gebhart/patrepeval huggingface dataset:
Neutrophil extracellular traps (NETs) - formation and implications. (2013)

Neutrophils are cells of the immune system which freely circulate in blood vessels and are recruited to the inflammation sites when the human organism responds to microbial infections. One of the mechanisms of neutrophil action is the formation of neutrophil extracellular traps (NETs) The process of NET generation, called netosis, is a specific type of cell death, different from necrosis and apoptosis. NETs are formed by neutrophils upon contact with various bacteria or fungi as well as with activated platelets or under the influence of numerous inflammatory stimuli, and this process is associated with dramatic changes in the morphology of the cells. The main components of NETs, DNA and granular antimicrobial proteins, determine their antimicrobial properties. The pathogens trapped in NETs are killed by oxidative and non-oxidative mechanisms. On the other hand, it was also discovered that chromatin and proteases released into the circulatory system during NET formation can regulate procoagulant and prothrombotic factors and take part in clot formation in blood vessels. NETs have also been detected in lungs where they are involved in chronic inflammation processes in ALI/ARDS patients. Moreover, DNA-proteins complexes have been found in the airway fluids of cystic fibrosis patients where they can increase the viscosity of the sputum and have a negative impact on the lung functions. The DNA-complexed granular proteins and other proteins released by neutrophils during netosis lead to autoimmunity syndromes such as systemic lupus erythematosus (SLE), small-vessel vasculitis (SVV) or autoimmune diseases associated with the formation of autoantibodies against chromatin and neutrophil components. A possible involvement of NETs in metastasis is also considered.
Unimolecular decomposition of NO3 to form NO and O2 and a review of N2O5/NO3 kinetics (1986)

The nitrate free radical NO 3 has been observed by several investigators in the troposphere at night. It increases during the night much less than predicted in terms of known processes, and there has been a search for an unknown NO 3 scavenger. In this article we report evidence in the chemical literature for the thermal decomposition of NO 3 to form nitric oxide and molecular oxygen, where the reaction w is NO 3 → NO + O 2 , and the rate is such that this reaction is proposed as a scavenging process in the troposphere. By straightforward reinterpretation of three room temperature kinetic studies which used reactors of widely different volumes, we find the first‐order rate constant at one atmosphere pressure to be w = (3 ± 2) × 10 −3 s −1 ; in these systems the otherwise unexplained first‐order loss of NO 3 accounted for 5–74% of the observed rate. Using high‐temperature shock tube experiments, Schott and Davidson [1958] evaluated rate constants for reaction e (NO 2 + NO 3 → NO + O 2 + NO 2 ) and reaction g (2NO 3 → 2NO 2 + O 2 ), but these values are much higher than the extrapolated results of Graham and Johnston [1978]. This difference is ascribed to the unrecognized contribution of reaction w in Schott and Davidson's system; with this assumption we evaluated by two methods the rate constants for w at high temperatures, which combine with the room temperature values to give the Arrhenius expression w = 2.5 × 10 6 exp (−6.1 × 10 3 / T ) s −1 . This relation implies that the unimolecular reaction has a low frequency factor and a low activation energy, which are ascribed to a forbidden transition to the low‐lying excited electronic state ( 2 E 2 ″) of NO 3 . The rate of this channel of decomposition is compared with the much slower process leading to NO 2 and O as products. Although this article gives evidence that the reaction NO 3 → NO + O 2 occurs, the quantitative values of rate coefficients are uncertain, and there are no data concerning the effect of foreign gas pressure. This article points out two methods (equations (14) and (17)) whereby deliberate studies of this reaction can be used to establish its rate coefficients and to find its M gas dependence. The recommended rate expression for reaction e is 2.05 × 10 13 exp (−1.24 × 10 4 / T )/ K eq and that for g is 8.5 × 10 −13 exp (−2.45 × 10 3 / T ) cm 3 molecule −1 s −1 , where K eq refers to the equilibrium N 2 O 5 = NO 3 + NO 2 .
Ski-related novel protein N (SnoN), a negative controller of transforming growth factor-beta signaling, is a prognostic marker in estrogen receptor-positive breast carcinomas. (2003)

