gebhart/patrepeval huggingface dataset:
Energy Barriers to Chemical Reactions. Why, How, and How Much? Non-Arrhenius Behavior in Hydrogen Abstractions by Radicals (1998)

Using free-radical hydrogen abstractions of the type X−H + •Y → X• + H−Y as a model for reactions involving simultaneous bond breaking and bond making, we find that the enthalpy of activation may increase or decrease with temperature. This depends on changes in bond dissociation energies and their effect on (a) the enthalpy of reaction and (b) the triplet repulsion between the terminal groups X and Y. The variety of observed curvatures in plots of ln(k) vs 1/T for eight typical reactions can be described primarily by these two factors, over temperature ranges greater than 1000 K. The reactions treated are OCH2 + •H, CH4 + •H, H2 + •CH3, C2H6 + •CH3, C2H6 + •H, H2 + •C2H5, CH4 + •Br, and H2 + •Br.
254. Vaccination of Recurrent Glioma Patients with Tumour Lysate-Pulsed Dendritic Cells Elicits Immune Responses: Results of a Clinical Phase I/II Trial (2004)

In this Phase I/II trial, the patient's peripheral blood dendritic cells were pulsed with an autologous tumour lysate of the glioma. Fourteen patients with glioblastoma and 4 patients with anaplastic glioma, ranging in age from 20 to 73 years, participated in this study. The mean numbers of vaccinations of tumour lysate-pulsed dendritic cells were 4.8 times intradermally close to a cervical lymph node, and 4.2 times intratumourally via an Ommaya reservoir. The percentage of CD56-positive cells in the peripheral blood lymphocytes increased after immunization. There were 1 partial response, 2 minor responses and 7 no change cases evaluated by radiological findings. Dendritic cell vaccination elicited T-cell-mediated antitumour activity, as evaluated by ELISPOT assay after vaccination in 2 of 5 tested patients. Three patients showed DTH reactivity to the autologous tumour lysate, two of these had a minor clinical response, and two had an increased ELISPOT result. Intratumoural CD4 and CD8 T-cell infiltration was detected in two patients who underwent re-operation after vaccination. This study demonstrated the safety and antitumour effects of autologous tumour lysate-pulsed dendritic cell therapy for patients with malignant glioma.
Warburg effect in chemosensitivity: Targeting lactate dehydrogenase-A re-sensitizes Taxol-resistant cancer cells to Taxol (2010)

LDH-A plays an important role in Taxol resistance and inhibition of LDH-A re-sensitizes Taxol-resistant cells to Taxol. This supports that Warburg effect is a property of Taxol resistant cancer cells and may play an important role in the development of Taxol resistance. To our knowledge, this is the first report showing that the increased expression of LDH-A plays an important role in Taxol resistance of human breast cancer cells. This study provides valuable information for the future development and use of targeted therapies, such as oxamate, for the treatment of patients with Taxol-resistant breast cancer.
An Endoscopic System for DSPI (1993)

A digital speckle pattern interferometer with an endoscopic imaging system is proposed for nondestructive measurements in hidden or difficult to reach zones. Some particular applications are presented
Characterization and biological effects of the Pasteurella multocida toxin (1987)

A proteinaceous substance produced by a toxigenic type D strain of Pasteurella multocida was purified by anion exchange chromatography and preparative polyacrylamide gel electrophoresis (PAGE). The protein, the P. multocida toxin (PMT), had a molecular weight of 143 kDa (SDS-PAGE) and had the same biological properties as crude extracts from toxigenic strains of P. multocida i.e., dermonecrotic effect in guinea pigs, cytopathic effect in embryonic bovine lung cells, and a lethal effect to mice.
A Hands-Free Unit with Noise Reduction by Using Adaptive Beamformer (2008)

This paper presents an implementation of an adaptive beamformer in a hands-free unit. The proposed adaptive beamformer suppresses stationary noise and interference sound. The adaptive beamformer and acoustic echo canceller were implemented in a compact hands-free unit with a low-cost DSP. Experimental results demonstrate the noise reduction performance of the hands-free unit.
Development of Novel Pharmacotherapies for the Treatment of Alcohol Dependence: Focus on Antiepileptics (2004)

