gebhart/patrepeval huggingface dataset:
Release of Pertussis Toxin and Its Interaction With Outer-membrane Antigens (1987)

The absence of subunit S3 in cell-associated pertussis toxin (PT) from a mutant of Bordetella pertussis which failed to produce cell-free toxin suggested that this subunit was involved in the release of PT into the culture medium. The addition of methylated beta-cyclodextrin (MCD) to the culture medium caused a small but consistent increase in the release of lipopolysaccharide (LPS) by four wild-type strains of B. pertussis. Since previous studies have shown that MCD also enhances the levels of PT in culture supernates, it seemed probable that the increased shedding of outer-membranes vesicles (OMV) may explain the increased levels of both cell-free PT and LPS. Release of PT was inhibited in media buffered with HEPES but was unaffected in Tris/HC1 buffer. This suggested that in addition to shedding of the outer membrane, increased permeability and greater destabilization of the outer membrane, as caused by Tris/HC1 buffer, may be important in the release of PT. Our data do not support the idea that PT is packaged into OMV because only an insignificant proportion (0.01%) of the total cell-free PT was associated with LPS. The association of PT with small micelles derived from outer-membrane amphiphiles may be more important since the LPS content of PT purified from culture supernates (containing no large OMV) was nearly 18% by weight.
Sequencing and Validation of the Genome of a Campylobacter concisus Reveals Intra-Species Diversity (2011)

Campylobacter concisus is an emerging pathogen of the human gastrointestinal tract. Its role in different diseases remains a subject of debate; this may be due to strain to strain genetic variation. Here, we sequence and analyze the genome of a C. concisus from a biopsy of a child with Crohn's disease (UNSWCD); the second such genome for this species. A 1.8 Mb genome was assembled with paired-end reads from a next-generation sequencer. This genome is smaller than the 2.1 Mb C. concisus reference BAA-1457. While 1593 genes were conserved across UNSWCD and BAA-1457, 138 genes from UNSWCD and 281 from BAA-1457 were unique when compared against the other. To further validate the genome assembly and annotation, comprehensive shotgun proteomics was performed. This confirmed 78% of open reading frames in UNSWCD and, importantly, provided evidence of expression for 217 proteins previously defined as 'hypothetical' in Campylobacter. Substantial functional differences were observed between the UNSWCD and the reference strain. Enrichment analysis revealed differences in membrane proteins, response to stimulus, molecular transport and electron carriers. Synteny maps for the 281 genes not present in UNSWCD identified seven functionally associated gene clusters. These included one associated with the CRISPR family and another which encoded multiple restriction endonucleases; these genes are all involved in resistance to phage attack. Many of the observed differences are consistent with UNSWCD having adapted to greater surface interaction with host cells, as opposed to BAA-1457 which may prefer a free-living environment.
Understanding Basic Mechanisms and Optimizing Assays to Evaluate the Efficacy of Vaginal Microbicides (2009)

In Brief The ideal microbicide or microbicide combination must have activity against cell-free and cell-associated primary HIV isolates representing multiple clades, must inhibit transmission to relevant cell types within the mucosa, and must retain activity in the presence of cervicovaginal fluid and when virus is introduced in semen or seminal plasma. This summary briefly reviews some of the basic concepts underlying the optimization of assays to evaluate the efficacy of candidate microbicides against HIV/STI. The review is based on the presentations of Drs. Stuart Turville (Population Council), Dan Barouch (Harvard University), Scott McCoombe (Northwestern University), Betsy Herold (Albert Einstein College of Medicine), Sam Niedbala (Lehigh University), and the subsequent discussion led by Drs. Robin Shattock (St. George's Hospital Medical School) and Jim Turpin (National Institutes of Health) during a session entitled “Biomarkers of HIV/STI” held at the conference entitled “Biomarkers for evaluation of vaginal microbicides and contraceptives: discovery and early validation,” organized by CONRAD and the Alliance for Microbicide Development in November of 2006 as well as more recent published findings. This review highlights key concepts underlying the optimization of assays to evaluate the efficacy of microbicides to prevent HIV and other sexually transmitted infections.
Approach for estimating global landfill-methane emissions. Final report, April-September 1990 (1991)

