gebhart/patrepeval huggingface dataset:
Bax degradation by the ubiquitin/proteasome-dependent pathway: Involvement in tumor survival and progression (2000)

Previously we reported that proteasome inhibitors were able to overcome Bcl-2-mediated protection from apoptosis. Here we show that inhibition of the proteasome activity in Bcl-2-overexpressing cells accumulates the proapoptotic Bax protein to mitochondria/cytoplasm, where it interacts to Bcl-2 protein. This event was followed by release of mitochondrial cytochrome c into the cytosol and activation of caspase-mediated apoptosis. In contrast, proteasome inhibition did not induce any apparent changes in Bcl-2 protein levels. In addition, treatment with a proteasome inhibitor increased levels of ubiquitinated forms of Bax protein, without any effects on Bax mRNA expression. We also established a cell-free Bax degradation assay in which an in vitro-translated, (35)S-labeled Bax protein can be degraded by a tumor cell protein extract, inhibitable by addition of a proteasome inhibitor or depletion of the proteasome or ATP. The Bax degradation activity can be reconstituted in the proteasome-depleted supernatant by addition of a purified 20S proteasome or proteasome-enriched fraction. Finally, by using tissue samples of human prostate adenocarcinoma, we demonstrated that increased levels of Bax degradation correlated well with decreased levels of Bax protein and increased Gleason scores of prostate cancer. Our studies strongly suggest that ubiquitin/proteasome-mediated Bax degradation is a novel survival mechanism in human cancer cells and that selective targeting of this pathway should provide a unique approach for treatment of human cancers, especially those overexpressing Bcl-2.
ChemInform Abstract: A CONVENIENT PROCEDURE FOR THE CIS‐HYDROXYLATION OF OLEFINS (1974)

Abstract 5a‐Cholest‐2‐en (I) liefert bei der Behandlung mit J od/ Kaliumjodat in Eisessig das trans‐Jodhydrin (II), das zum cis‐Diol (III) mit Silberacetat, Kupferacetat oder auch durch Kochen in Eisessig/Wasser übergeführt werden kann.
GEISHA, a whole‐mount in situ hybridization gene expression screen in chicken embryos (2004)

Despite the increasing quality and quantity of genomic sequence that is available to researchers, predicting gene function from sequence information remains a challenge. One method for obtaining rapid insight into potential functional roles of novel genes is through gene expression mapping. We have performed a high throughput whole-mount in situ hybridization (ISH) screen with chick embryos to identify novel, differentially expressed genes. Approximately 1,200 5' expressed sequence tags (ESTs) were generated from cDNA clones of a Hamburger and Hamilton (HH) stage 4-7 (late gastrula) chick embryo endoderm-mesoderm library. After screening to remove ubiquitously expressed cDNAs and internal clustering and after comparison to GenBank sequences, remaining cDNAs (representing both characterized and uncharacterized genes) were screened for expression in HH stage 3-14 embryos by automated high throughput ISH. Of 786 cDNAs for which ISH was successfully performed, approximately 30% showed ubiquitous expression, 40% were negative, and approximately 30% showed a restricted expression pattern. cDNAs were identified that showed restricted expression in every embryonic region, including the primitive streak, somites, developing cardiovascular system and neural tube/neural crest. A relational database was developed to hold all EST sequences, ISH images, and corresponding BLAST report information, and to enable browsing and querying of data. A user interface is freely accessible at http://geisha.biosci.arizona.edu. Results show that high throughput whole-mount ISH provides an effective approach for identifying novel genes that are differentially expressed in the developing chicken embryo.
Emerging and diverse roles of protein kinase C in immune cell signalling (2003)

Members of the protein kinase C (PKC) family are expressed in many different cell types, where they are known to regulate a wide variety of cellular processes that impact on cell growth and differentiation, cytoskeletal remodelling and gene expression in the response to diverse stimuli. The broad tissue distribution and redundancy of in vitro function have often hampered the identification of definitive roles for each PKC family member. However, recent in vivo studies of PKC isoenzyme-selective knockout and transgenic mice have highlighted distinct functions of individual PKCs in the immune system. These genetic analyses, along with biochemical studies utilizing PKC isoenzyme-specific cDNA (wild-type, constitutively active and dominant-negative), antisense oligonucleotides (ASO), RNA interference (RNAi), and pharmacological inhibitors, indicate that PKC-regulated signalling pathways play a significant role in many aspects of immune responses, from development, differentiation, activation and survival of lymphocytes to macrophage activation. The importance of PKCs in cellular immune responses suggests that improved understanding of the molecular events that govern their actions could point to new avenues for development of treatments for immune disorders.
Metabolic and environmental origins of volatile organic compounds in breath. (1994)