This article represents the proceedings of a symposium, "Development of Novel Pharmacotherapies for the Treatment of Alcohol Dependence: Focus on Antiepileptics," presented at the 2003 annual meeting of the Research Society on Alcoholism in Fort Lauderdale, FL. The organizers and cochairs were Bankole A. Johnson and Robert M. Swift. The presentations were (1) Development of topiramate in the treatment of alcoholism, by Bankole A. Johnson; (2) Craving as a predictor of treatment outcome in pharmacotherapy trials for the treatment of alcoholism, by Nassima Ait-Daoud; (3) Use of biomarkers as a predictor of treatment response in treating alcoholism, by Martin A. Javors; (4) Psychotherapy to enhance compliance with pharmacotherapy in treatment trials for alcohol dependence, by Carlo C. DiClemente; (5) Synopsis of promising medications to treat alcoholism, by Robert M. Swift; and (6) New knowledge on the development of antiepileptic medications for the treatment of alcoholism, by Robert J. Malcolm, Jr.
The Derivation of Highly Germline-Competent Embryonic Stem Cells Containing NOD-Derived Genome (2003)

It would be extremely advantageous to the analysis of disease mechanisms in the spontaneous mouse model of type 1 diabetes, the nonobese diabetic (NOD) strain, if genes in this strain could be modified in vivo using embryonic stem (ES) cells and homologous recombination. However, a NOD ES cell line with adequate germline transmission has not yet been reported. We report the development of highly germline-competent ES cell lines from the F1 hybrid of NOD and 129 for use in NOD gene targeting. Consequently, we developed ES cell lines derived from (NOD x 129)F1 x 129 backcross 1 mice, which were intercrossed to select for homozygosity of particular regions of NOD genome known to contain disease loci.
[Immunotargeting of tumors: state of the art and prospects in 2000]. (2000)

Following 15 years of experimental studies, tumor immunotargeting using monoclonal antibodies directed against tumor associated antigens shows now important monoclonal antibodies directed against tumor associated antigens shows now important clinical developments. This is mainly due to encouraging therapeutic results which have obtained using humanized antibodies such as the anti-CD20 rituximab in follicular B lymphomas and the anti-DrbB2 herceptin in breast carcinomas. Thanks to genetic engineering it is possible to graft variable or hypervariable regions from murine antibodies to human IgG, and even to obtain fully human antibodies by using either transgenic mice containing a large part of the human repertoire of human IgG, or selection of human antibody fragments expressed by phages. Radiolabeling of antibodies played a major role to demonstrate the tumor immunotargeting specificity and remains attractive for the diagnosis by immunoscintigraphy as well as for the treatment by radioimmunotherapy of some cancers. In this review, the current results and the prospects of diagnostic and therapeutic uses of anti-tumor antibodies and their fragments will be described. Concerning diagnosis, 123-iodine or 99m-technetium labeled Fab fragments allowed very demonstrative tumor images but this technique has a limited effect upon the therapeutic attitude. Immuno-PET (positron emission tomography) could enhance the sensitivity of this imaging method. Radio-immunoguided surgery and immunophotodetection are attractive techniques still under evaluation. Concerning therapy, 131-iodine labeled anti-CD20 antibodies gave spectacular results in non-Hodgkin's B lymphomas. In solid tumors which as less radiosensitive, radioimmunotherapy could concern small tumors and need the use of two-steps targeting and/or alpha emitters radioisotopes. Some other strategies will be described such as bispecific antibodies directed against tumors and immune effector cells, some antibody fragments expressed on T cells called T-bodies or some biological studies using intrabodies. Published data and works in progress demonstrate that immunotargeting of tumors will have a growing place in the treatments of cancer patients.
Lateral Proppant Distribution: The Good, the Bad, and the Ugly of Putting Frac Jobs Away (1999)

