gebhart/patrepeval huggingface dataset:
Ganglioside vaccines with emphasis on GM2. (1998)

Gangliosides are neuraminic acid-containing glycosphingolipids that are anchored into the cell membrane lipid bilayer by lipophilic ceramide chains. They are overexpressed on tissues of neuroectodermal origin, and particularly in tumors such as melanomas, sarcomas, neuroblastomas, astrocytomas, and small cell lung cancers. Both active and passive immunotherapy trials have identified gangliosides as uniquely effective targets for antibody mediated melanoma immunotherapy. Induction of antibodies against GM2 by vaccination has correlated with an improved prognosis in American Joint Committee on Cancer (AJCC) stage III melanoma patients and vaccines containing GM2 chemically conjugated to keyhole limpet hemocyanin (KLH; GM2-KLH) plus the immunologic adjuvant QS-21 have proven to be consistently immunogenic. Phase III trials with this vaccine are ongoing in patients with melanoma in the United States, Canada, Europe, Australia, and New Zealand. GD2, fucosylated GMI, and GD3-KLH conjugates plus QS-21 are also consistently immunogenic, inducing IgM and IgG antibodies in the majority of patients. Polyvalent ganglioside-KLH conjugate plus QS-21 vaccines should be available in early 1999 for testing in phase II and III clinical trials.
Production and application of methylotrophic yeast <i>Pichia pastoris</i> (1988)

Pichia pastoris is a methylotrophic yeast that makes use bf the enzyme alcohol oxidase to catalyze the first step of the dissimilatory pathway that enables it to grow on methanol. Because of its stability and low substrate specificity, alcohol oxidase is of considerable interest for a range of biotechnological processes. Various feeding regimes were evaluated in an effort to increase the biomass concentration and productivity that could be achieved from fermentations using this organism. Through continuous or semicontinuous feeding, biomass concentrations were increased 10-fold over those achieved in batch fermentations. In subsequent trials, nongrowing whole cells were applied successfully to convert ethanol to acetaldehyde. Quantitative conversions of 20-g/L solutions of ethanol have been achieved in 2 h, and acetaldehyde concentrations of up to 35 g/L have been achieved using extended reaction times of 5 h. The conversion reaction was limited by end product inhibition and by acetaldehyde holdup within the yeast cells.
Effects of tumor necrosis factor alpha (TNF-alpha) on collagen arthritis. (1992)

Louvain rats were administered tumor necrosis factor alpha (TNF-alpha) via a continuous osmotic infusion pump. These rats were then immunized with native type II collagen (CII) to determine the effects of exogenous TNF-alpha on collagen-induced arthritis (CIA), an animal model of rheumatoid arthritis (RA). In this highly susceptible strain, 100% of experimental and control rats developed arthritis although TNF-alpha-treated rats had more severe disease as judged by both clinical and blinded radiographic parameters. Humoral responses to collagen were high in both groups, but cellular responses to CII were augmented by TNF-alpha. Serum IL-6 levels were significantly increased in all arthritic rats. This study suggests that TNF-alpha is a proinflammatory cytokine in CIA and that future studies targeting TNF-alpha might be therapeutic.
Natural killer (NK) cells as a responder to interleukin 2 (IL 2). II. IL 2-induced interferon <i>gamma</i> production. (1983)

In the accompanying paper, we showed that natural killer (NK) cells were a major population in the naive spleens of normal mice that responded directly to a T cell growth factor, interleukin 2 (IL 2), and clonally replicated without other stimulating agents. The cloned cells growing in IL 2 showed a potent NK activity against several NK targets without addition of an NK-activating agent, interferon (IFN). In the present study, therefore, we examined whether these cloned NK cells on their own produced IFN. It was found that all NK clones growing in IL 2 produced IFN in the culture fluids. The titers of IFN produced in the IL 2-containing media correlated well with the number of growing cells. With the culture in the absence of IL 2, neither cell growth nor IFN production could be detected. Addition of Con A into the culture in the IL 2-free media showed no IFN production. The antiserum neutralizing IFN alpha and IFN beta failed to significantly neutralize IFN produced by NK clones. Treatment with either a pH of 2.0 or antiserum neutralizing mouse IFN gamma resulted in a marked reduction of IL 2-induced NK IFN, indicating that a major part of IFN produced was IFN gamma. These results indicate that IL 2 stimulates NK clones to proliferate, accompanied by IFN gamma production. The results also show that an NK clone, when stimulated with Sendai virus, produced a type 1 IFN (IFN alpha and/or IFN beta), suggesting that murine NK cells can produce both type 1 (alpha and/or beta) and type 2 (gamma) IFN, depending on inducers.
Mechanics of carbon nanotubes (2002)

