gebhart/patrepeval huggingface dataset:
Elevated Serum Levels of Interleukin-8 in Advanced Non-Small Cell Lung Cancer Patients: Relationship with Prognosis (2002)

Interleukin-8 (IL-8) is a pleiotropic cytokine that has also been shown to exert effects relevant to cancer growth and progression. Cancer progression is believed to be contributed to by the ability of this cytokine to promote angiogenesis and mitogenic effects. As IL-8 production at the tumor site may determine elevated serum levels of this cytokine because of hematogenous leakage, it is conceivable that patients with high IL-8 serum levels may have tumors actively producing this cytokine. The aim of this study was, therefore, to assess IL-8 serum levels in 60 non-small cell lung cancer (NSCLC) patients undergoing chemotherapy and to correlate them with prognosis. IL-8 serum levels were found to be significantly elevated in cancer patients with respect to controls. Moreover, IL-8 serum levels were shown to be significantly increased in stage IV patients compared with stage III patients. When basal IL-8 serum levels in cancer patients were analyzed according to response to chemotherapy, responders were shown to have significantly lower IL-8 serum levels than nonresponders. On univariate analysis, the IL-8 serum level was included among the variables capable of affecting both overall survival (OS) and time to treatment failure (TTF). However, multivariate analysis failed to demonstrate an independent prognostic significance for IL-8 serum levels. In conclusion, this study showed that IL-8 serum levels were elevated in advanced NSCLC patients and correlated with both OS and TTF, but they were shown not to be an independent prognostic factor.
Calcium cyclotron resonance and diatom mobility (1987)

The hypothesis that movement of biological ions may be predicted by cyclotron resonance theory applied to cell membranes is tested in these experiments. Diatoms (Amphora coffeaeformis) were chosen as the biosystem since they move or don't move, depending on how much calcium is transported across the membrane. The experiments demonstrate that a particular ion (calcium) is apparently moved across the cell membrane in response to the DC and AC values of magnetic flux densities (B) and the frequency derived from the cyclotron resonance theory. A clear resonance is shown and a rather sharp frequency response curve is demonstrated. The experiments also show a dose response as the AC value of the flux density is varied, and that odd harmonics of the basic cyclotron frequency are also effective.
Next-generation ammonia pretreatment enhances cellulosic biofuel production (2016)

Extractive ammonia pretreatment converts crystalline cellulose I<sub>β</sub> to a highly digestible cellulose III<sub>I</sub> and selectively extracts up to ∼45% of the lignin from lignocellulosic biomass with near-quantitative retention of all polysaccharides.
New Bioorganic Reagents: Evolved Cyclohexanone Monoxygenase — Why Is it more Selective? (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Ability of Serum Glial Fibrillary Acidic Protein, Ubiquitin C-Terminal Hydrolase-L1, and S100B To Differentiate Normal and Abnormal Head Computed Tomography Findings in Patients with Suspected Mild or Moderate Traumatic Brain Injury (2015)

Head computed tomography (CT) imaging is still a commonly obtained diagnostic test for patients with minor head injury despite availability of clinical decision rules to guide imaging use and recommendations to reduce radiation exposure resulting from unnecessary imaging. This prospective multicenter observational study of 251 patients with suspected mild to moderate traumatic brain injury (TBI) evaluated three serum biomarkers' (glial fibrillary acidic protein [GFAP], ubiquitin C-terminal hydrolase-L1 [UCH-L1] and S100B measured within 6 h of injury) ability to differentiate CT negative and CT positive findings. Of the 251 patients, 60.2% were male and 225 (89.6%) had a presenting Glasgow Coma Scale score of 15. A positive head CT (intracranial injury) was found in 36 (14.3%). UCH-L1 was 100% sensitive and 39% specific at a cutoff value >40 pg/mL. To retain 100% sensitivity, GFAP was 0% specific (cutoff value 0 pg/mL) and S100B had a specificity of only 2% (cutoff value 30 pg/mL). All three biomarkers had similar values for areas under the receiver operator characteristic curve: 0.79 (95% confidence interval; 0.70-0.88) for GFAP, 0.80 (0.71-0.89) for UCH-L1, and 0.75 (0.65-0.85) for S100B. Neither GFAP nor UCH-L1 curve values differed significantly from S100B (p = 0.21 and p = 0.77, respectively). In our patient cohort, UCH-L1 outperformed GFAP and S100B when the goal was to reduce CT use without sacrificing sensitivity. UCH-L1 values <40 pg/mL could potentially have aided in eliminating 83 of the 215 negative CT scans. These results require replication in other studies before the test is used in actual clinical practice.
Nonlithographic Patterning and Metal-Assisted Chemical Etching for Manufacturing of Tunable Light-Emitting Silicon Nanowire Arrays (2010)

