gebhart/patrepeval huggingface dataset:
Pydron: semi-automatic parallelization for multi-core and the cloud (2014)

The cloud, rack-scale computing, and multi-core are the basis for today's computing platforms. Their intrinsic parallelism is a challenge for programmers, specially in areas lacking the necessary economies of scale in application/ code reuse because of the small number of potential users and frequently changing code and data. In this paper, based on an on-going collaboration with several projects in astrophysics, we present Pydron, a system to parallelize and execute sequential Python code on a cloud, cluster, or multi-core infrastructure. While focused on scientific applications, the solution we propose is general and provides a competitive alternative to moving the development effort to application specific platforms. Pydron uses semi-automatic parallelization and can parallelize with an API of only two decorators. Pydron also supports the scheduling and run-time management of the parallel code, regardless of the target platform. First experiences with real astrophysics data pipelines indicate Pydron significantly simplifies development without sacrificing the performance gains of parallelism at the machine or cluster level.
Cell loss in the aging retina. Relationship to lipofuscin accumulation and macular degeneration. (1989)

We examined the impact of aging on the numbers of photoreceptors and retinal pigment epithelium (RPE) cells, and the number of photoreceptors per RPE cell profile, in selected regions of 30 human eyes. The mean ratio of photoreceptors to RPE cell was higher in the macula than in the paramacula (P less than 0.01) or the equatorial area (P less than 0.001). We found evidence for an age-related loss of RPE in both whites (P less than 0.02) and blacks (P less than 0.0006), although the rate of loss in whites was significantly slower than in blacks. Photoreceptor loss in blacks was inversely correlated with age (P less than 0.04). In whites, however, photoreceptor loss was very significantly and directly correlated with lipofuscin concentration in the opposing RPE (P less than 0.0001) and unrelated to age. The disparity in the rates of photoreceptor and RPE cell loss produced, in older eyes, a higher ratio of photoreceptors per RPE cell profile. In the macula, the ratio for whites over 50 years of age was significantly higher (P less than 0.05) than that in blacks over 50. Our data suggest that the increased phagocytic and metabolic load on the RPE, which ultimately the macula causes a preferential age-related accumulation of lipofuscin in the RPE, which ultimately leads to photoreceptor death. This may prove a useful model of age-related macular degeneration and Stargardt's disease.
Performance without pain = productivity (2008)

The next generations of supercomputers are projected to have hundreds of thousands of processors. However, as the numbers of processors grow, the scalability of applications will be the dominant challenge. This forces us to reexamine some of our fundamental ways that we approach the design and use of parallel languages and runtime systems.
Crusted Demodicosis in an Immunocompetent Pediatric Patient (2014)

Demodicosis refers to the infestation by Demodex spp., a saprophytic mite of the pilosebaceous unit. Demodex proliferation can result in a number of cutaneous disorders including pustular folliculitis, pityriasis folliculorum, papulopustular, and granulomatous rosacea, among others. We report the case of a 7-year-old female presenting with pruritic grayish crusted lesions over her nose and cheeks, along with facial erythema, papules, and pustules. The father referred chronic use of topical steroids. A potassium hydroxide mount of a pustule scraping revealed several D. folliculorum mites. Oral ivermectin (200 μ g/kg, single dose) plus topical permethrin 5% lotion applied for 3 consecutive nights were administered. Oral ivermectin was repeated every week and oral erythromycin plus topical metronidazole cream was added. The facial lesions greatly improved within the following 3 months. While infestation of the pilosebaceous unit by Demodex folliculorum mites is common, only few individuals present symptoms. Demodicosis can present as pruritic papules, pustules, plaques, and granulomatous facial lesions. To our knowledge, this is the first reported case of facial crusted demodicosis in an immunocompetent child. The development of symptoms in this patient could be secondary to local immunosuppression caused by the chronic use of topical steroids.
Genetic Differentiation between Fake Abalone and Genuine Haliotis Species Using the Forensically Informative Nucleotide Sequencing (FINS) Method (2011)

