gebhart/patrepeval huggingface dataset:
An Enzyme-Linked Immunosorbent Assay for Quantifying Adherence of Candida to Human Vascular Endothelium (1987)

Success in elucidating the pathogenesis of certain bacterial infections through studies of bacterial adherence to host cells has stimulated interest in parallel investigations of fungal adherence. Fungal adherence differs from bacterial adherence, especially when fungal coadherence (adherence of fungal cells to each other) is a factor. Using human umbilical vein endothelial cells cultured in a living monolayer in microtiter plates, we developed an ELISA to study adherence of Candida albicans to endothelial cells in the absence of yeast coadherence. A rabbit antibody to Candida detected the adherent Candida, and an alkaline phosphatase-conjugated antibody to rabbit IgG was the developing antibody. A linear relationship between the log of the optical density and the log of the number of adherent organisms was seen for wells containing 3 X 10(4)-1 X 10(6) organisms (r = .923- .965). In addition to measuring adherence of living Candida to living target cells and avoiding Candida coadherence, this assay makes it possible to investigate adherence limited to lumenal surfaces, conserves reagents, and facilitates the testing of large numbers of potential adherence modifiers.
New Insights into the Troubles of Aneuploidy (2012)

Deviation from a balanced genome by either gain or loss of entire chromosomes is generally tolerated poorly in all eukaryotic systems studied to date. Errors in mitotic or meiotic cell division lead to aneuploidy, which places a burden of additional or insufficient gene products from the missegregated chromosomes on the daughter cells. The burden of aneuploidy often manifests itself as impaired fitness of individual cells and whole organisms, in which abnormal development is also characteristic. However, most human cancers, noted for their rapid growth, also display various levels of aneuploidy. Here we discuss the detrimental, potentially beneficial, and sometimes puzzling effects of aneuploidy on cellular and organismal fitness and tissue function as well as its role in diseases such as cancer and neurodegeneration.
A CMOS scheme for 0.5 V supply voltage with pico-ampere standby current (2002)

Recently, low-power requirements are getting stronger in VLSI designs. Since the power consumption of CMOS VLSIs quadratically depends on the supply voltage, low-voltage circuits have been exploited. If a VLSI is operated in 0.5 V-0.8 V V/sub DD/ range for low-power consumption, the threshold voltage of MOSFETs, V/sub TH/, should be well below 0.5 V to turn the MOSFETs on. V/sub TH/ between 0.1 V and 0.2 V causes 10 nA-order subthreshold leakage current per logic gate in a standby mode, which leads to 10 mA standby current for 1M-gate VLSIs. This hinders application of the VLSIs in mobile equipment powered by a small battery. The super cut-off CMOS (SCCMOS) circuit overcomes this problem. With the SCCMOS, operation is possible below 0.5 V-0.8 V V/sub DD/ with 0.1 V-0.2 V V/sub TH/ and, at the same time, pA-order standby current per logic gate can be achieved.
Maxillo-mandibular surgery for obstructive sleep apnoea (1989)

Many therapeutic approaches, including mandibular surgery, have been proposed for the treatment of obstructive sleep apnoea syndrome. In the largest study of its type yet reported, 54 patients (population A) underwent mandibular surgery: 36 had palato-pharyngoplasty and inferior sagittal osteotomy of the mandible with hyoid myotomy and resuspension, and 18 (population B) had maxillo-mandibular hyoid advancement, a procedure consisting of palato-pharyngoplasty, inferior sagittal osteotomy of the mandible with hyoid myotomy and, several months later, a maxillo-mandibular osteotomy. Criteria for procedure selection and for evaluation of results were pre-set, and clinical and polygraphic follow-up occurred 6-8 months after final surgery. In population A, 32 of the 36 patients had improved; but only 20 were evaluated as "satisfactory". In contrast, all of the population B patients were judged satisfactory. Four of the population B patients received nasal continuous positive airway pressure (CPAP) before any surgery, and both approaches gave similar good polygraphic results. The degree of skeletal cranio-facial deficiencies, particularly retrognathia, is crucial for procedure selection. We describe potential procedural risks and problems.
The Thiobarbituric Acid Assay of Sialic Acids (1959)