Semiconductor nanowires have potential applications in photovoltaics, batteries, and thermoelectrics. We report a top-down fabrication method that involves the combination of superionic-solid-state-stamping (S4) patterning with metal-assisted-chemical-etching (MacEtch), to produce silicon nanowire arrays with defined geometry and optical properties in a manufacturable fashion. Strong light emission in the entire visible and near infrared wavelength range at room temperature, tunable by etching condition, attributed to surface features, and enhanced by silver surface plasmon, is demonstrated.
Protein Detection with Aptamer Biosensors (2008)

Aptamers have been developed for different applications. Their use as new biological recognition elements in biosensors promises progress for fast and easy detection of proteins. This new generation of biosensor (aptasensors) will be more stable and well adapted to the conditions of real samples because of the specific properties of aptamers.
Three‐color immunofluorescence analysis of mouse B‐lymphocyte subpopulations (1984)

We have modified a fluorescence-activated cell sorter (FACS) to make three independent immunofluorescence measurements on each cell and used this system to study mouse B-lymphocyte subpopulations. An argon-ion laser (emitting at 488 nm) excites fluorescein- and phycoerythrin-labeled reagents, and a tunable dye laser charged with rhodamine 6G (emitting at 615 nm) excites an allophycocyanin-labeled reagent. We report simultaneous measurements of IgM, IgD, and the recently-defined mouse B lymphocyte antigens BLA-1 and BLA-2 on splenic lymphocytes of CBA/J mice and mice of the congenic strain CBA/N (which have an X-linked immunodeficiency [xid]). These data provide information on relationships among the B-cell populations in CBA/J "normal" mice and the defective CBA/N that could not be derived from one- or two-color immunofluorescent measurements. We believe this is the first use of allophycocyanin as an immunofluorescence label.
Analysis of the cytolytic T lymphocyte response of melanoma patients to the naturally HLA-A*0201-associated tyrosinase peptide 368-376. (1999)

The human tyrosinase gene codes for two distinct antigens that are recognized by HLA-A*0201-restricted CTLs. For one of them, tyrosinase peptide 368-376, the sequence identified by mass spectrometry in melanoma cell eluates differs from the gene-encoded sequence as a result of posttranslational modification of amino acid residue 370 (asparagine to aspartic acid). Here, we used fluorescent tetrameric complexes ("tetramers") of HLA-A*0201 and tyrosinase peptide 368-376 (YMDGTMSQV) to characterize the CD8+ T-cell response to this antigen in lymphoid cell populations from HLA-A2 melanoma patients. Taking advantage of the presence of significant numbers of tetramer-positive CD8+ T cells in tumor-infiltrated lymph node cells from a melanoma patient, we derived polyclonal and monoclonal tyrosinase peptide 368-376-specific CTLs by tetramer-guided flow cytometric sorting. These CTLs efficiently and specifically lysed HLA-A*0201- and tyrosinase-positive melanoma cells. As assessed with tyrosinase peptide variants, the fine antigen specificity of the CTLs was quite diverse at the clonal level. Flow cytometric analysis of PBMCs stained with tetramers showed that tyrosinase peptide 368-376-specific CD8+ T cells were hardly detectable in peripheral blood of melanoma patients. However, significant numbers of such cells were detected after short-term stimulation of CD8+ lymphocytes with tyrosinase peptide 368-376 in 6 of 10 HLA-A2 melanoma patients. Taken together, these findings emphasize the significant contribution of the natural tyrosinase peptide 368-376 to the antigenic specificities recognized by the tumor-reactive CTLs that may develop in HLA-A2 melanoma patients.
Google Glass (2014)

Discussions of these identified benefits are framed within the potential of new in-vehicle systems that bring both novel forms of distraction and tools for mitigation into the driver's seat.
Protective immunization with invariant peptides of the Plasmodium falciparum antigen MSA2 (1992)