Although more than 200 volatile organic compounds (VOCs) have been identified in human alveolar breath, their origins are still mostly unknown. An attempt was made to determine whether the major VOCs in breath were derived from inside or outside the body--that is, were they products of metabolism or contaminants from the environment? The concentrations were measured of the 24 most abundant VOCs in the alveolar breath of 12 normal volunteers and also in the air they inspired. The polarity of the mean alveolar gradient (concentration in breath minus concentration in inspired air) was positive in 15 VOCs and negative in nine. The mean alveolar gradient varied from strongly positive (for example, 2,3,3-trimethylpentane), consistent with a metabolite manufactured in the body, to strongly negative (for example, isoprene), consistent with ingestion of an air pollutant which was then catabolised in vivo or excreted via an extra-pulmonary pathway.
Both Enantiomers of <i>N</i>-Boc-indoline-2-carboxylic Esters (2004)

Abstract An immobilized form of Candida antarctica lipase (Chirazyme L-2) catalyzed enantioselective hydrolysis (E &gt; 1000) of N-Boc-indoline-2-carboxylic acid methyl ester. The reaction proceeded efficiently at 60 °C, a temperature over the melting point of substrate, in the conversion of 49.9% to provide the hydrolyzed product, (S)-carboxylic acid with &gt;99.9% ee and the unreacted (R)-ester with 99.6% ee. A newly developed expeditious route to the racemic substrate (a total of six steps, 60% yield), starting from aniline and ethyl α-methylacetoacetate, established the scalable chemo-enzymatic synthesis of the desired compounds in both enantiomerically pure forms.
Relationship between cytotoxic activity and radical intensity of isoflavones from Sophora species. (2001)

Among 11 isoflavones tested, genistein [YS13] produced higher cytotoxic activity against human oral tumor cell lines (HSC-2, HSG) than against normal cells (human gingival fibroblast, HGF), suggesting its tumor-specific action. Electron spin resonance (ESR) spectroscopy showed that YS13 did not produce radical, nor scavenged O2*- generated by hypoxanthine-xanthine oxidase reaction system, suggesting that radical-mediated oxidation mechanism is not be involved in the YS13-induced cytotoxicity. Addition of one prenyl group produced YS18 and YS19 with higher anti-Helicobacter pylori activity. Addition of two prenyl groups produced YS21 with the highest cytotoxic activity but lower tumor-specificity. Since YS21 produced the highest amount of radical and most efficiently scavenged O2*-, this compound may induce cytotoxicity by radical-mediated oxidation mechanism. All isoflavones failed to induce anti-human immunodeficiency virus (HIV) activity. These data suggest the medicinal efficacy of isoflavones.
LaRASideCam: a Fast and Robust Vision-Based Blindspot Detection System (2007)

While shifting lane on the road, the presence of a car in the blindspot can cause many accidents, since the driver does not always turn his head. Therefore, a blindspot car detection is likely to become an essential part of modern vehicles. We developed a program that detects cars in the particular configuration of blindspot using video data taken from the left or right mirror of a car, using on the one hand edge detection and support vector machine (SVM) learning and on the other hand template matching. This makes this program simple, fast and adaptative thanks to SVM learning. The program only uses basical functions of the Ecole des Mines' Camellia open-source image processing library [1], which is close to Intel's IPL library. Thus the program is easy to adapt to another API; it has already been adapted to an embedded system currently in development at NXP Semiconductors (formerly Philips Semiconductors). The source code was tested using the valgrind code checking tool [3] and was validated on real-world video sequences.
Safety and effect of topical recombinant human interleukin‐1β in the management of pressure sores (1994)