Publisher Summary This chapter discusses the different aspects of thiobarbituric acid assay of sialic acid. Periodate oxidation of the neuraminic acid backbone of sialic acids results in the formation of β -formylpyruvic acid from carbon atoms 1 to 4. The N -acetyl or N -glycolyl group of sialic acids apparently does not interfere with periodate oxidation. β -Formylpyruvic acid is coupled with 2-thiobarbituric acid to form a red chromophore with a maximum absorption at 549 mμ. It is found that as only free sialic acids are reactive in the assay, hydrolysis of sialic acid-containing material must be carried out for the measurement of total sialic acids. The assay is suitable for measuring the release of bound sialic acid by sialidase. A series of 2-keto, 3-deoxy sugar acids, found in bacteria, also react in the thiobarbituric acid assay. These produce a chromogen with a peak at 549 mμ. They can be readily distinguished from sialic acids because they are not reactive in the orcinol or direct Ehrlich assays for sialic acids. The hydrolysis frees all the sialic acids from several mucoproteins that have been tested except for brain tissue where release of sialic acids takes place for several hours.
Simple canonical views (2005)

This paper demonstrates how to determine canonical views of objects in a way that is simple, robust and versatile. Common parlance loosely defines canonical views as the “front”, “side”, and “top” views of an object. Our approach determines these views for objects whether represented by images or three-dimensional points; neither image segmentation nor model analysis is required. It is easy to introduce constraints so that other views can be determined, as desired. We explain our method and compare it qualitatively to alternatives.
Organization of human T-cell receptor beta-chain genes: clusters of V beta genes are present on chromosomes 7 and 9. (1993)

To ascertain the extent and organization of the germ-line human T-cell receptor (TCR) beta-chain gene repertoire, beta-chain variable region (V beta) genes were mapped by pulsed-field gel electrophoresis, cosmid cloning, and in situ hybridization. Probes derived from the 24 known V beta families were mapped to a total of six Sfi I fragments in DNA samples from multiple individuals representing all possible haplotypes of TCR V- and C (constant)-region insertion/deletion-related polymorphisms. Four of the Sfi I fragments were linked to one another to develop an extended map of the TCR beta-chain gene complex previously localized to chromosome 7q35. The remaining two Sfi I fragments, containing 6 V beta genes, could not be linked to the TCR beta-chain gene complex. Using human-hamster somatic cell hybrids and in situ hybridization, these orphon genes were localized to chromosome 9p. Nucleotide sequences of the orphon V beta genes, derived from cosmid clones, were 93-97% identical to V beta genes in the TCR beta-chain gene complex. Open reading frames in three of the orphon V beta genes were intact as were the recombination signal sequences. As expected, based on their orphon status, none of the V beta genes of chromosome 9 was detected in transcripts containing C beta. These results indicate that the functional germ-line V beta repertoire in humans is substantially (10%) smaller than previously estimated.
STUDIES ON DIHYDROISOCOUMARIN (I). A PRACTICAL SYNTHESIS OF 3-HYDROXYHOMOPHTHALIC ACID (1973)

(1973). STUDIES ON DIHYDROISOCOUMARIN (I). A PRACTICAL SYNTHESIS OF 3-HYDROXYHOMOPHTHALIC ACID. Organic Preparations and Procedures International: Vol. 5, No. 2, pp. 65-70.
Optimum mask and source patterns to print a given shape (2002)

New degrees of freedom can be optimized in mask shapes when the source is also adjustable, because required image symmetries can be provided by the source rather than the collected wave front. The optimized mask will often consist of novel sets of shapes that are quite different in layout from the target integrated circuit patterns. This implies that the optimization algorithm should have good global convergence properties, since the target patterns may not be a suitable starting solution. We have developed an algorithm that can optimize mask and source without using a starting design. Examples are shown where the process window obtained is between two and six times larger than that achieved with standard reticle enhancement techniques (RET). The optimized masks require phase shift, but no trim mask is used. Thus far we can only optimize two-dimensional patterns over small fields (periodicities of ;1 mm or less), though patterns in two separate fields can be jointly optimized for maximum common window under a single source. We also discuss mask optimization with fixed source, source optimization with fixed mask, and the retargeting of designs in different mask regions to provide a common exposure level.
Proapoptotic Activity of Cell-Permeable Anti-Akt Single-Chain Antibodies (2005)