Abstract This paper shows proppant induced pressure increase (i.e., "tip screenout", "pack", "body pack", etc.) can relate to restricted vertical and lateral proppant distribution in hydraulic fractures. We discuss a way of interpreting the character of the pressure response during the proppant stages of a fracture stimulation. The pressure response during the proppant stages will determine the quality of the production response and the level of success that is achieved. The technology presented has been found to apply to all rock types and most formations. This area of study is based upon common sense observations and extensive engineering. It fits the reservoir engineering of the producing character and advanced fracture treatment pressure interpretation on over 1,000 wells. When early proppant bridging occurs in the fracture, the lateral and vertical proppant distribution adjacent to the pay interval can be negatively affected. This results in less effective stimulation because the pay interval, both vertically and laterally, is not effectively propped. The fracture stimulation may have been "put away"; but the negative aspects of how the stimulation was designed and implemented may have a significant affect on the resultant production response. To lay the basis for additional thought and investigation, there is discussion about deficiencies in overly simplified pretreatment mini-fracture analysis procedures. These analysis methods are not focused on the proppant induced friction character, and therefore can not optimize fracture length. An evolved approach is presented, that addresses leakoff, fracture geometry, and proppant induced friction, to optimize the proppant distribution, and overall stimulation of the pay interval.
Synthesis of a Structurally Defined Antigen-Immunostimulant Combination for Use in Cancer Vaccines (1999)

A carbohydrate antigen gangliosideGM2 linked by a spacer to the B-cell stimulatory glycolipid BAY R 1005 led to the depicted neoglycolipid 1. This new concept provides useful immunogens for inducing antibodies to carbohydrate antigens.
Transcription factor veracity: is GBF3 responsible for ABA-regulated expression of Arabidopsis Adh? (1996)

Assignment of particular transcription factors to specific roles in promoter elements can be problematic, especially in systems such as the G-box, where multiple factors of overlapping specificity exist. In the Arabidopsis alcohol dehydrogenase (Adh) promoter, the G-box regulates expression in response to cold and dehydration, presumably through the action of abscisic acid (ABA), and is bound by a nuclear protein complex in vivo during expression in cell cultures. In this report, we test the conventional wisdom of biochemical approaches used to identify DNA binding proteins and assess their specific interactions by using the G-box and a nearby half G-box element of the Arabidopsis Adh promoter as a model system. Typical in vitro assays demonstrated specific interaction of G-box factor 3 (GBF3) with both the G-box and the half G-box element. Dimethyl sulfate footprint analysis confirmed that the in vitro binding signature of GBF3 essentially matches the footprint signature detected in vivo at the G-box. Because RNA gel blot data indicated that GBF3 is itself induced by ABA, we might have concluded that GBF3 is indeed the GBF responsible in cell cultures for binding to the Adh G-box and is therefore responsible for ABA-regulated expression of Adh. Potential limitations of this conclusion are exposed by the fact that other GBFs bind the G-box with the same signature as GBF3, and subtle differences between in vivo and in vitro footprint signatures indicate that factors other than or in addition to GBF3 interact with the half G-box element.
Privatizing the University--the New Tragedy of the Commons (2000)

Teaching and research at universities is increasingly funded from private sources. In this essay, Brown highlights the problems associated with this approach and calls for a return to largely public funding. He argues that the public, rather than corporations or individual scientists or even secretive governments, should own the results.
Corrosion Monitoring of Reinforced Concrete Structures – A Review (2007)

Reinforced concrete structures have the potential to be very durable and capable of withstanding a variety of adverse environmental conditions. However, failures in the structures do still occur as a result of premature reinforcement corrosion. The maintenance and repair of bridges and buildings for their safety requires effective inspection and monitoring techniques for assessing the reinforcement corrosion. Engineers need better techniques for assessing the condition of the structure when the maintenance or repair is required. These methods need to be able to identify any possible durability problems within structures before they become serious. This paper reviews all the electrochemical and nondestructive techniques from the point of view of corrosion assessment and their applications to bridges, buildings and other civil engineering structures.
Synthesis and Manipulation of Orthogonally Protected Dendrimers: Building Blocks for Library Synthesis (2004)

Laborfrüchte: Dendrimere mit bis zu sechs unterschiedlichen funktionellen Gruppen werden in vielstufigen Eintopfreaktionen mithilfe selektiver Schutzgruppenoperationen erhalten (siehe Beispiel). Die Autoren bezeichnen diese multifunktionellen Dendrimere als molekulare Obstsalatbäume; sie könnten nützliche Bausteine für Wirkstoff-Freisetzungssysteme und neuartige Materialien sein.
Foxa2 Controls Pdx1 Gene Expression in Pancreatic β-Cells In Vivo (2002)