Soon after the discovery of carbon nanotubes, it was realized that the theoretically predicted mechanical properties of these interesting structures–including high strength, high stiffness, low density and structural perfection–could make them ideal for a wealth of technological applications. The experimental verification, and in some cases refutation, of these predictions, along with a number of computer simulation methods applied to their modeling, has led over the past decade to an improved but by no means complete understanding of the mechanics of carbon nanotubes. We review the theoretical predictions and discuss the experimental techniques that are most often used for the challenging tasks of visualizing and manipulating these tiny structures. We also outline the computational approaches that have been taken, including ab initio quantum mechanical simulations, classical molecular dynamics, and continuum models. The development of multiscale and multiphysics models and simulation tools naturally arises as a result of the link between basic scientific research and engineering application; while this issue is still under intensive study, we present here some of the approaches to this topic. Our concentration throughout is on the exploration of mechanical properties such as Young’s modulus, bending stiffness, buckling criteria, and tensile and compressive strengths. Finally, we discuss several examples of exciting applications that take advantage of these properties, including nanoropes, filled nanotubes, nanoelectromechanical systems, nanosensors, and nanotube-reinforced polymers. This review article cites 349 references.
Enhancement of methionine production by methionine analogue ethionine resistant mutants of <i>Brevibacterium heali</i> (1994)

Abstract In order to improve the methionine yield of the isolate B. heali , attempts were made to isolate mutants resistant to the methionine analogue DL ‐ethionine after mutagenesis with N‐methyl‐N′‐nitro‐N‐nitrosoguanidine (NTG). The minimum inhibitory concentration (MIC) of ethionine for B. heali was found to be 2 mM. After mutagenesis and screening, five mutants resistant to 50 mM of ethionine were isolated. The yield of the best ethionine resistant mutant, B. heali Br EthR , was 13 mg/l of methionine medium under optimum cultivation conditions.
The heterogeneous nucleation of microcellular foams assisted by the survival of microvoids in polymers containing low glass transition particles. Part I: Mathematical modeling and numerical simulation (1994)

Abstract The existing models based on classical nucleation theory are not able to explain satisfactorily the nucleation phenomenon of microcellular foams in thermoplastics. Here, we extend the analysis of Kweeder (24), who developed a new model that considers the presence of microvoids, resulting from the thermal processing history of the polymer, as potential nucleation sites. The nucleation model “concentrates” on the stresses and thus void formations in the rubber particles. Since these are pre‐existing microvoids, bubble nucleation depends on the survival of these voids to grow rather than the formation of a new phase as modeled by classical nucleation theory. The population of viable microvoids with a sufficiently large radius to survive and overcome surface and elastic forces has been modeled to yield the cell density. A log‐normal distribution, which relates to the rubber particle size, has been used to model the distribution of microvoids in the polymer composite material. The model depends on various process parameters such as saturation pressure, foaming temperature, concentration of nucleating agents, solubility of the blowing agent in the polymer, and the modulus. High impact polystyrene (HIPS) was added to polystyrene to obtain polymers with different concentrations of rubber gel particles, the nucleating agent, and used here for this study.
An improved genome release (version Mt4.0) for the model legume Medicago truncatula (2014)

Mt4.0 and its associated resources, such as genome browsers, BLAST-able datasets and gene information pages, can be found on the JCVI Medicago web site (http://www.jcvi.org/medicago). The assembly and annotation has been deposited in GenBank (BioProject: PRJNA10791). The heavily curated chromosomal sequences and associated gene models of Medicago will serve as a better reference for legume biology and comparative genomics.
Presence in immersive virtual environments (2002)