Abalones ( Haliotis species) are a popular delicacy and commonly preserved in dried form either whole or in slices or small pieces for consumption in Asian countries. Driven by the huge profit from trading abalones, dishonest traders may substitute other molluscan species for processed abalone, of which the morphological characteristics are frequently lost in the processed form. For protection of consumer rights and law enforcement against fraud, there is a need for an effective methodology to differentiate between fake and genuine abalone. This paper describes a method (validated according to the international forensic guidelines provided by SWGDAM) for the identification of fake abalone species using forensically informative nucleotide sequence (FINS) analysis. A study of the local market revealed that many claimed "abalone slice" samples on sale are not genuine. The fake abalone samples were found to be either volutids of the genus Cymbium (93%) or the muricid Concholepas concholepas (7%). This is the first report of Cymbium species being used for the preparation and sale as "abalone" in dried sliced form in Hong Kong.
Effect of a single injection of humanized anti-CD154 monoclonal antibody on the platelet-specific autoimmune response in patients with immune thrombocytopenic purpura (2003)

Blockade of the CD40/CD154 signal is a potential immunomodulatory strategy for T-cell-mediated diseases. As a part of a phase 1, multicenter, dose-escalating trial of humanized monoclonal antibody to CD154 (IDEC-131/E6040) in patients with refractory immune thrombocytopenic purpura (ITP), the autoimmune response to glycoprotein IIb/IIIa (GPIIb/IIIa) was evaluated at successive time points. Five patients each were given a single infusion of 1, 2, 5, or 10 mg/kg IDEC-131/E6040 and followed for 3 months. All adverse events were mild, and there were no severe infections or thromboembolic events. No increase in platelet count was observed in patients treated at 1, 2, or 5 mg/kg, but an increase was observed in 3 patients treated at 10 mg/kg. In only the patients treated at 5 or 10 mg/kg, the frequency of B cells producing anti-GPIIb/IIIa antibodies, GPIIb/IIIa-induced T-cell proliferation, and anti-GPIIb/IIIa antibody production by antigen-dependent T-B-cell collaboration were all suppressed in parallel after the treatment, with a slow return to baseline. In contrast, T-cell response to an irrelevant antigen was not affected. These findings suggest that CD40/CD154 blockade therapy is potentially effective for refractory ITP, through selective suppression of autoreactive T and B cells to platelet antigens.
Truxene Derivatives (1981)

Abstract Eight hexa-n-alkanoyloxy truxenes are presented. These new disc-like liquid crystals exhibit both columnar and N D nematic phases. The N D nematic phase is the first low temperature one. All these compounds show an inverted nematic-columnar sequence: the fluid N D nematic phase is observed while heating after the crystalline phase below one or two viscous columnar phases and shows a phenomenon quite similar to the reentrant nematic behaviour.
Prevention of Persistent Human Papillomavirus Infection by an HPV16/18 Vaccine: A Community-Based Randomized Clinical Trial in Guanacaste, Costa Rica (2011)

Target groups for human papillomavirus (HPV) vaccination are controversial. We evaluated vaccine efficacy (VE) against 1-year persistent infection, stratified by age and sexual behavior, among young women in Costa Rica. We randomized 7,466 healthy women 18 to 25 years of age to HPV16/18 or hepatitis A vaccine (follow-up, 50.4 months). According-to-protocol (ATP) cohorts included compliant HPV-negative women; intention-to-treat (ITT) included all randomized women. ATP VE was 90.9% (95% CI, 82.0-95.9) against HPV16/18 infections, 44.5% against HPV31/33/45 (95% CI, 17.5-63.1), and 12.4% (95% CI, -3.2 to 25.6) against any oncogenic infection. Overall ITT VE against HPV16/18 infections was 49.0%, but ATP and ITT VE almost reached 100% in year 4 of follow-up. ATP efficacy against HPV16/18 was similar by age, but ITT VE was greatest among youngest women (68.9% among those 18-19 years of age; 21.8% among those 24-25 years of age) and 79.8% among virgins. Among previously unexposed women, vaccination is highly efficacious against HPV16/18 and partially against HPV31/33/45. Vaccination is most effective in women and girls before they initiate sexual activity, with programmatic and individual decision implications.
Role of Hydrogen Bonds in the Reaction Mechanism of Chalcone Isomerase (2002)