Transforming growth factor (TGF)-beta arrests the growth of breast epithelial cells, whereas breast cancer cells are highly resistant to its growth restrictive properties. To define causes for the defect in TGF-beta action, we present here the first in vivo analysis of Ski-related novel protein N (SnoN), a negative regulator of TGF-beta signaling, in human breast carcinomas. SnoN expression was analyzed by immunohistochemistry in a tissue microarray of 1122 breast carcinomas and 10 reduction mammoplasties. In the normal breast, SnoN was located predominantly in nuclei of large duct epithelial cells and the cytoplasm of terminal duct epithelial cells. Breast cancers displayed variances in both SnoN expression levels and subcellular localizations. High levels of cytoplasmic SnoN were more often observed in tumors of ductal histological type and associated with adverse prognostic features, such as lack of hormone receptors; high levels of p53, Ki-67, and cyclooxygenase-2; and amplifications of HER-2. High levels of nuclear SnoN were associated with lobular histology and favorable features, including presence of hormone receptors, low expression of p53 and Ki-67, and lack of HER-2 amplifications. Reduced expression of SnoN significantly correlated with longer distant disease-free survival in estrogen receptor-positive patients (P = 0.0027, relative risk = 3.27; 95% confidence interval = 1.44-7.41). The results suggest that the subcellular localization of SnoN may have clinical significance and that reduced expression of SnoN is associated with favorable outcome in estrogen receptor-positive breast cancer.
Spinosyn G:  Proof of Structure by Semisynthesis (2005)

[reaction: see text] Spinosyn G was isolated in the late 1980s as a minor component from the broth of our potent, fermentation-derived insecticide spinosad. Its structure was then tentatively identified as 5' '-epispinosyn A (3) on the basis of (1)H and (13)C NMR data, but the 4' '-epi compound 4 could not be conclusively ruled out with the data available. Described herein are unambiguous syntheses of both 3 and 4, whereby 3 was proved identical to the natural product. Compound 4 was prepared from intact spinosyn A by a novel F-TEDA-promoted oxidative deamination to the 4' '-ketone 5, stereoselective reduction to the equatorial alcohol 6, and nitrogen incorporation via the axial azide 7. Compound 3 was obtained by coupling spinosyn A 17-pseudoaglycone (9) with the N-protected dihydropyran 16 derived from methyl l-ossaminide (14). This gave an approximately 2:1 mixture of anomeric products 17 with the desired equatorial glycoside predominating, which was then converted to 3 by N-deprotection and methylation.
The influence of atmospheric carbonic acid upon the surface tension of aqueous solutions of sodium salts of fatty acids (1935)

The first page of this article is displayed as the abstract.
Quality of thrombin produced from the patient's own plasma using the TPD, a new Thrombin-processing Device. (2005)

Thrombin derived from bovine sources commonly is used to arrest bleeding during surgical procedures. However, complications such as postoperative hemorrhage can occur because of the development of cross-reactive anti-bovine antibodies that inhibit human coagulation factor V. It would thus be advantageous to develop techniques to generate human thrombin. This study evaluated thrombin produced from human plasma using a new Thrombin-Processing Device (TPD). Plasma was introduced into the TPD, mixed with an ethanol/ CaCl2 reagent, incubated for 1 h, and the harvested thrombin was assayed for activity and the ability to activate platelets by in vitro assays. TPD-produced thrombin activity was found to be 51.8 +/- 12.4 IU/mL (n = 145). TPD-produced thrombin also stimulated P-selectin (CD62) expression (83 +/- 13% of the platelet population) and Annexin V binding (10.3 +/- 2% of the platelet population) on platelets in a similar fashion to commercial thrombin (P-selectin expression: 88 +/- 3%; Annexin-V binding: 11.4 +/- 3%). Compared with CaCl2 and batroxobin, TPD-produced thrombin had a significantly greater ability to activate platelets. TPD-produced thrombin from human plasma has consistent activity and significantly activates platelets and, thus, may have attractive applications such as the production of autologous thrombin for surgical patients.
Surface Functionalization of Living Cells with Multilayer Patches (2008)

We demonstrate that functional polyelectrolyte multilayer (PEM) patches can be attached to a fraction of the surface area of living, individual lymphocytes. Surface-modified cells remain viable at least 48 h following attachment of the functional patch, and patches carrying magnetic nanoparticles allow the cells to be spatially manipulated using a magnetic field. The patch does not completely occlude the cellular surface from the surrounding environment; this approach allows a functional payload to be attached to a cell that is still free to perform its native functions, as suggested by preliminary studies on patch-modified T-cell migration. This approach has potential for broad applications in bioimaging, cellular functionalization, immune system and tissue engineering, and cell-based therapeutics where cell-environment interactions are critical.
Generation of Potent T-cell Immunotherapy for Cancer Using DAP12-Based, Multichain, Chimeric Immunoreceptors (2015)

