (EBOV-GP) gene was used to generate pseudotype viruses for screening of chemical libraries. A benzodiazepine derivative (compound 7) was identified from a high-throughput screen (HTS) of small-molecule compound libraries utilizing the pseudotype virus. Compound 7 was validated as an inhibitor of infectious EBOV and Marburg virus (MARV) in cell-based assays, with 50% inhibitory concentrations (IC(50)s) of 10 μM and 12 μM, respectively. Time-of-addition and binding studies suggested that compound 7 binds to EBOV-GP at an early stage during EBOV infection. Preliminary Schrödinger SiteMap calculations, using a published EBOV-GP crystal structure in its prefusion conformation, suggested a hydrophobic pocket at or near the GP1 and GP2 interface as a suitable site for compound 7 binding. This prediction was supported by mutational analysis implying that residues Asn69, Leu70, Leu184, Ile185, Leu186, Lys190, and Lys191 are critical for the binding of compound 7 and its analogs with EBOV-GP. We hypothesize that compound 7 binds to this hydrophobic pocket and as a consequence inhibits EBOV infection of cells, but the details of the mechanism remain to be determined. In summary, we have identified a novel series of benzodiazepine compounds that are suitable for optimization as potential inhibitors of filoviral infection.
Involvement of phosphatidylinositol 3-kinase in Fc gamma receptor signaling. (1994)

Wortmannin, a potent and selective inhibitor of phosphatidylinositol (PI) 3-kinase (Okada, T., Sakuma, L., Fukui, Y., Hazeki, O., and Ui, M. (1994) J. Biol. Chem. 269, 3563-3567), prevented Fc receptor for IgG (Fc gamma R)-dependent phagocytosis of the human monocytic cell line U937 or guinea pig neutrophils. Cross-linking of Fc gamma R on the surface of U937 cells increased PI 3-kinase activity that was immunoprecipitated with antibody against phosphotyrosine or antibody against the 85-kDa regulatory subunit of PI 3-kinase. Specific cross-linking of Fc gamma R subclass Fc gamma RI or Fc gamma RII, using monoclonal antibodies against each receptor subclass and the F(ab')2 fragment of goat antibody against mouse IgG, increased anti-phosphotyrosine-precipitable PI 3-kinase activity. Treatment of cells with anti-Fc gamma RIII antibody plus the same F(ab')2 did not affect the activity, reflecting the lack of Fc gamma RIII in U937 cells. Fcy gamma R stimulation triggered prominent tyrosine phosphorylation of several proteins, among which the 115-kDa peptide showed strong association with PI 3-kinase. Thus, Fc gamma R appears to be coupled functionally, via a tyrosine kinase, to PI 3-kinase, which may regulate the phagocytotic activity of the cells.
Production and Evaluation of Biodiesel from Field Pennycress (Thlaspi arvenseL.) Oil† (2009)

Field pennycress (Thlaspi arvense L.) oil is evaluated for the first time as a feedstock for biodiesel production. Biodiesel was obtained in 82 wt % yield by a standard transesterification procedure with methanol and sodium methoxide catalyst at 60 °C and an alcohol to oil molar ratio of 6:1. Acid-catalyzed pretreatment to reduce the acid value of crude field pennycress oil resulted in a yield after methanolysis of 94 wt %. Field pennycress oil had high contents of erucic (13(Z)-docosenoic; 32.8 wt %) and linoleic (9(Z),12(Z)-octadecadienoic; 22.4 wt %) acids with other unsaturated fatty acids comprising most of the remaining fatty acid profile. As a result, the methyl esters (biodiesel) obtained from this oil exhibited a high cetane number of 59.8 and excellent low temperature properties, as evidenced by cloud, pour, and cold filter plugging points of −10, −18, and −17 °C, respectively. The kinematic viscosity and oxidative stability (Rancimat method) of field pennycress oil methyl esters were 5.24 mm2/s (40 °C) and 4.4 h (110 °C), respectively. Other fuel properties such as acid value, lubricity, free and total glycerol content, surface tension, as well as sulfur and phosphorus contents were also determined and are discussed in light of biodiesel standards such as ASTM D6751 and EN 14214. Also reported for the first time are cetane numbers of methyl esters of erucic and gondoic (methyl 11(Z)-eicosenoate) acids, which were found to be 74.2 and 73.2, respectively. In summary, field pennycress oil appears to an acceptable feedstock for biodiesel production.
Use of Galactose-Fermenting Streptococcus thermophilus in the Manufacture of Swiss, Mozzarella, and Short-Method Cheddar Cheese (1986)

