gebhart/patrepeval huggingface dataset:
Assembly of Positively Charged Porphyrins Driven by Metal Ions:  A Novel Polymeric Arrangement of Cationic Metalloporphyrin (2004)

Crystallization and crystal structure analysis of chlorohydrates of either tri- or tetracationic copper porphyrins, namely copper(5,10,15-tris(N-methyl-pyridinium-4-yl)-20-pyridine-porphyrinato) (1) and copper(5,10,15,20-tetrakis(N-methyl-pyridinium-4-yl)-porphyrinato), respectively, have been performed. Two crystalline forms, 2 and 3, of the latter have been obtained under different preparation conditions. A novel kind of slipped stack chains of these cationic porphyrins has been detected. The pronounced saddle conformation of the porphyrin reveals pi-like interactions between the peripheral pyrrole Cb-Cb- "double bond" and the metal center. DFT calculations on the isolated porphyrins clearly show the HOMO orbitals with the correct topology to yield a bonding interaction among the stacked porphyrin units. To our knowledge, a slipped stack chain of positively charged porphyrins has never been previously reported, if the arrangement of faced units of monocationic metalloporphyrins or phthalocyanins is excluded.
Pathogenicity and drug resistance in Candida albicans and other yeast species (2007)

Pathogenic yeasts from the genus Candida can cause serious infection in humans particularly, in immunocompromised patients and are now recognized as major agents of hospital acquired (nosocomial) infections. In the recent years, there has been a marked increase in the incidence of treatment failures in candidiasis patients receiving long-term antifungal therapy, which has posed a serious problem in its successful use in chemotherapy. Candida cells acquire drug resistance (MDR) during the course of the treatment. The mechanisms of resistance to azole antifungal agents have been elucidated in Candida species and can be mainly categorized as (i) changes in the cell wall or plasma membrane, which lead to impaired drug (azole) uptake; (ii) alterations in the affinity of the drug target Erg11p (lanosterol 14alpha-demethylase) especially to azoles or in the cellular content of Erg11p due to target site mutation or overexpression of the ERG11 gene; and (iii) the efflux of drugs mediated by membrane transport proteins belonging to the ATP-binding cassette (ABC) transporters, namely CDR1 and CDR2 or to the major facilitator superfamily (MFS) transporter, CaMDR1. Many such manifestations are associated with the formation of Candida biofilms including those occurring on devices like indwelling intravascular catheters. Biofilm-associated Candida show uniform resistance to a wide spectrum of antifungal drugs. A combination of different resistance mechanisms is responsible for drug resistance in clinical isolates of Candida species.
mdm2 deletion does not alter growth characteristics of p53-deficient embryo fibroblasts. (1996)

The mdm2 gene encodes a protein that is necessary for the negative regulation of p53 function in vivo. Deletion of the mdm2 gene in mice results in early embryonic death while concomitant mdm2 and p53 deletion results in viable offspring. The viability of these mice prompted us to ask if MDM2 had an important growth regulatory function independent of p53. We established mouse embryo fibroblasts null for both p53 and mdm2 and compared them with p53-null fibroblasts. The cells did not differ in their growth rates or their ability to bypass a G1 arrest. Both cell lines formed colonies efficiently when plated at low density and showed a similar degree of genetic instability. Thus, the analysis of several growth parameters indicated no difference between p53-null and p53/mdm2-null cell lines.
How java programs interact with virtual machines at the microarchitectural level (2003)