Immersive virtual environments (IVEs) provide a tightly coupled human-computer interface; input to the sensory organs of the human participant are directly generated through computer displays, in the visual, auditory, tactile and haptic modalities. Some of the results of a pilot experimental study of presence in IVEs are outlined. This is a contribution to a project involved in constructing a system for architectural walkthrough, where architects and their clients are able to navigate through and effect changes to a virtual building interior. Emphasis is placed on the interface provided by the virtual environment generator (VEG) to the human user, and initially on the problem of the establishment of the presence of the human inside the virtual environment (VE).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Estimation of Left Ventricular Function in Patients With a Left Ventricular Assist Device (1995)

Patients with profound left ventricular (LV) dysfunction supported by a left ventricular assist device (LVAD) may have recovery of LV function, but current methods for assessing this are difficult or not readily available. A new method to estimate LV performance was tested in 6 patients on LVAD (age, 47 +/- 12 years). Simultaneous measures of LV cross-sectional area (substitute for volume) using transesophageal echocardiographic automated border detection and femoral arterial pressure (substitute for LV ejection pressure) were recorded during brief periods on and off LVAD. During the LVAD off period, femoral arterial pressure and LV area signals were combined on-line to generate arterial pressure-LV area loops. The slope of the linear regression line connecting the end systolic points generated during LV filling after LVAD off was used as an estimate of end systolic elastance denoted by Ees. The average Ees was 3.8 +/- 3.1 mmHg/cm2. These values are significantly lower than those of 13 control patients (22.3 +/- 15.4 mmHg/cm2). This method of estimating Ees may be clinically useful in assessing LV recovery in patients on LVAD after extended support.
InfoTrac TFD: a microcomputer implementation of the Transcription Factor Database TFD with a graphical user interface (1994)

InfoTrac TFD provides a graphical user interface (GUI) for viewing and manipulating datasets in the Transcription Factor Database, TFD. The interface was developed in Filemaker Pro 2.0 by Claris Corporation, which provides cross platform compatibility between Apple Macintosh computers running System 7.0 and higher and IBM-compatibles running Microsoft Windows 3.0 and higher. TFD ASCII-tables were formatted to fit data into several custom data tables using Add/Strip, a shareware utility and Filemaker Pro's lookup feature. The lookup feature was also put to use to allow TFD data tables to become linked within a flat-file database management system. The ‘Navigator’, consisting of several pop-up menus listing transcription factor abbreviations, facilitates the search for transcription factor entries. Data are presented on-screen in several layouts, that can be further customized by the user. InfoTrac TFD makes the transcription factor database accessible to a much wider community of scientists by making it available on two popular microcomputer platforms.
Acholeplasma laidlawii B-PG9 adenine-specific purine nucleoside phosphorylase that accepts ribose-1-phosphate, deoxyribose-1-phosphate, and xylose-1-phosphate (1988)

An adenylate-specific purine nucleoside phosphorylase (purine nucleoside:orthophosphate ribosyltransferase, EC12.4.2.1) (PNP) was isolated from a cytoplasmic fraction of Acholeplasma laidlawii B-PG9 and partially purified (820-fold). This partially purified PNP could only ribosylate adenine and deribosylate adenosine and deoxyadenosine. The A. laidlawii partially purified PNP could not use hypoxanthine, guanine, uracil, guanosine, deoxyguanosine, or inosine as substrates, but could use ribose-1-phosphate, deoxyribose-1-phosphate, or xylose-1-phosphate as the pentose donor. Mg2+ and a pH of 7.6 were required for maximum activity for each of the pentoses. The partially purified enzyme in sucrose density gradient experiments had an approximate molecular weight of 108,000 and a sedimentation coefficient of 6.9, and in gel filtration experiments it had an approximate molecular weight of 102,000 and a Stoke's radius of 4.1 nm. Nondenaturing polyacrylamide tube gels of the enzyme preparation produced one major and one minor band. The major band (Rf, 0.57) corresponded to all enzyme activity. The Kms for the partially purified PNP with ribose-1-phosphate, deoxyribose-1-phosphate, and xylose-1-phosphate were 0.80, 0.82, and 0.81 mM, respectively. The corresponding Vmaxs were 12.5, 14.3, and 12.0 microM min-1, respectively. The Hill or interaction coefficients (n) for all three pentose phosphates were close to unity. The characterization data suggest the possibility of one active site on the enzyme which is equally reactive toward each of the three pentoses. This is the first report of an apparently adenine-specific PNP activity.
Rapidly Deployable Blast Barriers for Lunar Surface Operations (2008)

