gebhart/patrepeval huggingface dataset:
Early Detection of Head and Neck Cancer: Development of a Novel Screening Tool Using Multiplexed Immunobead-Based Biomarker Profiling (2007)

Squamous cell carcinoma of the head and neck (SCCHN) is an aggressive disease that has been linked to altered immune, inflammatory, and angiogenesis responses. A better understanding of these aberrant responses might improve early detection and prognosis of SCCHN and provide novel therapeutic targets. Previous studies examined the role of multiplexed serum biomarkers in small cohorts or SCCHN sera. We hypothesized that an expanded panel comprised of multiple cytokines, chemokines, growth factors, and other tumor markers, which individually may show some promising correlation with disease status, might provide higher diagnostic power if used in combination. Thus, we evaluated a novel multianalyte LabMAP profiling technology that allows simultaneous measurement of multiple serum biomarkers. Concentrations of 60 cytokines, growth factors, and tumor antigens were measured in the sera of 116 SCCHN patients before treatment (active disease group), 103 patients who were successfully treated (no evidence of disease group), and 117 smoker controls without evidence of cancer. The multimarker panel offering the highest diagnostic power was comprised of 25 biomarkers, including epidermal growth factor, epidermal growth factor receptor, interleukin (IL)-8, tissue plasminogen activator inhibitor-1, alpha-fetoprotein, matrix metalloproteinase-2, matrix metalloproteinase-3, IFN-alpha, IFN-gamma, IFN-inducible protein-10, regulated on activation, normal T-cell expressed and secreted (RANTES), macrophage inflammatory protein-1alpha, IL-7, IL-17, IL-1 receptor-alpha, IL-2 receptor, granulocyte colony-stimulating factor, mesothelin, insulin-like growth factor binding protein 1, E-selectin, cytokeratin-19, vascular cell adhesion molecule, and cancer antigen-125. Statistical analysis using an ADE algorithm resulted in a sensitivity of 84.5%, specificity of 98%, and 92% of patients in the active disease group correctly classified from a cross-validation serum set. The data presented show that simultaneous testing using a multiplexed panel of serum biomarkers may present a promising new approach for the early detection of head and neck cancer.
Selective inhibition of Aβ42 production by NSAID R‐enantiomers (2002)

Non-steroidal anti-inflammatory drugs (NSAIDs) have been associated with reduced risk for Alzheimer's disease (AD) and selected NSAIDs racemates suppress beta-amyloid (Abeta) accumulation in vivo and Abeta42 production in vitro. Clinical use of NSAIDs for preventing or treating AD has been hampered by dose-limiting toxicity believed to be due to cyclooxygenase (COX)-inhibition that is reportedly not essential for selective Abeta42 reduction. Profens have racemates and R-enantiomers were supposed to be inactive forms. Here we demonstrate that R-ibuprofen and R-flurbiprofen, with poor COX-inhibiting activity, reduce Abeta42 production by human cells. Although these R-enantiomers inhibit nuclear factor-kappaB (NF-kappaB) activation and NF-kappaB can selectively regulate Abeta42, Abeta42 reduction is not mediated by inhibition of NF-kappaB activation. Because of its efficacy at lowering Abeta42 production and low toxicity profile, R-flurbiprofen is a strong candidate for clinical development.
Fluorescence energy transfer detection as a homogeneous DNA diagnostic method (1997)

A homogeneous DNA diagnostic assay based on template-directed primer extension detected by fluorescence resonance energy transfer, named template-directed dye-terminator incorporation (TDI) assay, has been developed for mutation detection and high throughput genome analysis. Here, we report the successful application of the TDI assay to detect mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, the human leukocyte antigen H (HLA-H) gene, and the receptor tyrosin kinase (RET) protooncogene that are associated with cystic fibrosis, hemochromatosis, and multiple endocrine neoplasia, type 2, respectively. Starting with total human DNA, the samples are amplified by the PCR followed by enzymatic degradation of excess primers and deoxyribonucleoside triphosphates before the primer extension reaction is performed. All these standardized steps are performed in the same tube, and the fluorescence changes are monitored in real time, making it a useful clinical DNA diagnostic method.
Can Droplets and Bubbles Think? (2007)