Chimeric antigen receptors (CAR) bearing an antigen-binding domain linked in cis to the cytoplasmic domains of CD3ζ and costimulatory receptors have provided a potent method for engineering T-cell cytotoxicity toward B-cell leukemia and lymphoma. However, resistance to immunotherapy due to loss of T-cell effector function remains a significant barrier, especially in solid malignancies. We describe an alternative chimeric immunoreceptor design in which we have fused a single-chain variable fragment for antigen recognition to the transmembrane and cytoplasmic domains of KIR2DS2, a stimulatory killer immunoglobulin-like receptor (KIR). We show that this simple, KIR-based CAR (KIR-CAR) triggers robust antigen-specific proliferation and effector function in vitro when introduced into human T cells with DAP12, an immunotyrosine-based activation motifs-containing adaptor. T cells modified to express a KIR-CAR and DAP12 exhibit superior antitumor activity compared with standard first- and second-generation CD3ζ-based CARs in a xenograft model of mesothelioma highly resistant to immunotherapy. The enhanced antitumor activity is associated with improved retention of chimeric immunoreceptor expression and improved effector function of isolated tumor-infiltrating lymphocytes. These results support the exploration of KIR-CARs for adoptive T-cell immunotherapy, particularly in immunotherapy-resistant solid tumors.
Joint time-frequency measurements of modelocked semiconductor diode lasers and dynamics using frequency-resolved optical gating (1999)

Joint time-frequency ultrafast measurements using frequency-resolved optical gating (FROG) have been used to provide a fundamental understanding of: (1) ultrashort pulse propagation in semiconductor optical amplifiers; (2) the modelocking dynamics in external cavity semiconductor diode lasers; and (3) correlated multiple-wavelength generation from mode locked semiconductor lasers. The pulse shaping and chirping effects measured by FROG are shown to be attributed to intracavity gain and saturable absorbing dynamics, as well as group velocity dispersion. In addition, the intracavity gain dynamics show a regime of transient unsaturated gain, which can be exploited to allow phase-correlated multiple-wavelength modelocked operation from a single-stripe external-cavity semiconductor diode laser. In this case, FROG techniques are used to understand the underlying mechanisms involved in the phase correlation process.
Erythrocyte engineering for drug delivery and targeting (1998)

A new procedure for the encapsulation of non-diffusible drugs into human erythrocytes was developed. With as little as 50 ml of blood and by using a new apparatus, it was possible to encapsulate a variety of biologically active compounds into erythrocytes in 2 h at room temperature and under blood-banking conditions. The process, which is based on two sequential hypotonic dilutions of washed red cells followed by concentration with a haemofilter and resealing of red cells, allows a 35-50% cell recovery and approx. 30% encapsulation of added drugs. The resulting processed erythrocytes have a normal survival in vivo and can be modified further, with the same apparatus, to increase their recognition by tissue macrophages to perform as a drug-targeting system. The new equipment designed and built for this procedure was named 'Red Cell Loader'.
Growth Factors, Matrices, and Forces Combine and Control Stem Cells (2009)

Stem cell fate is influenced by a number of factors and interactions that require robust control for safe and effective regeneration of functional tissue. Coordinated interactions with soluble factors, other cells, and extracellular matrices define a local biochemical and mechanical niche with complex and dynamic regulation that stem cells sense. Decellularized tissue matrices and synthetic polymer niches are being used in the clinic, and they are also beginning to clarify fundamental aspects of how stem cells contribute to homeostasis and repair, for example, at sites of fibrosis. Multifaceted technologies are increasingly required to produce and interrogate cells ex vivo, to build predictive models, and, ultimately, to enhance stem cell integration in vivo for therapeutic benefit.
Ultra‐Small Iron Oxide Doped Polypyrrole Nanoparticles for In Vivo Multimodal Imaging Guided Photothermal Therapy (2013)