Java workloads are becoming increasingly prominent on various platforms ranging from embedded systems, over general-purpose computers to high-end servers. Understanding the implications of all the aspects involved when running Java workloads, is thus extremely important during the design of a system that will run such workloads. In other words, understanding the interaction between the Java application, its input and the virtual machine it runs on, is key to a succesful design. The goal of this paper is to study this complex interaction at the microarchitectural level, e.g., by analyzing the branch behavior, the cache behavior, etc. This is done by measuring a large number of performance characteristics using performance counters on an AMD K7 Duron microprocessor. These performance characteristics are measured for seven virtual machine configurations, and a collection of Java benchmarks with corresponding inputs coming from the SPECjvm98 benchmark suite, the SPECjbb2000 benchmark suite, the Java Grande Forum benchmark suite and an open-source raytracer, called Raja with 19 scene descriptions. This large amount of data is further analyzed using statistical data analysis techniques, namely principal components analysis and cluster analysis. These techniques provide useful insights in an understandable way.From our experiments, we conclude that (i) the behavior observed at the microarchitectural level is primarily determined by the virtual machine for small input sets, e.g., the SPECjvm98 s1 input set; (ii) the behavior can be quite different for various input sets, e.g., short-running versus long-running benchmarks; (iii) for long-running benchmarks with few hot spots, the behavior can be primarily determined by the Java program and not the virtual machine, i.e., all the virtual machines optimize the hot spots to similarly behaving native code; (iv) in general, the behavior of a Java application running on one virtual machine can be significantly different from running on another virtual machine. These conclusions warn researchers working on Java workloads to be careful when using a limited number of Java benchmarks or virtual machines since this might lead to biased conclusions.
Single page architecture as basis for web applications (2015)

Content of the web has evolved from simple documents to rich and interactive applications. It has been predicted that, in the future, the vast majority of end user software will be built with web technologies, whereas binary programs will be limited to system software. In order to truly succeed, web applications have to overcome many challenges. Some of these challenges have been solved by single page architecture (SPA).\n\nConventional web applications are rendered on the server and might use APIs (Application Programming Interface) to partially update the views. In SPA, the application is fully loaded at once and the business logic is transferred from the server to the client. This results in client-heavy applications, which communicate with the server through an API.\n\nThe goal of this thesis is to evaluate single page architecture as a foundation for web applications. I will assess the challenges and advantages of the web as an application platform. I present the current web technologies and trends in development of single page applications. Moreover, I present three applications I built, which helped me to evaluate the significance of the architectural model.\n\nThe study shows that single page architecture greatly simplifies the creation of application-like user interfaces, which results in enhanced user experience. I also found that HTML and web browser semantics hinder the development of web applications. The study of frameworks showed that SPA is suitable to mobile, tablet and desktop platforms.
Ehrlichia chaffeensis Uses Its Surface Protein EtpE to Bind GPI-Anchored Protein DNase X and Trigger Entry into Mammalian Cells (2013)

Ehrlichia chaffeensis, an obligatory intracellular rickettsial pathogen, enters and replicates in monocytes/macrophages and several non-phagocytic cells. E. chaffeensis entry into mammalian cells is essential not only for causing the emerging zoonosis, human monocytic ehrlichiosis, but also for its survival. It remains unclear if E. chaffeensis has evolved a specific surface protein that functions as an 'invasin' to mediate its entry. We report a novel entry triggering protein of Ehrlichia, EtpE that functions as an invasin. EtpE is an outer membrane protein and an antibody against EtpE (the C-terminal fragment, EtpE-C) greatly inhibited E. chaffeensis binding, entry and infection of both phagocytes and non-phagocytes. EtpE-C-immunization of mice significantly inhibited E. chaffeensis infection. EtpE-C-coated latex beads, used to investigate whether EtpE-C can mediate cell invasion, entered both phagocytes and non-phagocytes and the entry was blocked by compounds that block E. chaffeensis entry. None of these compounds blocked uptake of non-coated beads by phagocytes. Yeast two-hybrid screening revealed that DNase X, a glycosylphosphatidyl inositol-anchored mammalian cell-surface protein binds EtpE-C. This was confirmed by far-Western blotting, affinity pull-down, co-immunoprecipitation, immunofluorescence labeling, and live-cell image analysis. EtpE-C-coated beads entered bone marrow-derived macrophages (BMDMs) from wild-type mice, whereas they neither bound nor entered BMDMs from DNase X(-/-) mice. Antibody against DNase X or DNase X knock-down by small interfering RNA impaired E. chaffeensis binding, entry, and infection. E. chaffeensis entry and infection rates of BMDMs from DNase X(-/-) mice and bacterial load in the peripheral blood in experimentally infected DNase X(-/-) mice, were significantly lower than those from wild-type mice. Thus this obligatory intracellular pathogen evolved a unique protein EtpE that binds DNase X to enter and infect eukaryotic cells. This study is the first to demonstrate the invasin and its mammalian receptor, and their in vivo relevance in any ehrlichial species.
Searching for Storiness: Story-Generation from a Reader's Perspective (1999)