Bubbles flowing through narrow channels can be encoded with information and made to perform logic operations like those in a computer.
An Analysis of The Candidates Remarks on Twitter in 2014 Presidency Election in Terms of Values (2015)

Siyasal iletişim süreci teknolojiyle birlikte yön değiştirmiş, Siyasi aktörler kampanyalarında günlük duygu, düşünce ve faaliyetlerini aktarmalarının yanı sıra seçim kampanyalarının içerik ve boyutları yeni şartlara göre değişmiştir. Siyasi aktörlerin yanı sıra özellikle liderler, geleneksel medyanın yanı sıra sosyal medyada kullanılan iletişim yöntemleriyle birlikte kendilerinin “marka kişilik” olarak sunulması konusunda profesyonel çalışanlardan ve imaj tasarımcılarından yararlanmaktadırlar. Bunun nedeni Türkiye’de liderlerin siyasette en önemli figür olmaları gerçeğidir. Türk siyasal yaşamında milletvekili seçimlerinin yanı sıra 10 Ağustos 2014 yılında Türkiye’de ilk defa halkoylamasıyla yapılan Cumhurbaşkanlığı seçiminde de adaylar sosyal medyayı yoğun olarak kullanmışlardır. Cumhurbaşkanı adayları Recep Tayyip Erdoğan, Ekmeleddin İhsanoğlu ve Selahattin Demirtaş özellikle Twitter aracılığıyla seçime yönelik iletilerinde bir takım değerleri kullanarak kişisel imaj tasarlamaya çalışmış, seçmenlerine güvenilir, dürüst, demokrat, barışçıl v.s. bir cumhurbaşkanı olacakları yönünde iletiler sunmuşlardır.
A Biochemical Guide to Yeast Adhesins: Glycoproteins for Social and Antisocial Occasions (2007)

Fungi are nonmotile eukaryotes that rely on their adhesins for selective interaction with the environment and with other fungal cells. Glycosylphosphatidylinositol (GPI)-cross-linked adhesins have essential roles in mating, colony morphology, host-pathogen interactions, and biofilm formation. We review the structure and binding properties of cell wall-bound adhesins of ascomycetous yeasts and relate them to their effects on cellular interactions, with particular emphasis on the agglutinins and flocculins of Saccharomyces and the Als proteins of Candida. These glycoproteins share common structural motifs tailored to surface activity and biological function. After being secreted to the outer face of the plasma membrane, they are covalently anchored in the wall through modified GPI anchors, with their binding domains elevated beyond the wall surface on highly glycosylated extended stalks. N-terminal globular domains bind peptide or sugar ligands, with between millimolar and nanomolar affinities. These affinities and the high density of adhesins and ligands at the cell surface determine microscopic and macroscopic characteristics of cell-cell associations. Central domains often include Thr-rich tandemly repeated sequences that are highly glycosylated. These domains potentiate cell-to-cell binding, but the molecular mechanism of such an association is not yet clear. These repeats also mediate recombination between repeats and between genes. The high levels of recombination and epigenetic regulation are sources of variation which enable the population to continually exploit new niches and resources.
Evaluating two methods for fingerprinting genomes of Actinobacillus actinomycetemcomitans (1993)

The arbitrary primer polymerase chain reaction (AP-PCR) and Southern blot restriction fragment length polymorphism (RFLP) were used to genotype the periodontal pathogen A. actinomycetemcomitans. Total genomic DNA from 73 strains was extracted by conventional methods. Three random-sequence 10-base oligonucleotide primers were chosen for AP-PCR. The amplified DNA products were separated electrophoretically in a 1% agarose gel containing ethidium bromide and the banding patterns were compared among different strains. For RFLP analysis, DNA was digested with EcoRI, separated on a 0.8% agarose gel and transferred to a nylon membrane. The membrane was probed with a previously characterized 5.2 kilobases (kb) DNA fragment cloned from A. actinomycetemcomitans strain Y4. The probe was labeled with digoxigenin, and hybridized fragments were detected with anti-digoxigenin antibody. AP-PCR produced 4-10 DNA bands in the 0.5-5 kb regions and distinguished 9, 13 or 17 genotypes, depending on the specific primer used. Southern blot RFLP analysis revealed 12 hybridization patterns consisting of 1 or 2 DNA fragments (2-23 kb). The addition of the Southern blot analysis to the AP-PCR analysis gave rise to a total of 30 DNA profiles among the 73 A. actinomycetemcomitans study strains. The results indicate that both AP-PCR and Southern blot analysis are useful in clonal analysis of A. actinomycetemcomitans.
Placental anticoagulant proteins: isolation and comparative characterization of four members of the lipocortin family (1988)