Three octapeptides from the N and C terminal C regions of the merozoite surface Ag 2 (MSA2) of Plasmodium falciparum elicit anti-MSA2 antibody when given as diphtheria toxoid conjugates. These antibodies also bind to the MSA2 homolog from the rodent malaria Plasmodium berghei. All mice vaccinated with these conjugates and challenged with an otherwise lethal inoculum of P. berghei showed substantial protection with most surviving. There was a inverse correlation between the development of the parasitemia and the antibody titer, with alum, algammulin, and CFA giving comparable results. These observations show that the conserved region of MSA2 could form the basis of a malaria vaccine when presented in a suitably immunogenic form, thus avoiding the problems of antigenic diversity [corrected].
Effects of mechanical stretching on trabecular matrix metalloproteinases. (2001)

These results are compatible with the hypothesis that elevations in IOP are sensed by TM cells as ECM stretch/distortion. TM cells respond by increasing gelatinase A and MT1-MMP, while decreasing TIMP-2 levels. This will increase ECM turnover rates, reduce the trabecular resistance to aqueous humor outflow, and restore normal IOP levels. This hypothesis provides a regulatory feedback mechanism for IOP homeostasis.
Prospects for adenovirus-mediated gene therapy of inherited diseases of the myocardium (1997)

Time for primary review 30 days.

Many genetic loci linked to a variety of diseases have been identified, and disease-causing mutations characterized. These have included diseases of the myocardium, such as X-linked dilated cardiomyopathy [1–3], hypertrophic cardiomyopathy [4–6], and Long QT syndrome [7–9]. The elucidation of gene defects has allowed different therapeutic strategies to be proposed, including the use of pharmaceutical agents to replace or to antagonize the mutated protein, and replacement of the defective gene with a functional one (gene therapy). There have been many publications describing the use of vectors to transduce target cells for the correction of gene defects or for anti-viral therapy (for reviews see [10–14]). Such vectors have included recombinant retroviruses, adenoviruses, adeno-associated viruses, and herpes viruses, as well as non-viral vectors. Each vector has inherent advantages and disadvantages. At this time the adenoviruses are most commonly used and represent the most likely vector for efficient transduction of the myocardium. While many groups have reported the use of recombinant adenoviruses to transduce cells in vitro and in vivo, and even their use in clinical trials for the correction of the cystic fibrosis gene defect [15, 16], there have been few reports describing the targeted expression of gene products for the correction of myocardial diseases. In this review we will discuss the potential of gene therapeutic approaches for the treatment of myocardial disease, as well as consider some of the limitations and risks associated with the use of the adenovirus-based vectors.

Recombinant adenoviruses have been the most commonly utilized vectors for the transduction of cells both in vitro and in vivo. This has primarily been due to their ability to be propagated and purified to high titers, their ability to transduce non-dividing cells, and their broad spectrum of target tissues. Most studies … 

* Corresponding author. Pediatric Cardiology, Baylor College of Medicine, One Baylor Plaza, Room 333E, Houston TX 77030, USA. Tel.: +1 713 7987342; Fax: +1 713 7988085; E-mail: jtowbin@bcm.tmc.edu
Determination of interactive thiol ionizations in bovine serum albumin, glutathione, and other thiols by potentiometric difference titration (1980)

A potentiometric difference titration (PDT) method is used to study the ionization behavior of the thiol group in bovine serum albumin and in the following less complex compounds: glutathione, cysteine, 2-mercaptoethanol, 3-mercaptopropionic acid, 2-mercaptoethylamine, cis-2-mercaptocyclobutylamine, 2-aminothiophenol, and 5-mercapto-2-nitrobenzoic acid. In the PDT method the pH dependence of the amount of protons released in the reaction RSH + CH3SO2SCH3 leads to RSSCH3 + CH3SO2- + H+ is measured in order to obtain the pH dependence of the molar proton content of the thiol (hu) relative to the molar proton content of its methylthio derivative (hm). The pH dependence of hu--hm reflects the ionization behavior of the thiol group and of other groups whose ionization is thermodynamically linked to that of the thiol group. Data presented here indicate that the ionization behavior of the single thiol group in albumin is strikingly different in the native and the urea-denatured proteins. Three ionizable groups appear to affect ionization of the thiol in the native protein whereas only one group appears to affect ionization of the thiol in the urea-denatured protein. Furthermore, the measured PDT curves are consistent with an abnormally high acidity (pK less than 5) for the thiol in native albumin and a normal acidity for the thiol in the urea-denatured protein. Comparisons of microscopic ionization constants determined for cysteine by using the PDT method with those determined by other methods indicate that the PDT method should be useful in characterizing the ionization behavior of thiol groups in proteins and other polyprotic substances.
A Functional Sp1 Binding Site Is Essential for the Activity of the Adult Liver-Specific Human Insulin-Like Growth Factor II Promoter (1997)