Poly(epsilon-caprolactone) (PCL) is a biodegradable polyester whose biocompatibility has been widely demonstrated both in vivo and in vitro. In the last few years, our group has confirmed that NaOH-treated PCL films can serve as a suitable biomaterial for vascular tissue engineering by supporting the culture of primary vascular cells and, more recently, endothelial-like EC(2) cells derived from endothelial progenitor cells (EPC). In the present study, NO production in basal conditions and after stimulation with different agents has been evaluated and related to the reactive oxygen species (ROS) content and the intracellular calcium levels on EC(2) cells cultured on NaOH-treated PCL films. The results obtained demonstrate that EC(2) seeded on NaOH-treated PCL films enhance the basal NO levels and show a faster, more intense response to physiological stimuli such as VEGF, bradykinin and thrombin than vein endothelial cells (ECv). This result could be indicative of a better capacity of EC(2) cells to maintain their endothelial functionality when seeded on polymers. On the other hand, the culture of both EC(2) and ECv cells on NaOH-treated PCL films induces a significant increase in both ROS content and intracellular calcium that is balanced out through the stimulation of NO production in these cells. In conclusion, these results demonstrate the ability of NaOH-treated PCL films to support endothelial cell production of nitric oxide and reinforce the idea of considering the endothelial-like EC(2) cells derived from blood progenitors as an adequate source of endothelial cells to functionalize vascular grafts. Furthermore, NaOH-treated PCL films could be considered as a promising cellular NO production-inducing biomaterial for vascular tissue engineering applications.
Identification of Genes That Promote or Antagonize Somatic Homolog Pairing Using a High-Throughput FISH–Based Screen (2012)

The pairing of homologous chromosomes is a fundamental feature of the meiotic cell. In addition, a number of species exhibit homolog pairing in nonmeiotic, somatic cells as well, with evidence for its impact on both gene regulation and double-strand break (DSB) repair. An extreme example of somatic pairing can be observed in Drosophila melanogaster, where homologous chromosomes remain aligned throughout most of development. However, our understanding of the mechanism of somatic homolog pairing remains unclear, as only a few genes have been implicated in this process. In this study, we introduce a novel high-throughput fluorescent in situ hybridization (FISH) technology that enabled us to conduct a genome-wide RNAi screen for factors involved in the robust somatic pairing observed in Drosophila. We identified both candidate "pairing promoting genes" and candidate "anti-pairing genes," providing evidence that pairing is a dynamic process that can be both enhanced and antagonized. Many of the genes found to be important for promoting pairing are highly enriched for functions associated with mitotic cell division, suggesting a genetic framework for a long-standing link between chromosome dynamics during mitosis and nuclear organization during interphase. In contrast, several of the candidate anti-pairing genes have known interphase functions associated with S-phase progression, DNA replication, and chromatin compaction, including several components of the condensin II complex. In combination with a variety of secondary assays, these results provide insights into the mechanism and dynamics of somatic pairing.
Can online auctions beat online catalogs (1999)

In this paper, we report the results of an extensive study comparing the price paid in 473 online auctions with the prevailing prices of identical goods sold through online catalogs. Our results reveal a striking phenomenon: auction winners enjoy an average discount of 25% relative to the catalog prices for identical items sold at the same site. The average discount grows to 39% if identical items are on sale only on other sites. We also find that this discount is a function of the monetary value of the items being auctioned and more expensive items are typically associated with lower discount rates. We use these results to characterize the major costs that are imposed on online auction participants and we analyze the impact of these costs on the resulting auction closing price. Our information economics model provides an explanation for the deep discounts observed in our research and provides some conceptual guidelines for online auction design.
Quantitative Image Analysis of Broadband CARS Hyperspectral Images of Polymer Blends (2011)