Interleukin-1beta is produced by numerous cell types including monocytes and fibroblasts. It has been shown to stimulate multiple cell types including fibroblasts, keratinocytes, endothelial cells, neutrophils, macrophages, and lymphocytes. Previously, interleukin-1beta was shown to accelerate healing in partial-thickness and full-thickness wounds in animals and was also shown to be safe when applied topically in Phase I human trials. Therefore a prospectively randomized, blind, placebo-controlled trial was performed with patients with chronic pressure ulcers. Doses of interleukin-1beta of .01 microg, .10 microg, and 1.0 microg per square centimeter did not show acceleration of healing of the pressure ulcers. Therefore use of recombinant human interleukin-1beta in this study was safe but, at the dose levels tested, did not result in improvement in the healing ratio.
C3 Glomerulopathy and Therapeutic Potential of C5 Complement Inhibitors (2016)

C3 glomerulopathy is a disease including both dense deposit disease and C3 glomerulonephritis has an estimated prevalence of 2 to 3 per million. Originally, these pathologies were defined as glomerular pathology characterized by accumulation of C3 with absent or scanty immunoglobulin deposition. The keystone defect in both of these pathologies is the unregulated hyperactivity of alternative complement pathway. Specifically, in C3 glomerulopathy patients, there exists a prolongation of C3 cleavage which causes the uncontrolled alternative pathway activation. Many treatments have been investigated for treating C3 glomerulopathy to little or no avail, including calcineurin inhibitors, plasmapharesis, and anti-CD20 monoclonal antibodies. The next logical step is exploring the efficacy of anti-C5 monoclonal antibody therapy in C3 glomerulopathies to target the specific pathophysiology of this particular disease. Eculizumab is an anti-C5 monoclonal antibody that blocks the terminal step of complement activation. This drug has proven to be an effective treatment in other nephrologic pathologies that are caused by complement dysregulation. Here in this paper we discuss and present various case studies and clinical trials available that experiment with Eculizumab in patients with either dense deposit disease or C3 glomerulonephritis. In most of these patients, treatment with Eculizumab has demonstrated clinical and biochemical improvements in kidney function. These results provide encouraging evidence that suggest Eculizumab as a promising therapy for patients with C3 glomerulopathy and warrant that more extensive clinical trials can be designed as a next step.
PIERS Timings on Various Parallel Supercomputers (1994)

Summary A parallel implicit research reservoir simulator (PIERS), designed for experimentation rather than production yet with many of the features of realistic petroleum reservoir models, was made available to us as a test program. This article reports results of timing PIERS on five parallel supercomputers. Graphs illustrate performance as a function of the number of processors for several problem sizes. Results indicate that parallel computation provides substantial speed improvement in reservoir simulator codes. Also, the raw timings provide an interesting comparison of machine performance, though one should remember that they apply directly only to PIERS and may vary with different simulators, compilers, operating systems, and hardware configurations.
Bayesian Estimation of Beta Mixture Models with Variational Inference (2011)

Bayesian estimation of the parameters in beta mixture models (BMM) is analytically intractable. The numerical solutions to simulate the posterior distribution are available, but incur high computational cost. In this paper, we introduce an approximation to the prior/posterior distribution of the parameters in the beta distribution and propose an analytically tractable (closed form) Bayesian approach to the parameter estimation. The approach is based on the variational inference (VI) framework. Following the principles of the VI framework and utilizing the relative convexity bound, the extended factorized approximation method is applied to approximate the distribution of the parameters in BMM. In a fully Bayesian model where all of the parameters of the BMM are considered as variables and assigned proper distributions, our approach can asymptotically find the optimal estimate of the parameters posterior distribution. Also, the model complexity can be determined based on the data. The closed-form solution is proposed so that no iterative numerical calculation is required. Meanwhile, our approach avoids the drawback of overfitting in the conventional expectation maximization algorithm. The good performance of this approach is verified by experiments with both synthetic and real data.
Development of multipurpose peroxisomes in Candida boidinii grown in oleic acid-methanol limited continuous cultures (1992)