Previous work in the field of automatic story-generation has largely neglected reader-response as an important aspect of the success of a story. This paper describes an approach to automatic story-generation based on an intuitive model of the cognitive states and processes within the mind of an imagined reader of the story. Generation assumes a privileged access to the responses of the reader, and proceeds by heuristically searching for story elements which create preferred abstract ‘storiness’ effects for the reader. It is claimed that the model is sensitive to the idiosyncracies of individual readers, but also that it captures useful general properties of stories. Previous work in the field of automatic storygeneration is briefly reviewed, and this new model is placed in context. The model is then motivated, and described in more detail. Finally, the strengths and weaknesses of the model are discussed, and issues of implementation are summarised. The model described in this paper is work-in-progress as part of a PhD at the University of Edinburgh.
Susceptibility to fluconazole of Candida clinical isolates determined by FUN-1 staining with flow cytometry and epifluorescence microscopy (2001)

The susceptibility of clinical Candida isolates to fluconazole was assayed by flow cytometry (FCM) and epifluorescence microscopy (EFM), with FUN-1 staining. In all, 25 clinical isolates of Candida spp. (12 sensitive, 3 dose-dependently sensitive and 10 resistant to fluconazole according to the NCCLS M27-A protocol) were treated with increasing concentrations of fluconazole during 1 or 2 h staining with FUN-1 for 30 min and analysed, respectively, by FCM at 575 nm (FL2) and by EFM. Fluconazole-susceptible strains showed an increased accumulation of FUN-1 in comparison with controls as determined by FCM and a reduced metabolic processing of the probe, confirmed by EFM. Conversely, resistant strains showed decreased FUN-1 staining and were able to process the probe. The fluconazole minimal inhibitory concentrations (MICs) determined by FCM or EFM after FUN-1 staining compared very well with the corresponding values determined by the M27-A protocol, indicating that FUN-1 staining can be used as an alternative to the conventional method. MIC values of resistant strains, with the exception of C. krusei, were lower when treatment with fluconazole followed pre-incubation with 0.1 mM sodium azide, a concentration known to inhibit the activity of efflux pumps. These results show that FUN-1 staining can be used as an alternative and rapid method for the assessment of susceptibility of Candida clinical isolates to fluconazole. Furthermore, the results suggest that resistance of Candida cells to fluconazole, with the exception of C. krusei strains, is likely to be due to the activity of efflux pumps.
On orthogonal space-time block codes and transceiver signal linearization (2006)

We present a necessary and sufficient condition for any orthogonal space-time block code (STBC) to allow transceiver signal linearization (as in the well-known case of the Alamouti scheme). Then, we show that all square orthogonal STBC's that satisfy the condition have rate that goes to zero linearly with the number of transmit antennas. Hence, multiple-antenna systems with orthogonal STBC's and satisfactory rate are possible only If we abandon the linearization property or utilize non-square codes (except for the 2 /spl times/ 2 Alamouti code).
An Update on CRF Mechanisms Underlying Alcohol Use Disorders and Dependence (2016)