We demonstrate that broadband coherent anti-Stokes Raman scattering (CARS) microscopy can be very useful for fast acquisition of quantitative chemical images of multilayer polymer blends. This is challenging because the raw CARS signal results from the coherent interference of resonant Raman and nonresonant background and its intensity is not linearly proportional to the concentration of molecules of interest. Here we have developed a sequence of data-processing steps to retrieve background-free and noise-reduced Raman spectra over the whole frequency range including both the fingerprint and C-H regions. Using a classical least-squares approach, we are able to decompose a Raman hyperspectral image of a tertiary polymer blend into quantitative chemical images of individual components. We use this method to acquire 3-D sectioned quantitative chemical images of a multilayer polymer blend of polystyrene, styrene-ethylene/propylene copolymer, and polypropylene that have overlapping spectral peaks.
Virtual Reality Unbound (1995)

Virtual reality involves a compelling vision: using computers to create three-dimensional environments that immerse the user in application-specific objects. These objects have a strong sense of spatial presence, and have programmed appearances and behaviors tailored to the virtual environment's task. What could be more compelling than an environment you step into, specially built for your 3D task?
Arginine-164-tryptophan substitution in connexin32 associated with X linked dominant Charcot-Marie-Tooth disease. (1996)

A Spanish family with X linked dominant Charcot-Marie-Tooth (CMTX1) neuropathy was screened for point mutations in the connexin32 gene (GJ beta 1). The patients showed a C-T transition at position 552 which predicts arginine to tryptophan substitution at amino acid 164 (R164K). This mutation destroys an AciI restriction site at position 552 and creates a PflMI restriction site.
Sperm phospholipases and acrosomal exocytosis (2006)

At the time of fertilization, the sperm cell undergoes regulated exocytosis in response to the oocyte-associated agonists progesterone and zona pellucida. An early response generated by agonist-receptor interaction in spermatozoa is the activation of mechanisms leading to Ca2+ influx, this ion being essential for the activation of phospholipases and for the fusion of the plasma membrane with the outer acrosomal membrane. Both a phosphoinositide-specific, and a phosphatidylcholine-specific phospholipase C are involved in the generation of a variety of diacylglycerol molecular species. Phospholipase D, on the other hand, does not seem to play a significant role in the generation of diacylglycerol. Hydrolysis of phospholipids by phospholipase A2 generates free fatty acids and lysophospholipids; these are important either as substrates for the generation of other metabolites (e.g., eicosanoids) or having a direct, essential action in the final stages of membrane fusion. There is still much work to be done in the future in order to characterize phospholipase isozymes and their regulation during acrosomal exocytosis in spermatozoa.
Three-Axis Teslameter With Integrated Hall Probe (2007)

The first commercially available teslameter with a fully integrated three-axis Hall probe is described. The Hall probe chip contains horizontal and vertical Hall elements, analog electronics, and a synchronization circuit. A horizontal Hall element measures the perpendicular component, and two vertical Hall devices measure the two in-plane components of a magnetic flux density vector. Current spinning in the Hall devices cancels offset, 1/f noise, and the planar Hall voltage. The analog electronic module of the teslameter cancels the residual offset and compensates temperature dependence and nonlinearity of the Hall voltages. The digital module provides analog-to-digital conversion and communication to a computer.
Editorial (2007)

Improving Cardiovascular Outcomes in Nova Scotia."This paper provides an analysis of a provincewide disease-management project that demonstrated a positive economic impact of investing in community and evidencebased health partnerships.The results showed the significant multiplier effect of a private-sector investment in the management of burdensome diseases for a whole population.The second article, by Anu MacIntosh-Murray, of the University of Toronto, describes the challenges of implementing collaborative improvement in complex continuing care.The article discusses key points for organizations to consider before they engage in an improvement collaborative, based on participants' views of what worked well and challenges they experienced, and suggestions about what they would do differently.Next, we provide the fourth part in a series of articles by Joann Trypuc, Alan Hudson and Hugh MacLeod, of the Ontario Ministry of Health and Long-Term Care.The authors suggest that it is widely recognized that Ontario's Wait Time Strategy is a significant change management initiative.But they raise the question of whether the province achieved the goal that it set out for itself in November 2004.The article begins with a brief overview of the major inputs or foundational building blocks of the strategy, and follows with a detailed analysis of the major outputs or outcomes of the strategy to date.Wendy Nicklin and Gilles Lanteigne, of the Canadian Council on Health Services Accreditation, describe how the national accreditation program is undergoing a significant transformation.The article outlines the rationale for the changes, objectives, key enhancements, development process, critical path and key messages.Sharon King and Larry Peterson, of Starfield Consulting, provide the second article in a series on how effective leaders achieve success in critical change initiatives.In this article, the authors focus on why change leadership must transcend project management for complex initiatives to be successful.In our Ideas at Work section, we provide three different scenarios.Bill MacLeod and Murray Martin describe how Hamilton Health Sciences put cogeneration to work.Spanning three acute care hospitals and generating a combined total of 22.75 megawatts of electricity, Hamilton Health Sciences' cogeneration plants address energy supply issues by offering a clean and reliable power source and offer the potential to generate revenue by selling excess electricity back to the province.
Mammalian nitrobenzylthioinosine-sensitive nucleoside transport proteins. Immunological evidence that transporters differing in size and inhibitor specificity share sequence homology. (1992)