We developed anti-Akt1 single-chain antibodies (scFv) by panning a mouse phage-displayed scFv recombinant antibody library. Recombinant scFv that bound glutathione S-transferase (GST)-Akt1 were screened for their ability to inhibit Akt activity in vitro in a kinase reaction containing human recombinant Akt1 and an Akt/serum glucocorticoid-inducible kinase (SGK) substrate. Michaelis-Menten analysis of kinase inhibition by a selected scFv was consistent with scFv-mediated competition with enzyme's substrate for the catalytic site of Akt. To generate a membrane-permeable version of the anti-Akt1 scFv, the scFv gene was subcloned into a GST expression vector carrying a membrane-translocating sequence (MTS) from Kaposi fibroblast growth factor. A purified GST-anti-Akt1-MTS fusion protein accumulated intracellularly in 293T, BT-474, and PyVmT cells in a dose- and time-dependent fashion. Intracellular accumulation correlated temporally with inhibition of p-Ser(473) Akt and GSK-3alpha/beta phosphorylation, suggesting that Ser(473) is an Akt autophosphorylation site. Phosphorylated (activated) phosphoinositide-dependent kinase 1, mitogen-activated protein kinase, p38, and HER2 (erbB2) were not affected, supporting Akt kinase specificity for the inhibitory scFv. Exogenously expressed constitutively active Akt2 and Akt3 were also inhibited in vitro by the anti-Akt1 fusion protein. Furthermore, GST-anti-Akt1-MTS induced apoptosis in three cancer cell lines that express constitutively active Akt. Finally, systemic treatment with the anti-Akt scFv reduced tumor volume and neovascularization and increased apoptosis in PyVmT-expressing transgenic tumors implanted in mouse dorsal window chambers. Thus, GST-anti-Akt1-MTS is a novel cell-permeable inhibitor of Akt, which selectively inhibits Akt-mediated survival in intact cells both in vitro and in vivo.
CRISPR interference and priming varies with individual spacer sequences (2015)

CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring 'spacer' sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR interference. Mutations in the protospacer adjacent motif (PAM) and seed regions block interference but promote rapid 'primed' adaptation. Here, we use multiple spacer sequences to reexamine the PAM and seed sequence requirements for interference and priming in the Escherichia coli Type I-E CRISPR-Cas system. Surprisingly, CRISPR interference is far more tolerant of mutations in the seed and the PAM than previously reported, and this mutational tolerance, as well as priming activity, is highly dependent on spacer sequence. We identify a large number of functional PAMs that can promote interference, priming or both activities, depending on the associated spacer sequence. Functional PAMs are preferentially acquired during unprimed 'naïve' adaptation, leading to a rapid priming response following infection. Our results provide numerous insights into the importance of both spacer and target sequences for interference and priming, and reveal that priming is a major pathway for adaptation during initial infection.
Cerebral microdialysis combined with single-neuron and electroencephalographic recording in neurosurgical patients (1999)

Monitoring physiological changes in the brain parenchyma has important applications in the care of neurosurgical patients. A technique is described for measuring extracellular neurochemicals by cerebral microdialysis with simultaneous recording of electroencephalographic (EEG) and single-unit (neuron) activity in selected targets in the human brain. Forty-two patients with medically intractable epilepsy underwent stereotactically guided implantation of a total of 423 intracranial depth electrodes to delineate potentially resectable seizure foci. The electrodes had platinum alloy contacts for EEG recordings and four to nine 40-microm microwires for recording single-unit neuron activity. Eighty-six electrodes also included microdialysis probes introduced via the electrode lumens. During monitoring on the neurosurgical ward, electrophysiological recording and cerebral microdialysis sampling were performed during seizures, cognitive tasks, and sleep-waking cycles. The technique described here could be used in developing novel approaches for evaluation and treatment in a variety of neurological conditions such as head injury, subarachnoid hemorrhage, epilepsy, and movement disorders.
Human Serial Learning: Enhancement with Arecholine and Choline Impairment with Scopolamine (1978)

