gebhart/patrepeval huggingface dataset:
2-Deoxy-d-Glucose Combined with Cisplatin Enhances Cytotoxicity via Metabolic Oxidative Stress in Human Head and Neck Cancer Cells (2007)

Glucose deprivation has been hypothesized to cause cytotoxicity by inducing metabolic oxidative stress in human cancer cells. The current work tests the hypothesis that 2-deoxy-d-glucose (2DG) combined with cisplatin [cis-diamminedichloroplatinum(II)] can enhance cytotoxicity in human head and neck cancer cells (FaDu) by mechanisms involving oxidative stress. Exposure of FaDu cells to the combination of 2DG and cisplatin resulted in a significant decrease in cell survival when compared with 2DG or cisplatin alone. Treatment with 2DG and cisplatin also caused perturbations in parameters indicative of oxidative stress, including decreased intracellular total glutathione and increased percentage of glutathione disulfide. Simultaneous treatment with the thiol antioxidant N-acetylcysteine (NAC) inhibited parameters indicative of oxidative stress, as well as protected FaDu cells from the cytotoxic effects of cisplatin alone and the combination of 2DG and cisplatin. In addition, polyethylene glycol-conjugated antioxidant enzymes (PEG-superoxide dismutase and PEG-catalase) also protected FaDu cells from 2DG toxicity. An inhibitor of glutathione synthesis, l-buthionine-[S,R]-sulfoximine (BSO), sensitized FaDu cells to the cytotoxic effects of 2DG and cisplatin, and these effects were inhibited by NAC. Furthermore, the combination of 2DG, cisplatin, and BSO significantly increased the percentage of glutathione disulfide, which was also inhibited by NAC. These results support the hypothesis that exposure of human head and neck cancer cells to 2DG combined with cisplatin enhances cytotoxicity via metabolic oxidative stress. These findings provide a strong biochemical rationale for evaluating inhibitors of glucose and hydroperoxide metabolism in combination with cisplatin for the treatment of head and neck cancer.
Imbalance of bacteriome profiles within the Finnish Diabetes Prediction and Prevention study: Parallel use of 16S profiling and virome sequencing in stool samples from children with islet autoimmunity and matched controls (2016)

The results confirm previous findings that an imbalance within the prevalent Bacteroides genus is associated with islet autoimmunity. The detected quantitative relation of the novel "orphan" bacteriophage CrAssphage with a prevalent species of the Bacteroides genus may exemplify possible modifiers of the bacteriome.
Temperature Control and Recovery of Bowel Function After Laparoscopic or Laparotomic Colorectal Surgery in Patients Receiving Combined Epidural/General Anesthesia and Postoperative Epidural Analgesia (2002)

We compared the effects of a laparoscopic (n = 23) versus laparotomic (n = 21) technique for major abdominal surgery on temperature control in 44 patients undergoing colorectal surgery during a combined epidural/general anesthesia. A thoracic epidural block up to T4 was induced with 6–10 mL of 0.75% ropivacaine; general anesthesia was induced with thiopental, fentanyl, and atracurium IV and maintained with isoflurane. Core temperature was measured with a bladder probe and recorded every 15 min after the induction. In both groups, core temperature decreased to 35.2°C (range, 34°C–36°C) at the end of surgery. After surgery, normothermia returned after 75 min (60–120 min) in the Laparoscopy group and 60 min (45–180 min) in the Laparotomy group (P = 0.56). No differences in postanesthesia care unit discharge time were reported between the two groups. The degree of pain during coughing was smaller after laparoscopy than laparotomy from the 24th to the 72nd observation times (P < 0.01). Morphine consumption was 22 mg (2–65 mg) in the Laparotomy group and 5 mg (0–45 mg) in the Laparoscopy group (P = 0.02). The time to first flatus was shorter after laparoscopy (24 h [16–72 h]) than laparotomy (72 h [26–96 h]) (P = 0.0005), and the first intake of clear liquid occurred after 48 h (24–72 h) in the Laparoscopy group and after 96 h (90–96 h) in the Laparotomy group (P = 0.0005). Although laparoscopic surgery provides positive effects on the degree of postoperative pain and recovery of bowel function, the reduction in heat loss produced by minimizing bowel exposure with laparoscopic surgery does not compensate for the anesthesia-related effects on temperature control, and active patient warming must also be used with laparoscopic techniques.
Prediction of Drug Solubility by the General Solubility Equation (GSE) (2001)