Polyclonal antibodies were raised against the nitrobenzylthioinosine (NBMPR)-sensitive nucleoside transporter of human erythrocyte membranes. On Western blots of these membranes they labeled the broad "band 4.5" region (average apparent M(r) 55,000), which contains both the nucleoside and glucose transport proteins. However, they did not recognize the glucose transporter when this was prepared free of nucleoside transporter by expression from a cDNA clone. Their specificity for the nucleoside transporter was confirmed by the ability to immunoadsorb NBMPR- but not cytochalasin B-binding sites from a detergent-solubilized mixture of band 4.5 proteins. Although a large proportion of the antibodies recognized extracellular epitopes, these appeared to be located primarily on the polypeptide moiety of the glycoprotein, as demonstrated by the ability of the antibodies strongly to label the deglycosylated transporter (apparent M(r) 45,000) on Western blots. The antibodies were species-cross-reactive, recognizing nucleoside transporters from pig and rabbit erythrocytes and from rat liver. The pig protein is similar to the human transporter in its inhibitor sensitivity but is considerably larger (apparent M(r) 57,000 after deglycosylation). In contrast, the rat protein is similar in size to the human transporter (apparent M(r) 45,000 after deglycosylation) but much less sensitive to the inhibitors dilazep and dipyridamole. These findings indicate that despite their differences in size and inhibitor specificity, the NBMPR-sensitive nucleoside transporters of these mammalian species are related in amino acid sequence.
Characterization of polyphenol oxidase during three ripening stages of an eggplant (Solanum melongena L.) fruit: a local type in northeast Anatolia (2015)

Objective: A relatively new cultivar of eggplant, Solanum melongena L. 'Kadife' is widely consumed in Turkey because of its economic availability and good nutritional qualities. However, the high polyphenol content of eggplant renders it susceptible to unattractive oxidative browning catalyzed by polyphenol oxides (PPOs). Therefore, the main aim of this study was to characterize PPO in this eggplant cultivar at three stages of its development. Methods: In this study, we determined substrate specificity, optimum pH and temperature, and optimum substrate concentration of the partial purified eggplant fruits PPO during ripening. Results: L-DOPA was proved to be the preferred PPO substrate in all three stages of ripening. Optimum activity was observed at pH 7.0 for PPO in extracts of ripening and overly-ripe eggplant, while activity in extracts of immature eggplant exhibited a broad pH optimum between, pH 5.0 and 7.0. In general, at all ripening stages, PPO was most active at 30C and was most sensitive to inhibition by sodium metabisulphite and ascorbic acid. The metal ions (Hg 2+ , Mn 2+ , Fe 3+ and Co 2+ ) mostly inhibited PPO activities. Conclusion: These data regarding the properties of PPO should enhance understanding of the browning reaction in eggplant and lead to the development of techniques for controlling this undesirable process.
<i>In Vivo</i> Evaluation of a PAMAM-Cystamine-(Gd-DO3A) Conjugate as a Biodegradable Macromolecular MRI Contrast Agent (2007)