Previously we isolated and characterized a placental anticoagulant protein (PAP or PAP-I), which is a Ca2+-dependent phospholipid binding protein [Funakoshi et al. (1987) Biochemistry 26, 5572] and a member of the lipocortin family [Funakoshi et al. (1987) Biochemistry 26, 8087]. In this study, three additional anticoagulant proteins (PAP-II, PAP-III, and PAP-IV) were simultaneously isolated from human placental homogenates prepared in the presence of 5 mM ethylenediaminetetraacetic acid. The isoelectric points of PAP-I, PAP-II, PAP-III, and PAP-IV were 4.8, 6.1, 5.9, and 8.1, respectively, and their apparent molecular weights were 32,000, 33,000, 34,000, and 34,500, respectively. Amino acid sequences of cyanogen bromide fragments of these proteins showed that PAP-III was a previously unrecognized member of the lipocortin family, while PAP-II was probably the human homologue of porcine protein II and PAP-IV was a derivative of lipocortin II truncated near the amino terminus. Comparative studies showed that all four proteins inhibited blood clotting and phospholipase A2 activity with potencies consistent with their measured relative affinities for anionic phospholipid vesicles. However, PAP-IV bound to phospholipid vesicles approximately 160-fold more weakly than PAP-I, while PAP-II and PAP-III bound only 2-fold and 3-fold more weakly. These results increase to six the number of lipocortin-like proteins known to exist in human placenta. The observed differences in phospholipid binding may indicate functional differences among the members of the lipocortin family despite their considerable structural similarities.
Comparison of Oxybutynin and its Active Metabolite, N-Desethyl-Oxybutynin, in the Human Detrusor and Parotid Gland (1997)

We conclude that oxybutynin and N-desethyl-oxybutynin have a similar antimuscarinic effect in the human detrusor, and the same binding characteristics in detrusor and parotid gland, respectively.
Sensitivity toward tyrosine kinase inhibitors varies between different activating mutations of the FLT3 receptor (2003)

Activating mutations of FLT3 have been detected in patients with acute myeloid leukemia (AML). Two distinct types of FLT3 mutations are most common: internal tandem duplication (ITD) of sequences coding for the juxtamembrane domain and point mutations at codon 835 (Asp835) within the kinase domain. Both types of mutations constitutively activate the tyrosine kinase activity of FLT3 in experimental systems and result in factor-independent proliferation of Ba/F3 and 32D cells. Recently, novel mutations within the activation loop were identified in patients with AML: deletion of isoleucine 836 (Ile836del) and an exchange of isoleucine 836 to methionine plus an arginine insertion (Ile836Met+Arg). To examine whether the Ile836 mutations result in constitutive activation of the FLT3 receptor, we introduced both mutant FLT3 cDNAs transiently into HEK 293 cells. Both mutant FLT3 receptors were constitutively autophosphorylated in the absence of ligand and kinase activity led to constitutive activation of downstream signaling cascades as determined by activation of the STAT5 (signal transducer and activator of transcription 5) pathway. When stably expressed in the growth factor-dependent cell lines Ba/F3 and 32D, both deletion and insertion mutants led to factor-independent proliferation, indicating that both mutants have transforming capabilities. We then examined the sensitivity of the FLT3 ITD, FLT3 Asp835Tyr, and the novel FLT3 receptor mutants toward the kinase inhibitors AG1296, PKC412, and SU5614. We show that these FLT3 kinase inhibitors have distinct inhibitory potencies against different activating FLT3 receptor mutants. These results suggest that it may be useful to determine the exact kind of FLT3 mutation when applying receptor kinase inhibitors in clinical trials.
Observation of Coherent Transients in Ultrashort Chirped Excitation of an Undamped Two-Level System (2001)

