gebhart/patrepeval huggingface dataset:
Peroxisome induction potential and lipid-regulating activity in rats. Quantitative microscopy and chemical structure-activity relationships. (1991)

Structurally diverse lipid-regulating agents induce hepatomegaly, hepatic peroxisome proliferation, and hepatocarcinoma in rats by mechanisms not fully understood. Nevertheless the initial hepatic response is a prompt, florid proliferation of peroxisomes. In investigations reported here, changes in the rat hepatic peroxisome compartment were measured by quantitative microscopy to determine chemical structure requirements that relate to peroxisome proliferation and lipid regulation. Aryloxyalkanoic acids plus amide analogs, and thio, benzimidazole, phenylpiperazine, and oxazole derivatives induced peroxisome proliferation and generally decreased plasma triglyceride and total cholesterol levels. These compounds contain an acidic function or are readily metabolized to a chemical with an acidic function. Substitution of the acidic function with an adamantyloxy eliminated peroxisome proliferation and induced contrasting effects on lipid profile, increasing triglycerides and decreasing total cholesterol. A previously unreported, direct correlation emerged between peroxisome proliferation and plasma high-density lipoprotein-cholesterol levels. These effects could not be elicited separately, negating identification of functional groups that could be associated with either activity. Chemical structure and resulting peroxisome proliferation with changes in plasma lipoproteins are therefore closely interrelated in rats.
Therapeutic Potential of T Cell Chimeric Antigen Receptors (CARs) in Cancer Treatment: Counteracting Off-Tumor Toxicities for Safe CAR T Cell Therapy (2016)

A chimeric antigen receptor (CAR) is a recombinant fusion protein combining an antibody-derived targeting fragment with signaling domains capable of activating T cells. Recent early-phase clinical trials have demonstrated the remarkable ability of CAR-modified T cells to eliminate B cell malignancies. This review describes the choice of target antigens and CAR manipulations to maximize antitumor specificity. Benefits and current limitations of CAR-modified T cells are discussed, with a special focus on the distribution of tumor antigens on normal tissues and the risk of on-target, off-tumor toxicities in the clinical setting. We present current methodologies for pre-evaluating these risks and review the strategies for counteracting potential off-tumor effects. Successful implementation of these approaches will improve the safety and efficacy of CAR T cell therapy and extend the range of cancer patients who may be treated.
Fingerprint patterning of solid nanoparticles embedded in a cholesteric liquid crystal (2004)

International audience
A Family of Adaptive Filter Algorithms in Noise Cancellation for Speech Enhancement (2010)

In many application of noise cancellation, the changes in signal characteristics could be quite fast. This requires the utilization of adaptive algorithms, which converge rapidly. Least Mean Squares (LMS) and Normalized Least Mean Squares (NLMS) adaptive filters have been used in a wide range of signal processing application because of its simplicity in computation and implementation. The Recursive Least Squares (RLS) algorithm has established itself as the "ultimate" adaptive filtering algorithm in the sense that it is the adaptive filter exhibiting the best convergence behavior. Unfortunately, practical implementations of the algorithm are often associated with high computational complexity and/or poor numerical properties. Recently adaptive filtering was presented, have a nice tradeoff between complexity and the convergence speed. This paper describes a new approach for noise cancellation in speech enhancement using the two new adaptive filtering algorithms named fast affine projection algorithm and fast Euclidean direction search algorithms for attenuating noise in speech signals. The simulation results demonstrate the good performance of the two new algorithms in attenuating the noise.
Design guidelines and characteristics of a four-layer large flattened mode fiber (2007)

A refractive index profile design, which can enable us to obtain a flat-top fundamental mode field around the center, is presented. The theoretical method to analyze the four-layer large flattened mode (LFM) fibers is given. The properties of the fiber, including the fundamental and higher order modal fields, effective area, and bending loss, are discussed. The reasons forming the different modal fields are explained. By discussion, the larger effective area of the LFM fiber compared with conventional step-index fiber is proven and the feasibility to suppress the higher order modes via bending is given.
Identification of a novel integrin beta subunit expressed on cultured monocytes (macrophages). Evidence that one alpha subunit can associate with multiple beta subunits. (1990)