Differentiation of early foregut endoderm into pancreatic endocrine and exocrine cells depends on a cascade of gene activation events controlled by various transcription factors. Prior in vitro analysis has suggested that the forkhead/winged helix transcription factor Foxa2 (formerly HNF-3beta) is a major upstream regulator of Pdx1, a homeobox gene essential for pancreatic development. Pdx1 is also essential for the maintenance of glucose homeostasis, as its human orthologue, IPF-1, is mutated in a subset of patients with early-onset type 2 diabetes (MODY4). To analyze the Foxa2/Pdx1 regulatory cascade during pancreatic beta-cell differentiation, we used conditional gene ablation of Foxa2 in mice. We demonstrated that the deletion of Foxa2 in beta-cell-specific knockout mice results in downregulation of Pdx1 mRNA and subsequent reduction of PDX-1 protein levels in islets. These data represent the first in vivo demonstration that Foxa2 acts upstream of Pdx1 in the differentiated beta-cell.
Molecular Recognition of Protein Surfaces:  High Affinity Ligands for the CBP KIX Domain (2003)

Potent and specific inhibitors of protein.protein interactions have potential both as therapeutic compounds and biological tools, yet discovery of such molecules remains a challenge. Our laboratory has recently described a strategy, called protein grafting, for the identification of miniature proteins that bind protein surfaces with high affinity and specificity and inhibit the formation of protein.protein complexes. In protein grafting, those residues that comprise a functional alpha-helical binding epitope are stabilized on the solvent-exposed alpha-helical face of the small yet stable protein avian pancreatic polypeptide (aPP). Here we use protein grafting in combination with molecular evolution by phage display to identify phosphorylated peptide ligands that recognize the shallow surface of CBP KIX with high nanomolar to low micromolar affinity. Furthermore, we show that grafting of the CBP KIX-binding epitope of CREB KID onto the aPP scaffold yields molecules capable of high affinity recognition of CBP KIX even in the absence of phosphorylation. Importantly, both classes of designed ligands exhibit high specificity for the target CBP KIX domain over carbonic anhydrase and calmodulin, two unrelated proteins that bind hydrophobic or alpha-helical molecules that might be encountered in vivo.
Immunological Response to A Strain of Staphylococcus Epidermidis in the Rabbit: Production of Protective Antibody (1978)

A rabbit was immunised with a heat-killed vaccine prepared from strain 1142 of Staphylococcus epidermidis. The HA titres of the antisera against a surface-polysaccharide antigen extracted from the homologous strain were highest in the 2nd-4th weeks after immunisation and subsequently declined. Only a minor amount of 2-ME-resistant antibody was formed, and this at a late state of the reaction. After a booster injection of the vaccine at the 10th week, there was a significantly greater HA-antibody response and a greater amount of 2-ME-resistant antibody was formed. The relative passive-protective activity of the sera in mice corresponded to their content of 2-ME-sensitive HA antibody. The protective activity of the sera was 2-ME sensitive and was not removed by absorption with anti-rabbit IgG goat serum. Further, 280 microgram of IgM-rich serum fraction obtained by sucrose-density-gradient ultracentrifugation passively protected against homologous challenge infection in mice, but even 910 microgram of IgG-rich fraction did not. These results indicated that the protective antibody was of the IgM class.
Depth-resolved two-dimensional Stokes vectors of backscattered light and Mueller matrices of biological tissue measured with optical coherence tomography (2000)

Mueller matrices provide a complete characterization of the optical polarization properties of biological tissue. A polarization-sensitive optical coherence tomography (OCT) system was built and used to investigate the optical polarization properties of biological tissues and other turbid media. The apparent degree of polarization (DOP) of the backscattered light was measured with both liquid and solid scattering samples. The DOP maintains the value of unity within the detectable depth for the solid sample, whereas the DOP decreases with the optical depth for the liquid sample. Two-dimensional depth-resolved images of both the Stokes vectors of the backscattered light and the full Mueller matrices of biological tissue were measured with this system. These polarization measurements revealed some tissue structures that are not perceptible with standard OCT.
Unforeseen decreases in dissolved oxygen levels affect tube formation kinetics in collagen gels (2011)