The revised general solubility equation (GSE) proposed by Jain and Yalkowsky is used to estimate the aqueous solubility of a set of organic nonelectrolytes studied by Jorgensen and Duffy. The only inputs used in the GSE are the Celsius melting point (MP) and the octanol water partition coefficient (K(ow)). These are generally known, easily measured, or easily calculated. The GSE does not utilize any fitted parameters. The average absolute error for the 150 compounds is 0.43 compared to 0.56 with Jorgensen and Duffy's computational method, which utilitizes five fitted parameters. Thus, the revised GSE is simpler and provides a more accurate estimation of aqueous solubility of the same set of organic compounds. It is also more accurate than the original version of the GSE.
Combined ultrasound and optoacoustic system for real-time high-contrast vascular imaging in vivo (2005)

In optoacoustic imaging, short laser pulses irradiate highly scattering human tissue and adiabatically heat embedded absorbing structures, such as blood vessels, to generate ultrasound transients by means of the thermoelastic effect. We present an optoacoustic vascular imaging system that records these transients on the skin surface with an ultrasound transducer array and displays the images online. With a single laser pulse a complete optoacoustic B-mode image can be acquired. The optoacoustic system exploits the high intrinsic optical contrast of blood and provides high-contrast images without the need for contrast agents. The high spatial resolution of the system is determined by the acoustic propagation and is limited to the submillimeter range by our 7.5-MHz linear array transducer. A Q-switched alexandrite laser emitting short near-infrared laser pulses at a wavelength of 760 nm allows an imaging depth of a few centimeters. The system provides real-time images at frame-rates of 7.5 Hz and optionally displays the classically generated ultrasound image alongside the optoacoustic image. The functionality of the system was demonstrated in vivo on human finger, arm and leg. The proposed system combines the merits and most compelling features of optics and ultrasound in a single high-contrast vascular imaging device.
Molecular characterization of the mycobacterial SenX3–RegX3 two-component system: evidence for autoregulation (2000)

Environmental regulation of bacterial gene expression is often mediated by two-component signal transduction systems, which are themselves tightly regulated. The response regulator RegX3 and the cytoplasmic portion of the histidine kinase SenX3 from Mycobacterium bovis BCG were overproduced in Escherichia coli and purified as N-terminally (His)(6)-tagged proteins. Phosphorylation assays demonstrated autophosphorylation of the cytoplasmic portion of SenX3 and a phosphotransfer from SenX3 to RegX3, involving conserved histidine and aspartate residues, respectively. In addition, as shown by electrophoretic mobility shift assays, (His)(6)RegX3 was able to specifically bind to the promoter region of the senX3-regX3 operon. Furthermore, operon fusion analyses indicated that the overexpression of the senX3-regX3 operon increases the activity of the senX3 promoter in Mycobacterium smegmatis. Together, these results indicate that the mycobacterial SenX3-RegX3 two-component system is positively autoregulated.
Refined Structure of an Intact IgG2a Monoclonal Antibody, (1997)

The structure of an intact, anti-canine lymphoma monoclonal antibody (Mab231) was determined by molecular replacement and refined in a triclinic cell to an R-value of 20.9%, using synchrotron diffraction data from 2.8 to 20 A resolution. All segments of the antibody, including the hinge region and carbohydrate component, are visible in electron density maps. There is no overall symmetry to the antibody, as the Fc is disposed in an entirely oblique manner with respect to the Fabs. The CH2 and CH3 domains do, however, possess a nearly exact, local 2-fold relationship. The Fab segments are related by a second, independent, local dyad axis, exact only with respect to constant domains. Variable domains exhibit no symmetry relationship as a consequence of the 16 degrees difference in Fab elbow angles. Variable domain pair associations VL:VH for the Fabs are virtually the same, and corresponding CDRs of the two Fabs also are nearly identical in structure. CDR-H3 displays the greatest difference. Hypervariable loops of both Fabs are involved in contacts with symmetry-related Fc segments at the CH2-CH3 switch junction, suggesting a "complex" structure. The hinge segment connecting Fabs with the Fc is quite extended and exhibits thermal factors indicative of a high degree of mobility. It consists of a well-defined upper hinge that partially maintains dyad symmetry and a fairly rigid core bounded above and below by fluid polypeptides that provide segmental flexibility. This structure represents the first visualization by X-ray analysis of a murine Fc segment, and its CH2 domains exhibit substantial rigid body conformational changes with respect to the human Fc used as an initial molecular replacement model. The oligosaccharides were found by difference Fourier syntheses to be very similar to those of the free human Fc fragment, although differences are present in the terminal residues. The detailed structure of the IgG presented here, and the distribution of effector binding sites, appears consistent with effector activation mechanisms involving translocation and/or aggregation of the Fc following antigen binding by the Fabs.
Universal Speech/Audio Coding Using Hybrid ACELP/TCX Techniques (2006)