The vitronectin receptor (VnR) is one member of a subset of cell adhesion receptors within the integrin supergene family which shares the beta 3 subunit (IIIa). We show here that the VnR is absent from the surface of monocytes freshly isolated from blood but is expressed on these cells after a period of in vitro culture. Such cultured monocytes (macrophages) from a patient with type I Glanzmann's thrombasthenia, however, failed to express the VnR. Instead, immunoprecipitation with a monoclonal antibody directed to the VnR alpha chain (alpha v) revealed a novel integrin comprising alpha v associated noncovalently with a 100-kDa beta subunit (beta 3b), immunologically unrelated to the VnR beta subunit (beta 3a). This same novel integrin complex was also identified on 10-day-old macrophages from healthy donors, but on these cells, the beta 3b subunit was co-expressed with the classical VnR complex of alpha v beta 3a. The novel beta 3b subunit was not identified by monoclonal or polyclonal antibodies to IIIa (beta 3a) nor by a monoclonal antibody to the classical VnR complex. The beta 3b subunit could be distinguished from beta 3a by its relatively greater migration on sodium dodecyl sulfate-polyacrylamide gel electrophoresis after reduction, by its distinct isoelectric point upon two-dimensional gel electrophoresis, and by one-dimensional peptide mapping. Neither platelets nor B lymphoblasts from this patient with Glanzmann's thrombasthenia expressed any VnR on their surface, whereas control cells from a normal donor expressed the classical VnR but not the beta 3b subunit. The two beta chains, and hence also the combined receptor complexes, appeared to be differentially regulated. These findings provide the first example of an integrin alpha chain complexed with more than a single beta chain in the same cell. Furthermore, the differential regulation of expression of the different beta subunits that associate with the VnR alpha chain on cultured monocytes suggests a role for the novel receptor complex during monocyte/macrophage differentiation.
Minimum number of spermatozoa required for normal fertility after deep intrauterine insemination in non-sedated sows (2002)

A fibreoptic endoscope procedure for non-surgical deep intrauterine insemination in non-sedated sows has been reported. However, the endoscope is an expensive and fragile instrument, and is unsuitable for use under field conditions. The aim of this study was to determine the minimum number of spermatozoa required to maintain optimal fertility using a flexible catheter (1.8 m in length, 4 mm in diameter) for deep intrauterine insemination in 2-6 parity non-sedated sows. Crossbred sows were treated with eCG 24 h after weaning and with hCG 72 h later to induce oestrus. Deep intrauterine insemination was performed 36 h after hCG treatment in 117, 126, 60 and 69 sows with 15.0, 5.0, 2.5 or 1.0 x 10(7) spermatozoa in 10 ml, respectively. Weaned sows (n = 147) not treated with hormones and used for standard artificial insemination (AI) (two inseminations per oestrus with 3 x 10(9) spermatozoa in 100 ml) served as controls. The flexible catheter was passed successfully through the cervix into one uterine horn in 95.4% of the sows in an average of 3.7 +/- 0.09 min. Farrowing rates after deep intrauterine insemination with 15 or 5 x 10(7) spermatozoa did not differ from those of the control group (82.9, 76.2 and 83.0%, respectively), but a significant decrease (P < 0.001) was observed in sows inseminated with 2.5 or 1.0 x 10(7) spermatozoa (46.7 and 39.1%, respectively). In contrast, the number of spermatozoa inseminated did not affect prolificacy. Laparotomy revealed that the tip of the flexible catheter reached approximately the anterior third of the uterine horn. Although deep intrauterine insemination was performed in only one uterine horn, the percentages of embryos collected from the tip of both uterine horns 2 days after deep insemination were not significantly different. The results show that in comparison with standard AI, a 20-60-fold reduction in the number of spermatozoa inseminated and an 8-10-fold reduction in the dose volume can be achieved without decreasing fertility when semen is deposited non-surgically into the upper first third of one uterine horn.
Receptor Affinity and Extracellular Domain Modifications Affect Tumor Recognition by ROR1-Specific Chimeric Antigen Receptor T Cells (2013)