Introduction: Apollo landing footage shows rocket blast streaking from the Lunar Module engines as the spacecraft approached the lunar surface. This blast streak (or ‘plume’) was mainly composed of small particles (10-60 microns) of lunar dust estimated to be traveling at speeds between 1.0-2.5 kilometers per second. The plume also consisted of engine exhaust gases powerful enough to move rocks up to 15 cm in size. Samples of the Surveyor 3 spacecraft returned to Earth revealed substantial lunar plume damage from the Apollo 12 landing in close proximity. If spacecraft land repeatedly at a permanent Constellation Program lunar outpost, special precautions will have to be made to prevent the plume from eroding hardware or causing jams in critical surface equipment mechanisms. Barrier Concepts: One possible blast solution is to use synthetic materials brought from Earth to build a mitigation barrier. The structure must be light-weight to reduce payload constraints and easy to deploy through robotic or astronaut surface operations. Our design concept for synthetic barriers focused primarily on two commercially available structures: inflatable barriers and textile fences. Inflatable Barrier: The inflatable concept shown in Figure 1 offers semi-automated deployment (for reducing EVA construction time); flexibility (for use on rugged lunar terrain), packaging efficiency (for minimal volume transport to lunar surface), and durability (for plume impacts) [1,2]. All materials were suppliedby SPM S.p.A. (Brescia, Italy) and purchased through World Cup Supply (Vermont, USA). The systems were integrated and assemblyed by our team to model the basic architecture of blast barriers. Advanced materials and assembly techniques more appropriate for the lunar environment must be implemented for Phase II designs. Inflatable Phase II Considerations: Weight reduction of our inflatable concept is a high priority (for reducing Earth-departure transportation cost). Our Phase II design will also explore pressurizing the barrier with a monopropellant generated gas. Any vacant spaces in the inflatable walls could then be injected with structural foam while the empty chamber space could be filled with compacted regolith to provide additional stability against strong blast forces [3]. To enhance lunar environment tolerance and prevent impact degradation, the intrinsic properties of the inflatable could consist of rigidizable materials (including Thin polymer film laminates and thermoplastic Figure 1: The KSC Phase I inflatable design stands 2.3 m tall and consists of two low pressure inflated walls, linked with a double zigzag tube chamber. The walls have loops for anchoring the structure with structural support poles (hollow, lightweight composites). These poles raise the height of the barrier with a fence extension. While only one section is depicted, multiple barrier sections can be linked, so the system may be made to any desired length or configuration.
Metal-Free Ring-Opening Metathesis Polymerization (2015)

We have developed a method to achieve ring-opening metathesis polymerization (ROMP) mediated by oxidation of organic initiators in the absence of any transition metals. Radical cations, generated via one-electron oxidation of vinyl ethers, were found to react with norbornene to give polymeric species with microstructures essentially identical to those traditionally obtained via metal-mediated ROMP. We found that vinyl ether oxidation could be accomplished under mild conditions using an organic photoredox mediator. This led to high yields of polymer and generally good correlation between M(n) values and initial monomer to catalyst loadings. Moreover, temporal control over reinitiation of polymer growth was achieved during on/off cycles of light exposure. This method demonstrates the first metal-free method for controlled ROMP.
A Conductimetric System Based on Polyaniline for Determination of Ammonia in Fertilizers (1997)