This paper presents a hybrid audio coding algorithm integrating an LP-based coding technique and a more general transform coding technique. ACELP is used in LP-based coding mode, whereas algebraic TCX is used in transform coding mode. The algorithm extends previously published work on ACELP/TCX coding in several ways. The frame length is increased to 80 ms, adaptive multi-length sub-frames are used with overlapping windowing, an extended multi-rate algebraic VQ is applied to the TCX spectrum to avoid quantizer saturation, and noise shaping is improved. Results show that the proposed hybrid coder has consistently high performance for both speech and music signals.
Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity. (1999)

The WWW version of FastM is accessible at: http://www.gsf.de/cgi-bin/fastm. pl and http://genomatix.gsf.de/cgi-bin/fastm2/fastm.pl
Anion Responsive Imidazolium‐Based Polymers (2012)

Stimuli responsiveness in polymer design is providing basis for diversely new and advanced materials that exhibit switchable porosity in membranes and coatings, switchable particle formation and thermodynamically stable nanoparticle dispersions, polymers that provide directed mechanical stress in response to intensive fields, and switchable compatibility of nanomaterials in changing environments. The incorporation of ionic liquid monomers has resulted in many new polymers based on the imidazolium group. These polymers exhibit all of the above-articulated material properties. Some insight into how these anion responsive polymers function has become empirically available. Much opportunity remains for extending our understanding as well as for designing more refined stimuli-responsive materials.
Molecular Pathways: Tumor Cells Co-opt the Brain-Specific Metabolism Gene CPT1C to Promote Survival (2012)

The metabolic adaptations of cancer cells are receiving renewed attention as potential targets for therapeutic exploitation. Recent work has highlighted the importance of fatty acid catabolism through β-oxidation to cellular energy homeostasis. In this article, we describe recent preclinical studies suggesting that a gene usually expressed only in the brain, carnitine palmitoyltransferase (CPT)1C, promotes cancer cell survival and tumor growth. CTP1C confers rapamycin resistance on breast cancer cells, indicating that this gene may act in a pathway parallel to mTOR-enhanced glycolysis. Because of CPT1C's normally brain-restricted expression and the inability of most drugs to pass the blood-brain barrier, CPT1C may be an ideal candidate for specific small-molecule inhibition. We further speculate that concurrent targeting of CPT1C activity and glycolysis in tumor cells could be a highly effective anticancer approach.
Gaseous core nuclear-driven engines featuring a self-shutoff mechanism to provide nuclear safety (1991)

Nuclear driven engines are described that could be run in either pulsed or steady state modes. In the pulsed mode nuclear energy is released by fissioning of uranium or plutonium in a supercritical assembly of fuel and working gas. In a steady state mode a fuel-gas mixture is injected into a magnetic nozzle where it is compressed into a critical state and produces energy. Engine performance is modeled using a code that calculates hydrodynamics, fission energy production, and neutron transport self-consistently. Results are given demonstrating a large negative temperature coefficient that produces self-shutoff or control of energy production. Reduced fission product inventory and the self-shutoff provide inherent nuclear safety. It is expected that nuclear engine reactor units could be scaled up from about 100 MW{sub e}.
Effects of Therapy for Dysphagia in Parkinson’s Disease: Systematic Review (2008)