Macromolecular Gd(III) chelates are superior magnetic resonance imaging (MRI) contrast agents for blood pool and tumor imaging. However, their clinical development is limited by the safety concerns related to the slow excretion and long-term gadolinium tissue accumulation. A generation 6 PAMAM Gd(III) chelate conjugate with a cleavable disulfide spacer, PAMAM-G6-cystamine-(Gd-DO3A), was prepared as a biodegradable macromolecular MRI contrast agent with rapid excretion from the body. T(1) and T(2) relaxivities of the contrast agent were 11.6 and 13.3 mM(-1)sec(-1) at 3T, respectively. Blood pool and tumor contrast enhancement of the agent were evaluated in female nude mice bearing MDA-MB-231 human breast carcinoma xenografts with a nondegradable conjugate PAMAM-G6-(Gd-DO3A) as a control. PAMAM-G6-cystamine-(Gd-DO3A) resulted in significant contrast enhancement in the blood for about 5 mins, and Gd-DO3A was released from the conjugate and rapidly excreted via renal filtration after the disulfide spacer was cleaved. The nondegradable control had much longer blood circulation and excreted more slowly from the body. PAMAM-G6-cystamine-(Gd-DO3A) also resulted in more prominent tumor contrast enhancement than the control. However, PAMAM-G6-cystamine-(Gd-DO3A) demonstrated high toxicity due to the intrinsic toxicity of PAMAM dendrimers. In conclusion, although PAMAM-G6-cystamine-(Gd-DO3A) showed some advantages compared with the nondegradable control, PAMAM dendrimers are not suitable carriers for biodegradable macromolecular MRI contrast agents, due to their high toxicity.
Positive and negative elements regulate a melanocyte-specific promoter. (1992)

Melanocytes are specialized cells residing in the hair follicles, the eye, and the basal layer of the human epidermis whose primary function is the production of the pigment melanin, giving rise to skin, hair, and eye color. Melanogenesis, a process unique to melanocytes that involves the processing of tyrosine by a number of melanocyte-specific enzymes, including tyrosinase and tyrosinase-related protein 1 (TRP-1), occurs only after differentiation from the melanocyte precursor, the melanoblast. In humans, melanogenesis is inducible by UV irradiation, with melanin being transferred from the melanocyte in the epidermis to the surrounding keratinocytes as protection from UV-induced damage. Excessive exposure to UV, however, is the primary cause of malignant melanoma, an increasingly common and highly aggressive disease. As an initial approach to understanding the regulation of melanocyte differentiation and melanocyte-specific transcription, we have isolated the gene encoding TRP-1 and examined the cis- and trans-acting factors required for cell-type-specific expression. We find that the TRP-1 promoter comprises both positive and negative regulatory elements which confer efficient expression in a TRP-1-expressing, pigmented melanoma cell line but not in NIH 3T3 or JEG3 cells and that a minimal promoter extending between -44 and +107 is sufficient for cell-type-specific expression. Assays for DNA-protein interactions coupled with extensive mutagenesis identified three factors, whose binding correlated with the function of two positive and one negative regulatory element. One of these factors, termed M-box-binding factor 1, binds to an 11-bp motif, the M box, which acts as a positive regulatory element both in TRP-1-expressing and -nonexpressing cell lines, despite being entirely conserved between the melanocyte-specific tyrosinase and TRP-1 promoters. The possible mechanisms underlying melanocyte-specific gene expression are discussed.
Studies on Ponstan (Mefenamic Acid): I. Gastro-Intestinal Blood Loss; II. Absorbtion and Excretion of a New Formulation (1975)

Using improved techniques in a study of faecal blood loss no significant change over control level occurred during administration of mefenamic acid 500 mg t.i.d. for six days. This lack of gastro-intestinal bleeding is at variance with earlier findings for this compound. Studies of two mefenamic acid formulations (250 mg capsule and 500 mg filmseal tablet) showed no significant difference in area under blood level curves or in urinary output data, indicating equivalent total absorption. The 500 mg film-coated tablet gave significantly higher serum levels at 0·5 hours, whereas the 250 mg capsule gave significantly higher serum levels at 6 and 8 hours.