In flavonoid, isoflavonoid, and anthocyanin biosynthesis, chalcone isomerase (CHI) catalyzes the intramolecular cyclization of chalcones into (S)-flavanones with a second-order rate constant that approaches the diffusion-controlled limit. The three-dimensional structures of alfalfa CHI complexed with different flavanones indicate that two sets of hydrogen bonds may possess critical roles in catalysis. The first set of interactions includes two conserved amino acids (Thr48 and Tyr106) that mediate a hydrogen bond network with two active site water molecules. The second set of hydrogen bonds occurs between the flavanone 7-hydroxyl group and two active site residues (Asn113 and Thr190). Comparison of the steady-state kinetic parameters of wild-type and mutant CHIs demonstrates that efficient cyclization of various chalcones into their respective flavanones requires both sets of contacts. For example, the T48A, T48S, Y106F, N113A, and T190A mutants exhibit 1550-, 3-, 30-, 7-, and 6-fold reductions in k(cat) and 2-3-fold changes in K(m) with 4,2',4'-trihydroxychalcone as a substrate. Kinetic comparisons of the pH-dependence of the reactions catalyzed by wild-type and mutant enzymes indicate that the active site hydrogen bonds contributed by these four residues do not significantly alter the pK(a) of the intramolecular cyclization reaction. Determinations of solvent kinetic isotope and solvent viscosity effects for wild-type and mutant enzymes reveal a change from a diffusion-controlled reaction to one limited by chemistry in the T48A and Y106F mutants. The X-ray crystal structures of the T48A and Y106F mutants support the assertion that the observed kinetic effects result from the loss of key hydrogen bonds at the CHI active site. Our results are consistent with a reaction mechanism for CHI in which Thr48 polarizes the ketone of the substrate and Tyr106 stabilizes a key catalytic water molecule. Hydrogen bonds contributed by Asn113 and Thr190 provide additional stabilization in the transition state. Conservation of these residues in CHIs from other plant species implies a common reaction mechanism for enzyme-catalyzed flavanone formation in all plants.
MOF bio-composites for biocatalysis (2017)

Among the different classes of Metal-Organic Framework (MOF) composites prepared during recent years using ceramic, metallic and polymeric nanoparticles, a new emerging type of MOF composite has been recently obtained by encapsulating bio-macromolecules.[1,2] Different water-based synthetic approaches such as co-precipitation and biomimetic mineralization methods, were used to self-assembly different types of MOFs around bio-active compounds (e.g. enzymes). These new biocatalytic porous compounds have shown unprecedented properties for the protection and release of enzymes.[1] Biomimetic mineralization methods overcome the need for MOFs with pores larger than the hosted biomolecules, and enable one-pot syntheses as an alternative preparation route to post infiltration methods.[8] Thus, MOFs are now considered promising materials for biotechnological applications as the encapsulation technique is rapid and inexpensive. [1] In this presentation, the progress from the encapsulation of enzymes [9] up to their combination with cells for their preservation. The functional properties of these composites will be disclosed providing examples of other methods used for the encapsulation of enzymes within MOFs.[3] Comparison of the protective properties will be illustrated and the applications of proteins for the controlled localization of MOFs discussed.
Identification of transcripts by macroarrays, RT–PCR and in situ hybridization in human ejaculate spermatozoa (2005)

Round spermatids contain high levels of extremely varied mRNAs that are synthesized either throughout early spermatogenesis or during spermiogenesis from the haploid genome. Concomitantly, with major changes in the chromatin organization, arrest of transcription occurs at midspermiogenesis. However, previous investigations using RT-PCR have revealed the persistence of numerous and different transcripts in ejaculated spermatozoa. In the present study, a step-by-step analysis by means of macroarray hybridization, RT-PCR and in situ hybridization was performed to identify more accurately the different mRNA species found in the human ejaculated spermatozoa. The data showed an extended pattern of various transcripts encoding a diverse range of proteins involved in signal transduction and cell proliferation. For the first time, they demonstrated that mRNAs coding for the transcription factors NFkappaB, HOX2A, ICSBP, protein kinase JNK2, growth factor HBEGF and receptors RXRbeta and ErbB3 accumulate within the sperm nucleus. The origin and fate of the sperm transcripts remain subject to discussion.
The architecture of the animal fatty acid synthetase. III. Isolation and characterization of beta-ketoacyl reductase. (1983)