Alcohol is the most commonly used and abused substance worldwide. The emergence of alcohol use disorders, and alcohol dependence in particular, is accompanied by functional changes in brain reward and stress systems, which contribute to escalated alcohol drinking and seeking. Corticotropin-releasing factor (CRF) systems have been critically implied in the transition toward problematic alcohol drinking and alcohol dependence. This review will discuss how dysregulation of CRF function contributes to the vulnerability for escalated alcohol drinking and other consequences of alcohol consumption, based on preclinical evidence. CRF signaling, mostly <i>via</i> CRF1 receptors, seems to be particularly important in conditions of excessive alcohol taking and seeking, including during early and protracted withdrawal, relapse, as well as during withdrawal-induced anxiety and escalated aggression promoted by alcohol. Modulation of CRF1 function seems to exert a less prominent role over low to moderate alcohol intake, or to species-typical behaviors. While CRF mechanisms in the hypothalamic-pituitary-adrenal axis have some contribution to the neurobiology of alcohol abuse and dependence, a pivotal role for extra-hypothalamic CRF pathways, particularly in the extended amygdala, is well characterized. More recent studies further suggest a direct modulation of brain reward function by CRF signaling in the ventral tegmental area, nucleus accumbens, and the prefrontal cortex, among other structures. This review will further discuss a putative role for other components of the CRF system that contribute for the overall balance of CRF function in reward and stress pathways, including CRF2 receptors, CRF-binding protein, and urocortins, a family of CRF-related peptides.
Integrating Online Multimedia into College Course and Classroom: With Application to the Social Sciences (2009)

Description centers on an approach for efficiently incorporating online media resources into course and classroom. Consideration is given to pedagogical rationale, types of media, locating programs and clips, content retrieval and delivery, copyright issues, and typical problems experienced by instructors and students using online resources. In addition, selected media-relevant websites appropriate to the social sciences along with samples of digital materials gleaned from these sites are listed and discussed.
Chlordecone (kepone®)‐potentiated carbon tetrachloride hepatotoxicity in partially hepatectomized rats — a histomorphometric study (1989)

Our previous studies indicated the involvement of some unidentified mechanisms, apart from the bioactivation phenomenon, in chlordecone (CD)-potentiated CCl4 hepatotoxicity and lethality. Recent studies revealed that hepatocellular regeneration is suppressed in CD + CCl4 toxicity. The present work is a continuation of our earlier work employing a partial hepatectomy model for stimulating hepatocellular division, in normal (N) or CD-treated (10 ppm for 15 days) rats. Male Sprague-Dawley rats maintained on an appropriate dietary protocol and undergoing sham (SH) or partial hepatectomies (PH) were employed. Hepatocellular regeneration was assessed by measuring the percentage mitotic figures and by autoradiography of liver sections from rats given 3H-thymidine in vivo. Hepatotoxicity was assessed by examining liver sections for necrotic cells, swollen cells and cells having lipid droplets. CCl4 (100 microliters kg-1)-induced histopathological alterations in CD-pretreated rats were significantly decreased in rats 2 days post-PH (PH2) as compared to SH rats or rats 7 days post-PH (PH7), indicating that amplification of CCl4 toxicity is significantly reduced when there is a greater regenerative activity. The percentage of mitoses as well as the percentage of labelled cells were significantly elevated at 2-6 h after CCl4 administration in N rats but remained suppressed in CD rats. In CD-pretreated PH2 rats where the percentage of mitoses and the percentage of labelled cells were many-fold greater when compared to SH or PH7 rats, a portion of the stimulated hepatocellular division decreased significantly at 2-6 h after CCl4 administration, but remained significantly greater when compared to basal level of regeneration.(ABSTRACT TRUNCATED AT 250 WORDS)
An implant-supported removable partial denture on milled bars to compromise the inadequate treatment plan: a clinical report. (2010)

SUMMARY This report illustrates how improper planning may pro-long treatment and give rise to complicated treatment proce-dure with poor prognosis. Countermeasures in this case con-sisted of correcting to an implant supported removable partialdenture in conjunction with careful evaluation of the oralcondition during treatment. Dental treatment should be basedon an adequate treatment plan, and procedures must be guid-ed by proper planning achieved by cooperation betweenimplant surgeon and restorative dentist. Implant-supported remov-able-type prosthesis with milled bar and attachment is aviable and useful treatment option in patients with improperlyplaced implants. REFERENCES 1. Budtz-Jo ¨ rgensen E. Restoration of the partially edentulousmouth-a comparison of overdentures, removable partial dentures,fixed partial dentures and implant treatment. J Dent 1996;24:237-44.2. Keltjens HM, Kayser AF, Hertel R, Battistuzzi PG. Distal ex-tension removable partial dentures supported by implants andresidual teeth: considerations and case reports. Int J OralMaxillofac Implants 1993;8:208-13.3. Halterman SM, Rivers JA, Keith JD, Nelson DR. Implant sup-port for removable partial overdentures: a case report. ImplantDent 1999;8:74-8.4. Schulte J, Flores AM, Weed M. Crown-to-implant ratios of sin-gle tooth implant-supported restorations. J Prosthet Dent2007;98:1-5.5. Chronopoulos V, Sarafianou A, Kourtis S. The use of dental im-plants in combination with removable partial dentures: a case re-port. J Esthet Restor Dent 2008;20:355-64.6. Starr NL. The distal extension case: an alternative restorative de-sign for implant prosthetics. Int J Periodontics RestorativeDent 2001;21:61-7.7. Mijiritsky E. Implants in conjunction with removable partial den-tures: a literature review. Implant Dent 2007;16:146-54.
New fluorescence assay for the quantitation of fungi (1989)