Abstract A simple conductimetric system to determine ammonia concentration using a sensor based on a conductor polymer was developed. The sensitive element to ammonia is a thin polyaniline film deposited by chemical synthesis in an acrylic substrate prepared before hand with two graphite electrodes. The conductance of the polyaniline film decreases when exposed to the ammonia gas and this variation can be related to the ammonia concentration. To determine ammonia in fertilizer samples a system consisting of a measurement cell, a conductivity meter and a strip chart recorder was used. The results were compared with those obtained by three different laboratories employing a Kjeldahl method and are in good agreement. The detection range of the system was 0.6 to 3.7 μg.mL−1 with a response time of 4 minutes. The relative standard deviation of the proposed method was about 5%.
Prognostic Value of Three Different Methods of MGMT Promoter Methylation Analysis in a Prospective Trial on Newly Diagnosed Glioblastoma (2012)

Hypermethylation in the promoter region of the MGMT gene encoding the DNA repair protein O(6)-methylguanine-DNA methyltransferase is among the most important prognostic factors for patients with glioblastoma and predicts response to treatment with alkylating agents like temozolomide. Hence, the MGMT status is widely determined in most clinical trials and frequently requested in routine diagnostics of glioblastoma. Since various different techniques are available for MGMT promoter methylation analysis, a generally accepted consensus as to the most suitable diagnostic method remains an unmet need. Here, we assessed methylation-specific polymerase chain reaction (MSP) as a qualitative and semi-quantitative method, pyrosequencing (PSQ) as a quantitative method, and methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) as a semi-quantitative method in a series of 35 formalin-fixed, paraffin-embedded glioblastoma tissues derived from patients treated in a prospective clinical phase II trial that tested up-front chemoradiotherapy with dose-intensified temozolomide (UKT-05). Our goal was to determine which of these three diagnostic methods provides the most accurate prediction of progression-free survival (PFS). The MGMT promoter methylation status was assessable by each method in almost all cases (n = 33/35 for MSP; n = 35/35 for PSQ; n = 34/35 for MS-MLPA). We were able to calculate significant cut-points for the continuous methylation signals at each CpG site analysed by PSQ (range, 11.5 to 44.9%) and at one CpG site assessed by MS-MLPA (3.6%) indicating that a dichotomisation of continuous methylation data as a prerequisite for comparative survival analyses is feasible. Our results show that, unlike MS-MLPA, MSP and PSQ provide a significant improvement of predicting PFS compared with established clinical prognostic factors alone (likelihood ratio tests: p<0.001). Conclusively, taking into consideration prognostic value, cost effectiveness and ease of use, we recommend pyrosequencing for analyses of MGMT promoter methylation in high-throughput settings and MSP for clinical routine diagnostics with low sample numbers.
Blockade of colony stimulating factor-1 (CSF-1) leads to inhibition of DSS-induced colitis (2006)

This is the first study to demonstrate that CSF-1 plays an important role in mediating intestinal mucosal inflammation and therefore may prove to be an attractive therapeutic target for intestinal diseases such as inflammatory bowel disease.
Humanized anti-Sialyl-Tn antibodies for the treatment of ovarian carcinoma (2018)

The expression of Sialyl-Tn (STn) in tumors is associated with metastatic disease, poor prognosis, and reduced overall survival. STn is expressed on ovarian cancer biomarkers including CA-125 (MUC16) and MUC1, and elevated serum levels of STn in ovarian cancer patients correlate with lower five-year survival rates. In the current study, we humanized novel anti-STn antibodies and demonstrated the retention of nanomolar (nM) target affinity while maintaining STn antigen selectivity. STn antibodies conjugated to Monomethyl Auristatin E (MMAE-ADCs) demonstrated in vitro cytotoxicity specific to STn-expressing ovarian cancer cell lines and tumor growth inhibition in vivo with both ovarian cancer cell line- and patient-derived xenograft models. We further validated the clinical potential of these STn-ADCs through tissue cross-reactivity and cynomolgus monkey toxicity studies. No membrane staining for STn was present in any organs of human or cynomolgus monkey origin, and the toxicity profile was favorable and only revealed MMAE-class associated events with none being attributed to the targeting of STn. The up-regulation of STn in ovarian carcinoma in combination with high affinity and STn-specific selectivity of the mAbs presented herein warrant further investigation for anti-STn antibody-drug conjugates in the clinical setting.