Recently, near‐infrared (NIR) absorbing conjugated polymeric nanoparticles have received significant attention in photothermal therapy of cancer. Herein, polypyrrole (PPy), a NIR‐absorbing conjugate polymer, is used to coat ultra‐small iron oxide nanoparticles (IONPs), obtaining multifunctional IONP@PPy nanocomposite which is further modified by the biocompatible polyethylene glycol (PEG) through a layer‐by‐layer method to acquire high stability in physiological solutions. Utilizing the optical and magnetic properties of the yielded IONP@PPy‐PEG nanoparticles, in vivo magnetic resonance (MR) and photoacoustic imaging of tumor‐bearing mice are conducted, revealing strong tumor uptake of those nanoparticles after intravenous injection. In vivo photothermal therapy is then designed and carried out, achieving excellent tumor ablation therapeutic effect in mice experiments. These results promise the use of multifunctional NIR‐absorbing organic‐inorganic hybrid nanomaterials, such as IONP@PPy‐PEG presented here, for potential applications in cancer theranostics.
Overexpression of Phospho-eIF4E Is Associated with Survival through AKT Pathway in Non–Small Cell Lung Cancer (2009)

This study shows that p-eIF4E expression in addition to p-AKT predicts poor prognosis in NSCLC. Moreover, the correlation between expression of p-eIF4E with p-AKT, as well as p-TSC2 and p-S6, indicates that eIF4E activation through the AKT pathway plays an important role in the progression of NSCLC.
A Synthetic TLR4 Antagonist Has Anti-Inflammatory Effects in Two Murine Models of Inflammatory Bowel Disease (2005)

Current evidence indicates that the chronic inflammation observed in the intestines of patients with inflammatory bowel disease is due to an aberrant immune response to enteric flora. We have developed a lipid A-mimetic, CRX-526, which has antagonistic activity for TLR4 and can block the interaction of LPS with the immune system. CRX-526 can prevent the expression of proinflammatory genes stimulated by LPS in vitro. This antagonist activity of CRX-526 is directly related to its structure, particularly secondary fatty acyl chain length. In vivo, CRX-526 treatment blocks the ability of LPS to induce TNF-alpha release. Importantly, treatment with CRX-526 inhibits the development of moderate-to-severe disease in two mouse models of colonic inflammation: the dextran sodium sulfate model and multidrug resistance gene 1a-deficient mice. By blocking the interaction between enteric bacteria and the innate immune system, CRX-526 may be an effective therapeutic molecule for inflammatory bowel disease.
A New Synthetic Route to Functionalized 2-Azabicyclo[2.2.2]octane (1994)

Functionalized 2-azabicyclo[2.2.2]octane ring system was prepared via intramolecular SN2 ring opening of epoxide by an amide anion.In the course of our stud~es on the enantioselective synthesis of natural products utilizing 5-trimethylsilyl-2cyclohexenone (I), we had a chance to examine diastereoselective 1,4-additions of various nucleophiles to 1, and found that the 14-addition of nitromethane to 1 proceeds in a highly diastereoselective manner.lThe result prompted us to examine new enantioselective routes to aza-containing bicyclic compounds from 1.Azabicyclo[2.2.2]octane, the isoquinuclidine system, was chosen as a target molecule since the system is common to --type indole alkalolds2 of which (+)-catharantine is of special interest because of its role as a synthetic precursor of clmical anticancer agent Vinblastine and related a ~k a l o i d s .~ The retro-synthetic route is shown in Figure 1.
Effect of keyhole limpet hemocyanin (KLH) and bacillus Calmette-Guérin (BCG) instillation on carcinoma in situ of the urinary bladder. (1996)

Patients with histologically verified carcinoma in situ (CIS) of the urinary bladder (13 primary and 8 secondary CIS) were treated with intravesical instillations of Keyhole Limpet Hemocyanin (KLH) (20 mg KLH weekly for 6 weeks, then monthly for 1 year or bimonthly for 2 subsequent years. Patients, non-responding to 2 courses of KLH were then treated with regular Bacillus Calmette-Guerin instillations (120 mg BCG-Connaught strain). The follow-up period ranged from 10 to 54 months (mean 23.5 months). 7 patients (33%) were free of tumor after the first therapeutical KLH course and 4 patients (19%) presented a complete-remission after the second KLH course (total primary response: 52%). 5 patients (24%) remained free of tumor during the established follow-up period (mean 31.7 months) and no evidence of further tumor progression occurred in patients after two courses of KLH treatment. However, 2 patients (9.5%) had to be cystectomized after KLH instillations because of progressive disease or tumor recurrence. 8 patients (38%) had to be radically cystectomized because of CIS persistence or progression after KLH and subsequent BCG treatment. Altogether 9 patients (42.8%) presented long-term remissions, with a mean duration of 31.3 months. Instillations of KLH did not induce major side effects; however, instillations of BCG caused severe dysuria in 60% and fever in 40% of patients.
An ultra-light and compact design and implementation of head-mounted projective displays (2002)