Galactose-fermenting (galactose-posirive) strains of Streptococcus tbermopbilus, alone and combined with galactosepositive and galactose-negative strains of Lactobacillus bulgaricus, were used as starter cultures in the manufacture of Swiss and Mozzarella cheese and were paired with Streptococcus lactis (also galactose-positive) in short-method Cheddar cheese manufacture. Experimental Swiss cheese made with the galactosepositive Streptococcus tbermopbilus starter alone contained a large amount of galactose (ca. 26 to 28 /amol/g of curd) 28 h after hooping compared with control Swiss (< 2/amol/g) made with a nongalactose fermenting strain of Streptococcus tbermopbilus and a galactosepositive strain of Lactobacillus bulgaricus. Mozzarella and short-method Cheddar made with only galactose-positive Streptococcus tbermopbilus also contained large amounts of galactose. Swiss cheese made with a galactose-positive strain of Streptococcus tberrnopbilus and a galacrose-negative strain of Lactobacillus bulgaricus had little galactose remaining after 28 h, indicating that the Lactobacillus had a stimulatory effect on galactose metabolism in Streptococcus tbermopbilus. These results indicate that galacrose-fermenting Streptococcus tbermopbilus may have limited potential when used as single strain starter cultures in Swiss cheese, but may be useful when combined with galactose-positive Lactobacillus in the manufacture of Mozzarella cheese.
Using Fibre-Optic Distributed Temperature Measurements to Provide Real-Time Reservoir Surveillance Data on Wytch Farm Field Horizontal Extended-Reach Wells (2000)

Abstract BP-Amoco operated Wytch Farm has installed fibre optic distributed temperature systems on 2 of their recent ERD (extended reach drilling) wells in order to provide real time reservoir surveillance. This novel new approach to reservoir monitoring has provided important information about the well and reservoir performance. This type of zonal contribution and fluid data would normally be acquired by running production logs on the end of coiled tubing at infrequent intervals, however the dual completion on Wytch Farm’s M-12 well made conventional production logging impossible. Distributed temperature data has been recorded over 2 years throughout well tests and shut-ins, as well as during normal periods of production. Data analysis is performed both visually, by correlating time related thermal events observed in the well with known reservoir and production anomalies, and theoretically by comparing recorded temperature data with that predicted by thermal profiles generated using nodal analysis fluid flow and heat transfer software*. Use of this software* allows estimates of production by zone to be compared to actual recorded temperature data, enabling a variety of production scenarios to be investigated and the most likely identified. The installation of real time fibre optic distributed temperature monitoring on Wytch Farm field has enabled the asset to recognise flow behind casing and cross flow during shut-in in the M-12 well and water finger encroachment to be identified in the M-17 well. This data has provided important information about both the reservoir and well performance in real time, which would not usually have become available until later in the wells life.
INCIDENT DETECTION ALGORITHM EVALUATION (2001)

This research examines a range of incident detection technologies to determine a recommended combination of approaches for use in the Utah Department of Transportation's (UDOT) Advanced Traffic Management System (ATMS). The technologies that were examined are computer-based Automatic Incident Detection (AID), Video Image Processing (VIP), and detection by cellular telephone call-ins. This project was originally scoped to include a rigorous testing of several computer-based algorithms. The projects Technical Advisory Committee, however, redirected this work to look more closely at the impact of cellular telephones in incident detection. Cellular telephone technology will continue to impact the power and speed with which incidents are detected. The Federal Communications Commission has mandated that all cellular telephone service providers give the name, number, and location of a cellular telephone caller to the Public Safety Answering Point by October 2001, for when that caller dials 911. This information will be helpful to identify locations of traffic incidents. The number of cellular telephones in use is also increasing. Incident detection by cellular telephones will continue to be the primary means of incident detection. Because the ATMS already possesses the All-Purpose Incident Detection (APID) and Double Exponential Smoothing (DES) algorithms as part of the Navigator software, they should be enabled and calibrated as a secondary form of incident detection. Other forms of incident detection can be evaluated from the ATMS. The neural network method and the video image processing method likely could be modified to work with existing ATMS equipment.
Random projection for high dimensional data clustering: a cluster ensemble approach (2003)

We investigate how random projection can best be used for clustering high dimensional data. Random projection has been shown to have promising theoretical properties. In practice, however, we find that it results in highly unstable clustering performance. Our solution is to use random projection in a cluster ensemble approach. Empirical results show that the proposed approach achieves better and more robust clustering performance compared to not only single runs of random projection/clustering but also clustering with PCA, a traditional data reduction method for high dimensional data. To gain insights into the performance improvement obtained by our ensemble method, we analyze and identify the influence of the quality and the diversity of the individual clustering solutions on the final ensemble performance. 1.