This systematic review explores the effects of dysphagia treatment for Parkinson's disease. The review includes rehabilitative, surgical, pharmacologic, and other treatments. Only oropharyngeal dysphagia is selected for this literature search, excluding dysphagia due to esophageal or gastric disorders. The effects of deep brain stimulation on dysphagia are not included. In general, the literature concerning dysphagia treatment in Parkinson's disease is rather limited. Most effect studies show diverse methodologic problems. Multiple case studies and trials are identified by searching biomedical literature databases PubMed and Embase, and by hand-searching reference lists. The conclusions of most studies cannot be compared with one another because of heterogeneous therapy methods and outcome measures. Further research based on randomized controlled trials to determine the effectiveness of different therapies for dysphagia in Parkinson's disease is required.
Range correlation effect on ISM band I/Q CMOS radar for non-contact vital signs sensing (2003)

A quadrature direct conversion microwave Doppler radar has been fully integrated in 0.25 /spl mu/m CMOS. This ISM band radar chip has been used to detect heart and respiration movement 50 cm from the subject. While oscillator phase noise is a performance-limiting factor in CW radar systems, the range correlation effect enables measurement of small phase modulations in spite of the notoriously high phase noise of the on-chip CMOS oscillator. This is the first reported quantitative experimental verification of the range correlation effect.
Preclinical Pharmacology and in Vitro Characterization of PR-047, An Oral Inhibitor of the 20S Proteasome (2008)

Abstract The clinical utility of proteasome inhibitors as treatment for multiple myeloma and non-Hodgkin’s lymphoma (NHL) has been validated with two parenterally administered agents: bortezomib, a dipeptide boronate that was approved by the FDA in 2003; and carfilzomib, a tetrapeptide epoxyketone that has shown promising activity in Phase 1 clinical trials. The clinical development of an orally bioavailable proteasome inhibitor would offer improvement in both dosing flexibility and patience convenience over intravenous (IV) administration. Furthermore, oral administration will allow a practical approach to investigating the affect of prolonged proteasome inhibition by repeated daily dosing in patients with advanced malignancies. Here we describe the preclinical pharmacology of PR-047, a tripeptide epoxyketone that was selected through a medicinal chemistry effort designed to find a selective inhibitor of the chymotrypsin-like (CT-L) activity of the proteasome that combined the efficacy and safety of carfilzomib with the patient convenience of oral dosing. In vitro, PR-047 demonstrated potency against the proteasome CT-L activity comparable to that of carfilzomib and induced tumor cell death across multiple tumor cell types with IC50s &lt;100 nM. In rodents and dogs, oral administration of PR-047 resulted in a prolonged dose-dependent inhibition of the proteasome in all tissues examined with the exception of brain. Proteasome inhibition following PO administration was rapid, resulting in maximal proteasome inhibition within 15 minutes. Plasma pharmacokinetics studies, also assessed in rodents and dogs, confirmed the rapid systemic exposure following oral administration. Absolute bioavailability, as measured by plasma levels of PR-047, was dose dependent and was &gt;20% across all species tested. Doses of PR-047 that resulted in significant (&gt;80%) proteasome inhibition in most tissues were 4–10 fold below the maximum tolerated dose (MTD) and were well tolerated when administered for five consecutive days. These data suggest that repeat daily dosing of PR-047 may be feasible. Single or repeated administrations of PR-047 did not affect kidney or liver function as measured by clinical chemistry. When assessed for anti-tumor activity, PR-047 induced consistent anti-tumor responses in human tumor xenograft models including multiple myeloma (MM1.S), NHL (RL) and solid tumors (HT-29, A549). The anti-tumor activity of PR-047 was equivalent or better than that of carfilzomib and was observed at well tolerated doses. Furthermore, TUNEL staining of tumor sections confirmed that the anti-tumor response was mediated in part by tumor cell apoptosis. PR-047 represents a promising orally bioavailable proteasome inhibitor with a favorable toxicologic profile. The results from these studies have facilitated further development of PR-047 in the treatment of malignant diseases.
A new approach for memory efficient ATV decoding (1997)