Head-mounted projective displays (HMPD) have been recently proposed as an alternative to conventional eyepiece-type head-mounted displays. HMPDs consist of a pair of miniature projection lenses and displays mounted on the helmet and retro-reflective sheeting materials placed strategically in the environment. Its novel concept and properties suggest solutions to part of the problems of state-of-the-art visualization devices and make it extremely suitable for multiple-user collaborative applications and wearable systems. A brief review of conventional visualization techniques is followed by an extensive discussion of HMPD technology, which includes a summary of its features and a comparison with conventional head-mounted displays (HMDs), projection-based displays, and HMPDs. An ultra-light and compact design (i.e. 8g) of a projection lens system using diffractive optical element (DOE) as well as plastic components for a HMPD is presented. Through the usage of fast prototyping technology, a compact stereoscopic head-mounted prototype with weight less than 700 grams was implemented, and optomechanical adjustments and ergonomic considerations are discussed. Finally, the motivated application in multiuser tele-collaboration is described.
Lattice BGK Models for Navier-Stokes Equation (1992)

We propose the lattice BGK models, as an alternative to lattice gases or the lattice Boltzmann equation, to obtain an efficient numerical scheme for the simulation of fluid dynamics. With a properly chosen equilibrium distribution, the Navier-Stokes equation is obtained from the kinetic BGK equation at the second-order of approximation. Compared to lattice gases, the present model is noise-free, has Galileian invariance and a velocity-independent pressure. It involves a relaxation parameter that influences the stability of the new scheme. Numerical simulations are shown to confirm the speed of sound and the shear viscosity.
Adenosquamous carcinoma of the pancreas: Molecular characterization of 23 patients along with a literature review (2015)

Adenosquamous carcinoma of the pancreas (ASCP) is a rare entity. Like adenocarcinoma of the pancreas, overall survival is poor. Characteristics of ASCP include central tumor necrosis, along with osteoclasts and hypercalcemia. Various theories exist as to why this histological subtype exists, as normal pancreas tissue has no benign squamous epithelium. Due to the rarity of this disease, limited molecular analysis has been performed, and those reports indicate unique molecular features of ASCP. In this paper, we characterize 23 patients diagnosed with ASCP through molecular profiling using immunohistochemistry staining, fluorescent in situ hybridization, chromogenic in situ hybridization, and gene sequencing, Additionally, we provide a comprehensive literature review of what is known to date of ASCP. Molecular characterization revealed overexpression in MRP1 (80%), MGMT (79%), TOP2A (75), RRM1 (42%), TOPO1 (42%), PTEN (45%), CMET (40%), and C-KIT (10%) among others. One hundred percent of samples tested were positive for KRAS mutations. This analysis shows heretofore unsuspected leads to be considered
Efficient Polymer Light‐Emitting Diode Using Air‐Stable Metal Oxides as Electrodes (2008)

Poly(phenylenevinylene)-based organic light-emitting diodes (OLEDs) are fabricated using air-stable metal oxides as electrodes, producing very efficient and bright electroluminescent devices. Efficiencies of 8 cd A−1 and luminances above 20000 cd m−2 are obtained, comparable to the values reported for classic OLED structures using reactive metals as cathodes.
Quantitative imaging of complex samples by spiral phase contrast microscopy (2006)

Recently a spatial spiral phase filter in a Fourier plane of a microscopic imaging setup has been demonstrated to produce edge enhancement and relief-like shadow formation of amplitude and phase samples. Here we demonstrate that a sequence of at least 3 spatially filtered images, which are recorded with different rotational orientations of the spiral phase plate, can be used to obtain a quantitative reconstruction of both, amplitude and phase information of a complex microscopic sample, i.e. an object consisting of mixed absorptive and refractive components. The method is demonstrated using a calibrated phase sample, and an epithelial cheek cell.