We have studied the development and metabolic significance of peroxisomes in the yeast Candida boidinii following adaptation of the organism to cultivation conditions which require the simultaneous presence and activity of two independent peroxisome-mediated pathways for growth. After the addition of methanol to oleic acid-grown cells at late exponentional growth, a number of new small peroxisomes developed which, apart from the presence of beta-oxidation enzymes, were characterized by the presence of enzymes involved in methanol metabolism (alcohol oxidase and dihydroxyacetone synthase). The latter proteins, however, were absent in the larger organelles which were originally present in the oleic acid-grown cells prior to the addition of methanol and which contained only enzymes of the beta-oxidation pathway. Subsequent experiments on cells from continuous cultures grown on a mixture of oleic acid and methanol at steady-state conditions revealed that both the enzymes of the beta-oxidation pathway and those involved in methanol metabolism were found in one and the same compartment. Thus, under these conditions the cells contained peroxisomes which were concurrently involved in the metabolism of two different carbon sources simultaneously used for growth. Our results indicated that the heterogeneity in the peroxisomal population of a single cell, observed in the transient state following the addition of methanol, is only temporary and due to heterogeneity among these organelles with respect to their capacity to incorporate newly synthesized matrix proteins.
Electrophysiological effects of alpha 2-adrenergic stimulation in canine cardiac Purkinje fibers (1995)

The effects of alpha 2-adrenergic stimulation on action potentials were measured in isolated canine Purkinje fibers. Action potential durations at 50 and 90% of repolarization (APD50 and APD90) were significantly prolonged by 0.25 microM l-norepinephrine + 0.5 microM dl-propranolol (NE+P) from baseline values of 166 +/- 7 and 249 +/- 9 (SE) ms (n = 7) to 174 +/- 7 and 265 +/- 9 ms, respectively (P < 0.05 for both). Selective alpha 2-blockade with 0.01 microM yohimbine (YO) reduced this prolongation by NE+P in APD50 and APD90 to 169 +/- 7 and 256 +/- 8 ms, respectively (P < 0.05 compared with NE+P). Additional selective alpha 1-blockade with 0.01 microM prazosin (PZ) completely blocked the effects of NE+P, returning APD50 and APD90 to 163 +/- 7 and 250 +/- 9 ms (not different from baseline). After incubation of isolated Purkinje fibers with pertussis toxin (1 microgram/ml), which reduced the availability of a 41-kDa membrane protein for ADP ribosylation by 70 +/- 7% (n = 4, P < 0.05), YO failed to reverse the prolongation in action potential durations brought on by NE+P, but the effects of PZ were intact. The effects of alpha 2-stimulation on beta-adrenergic-induced delayed afterdepolarizations (DADs) were studied by burst pacing of Purkinje fibers in Tyrode solution containing 7.5 mM Ca2+. The DADs induced in the presence of NE+PZ (beta- + alpha 2-stimulation) were significantly smaller in amplitude and required a shorter pacing cycle length to reach threshold than those induced in the presence of NE+PZ+YO (unopposed beta-adrenergic stimulation). Furthermore sustained triggered activity, seen in five of eight preparations under beta-stimulation, could no longer be elicited in the presence of beta- + alpha 2-stimulation. These results suggest that the postjunctional alpha 2-adrenergic receptors in canine Purkinje fibers are coupled to a pertussis toxin-sensitive G protein and that stimulation of these receptors leads to action potential prolongation and suppression of DADs induced by beta-adrenergic stimulation.
Nickel-Catalyzed Suzuki–Miyaura Reaction of Aryl Fluorides (2011)

Two protocols for the nickel-catalyzed cross-coupling of aryl fluorides with aryl boronic esters have been developed. The first employs metal fluoride cocatalysts, such as ZrF(4) and TiF(4), which enable Suzuki-Miyaura reactions of aryl fluorides bearing electron-withdrawing (ketones, esters, and CF(3)), aryl and alkenyl groups as well as those comprising fused aromatic rings, such as fluoronaphthalenes and fluoroquinolines. The second protocol employs aryl fluorides bearing ortho-directing groups, which facilitate the difficult C-F bond activation process via cyclometalation. N-heterocycles, such as pyridines, quinolines, pyrazoles, and oxazolines, can successfully promote cross-coupling with an array of organoboronic esters. A study into the substituent effects with respect to both coupling components has provided fundamental insights into the mechanism of the nickel-catalyzed cross-coupling of aryl fluorides.
Plasma-enhanced chemical-vapor-deposited oxide for low surface recombination velocity and high effective lifetime in silicon (1993)