In this paper we propose an efficient memory saving architecture for an ATV decoder. In this new architecture, the motion-compensation is performed in the frequency domain. This makes it possible for anchor frames to be saved as compressed bits, resulting in significant memory savings with the addition of several extra devices in the decoder. The increase in complexity is small compared to the reduction in memory requirements. The simulation results with the new decoder architecture have shown that the reconstructed image quality is close to that of the conventional decoder.
Generation and Characterization of Adeno-Associated Virus Producer Cell Lines for Research and Preclinical Vector Production (2013)

Adeno-associated virus (AAV) producer cell lines represent an effective method for large-scale production of AAV vectors. We set out to evaluate and characterize the use of an abbreviated protocol to generate "masterwells" (MWs; a nonclonal cell population) as a platform for research and preclinical vector production. In this system, a single plasmid containing three components, the vector sequence, the AAV rep, and cap genes, and a selectable marker gene is stably transfected into HeLaS3 cells. Producer cell lines generating an AAV2 vector expressing a secreted form of human placental alkaline phosphatase (SEAP) have been created. Several MWs showed vector yields in the 5×10(4) to 2×10(5) DNase-resistant particles/cell range, and the productivity was stable over >60 population doublings. Integrated plasmid copy number in three high-producing MWs ranged from approximately 12 to 50; copies were arranged in a head-to-tail configuration. Upon infection with adenovirus, rep/cap copy number was amplified approximately 100-fold and high yield appeared to be dependent on the extent of amplification. Rep/cap gene expression and vector packaging both reached a peak at 48 hr postinfection. AAV2-SEAP vector was produced in 1-liter shaker culture and purified for assessment of vector quality and potency. The data showed that the majority of the capsids from the MWs contained vector DNA (≥70%) and that purified vector was free of replication-competent AAV. In vitro and in vivo analyses demonstrated that potency of the producer cell-derived vector was comparable to vector generated via the standard transfection method.
Secretion by human fibroblasts of monocyte chemoattractant protein-1, the product of gene JE. (1990)

We recently purified human monocyte chemoattractant protein-1 (MCP-1) from culture fluids of either human glioma cell lines or mitogen-stimulated human peripheral blood mononuclear leukocytes. It has now been shown that MCP-1 is the product of the gene JE, which was first recognized by its expression in fibroblasts stimulated with platelet-derived growth factor (PDGF). We therefore studied secretion of MCP-1 by three human fibroblast cell lines. Monocyte chemotactic activity was found in culture fluids of all three lines after growth to confluence in DMEM-10% FCS, and the amounts secreted per cell were comparable for the three lines. The MRC-5 line was chosen for further study. Monocyte chemotactic activity secretion by confluent MRC-5 cultures continued after a switch to serum-free medium and was not inhibited by anti-PDGF antibody, indicating that secretion may not have been caused by autocrine release of PDGF. When concentrated serum-free MRC-5 culture fluid was injected into an HPLC gel filtration column, only one chemotactic activity peak was observed, which was in the same location as glioma-derived MCP-1. The activity was completely absorbed out by an anti-MCP-1 affinity column, which indicates that all the chemotactic activity in MRC-5 culture fluid was accounted for by MCP-1. PDGF caused a marked increase in chemotactic activity over that found in serum-free culture fluid of MRC-5 or 501T cells. Immunoprecipitation by anti-human MCP-1 showed two bands, corresponding to the two forms of MCP-1 previously described (MCP-1 alpha and beta); and the amounts increased in response to PDGF stimulation. Thus, the reported increase in human fibroblast JE mRNA in response to PDGF-containing serum stimulation is reflected in increased secretion of the MCP-1 gene product.
Bioinformatics: Volume I Data, Sequence Analysis and Evolution (Methods in Molecular Biology) (2008)

Not only is the quantity of life science data expanding, but new types of biological data continue to be introduced as a result of technological development and a growing understanding of biological systems. Methods for analyzing these data are an increasingly important component of modern biological research. In Bioinformatics, leading researchers in the field provide a selection of the most useful and widely applicable methods, able to be applied as is, or with minor variations, to many specific problems. Volume I: Data, Sequence Analysis and Evolution examines a selection of methods involving the generation and organization of data, including sequence data, RNA and protein structures, microarray expression data and functional annotations, methods for discovering the functional components of genomes, whether they be genes, alternative splice sites, non-coding RNAs or regulatory motifs, and several of the most interesting methods in phylogenetics and evolution.