The availability of oxygen (O(2)) is a critical parameter affecting vascular tube formation. In this study, we hypothesize that dissolved oxygen (DO) levels in collagen gels change during the three-dimensional (3D) culture of human umbilical vein endothelial cells (HUVECs) in atmospheric conditions and that such changes affect the kinetics of tube formation through the production of reactive oxygen species (ROS). We demonstrate a decrease in O(2) tension during 3D cultures of HUVECs. Noninvasive measurements of DO levels during culture under atmospheric conditions revealed a profound decrease that reached as low as 2% O(2) at the end of 24 h. After media replacement, DO levels rose rapidly and equilibrated at ∼15% O(2), creating a reoxygenated environment. To accurately estimate DO gradients in 3D collagen gels, we developed a 3D mathematical model and determined the Michaelis-Menten parameters, V(max) and K(m), of HUVECs in collagen gels. We detected an increase in ROS levels throughout the culture period. Using diphenyliodonium to inhibit ROS production resulted in the complete inhibition of tube formation. Interference RNA studies further showed that hypoxia-inducible factors (HIFs)-1α and -2α are not involved in the formation of 3D tubes in collagen gels. We conclude that ROS affect the tubulogenesis process through HIFα-independent pathways, where the levels of ROS are influenced by the uncontrolled variations in DO levels. This study is the first demonstration of the critical and unexpected role of O(2) during 3D in vitro culture models of tubulogenesis in atmospheric conditions.
mRNA structure regulates protein expression through changes in functional half-life (2019)

Messenger RNAs (mRNAs) encode information in both their primary sequence and their higher order structure. The independent contributions of factors like codon usage and secondary structure to regulating protein expression are difficult to establish as they are often highly correlated in endogenous sequences. Here, we used 2 approaches, global inclusion of modified nucleotides and rational sequence design of exogenously delivered constructs, to understand the role of mRNA secondary structure independent from codon usage. Unexpectedly, highly expressed mRNAs contained a highly structured coding sequence (CDS). Modified nucleotides that stabilize mRNA secondary structure enabled high expression across a wide variety of primary sequences. Using a set of eGFP mRNAs with independently altered codon usage and CDS structure, we find that the structure of the CDS regulates protein expression through changes in functional mRNA half-life (i.e., mRNA being actively translated). This work highlights an underappreciated role of mRNA secondary structure in the regulation of mRNA stability.
ChemInform Abstract: CONSTITUENTS OF MICROBIAL IRON CHELATORS. ALTERNATE SYNTHESES OF Δ‐N‐HYDROXY‐L‐ORNITHINE DERIVATIVES AND APPLICATIONS TO THE SYNTHESIS OF RHODOTORULIC ACID (1984)

Abstract Aus dem Glutaminsäurederivat (I) erhält man über das gemischte Anhydrid bei der Reduktion den Alkohol (II), der mit den Hydroxylamin‐Derivaten (III) zu den Folgeprodukten (IV) führt.
Ensemble and Single-Particle Fluorescence Photomodulation in Diarylethene-Doped Conjugated Polymer Nanoparticles (2011)

Fluorescent systems that can undergo intensity photomodulation in aqueous environments are finding increasing applications, particularly in high-resolution imaging of biological samples. We seek to develop conjugated polymer nanoparticles (CPNs) with bright fluorescence that can be modulated with a light signal. Here, we present CPNs, doped with a photochromic diarylethene dye, that exhibit efficient fluorescence photomodulation that is thermally irreversible. In their UV-absorbing open form, the diarylethenes have no effect on the fluorescence properties of the bright CPNs. A brief period of UV irradiation converts the dyes to their visible-absorbing closed form, which is an efficient fluorescence quencher for the CPNs, likely via a fluorescence resonance energy transfer mechanism. Aqueous suspensions of dye-doped CPNs prepared from the homopolymer poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV) or a polyfluorene-phenylenevinylene copolymer (PFPV) exhibit thermally stable bright and dark levels. The dye-doped MEH-PPV CPNs also exhibit photomodulation in single-nanoparticle imaging experiments, which reveal that nearly all CPNs retain a small amount of residual emission in the dark state. Their PFPV counterparts undergo irreversible fluorescence photobleaching rather than photomodulation in single-nanoparticle studies. The photostability of the CPNs under the UV irradiation conditions required for photochromic conversion is investigated on the single-particle level, and PFPV CPNs are found to be particularly susceptible to photobleaching upon 254 nm irradiation. These results will guide the selection of polymers and photochromes for CPNs intended for single-particle photomodulation.
Shape and Movement of Mesenchyme Cells as Functions of the Physical Structure of the Medium (1952)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.