It is shown that plasma-enhanced chemical-vapor deposition (PECVD) of thin SiO2 on Si wafers followed by rapid thermal annealing (RTA) can result in very high effective carrier lifetime (≳5 ms) and extremely low surface recombination velocity (≤2 cm/s). Thin SiO2 (∼100 Å) layers were prepared by direct PECVD at 250 °C and RTA was performed at 350 °C in forming gas. Detailed metal-oxide-semiconductor analysis and model calculations showed that such a low recombination velocity is the result of moderately high positive oxide charge (5×1011–1×1012 cm−2 ) and relatively low midgap interface-state density (5×1010–1×1011 cm−2 eV−1). RTA was found to be superior to furnace annealing, and a forming gas ambient was better than a nitrogen ambient for achieving a very low surface recombination velocity. Some degradation in the surface recombination velocity or effective lifetime was observed. It is found that a PECVD SiN cap on top of the thin SiO2 not only suppressed this degradation but also enhanced the effective lifetime.
25th Anniversary Article: Colloidal Quantum Dot Materials and Devices: A Quarter‐Century of Advances (2013)

Colloidal quantum dot (CQD) optoelectronics offers a compelling combination of low-cost, large-area solution processing, and spectral tunability through the quantum size effect. Since early reports of size-tunable light emission from solution-synthesized CQDs over 25 years ago, tremendous progress has been made in synthesis and assembly, optical and electrical properties, materials processing, and optoelectronic applications of these materials. Here some of the major developments in this field are reviewed, touching on key milestones as well as future opportunities.
Asymptotic disturbance rejection for momentum bias spacecraft (1992)

short duration is such that a right switch following closely on an initial left break by E ceases to be effective. The pursuer of course initially runs directly toward the evader, and in this case E breaks to one side or the other when the separation is only slightly more than L. The subsequent composite motions end with E at E2, where his heading makes only about 10 deg with the sideline. E has gained about 10 yd compared with the final position E}. The diagram here indicates that the players are in contact at the tackle range over the majority of the time, as shown by the curved dashed lines.
Feasibility study of semi‐selective protein precipitation with salt‐tolerant copolymers for industrial purification of therapeutic antibodies (2013)

We present a feasibility study for an antibody capturing process from clarified cell culture fluid using semi-selective protein precipitation with salt-tolerant copolymers. Protein precipitation is mediated by hydrophobic and electrostatic interactions with the copolymer that can be customized for the respective target. Precipitation yield with different copolymers at ionic strength of 2-22.5 mS cm⁻¹ and pH 5.0-pH 5.7 was evaluated using pure monoclonal antibody solutions. Optimized parameters were used to elucidate yield and purity of various antibodies precipitated at physiological conditions from cell culture fluid of CHO, NS0, and SP2/0 cell culture fluid. Precipitated protein was easily redissolved in small volume, enabling concentrating monoclonal antibodies (mAb) more than 40-fold and up to 100-fold, while residual polymer was removed to >98% using cationic polymer attached to silica flakes. mAb recovery of >90% and host cell protein clearance of >80% were achieved, not requiring any pre-dilution of cell culture fluid. Precipitation showed no impact on mAb binding affinity when compared to non-precipitated mAb. The obtained yield and purity were lower compared to a protein A based purification and loss of mAb was factor 1.5-3.0 higher. Yet, for high titer mAb purification processes being implemented in the future, precipitation is an attractive option due to its ease of scalability and cost-effectiveness.
[Study on the method of measurement of respiratory mechanical parameters]. (2006)

Respiratory mechanical parameters are the key indexes in evaluating the respiratory function of an anaesthetized patient during operation. The measurement of respiratory parameters plays an important role in clinic, and can dynamically monitor the working state of a respirator, direct the use of a respirator and monitor the respiratory function of a patient in intensive care unit(ICU). This paper introduces a new method that will break the traditional limitations, can measure eleven respiratory parameters and demonstrate the results by digital and diagrams.