Arecholine (4 milligrams), a cholinergic agonist, and choline (10 grams), a precursor of acetylcholine, significantly enhanced serial learning in normal human subjects. The subjects received methscopolamine prior to both arecholine and placebo injections. Conversely, scopolamine (0.5 milligram), a cholinergic antagonist, impaired learning and this impairment was reversed by arecholine and choline and the impairment after scopolamine were inversely proportional to the subject's performance on placebo; that is, "poor" performers were more vulnerable to both the enhancing effect of cholinergic agonist and precursor and the impairment after cholinergic antagonist than "good" performers.
Characterization of recombinant murine interleukin 5 expressed in Chinese hamster ovary cells (1992)

We have purified recombinant murine interleukin 5 (rmIL-5) from the supernatant of Chinese hamster ovary cells. Each peptide fragment of the purified rmIL-5 generated by Achromobacter protease I digestion was characterized and glycosylation sites were determined. Although rmIL-5 contains three potential sites of N-linked glycosylation (Asn-26, Asn-55 and Asn-69), Asn-69 is not glycosylated. The oligosaccharides released from the protein by hydrazinolysis were fractionated by paper electrophoresis, lectin column chromatography and gel permeation chromatography, and their structures were analysed by sequential exoglycosidase digestion in combination with methylation analysis. The results indicated that they are a mixture of bi-, tri- and tetraantennary complex-type sugar chains with and without a fucose at the C-6 position of the proximal N-acetylglucosamine residue and high-mannose-type sugar chains. Although > 80% of the sugar chains are neutral oligosaccharides similar to recombinant human IL-5 (rhIL-5; Kodama, S., Endo, T., Tsuroka, N., Tsujimoto, M. and Kobata, A. (1991) J. Biochem., 110, 693-701), rmIL-5 has more tetraantennary oligosaccharides than rhIL-5. A site differential study revealed that Asn-55 has more tetraantennary oligosaccharides than Asn-26.
The role of hypoxia in the maintenance of hematopoietic stem cells (1993)

Abstract Bone marrow cell liquid cultures were incubated at various oxygen concentrations ranging from 0% to 18% (air). The total number of cells in culture (CT) at the end of a 6-day incubation was found to be directly proportional to the oxygen concentration. As compared with air- incubated controls, cells recovered from severely hypoxic (1% oxygen) day-5 liquid cultures showed (1) the same day-7 colony-formation efficiency in semisolid culture (neutrophilic/monocytic colonies) or in spleen; (2) a higher day-14 spleen colony-formation efficiency; (3) an enhanced radio-protection ability; and (4) an increased marrow repopulation ability, as measured by determining either total cell number in recipient marrow MRAcell, or the capacity of the latter of generating day-7 neutrophilic/monocytic colonies in secondary in vitro assays (MRACFU-NM). Taking into account CT, the absolute numbers of progenitors in culture were also computed. The results showed that, with respect to time 0, incubation in air produced an increase in the number of day-7 CFUs and a decrease in the number of the other progenitors, whereas in hypoxic cultures all types of progenitors decreased. However, as compared with air-incubated controls, all progenitors, except cells sustaining MRACFU-NM, were reduced in hypoxic cultures. The degree of reduction paralleled the position of the progenitor in the hematopoietic hierarchy, being maximum for day-7 CFUs and null for cells sustaining MRACFU-NM, which, in fact, were better preserved in hypoxic cultures.
Considering biomodification and remineralization techniques as adjuncts to vital tooth-bleaching regimens. (2007)

Although in-office and dentist-monitored vital night-guard bleaching have proved successful for whitening teeth, in some cases involving stark white spots, additional efforts may be required. This clinical case demonstrates the use of a combination in-office and take-home whitening regimen, followed by the in-office and home application of a paste containing casein phosphopeptide and amorphous calcium phosphate, both of which are believed to help replace lost minerals in teeth, make teeth stronger, and help protect them from decay and erosion. The patient's teeth successfully lightened from an initial shade of A2 to a uniform shade of B1. The white spots that were still visible after the bleaching process had disappeared into the tooth structure after the 3-week at-home use of the remineralizing paste. However, at the 3-month recall appointment, some relapse in the appearance of the white spots was noted. Although more research is needed to assess the broader implications of the technique, the author concludes that this individualized result suggests that products with the potential to remineralize tooth structure might be useful adjuncts to traditional tooth-bleaching processes to achieve a uniform appearance when white spots are present.
In vivo and in vitro characteristics of interleukin 6-transfected B16 melanoma cells. (1992)