Abstract The human gene encoding insulin-like growth factor II contains four promoters (P1–P4) that are differentially activated in various tissues during development. Expression of insulin-like growth factor II in adult liver tissue is directed by P1, which is activated by liver-enriched members of the CCAAT/enhancer binding protein family of transcription factors. In the present report we show that the region around −48 relative to the transcription start site contains a high affinity Sp1 binding site. This was demonstrated by electrophoretic mobility shift assays using nuclear extracts from Hep3B hepatoma cells and with specific antibodies directed against Sp1. Competition electrophoretic mobility shift assays revealed that the Sp1 binding site of P1 and a consensus Sp1 binding site bind Sp1 with comparable efficiencies. Mutation of the Sp1 binding site results in an 85% decrease in P1 promoter activity in transient transfection assays using two different cell lines, COS-7 and Hep3B. Investigation of P1 mutants in which the spacing of the Sp1 binding site and the transcription start site was increased showed that the role of the Sp1 binding site in regulation of P1 is position dependent. Interestingly, the Sp1-responsive element cannot be exchanged by a functional TATA box. Activation of P1 by transactivators CCAAT/enhancer binding protein-β and hepatocyte nuclear factor-3β is strongly impaired after mutation of the Sp1 binding site. These results demonstrate that the specific presence of a binding site for the ubiquitously expressed transcription factor Sp1 is of eminent importance for efficient activation of P1 by liver-enriched transactivators.
Ultrastructure of the pineal cells of the homing pigeon Columba livia and magnetic fields (first trials). (1985)

The homing pigeon Columba livia was exposed to uniform 60 Hz AC magnetic fields, generated by Helmholtz coils with an intensity of 200 mG for 48 hrs. The microscopic studies performed revealed that only some of the pineal cells (between 20 and 30%) seemed to respond to the magnetic stimulation, and showed different ultrastructural morphological changes; the most striking effect was an apparent increase of apocrine secretion to the luminal spaces in the epiphyseal epithelium of this avian species.
O/W emulsion and W/O/W multiple emulsion: physical characterization and skin pharmacokinetic comparison in the delivery process of caffeine (1998)

The aim of this study was to compare the characteristics of an O/W emulsion and a W/O/W emulsion, formulated with similar ingredients. The physical properties of these two types of vehicles were characterized first. Using three types of in vitro models, human skin biopsies, nitrate acetate cellulose membranes and human reconstituted epidermis, the delivery potential of each vehicle for one hydrophilic drug, caffeine, was compared. The assessment of physical parameters, such as particle size, conductivity and rheological behavior enabled the nature of the test emulsions to be clearly identified. Clear differences were observed in the ability of each type of emulsion to deliver caffeine. Whatever the nature of the membrane used for the pharmacokinetic study, the absorption of caffeine was roughly two-fold lower (2.6 for human skin) when the W/O/W multiple emulsion was used as the vehicle. The concomitant determination of physical and kinetic properties of these two test emulsions allowed the W/O/W multiple emulsion and a simple O/W emulsion to be clearly differentiated.
Global analysis of tandem aromatic octapeptide repeats:The significance of the aromatic–glycine motif (2002)

The presence of aromatic-glycine conjugates appears to be significantly higher than aromatic conjugates to any other amino acid. Furthermore, all the six various combination of glycine occurrences before or after the three aromatic residues are present. No such pattern was observed for any other amino acid. The significance of the findings is being discussed in the context of the physicochemical properties of aromatic-glycine conjugates and its possible role in the facilitation of aggregates formation.
The ubiquitin-like proteins SMT3 and SUMO-1 are conjugated by the UBC9 E2 enzyme (1998)