Our results show that customizing spacer design and increasing affinity of ROR1-CARs enhances T-cell effector function and recognition of ROR1(+) tumors. T cells modified with an optimized ROR1-CAR have significant antitumor efficacy in a preclinical model in vivo, suggesting they may be useful to treat ROR1(+) tumors in clinical applications.
Alterations to both the Primary and Predicted Secondary Structure of Stem-Loop IIIc of the Hepatitis C Virus 1b 5′ Untranslated Region (5′UTR) Lead to Mutants Severely Defective in Translation Which Cannot Be Complemented in trans by the Wild-Type 5′UTR Sequence (1999)

Cap-independent translation of the hepatitis C virus (HCV) genomic RNA is mediated by an internal ribosome entry site (IRES) within the 5' untranslated region (5'UTR) of the virus RNA. To investigate the effects of alterations to the primary sequence of the 5'UTR on IRES activity, a series of HCV genotype 1b (HCV-1b) variant IRES elements was generated and cloned into a bicistronic reporter construct. Changes from the prototypic HCV-1b 5'UTR sequence were identified at various locations throughout the 5'UTR. The translation efficiencies of these IRES elements were examined by an in vivo transient expression assay in transfected BHK-21 cells and were found to range from 0.4 to 95.8% of the activity of the prototype HCV-1b IRES. Further mutational analysis of the three single-point mutants most severely defective in activity, whose mutations were all located in or near stem-loop IIIc, demonstrated that both the primary sequence and the maintenance of base pairing within this stem structure were critical for HCV IRES function. Complementation studies indicated that defective mutants containing either point mutations or major deletions within the IRES elements could not be complemented in trans by a wild-type IRES.
Modeling and Optimization of Lateral High Voltage IC Devices to Minimize 3-D Effects (1987)

High Voltage blocking capability of the RESURF or Lateral Charge Control (LCC) devices are strongly junction curvature dependent. A new charge model has been developed to translate 3-D curvature effect into 2-d plane. Existing 2-D computer program in conjunction with this new model has been utilized to model and optimize the LCC devices for high voltage 9C's. Theoretical predictions of this model are within 10% of the measured results.
Confronting Neutrality: Maximizing Success in the Analysis of Transition-Metal Catalysts by MALDI Mass Spectrometry (2016)

The elucidation of molecular identity is a central challenge in homogeneous transition-metal catalysis. Most exacting, despite advances in electrospray-ionization mass spectrometry (ESI-MS), are neutral complexes, which encompass the vast majority of metal catalysts. Insight into molecular constitution, readily achieved in other areas of the chemical sciences, is commonly thwarted by fragmentation of inorganic and organometallic compounds, particularly for highly reactive species. MALDI-MS, where coupled with charge-transfer ionization, stands out from all other current MS methods in its unique capacity to report on the molecular identity of intact metal complexes irrespective of their initial charge state. Identified in the present work are methods that enable routine, unambiguous identification of such complexes across a wide range of standard MALDI mass spectrometers. The origin of fragmentation during MALDI-MS analysis is explored on 13 different instruments at 9 facilities and across a range of mass analyzers, from TOF, TOF-TOF, and Q-TOF to Orbitrap. Selected as test analytes were the second-generation Hoveyda and Grubbs metathesis catalysts and the Grubbs resting-state methylidene complex, which span a very broad range in terms of ligand lability, and hence susceptibility to fragmentation. Three critical parameters emerge: (1) using the minimum applied laser energy necessary for sample volatilization; (2) minimizing the absorption cross-section of the analyte at the laser wavelength: (a) by appropriate laser choice, where options exist, (b) by using a matrix that absorbs as strongly as possible at the laser wavelength, in significant excess relative to the analyte (e.g., 500-fold), and (c) by prompt analysis, to limit matrix sublimation in the ion source; (3) using a charge-transfer matrix devoid of reactive protic or donor sites. A final, forward-looking section highlights relevant advances in state-of-the-art instrumentation, and instrumental features that would contribute to the optimization of next-generation MALDI mass spectrometers for this emerging application. These include fast-firing, contoured-profile, and, potentially, wavelength-tunable lasers, high-resolution mass analyzers, automatic plate rastering with software to support retroactive compilation of spectra from optimal sampling locations, and soft-vacuum or atmospheric-pressure sources, in conjunction with a standardized anaerobic interface.
Synthesis of Quinolines and 2H-Dihydropyrroles by Nucleophilic Substitution at the Nitrogen Atom of Oxime Derivatives (2003)