Interleukin 6 (IL-6) is a multifunctional cytokine important in the inflammatory response. Its potential role as an antitumor agent has been suggested by its demonstrated activity in a variety of tumor models. The mechanism of antitumor activity has been proposed to be its enhancement of cytotoxic T-cell function. In the current work we demonstrate clear antitumor activity for this cytokine in a nonimmunogenic tumor system. B16 melanoma cells transfected with the human IL-6 complementary DNA demonstrated slower tumor growth in vivo. Tumors that developed from these cells had a prominent stromal matrix, an easily recognized infiltration of inflammatory cells, fewer mitotic figures, and fewer blood vessels. These in vivo findings corresponded with a greater adhesion of the IL-6-transfected B16 cells to stromal matrix proteins (laminin, fibronectin, and vitronectin) and a less prominent vascular response in an intradermal angiogenesis assay. Therefore, we propose that with weakly antigenic tumors, such as B16 melanoma, IL-6 may mediate important antitumor responses by nonspecific proinflammatory mechanisms.
Alkyl Esters of Camptothecin and 9-Nitrocamptothecin:  Synthesis, in Vitro Pharmacokinetics, Toxicity, and Antitumor Activity (1998)

Eleven camptothecin esters, 6a-e and 7a-f, were prepared by straightforward acylation of camptothecins with the corresponding acylating reagents such as organic anhydrides and carboxylic acid chlorides. The in vitro pharmacokinetic determination of lactone levels of esters 6a and 7b showed that the biological life span of their lactone forms in human and mouse plasma significantly increased when compared with their mother compounds, camptothecin (3) and 9-nitrocamptothecin (4). The differences of lactone levels between human plasma and mouse plasma for 6a and 7b were much smaller than what was observed for their mother compounds. The in vivo antitumor activity and toxicity studies demonstrated that some of these esters were very active against human tumor xenografts in nude mice and had an exceptional lack of toxicity in nude mice, even at enormous doses.
Valuation by Approximation: A Comparison of Alternative Option Valuation Techniques (1985)

Robert Geske, Kuldeep Shastri, Valuation by Approximation: A Comparison of Alternative Option Valuation Techniques, The Journal of Financial and Quantitative Analysis, Vol. 20, No. 1 (Mar., 1985), pp. 45-71
Cloning and nucleotide sequence of luxR, a regulatory gene controlling bioluminescence in Vibrio harveyi (1990)

Mutagenesis with transposon mini-Mulac was used previously to identify a regulatory locus necessary for expression of bioluminescence genes, lux, in Vibrio harveyi (M. Martin, R. Showalter, and M. Silverman, J. Bacteriol. 171:2406-2414, 1989). Mutants with transposon insertions in this regulatory locus were used to construct a hybridization probe which was used in this study to detect recombinants in a cosmid library containing the homologous DNA. Recombinant cosmids with this DNA stimulated expression of the genes encoding enzymes for luminescence, i.e., the luxCDABE operon, which were positioned in trans on a compatible replicon in Escherichia coli. Transposon mutagenesis and analysis of the DNA sequence of the cloned DNA indicated that regulatory function resided in a single gene of about 0.6-kilobases named luxR. Expression of bioluminescence in V. harveyi and in the fish light-organ symbiont Vibrio fischeri is controlled by density-sensing mechanisms involving the accumulation of small signal molecules called autoinducers, but similarity of the two luminescence systems at the molecular level was not apparent in this study. The amino acid sequence of the LuxR product of V. harveyi, which indicates a structural relationship to some DNA-binding proteins, is not similar to the sequence of the protein that regulates expression of luminescence in V. fischeri. In addition, reconstitution of autoinducer-controlled luminescence in recombinant E. coli, already achieved with lux genes cloned from V. fischeri, was not accomplished with the isolation of luxR from V. harveyi, suggesting a requirement for an additional regulatory component.
Extensive Variation in Chromatin States Across Humans (2013)

The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.