The effects of coherent excitation of a two-level system with a linearly chirped pulse are studied theoretically and experimentally [in Rb (5s-5p)] in the low field regime. The coherent transients are measured directly on the excited state population on an ultrashort time scale. A sharp step corresponds to the passage through resonance. It is followed by oscillations resulting from interferences between off-resonant and resonant contributions. We finally show the equivalence between this experiment and Fresnel diffraction by a sharp edge.
Understanding wound inflammation. (2004)

Inflammation is the first stage in the wound-healing process. It is normally followed by two further phases: regeneration (sometimes also referred to as proliferation) and maturation. Inflammation is characterised by the classic signs of heat and redness, pain and swelling, raised temperature and fever. The overall function of inflammation is to neutralise and destroy any toxic agents at the site of an injury and to restore tissue homeostasis.
The Study of Surface Film Formation on Noble-Metal Electrodes in Alkyl Carbonates/Li Salt Solutions, Using Simultaneous in Situ AFM, EQCM, FTIR, and EIS (1999)

In this study, surface film formation on nonactive-metal electrodes was analyzed using several in situ spectroelectrochemical techniques. These techniques included in situ Fourier transform infrared spectroscopy in both internal and external reflectance modes, impedance spectroscopy, electrochemical quartz crystal microbalance, and atomic force microscopy. The solutions studied included ethylene carbonate−dimethyl carbonate (EC−DMC) and EC−tetrahydrofurane (EC−THF) mixtures with Li salts, such as LiAsF6, LiPF6, LiClO4, and LiBr, part of which are essential for practical Li ion batteries. This work aimed to determine the onset of surface film formation, the impact of the solvent and salt used, and to compare the stability of the surface films formed in the various systems. The onset of surface film formation in these systems usually approximated 1.5 V (Li/Li+). EC reduction products, probably (CH2OCO2Li)2, are dominant constituents in the surface films. However, in LiPF6 solutions, Li salt reduction products become dominant in the surface films. The surface film formation is accompanied by an injection of charge which does not form stable surface species and by dissolution processes of surface species (until the solution becomes saturated with them). The coherence of the data obtained from the four techniques mentioned above and the relative stability of the surface films formed in the various solutions are discussed.
High dose dexamethasone as first line therapy of multiple myeloma? A case report. (1998)

The authors describe a case of multiple myeloma in which a complete remission was obtained by treatment with high dose dexamethasone. This was the only therapy suitable for the patient because of heavy myelosuppression due to disease and to one course of conventional treatment with melphalan and prednisone. Further trials are needed to evaluate the usefulness and safety of this treatment as first line therapy, especially in the elderly, with pancytopenia and bad performance status.
Total Chemical Synthesis of Crambin (2004)

Crambin is a small (46 amino acids) protein isolated from the seeds of the plant Crambe abyssinica. Crambin has been extensively used as a model protein for the development of advanced crystallography and NMR techniques and for computational folding studies. We set out to establish synthetic access to crambin. Initially, we synthesized the 46 amino acid polypeptide by native chemical ligation of two distinct sets of peptide segments (15 + 31 and 31 + 15 residues). The synthetic polypeptide chain folded in good yield to give native crambin containing three disulfide bonds. The chemically synthesized crambin was characterized by LC-MS and by 2D-NMR. However, the 31-residue peptide segments were difficult to purify, and this caused an overall low yield for the synthesis. To overcome this problem, we synthesized crambin by the native chemical ligation of three segments (15 + 16 + 15 residues). Total synthesis using the ligation of three segments gave more than a 10-fold increase in yield and a protein product of exceptionally high purity. This work demonstrates the efficacy of chemical protein synthesis by the native chemical ligation of three segments and establishes efficient synthetic access to the important model protein crambin for experimental studies of protein folding and stability.
PageRank Computation and the Structure of the Web: Experiments and Algorithms (2002)

We describe some computational experiments carried out with variants of the &amp;quot;PageRank&amp;quot; model due to Page et al., with particular reference to the small and large scale structure of the Web.
Docetaxel in prostate cancer. (2001)