Isomerization of oxime derivatives was researched in detail to find out the methods for the syn-anti isomerization of O-substituted oximes. Based on these findings were developed simple methods for the preparation of aza-heterocycles from both stereo­isomers of oximes. Quinolines were synthesized from β-aryl ketone oximes by treatment with trifluoroacetic anhydride and 4-chloranil. γ,δ-Unsaturated O-methoxyacetyloximes were transformed to 2H-dihydropyrroles by reaction with methoxy-acetic acid.
Effects of the particle deformability on the critical separation diameter in the deterministic lateral displacement device (2014)

Abstract Deterministic lateral displacement (DLD) technology is a newly developed method which can separate microscale and nanoscale particles continuously and efficiently. In this paper, a direct numerical simulation method (i.e. a fictitious domain method) is used to simulate the motion of an elastic particle (modelled as homogeneously elastic body) in the DLD device. The effects of the particle deformability on the critical separation diameter are investigated. Our results indicate that there exists a critical deformability, below which the critical diameter decreases with increasing deformability, whereas beyond which the critical diameter increases with increasing deformability. The reasons are discussed via the consideration of the effects of the particle deformation and the lubrication force on the lateral position of the particle centre point. In addition, our results show that the increase in the gap distance between adjacent posts in both directions or in the longitudinal direction alone leads to the increase in the critical particle size with respect to the gap size, which can be explained by the lateral position of the separation streamline of the undisturbed flow.
Collective cell migration in morphogenesis and cancer (2004)

The movement of cells that maintain cell-cell junctions yet protrude along or within tissues is an important mechanism for cell positioning in morphogenesis, tissue repair and cancer. Collective cell migration shares similarities but also important differences to individually migrating cells. Coherent groups of cells are arranged and held together by cell-cell adhesion molecules, including cadherins, integrins, ALCAM and NCAM. Integrins of the beta 1 and beta 3 families further provide polarized interactions with the extracellular tissue environment, while matrix-degrading proteases become focalized to substrate contacts to widen tissue space for the advancing cell mass. By generating one functional unit, in contrast to individual cell migration, collective migration provides the active and passive translocation of mobile and non-mobile cells, respectively. This review highlights cellular and molecular principles of collective migration in the context of morphogenic tissue patterning and tumor cell invasion.
Oxcarbazepine: a new drug in the management of intractable trigeminal neuralgia. (1989)

The efficacy and tolerability of oxcarbazepine, a keto derivative of carbamazepine, has been assessed in six patients (two males, four females; mean age 61 years, range 42-77), with trigeminal neuralgia refractory to carbamazepine therapy, over a period of 6 months. An excellent therapeutic response to oxcarbazepine was seen in all patients with pain control correlating well with serum drug concentrations of oxcarbazepine and its primary active metabolite 10-OH-carbazepine. Onset of the effect was observed within 24 hours in all cases. An overall serum therapeutic concentration range, in the six patients, of 50-110 mumol/l of 10-OH-carbazepine corresponding to a daily effective dose range of 1200-2400 mg (14.6-35.6 mg/kg body weight) oxcarbazepine, was observed. There was a significant correlation between oxcarbazepine dose and serum oxcarbazepine (r = 0.695, p less than 0.05) and 10-OH-carbazepine (r = 0.957, p less than 0.001) concentrations. Oxcarbazepine was well tolerated and no significant side effects were identified, though a mild hyponatraemia was observed during high doses (greater than 28 and greater than 35 mg/kg/day) in two patients. It is concluded that oxcarbazepine has potent antineuralgic properties in the absence of significant side effects and therefore may be useful in the management of intractable trigeminal neuralgia.
Perspectives on the Physical Chemistry of Semiconductor Nanocrystals (1996)