Quantitative determination of fungal mass is easily achieved with a new procedure that detects particle epifluorescence. Fungi are detected after exposure to a fluorescent stain (Fungiqual; CIBA-GEIGY Corp., Summit, N.J.) by using a fluorescence particle concentration analyzer. This report describes a simple fluorescence method for quantitation of either yeast or mycelial forms of fungi. The nature of the staining reaction was studied, and a practical application of this procedure for determination of fungal susceptibility to an antifungal agent is presented.
3D stack packaging solution for BAW devices: 3D packaging demonstrator and RF performance (2011)

This paper presents a 3D integration concept as a solution to package FBAR or BAW devices providing at the same time additional RF functionality. The feasibility of this 3D packaging solution has been proven by the successful realization of a 3D packaging demonstration vehicle including FBAR device, solder ring, bumps, through substrate via, low loss interconnects and extra integrated RF functionality. A good RF performance has been obtained. This concept could also be used for the packaging of MEMS, since the requirements are similar.
[Clinical experience with enzymes (collagenase, protease) in the treatment of skin lesions caused by CO2-laser surgery]. (1998)

The authors applied collagenase and protease in lipofil solution for the treatment of skin lesions caused by CO2 laser interventions. 354 surgical interventions were performed on 91 patients (43 verruca vulgaris, 32 naevus intradermalis, 16 keratosis). The laser methods were excision or/and vaporisation of the lesion. The authors created methodological groups and all of the patients had a control laser wounds without enzymatic treatment. The patients were controlled periodically from the 1st to the 56th postoperative day. The first experience shows that, the use of enzymatic treatment is advantageous for the laser wounds healing. The colour, scar formation and other aspects proved to be better after the enzymatic treatment. The optimal method was the use of the cream for 2-4 postoperative days on very thin layer, without bandage. The result seemed to be better compared with the enzymatically untreated cases.
Transcription of the Escherichia coli adenylate cyclase gene is negatively regulated by cAMP-cAMP receptor protein. (1985)

The regulatory region of the Escherichia coli cya gene was analyzed by using S1 nuclease mapping and in vitro transcription experiments. The cya gene was transcribed, both in vivo and in vitro, from one major promoter (P2) and two weak promoters (P1 and P1') that are located about 200 base pairs upstream of P2. The transcription from P2 was specifically inhibited by cAMP-CRP (cAMP receptor protein) in vitro. This regulatory mechanism was shown to be physiologically relevant through quantitative analyses of the cya mRNA in intact cells by S1 and dot blot assays. DNase I protection experiments revealed that cAMP-CRP binds to the cya DNA region between +11 and -20, in which a consensus CRP binding sequence is present. Moreover, it was found that cAMP-CRP alters the binding of RNA polymerase to the promoter region, thus inhibiting the transcription of the cya gene.
Visualising the Score: Screening Scores in Realtime Performance (2011)

This paper examines the screening of music notations and the impact of this configuration in a live music performance situation. Before the development of graphical computing, Traditional music notation, was rarely shared with the anyone other than other musicians, composers and analysts; let alone displayed during the performance. However, some composers experiment with scores and their visual presence in performance by employing automated ‗score-players‘ or actual films specifically developed to be interpreted by musicians. This paper raises some questions and possibilities for this new way of sharing musical qualities of composition and performance.