In contrast to several other tumor types, there has been relatively little experience with docetaxel in hormone-refractory prostate cancer. However, two phase II trials investigated the combination of docetaxel with estramustine, and reported prostate-specific antigen response rates of 69 and 74% and objective responses in 23% and 57% of patients. This activity is comparable with that of other estramustine combinations. However, there is uncertainty about whether estramustine itself should be omitted from therapy because of its emetogenic and thromboembolic potential, and also over the optimal schedule of docetaxel to avoid neutropenia. Preliminary data suggest that weekly docetaxel, with or without limited exposure to estramustine, may provide the right balance between efficacy and tolerability. Phase III studies now in progress are comparing regimens containing docetaxel and estramustine with a recent standard therapy consisting of mitoxantrone plus prednisone. In the future, the efficacy of docetaxel plus estramustine may be enhanced by adding agents to this regimen.
A comparative study of two different doses of cytarabine for acute myeloid leukemia: a phase III trial of Cancer and Leukemia Group B (1991)

Between 1982 and 1986, 326 evaluable patients with acute myeloid leukemia (AML) were randomized to receive cytarabine (Ara-C) at 200 mg/m2 (A200) or 100 mg/m2 (A100) for induction and maintenance therapy. Cycle 1 of induction therapy consisted of 7 days of continuous intravenous (IV) Ara-C and 3 days of i.v. daunorubicin (DNR); cycle 2, if needed, consisted of 5 days of Ara-C and 2 days of DNR. Complete responders (CR) then received monthly subcutaneous (SC) Ara-C at the respective doses (A100 or A200) with 6-thioquanine (6TG) at months 1 and 5, with vincristine (VCR) and prednisone at months 2, 4, 6, and 8, and with DNR at months 3 and 7. Complete response rates were 58% (A100) and 64% (A200) (P = .29). Median survival was 46 weeks (A100) and 38 weeks (A200) (P = .64); 5-year survival was 10% (A200) and 8% (A100). Median time to remission was 6.7 weeks (A200) and 8.1 weeks (A100) (P = .18). Median disease-free survival was 41 weeks (A200) and 44 weeks (A100) (P = .86). Deaths were attributed to therapy-related toxicities in 21% (A200) and 13% (A100) (P = .05). The 5-year survival was 15% for patients with performance status (PS) 0, 8% for PS 1 to 2, and 2% for PS 3 to 4, 18% for patients less than 40 years, 8% for ages 40 to 59, and 3% for age 60 or greater. Stratification of data by age and PS suggested that A200 may improve survival in patients less than 60 years with a good PS 0 (P = .05). This trial does not support the superiority of A200 over A100 in the treatment of AML.
Toward Ecosystem-Based Fisheries Management (2003)

Considerable effort has been directed in the last decade towards the development of multispecies, ecosystem-based approaches to fisheries management. One aspect of this is the development of models that take into account direct and indirect ecological interactions among species and their environment. We review four multispecies modeling approaches that we feel have great potential for use in fisheries management: multispecies production models, multispecies virtual population analysis, Ecopath with Ecosim, and multispecies bioenergetics models. All four can predict biomass trajectories over time and under various fishing pressures, but with different spatial, temporal, and biological resolution, quantitative/qualitative nature of the results, and insight into system function. We present the data requirements of each model and give examples of field programs that have provided data for model construction and validation. We conclude with a set of issues to consider when designing a coupled field-modeling research program, including the scale of the problem, appropriate sampling platform, and data collection.
Bayesian multi-scale differential optical flow (1999)

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397 14.2 Differential formulation . . . . . . . . . . . . . . . . . . . . . 398 14.3 Uncertainty Model . . . . . . . . . . . . . . . . . . . . . . . . 400 14.4 Coarse-to-fine estimation . . . . . . . . . . . . . . . . . . . . 404 14.5 Implementation issues . . . . . . . . . . . . . . . . . . . . . . 411 14.5.1 Derivative filter kernels . . . . . . . . . . . . . . . . . 411 14.5.2 Averaging filter kernels . . . . . . . . . . . . . . . . . 412 14.5.3 Multi-scale warping . . . . . . . . . . . . . . . . . . . 412 14.5.4 Boundary handling . . . . . . . . . . . . . . . . . . . 414 14.6 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 414 14.6.1 Performance measures . . . . . . . . . . . . . . . . . 414 14.6.2 Synthetic sequences . . . . . . . . . . . . . . . . . . . 415 14.7 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . 419 14.8 References . . . . . . . . . . . . . . . . . . . . . . .