Semiconductor nanocrystals exhibit a wide range of size-dependent properties. Variations in fundamental characteristics ranging from phase transitions to electrical conductivity can be induced by controlling the size of the crystals. The present status and new opportunities for research in this area of materials physical chemistry are reviewed.
fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood (1994)

We have developed a new tool, called fastDNAml, for constructing phylogenetic trees from DNA sequences. The program can be run on a wide variety of computers ranging from Unix workstations to massively parallel systems, and is available from the Ribosomal Database Project (RDP) by anonymous FTP. Our program uses a maximum likelihood approach and is based on version 3.3 of Felsenstein's dnaml program. Several enhancements, including algorithmic changes, significantly improve performance and reduce memory usage, making it feasible to construct even very large trees. Trees containing 40-100 taxa have been easily generated, and phylogenetic estimates are possible even when hundreds of sequences exist. We are currently using the tool to construct a phylogenetic tree based on 473 small subunit rRNA sequences from prokaryotes.
Antagonistic but Complementary Actions of Phytochromes A and B Allow Optimum Seedling De-Etiolation (1997)

Using dichromatic radiation, we show that the actions of phytochromes A and B (phyA and phyB) in Arabidopsis thaliana are antagonistic in mediating red and far-red radiation effects on seedling de-etiolation and yet act in a complementary manner to regulate de-etiolation, irrespective of spectral composition. At low phytochrome photoequilibria inhibition of hypocotyl extension was strong, because of the action of a far-red high-irradiance response mediated by phyA. At high phytochrome photoequilibria inhibition of hypocotyl extension was also strong, because of the action of phyB. At intermediate photoequilibria hypocotyl inhibition was less strong. In their natural environment, this dual action will strongly retard hypocotyl growth and promote cotyledon opening and expansion both in open daylight and under dense vegetation. Overlapping action by phyA and phyB will substantially promote de-etiolation in sparse vegetation. The antagonistic and complementary actions of phyA and phyB, therefore, allow the optimum regulation of seedling growth after emergence from the soil.
Helper-independent transformation by unintegrated Harvey sarcoma virus DNA (1978)

We have studied the unintegrated infectious DNA of Harvey sarcoma virus (Ha-SV) and Moloney leukemia virus (Mo-MuLV). The source of infectious viral DNA was the Hirt supernatant fraction from cells acutely infected with Ha-SV and Mo-MuLV. To obtain a direct quantitative assay for infectious viral DNA, recipient mouse cells were first exposed to calcium phosphate-precipitated viral DNA and then treated with dimethyl sulfoxide. Infectivity was monitored by focus formation for Ha-SV and XC plaque formation for Mo-MuLV. The viral DNA titration pattern followed single-hit kinetics for both foci and plaques, indicating that a single molecule carried information for each function. Focus-forming and plaque-forming activity were present in different molecules, since these two biological activities could be separated from each other by agarose gel electrophoresis. The focus-forming molecule was linear DNA with a molecular weight of about 4 x 10(6) daltons. The focus-forming activity of the viral DNA was sensitive to EcoRI and resistant to XhoI restriction endonucleases, whereas the plaque-forming activity was resistant to EcoRI and sensitive to XhoI. The generation of helper-independent foci indicates that Ha-SV DNA can transform mouse cells in the absence of helper virus or its proteins.