The ubiquitin-like protein SMT3 from Saccharomyces cerevisiae and SUMO-1, its mammalian homolog, can be covalently attached to other proteins posttranslationally. Conjugation of ubiquitin requires the activities of ubiquitin-activating (E1) and -conjugating (E2) enzymes and proceeds via thioester-linked enzyme-ubiquitin intermediates. Herein we show that UBC9, one of the 13 different E2 enzymes from yeast, is required for SMT3 conjugation in vivo. Moreover, recombinant yeast and mammalian UBC9 enzymes were found to form thioester complexes with SMT3 and SUMO-1, respectively. This suggests that UBC9 functions as an E2 in a SMT3/SUMO-1 conjugation pathway analogous to ubiquitin-conjugating enzymes. The role of yeast UBC9 in cell cycle progression may thus be mediated through its SMT3 conjugation activity.
Wellbore Hydraulics in a SAGD Well Pair (2005)

Abstract In SAGD process a pair of horizontal wells is drilled at the base of a heavy oil and bitumen reservoir, vertically one above the other. Steam is injected into the upper well and the heated and mobilized bitumen drains to the bottom producer and is withdrawn either by natural lift or artificial lift. Uniform distribution of steam along the entire length of the well bore is very important for the uniform growth of the steam chamber. This is very important to make the entire length of the well productive. Pressure drop along the length of the injector and producer may cause steam break through in one segment and build up of liquid level between the wells. Generally steam is injected at the heel and the toe of the well and is distributed along the entire length primarily through slotted liner. It is expected that this will provide a higher quality steam at the toe end of the well. However, with out proper design the counter current heat transfer between the two streams may result in delivering a poor quality to the toe. In the producer it is necessary to withdraw fluid from the toe and heel. In a concentric design this may cause serious lifting problem if the tubulars are not designed properly and the split between the streams is not right. This paper presents the issues related to SAGD well bore design.
Fractionation of the Stable Isotopes of Inorganic Carbon by Seagrasses (1980)

The delta(13)C values for seagrasses collected along the Texas Gulf Coast range from -10.9 to -11.4 per thousand. These values are similar to the delta(13)C values of terrestrial C(4) plants, but seagrasses lack bundle sheath cells which are important in determining the delta(13)C values of C(4) plants. This work attempts to explain the reason the delta(13)C values of seagrasses resemble the delta(13)C values of C(4) plants.Investigations on the photosynthetic characteristics of seagrasses show that dissolved CO(2) is the species of inorganic carbon absorbed or accumulated by Thalassia testudinum. The rate of photosynthetic CO(2) fixation varies from 9.6 to 129.0 micromoles CO(2) per milligram chlorophyll per hour in the presence of 0.042 to 1.9 millimolar dissolved CO(2) due to the high resistances of Thalassia leaves to CO(2) diffusion. Phosphoglyceric acid is the first stable product of photosynthetic CO(2) fixation in Thalassia which is a Calvin cycle plant. The light/dark ratios of (14)CO(2) release from submerged Thalassia leaf sections at 1, 21, and 100% O(2) indicate a small apparent photorespiration. Dark respiration continues in the light and is stimulated by 21 and 100% O(2). The low apparent photorespiration may be due to membrane and H(2)O resistances to CO(2) diffusion with subsequent refixation of the photorespired CO(2). The internal pool of CO(2) is not in equilibrium with the external pool of CO(2) which results in a closed system in the seagrasses.The delta(13)C value of CO(2) in sea H(2)O in isotopic equilibrium with HCO(3) (-) is -10.3 per thousand and the delta(13)C value of hexoses isolated from the leaves of Thalassia is -11.5 per thousand. In the closed system of the seagrasses there is a -1.2 per thousand fractionation of CO(2) by ribulose-1,5-bisphosphate carboxylase and the Calvin cycle. This contrasts to a fractionation of about -17 to -27 per thousand of the stable carbon isotopes of CO(2) by the Calvin cycle in the open system of terrestrial C(3) plants where the internal pool of CO(2) is in equilibrium with atmospheric CO(2).Among C(3) plants the seagrasses are very unusual in fixing CO(2) by the Calvin cycle in a closed system. This closed system metabolism is analogous to the fixation of CO(2) by the Calvin cycle in the bundle sheath cells of C(4) plants where all of the (12)CO(2) and (13)CO(2) is fixed by ribulose-1,5-bisphosphate carboxylase. Therefore, the reasons the delta(13)C values of seagrasses and C(4) plants are similar are: (a) the delta(13)C value of dissolved CO(2) in seawater resembles the delta(13)C value of the C(4) acids and the delta(13)C value of CO(2) in the bundle sheath cells, and (b) there is no fractionation of the stable carbon isotopes of CO(2) in the closed systems of the seagrasses or the bundle sheath cells of C(4) plants.