Sequential treatment of the chicken liver fatty acid synthetase by trypsin and subtilisin cleaved the Mr 267,000 subunit to 6-8 polypeptides, ranging in molecular weights from 15,000 to 94,000. Fractionation of the digest by ammonium sulfate and chromatography on a Procion Red HE3B affinity column permitted the isolation of a polypeptide (Mr = 94,000) containing the beta-ketoacyl reductase activity but no other partial activities normally associated with the synthetase. The specific activity of the beta-ketoacyl reductase increased 2 to 3 times in this fraction, an increase that is within the expected range based on relative molecular weight. The kinetic parameters of this fraction towards NADPH and N-acetyl-S-acetoacetyl cysteamine were essentially the same as the beta-ketoacyl reductase component of the intact synthetase. However, the purified fragment did not catalyze the reduction of acetoacetyl-S-CoA derivative, a substrate that is readily reduced by the intact synthetase. Fluorescence measurements with etheno-NADP+ indicate the binding of about 1 mol of NADP+/94,000 daltons, a value which is in agreement with the results obtained from fluorescence measurements with NADPH and the binding of a radiolabeled photoaffinity analog of NADP+. Phenylglyoxal inhibits the beta-ketoacyl reductase activity of either the intact synthetase or the isolated fragment, suggesting the involvement of an essential arginine at or near the active site. Another fragment (Mr 36,000) containing beta-ketoacyl reductase activity was isolated from the synthetase after kallikrein/subtilisin double digestion. Previous mapping studies had shown that this fragment lies adjacent to the COOH-terminal thioesterase domain and overlaps the tryptic Mr 94,000 peptide by approximately 21 daltons. This fragment, but not the Mr 94,000 fragment, was found to contain the phosphopantetheine prosthetic group, indicating that the acyl carrier protein moiety is located in the 15,000-dalton segment that separates the beta-ketoacyl reductase from the thioesterase domain.
Storage of vaccines in the community: weak link in the cold chain? (1992)

Vaccines were exposed to temperatures that may reduce their potency. Safe storage of vaccines in the clinics cannot be ensured without adhering to the recommended guidelines. Provision of adequate equipment and training for staff in maintaining the "cold chain" and the use and care of equipment are important components of a successful immunisation programme.
Multi-channel sampling of low-pass signals (1981)

A deterministic signal x(t) band limited to <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">|\omega| &lt; \sigma</tex> is passed through m linear time-invariant filters (channels) to obtain the m outputs <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">z_1(t),\cdots,Z_m(t)</tex> . If the filters are independent in a sense to be defined, then It Is shown that the common input <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x(t)</tex> may be reconstructed from samples of the outputs <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">(Z_k)</tex> , each output being sampled at <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m \Pi</tex> samples per second or <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">(1/m)</tex> th the rate associated with the Input signal. A rigorous derivation of this result Is given which proceeds from a minimum error energy criterion and leads to a system of linear algebraic equations for the optimal reconstruction filters. The system of equations derived here, which differs from the system given recently by Papoulis [1], has the advantage of depending on only one parameter <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\omega</tex> rather than on the two parameters <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\omega</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</tex> ; it also puts into evidence the fact that the spectra of the optimal reconstruction filters can be pieced together directly, without additional computation, from the elements of the system's inverse matrix. Lastly, the solutions of the system obtained in the Papoulis formulation are shown to be time-varying linear combinations of the simpler one-parameter solutions.
A Comparative Study on Two Cationic Porphycenes: Photophysical and Antimicrobial Photoinactivation Evaluation (2015)

Over the last decades, the number of pathogenic multi-resistant microorganisms has grown dramatically, which has stimulated the search for novel strategies to combat antimicrobial resistance. Antimicrobial photodynamic therapy (aPDT) is one of the promising alternatives to conventional treatments based on antibiotics. Here, we present a comparative study of two aryl tricationic porphycenes where photoinactivation efficiency against model pathogenic microorganisms is correlated to the photophysical behavior of the porphycene derivatives. Moreover, the extent of photosensitizer cell binding to bacteria has been assessed by flow cytometry in experiments with, or without, removing the unbound porphycene from the incubation medium. Results show that the peripheral substituent change do not significantly affect the overall behavior for both tricationic compounds neither in terms of photokilling efficiency, nor in terms of binding.
EXTH-56. TARGETING GBM WITH AN ONCOLYTIC PICORNAVIRUS SVV-001 ALONE AND IN COMBINATION WITH FRACTIONATED RADIATION IN A NOVEL PANEL OF ORTHOTOPIC PDX MODELS (2022)

Abstract BACKGROUND Large panels of clinically relevant animal models are needed for the development of new therapies for GBM. SVV-001, a replication-competent oncolytic virus that can pass through the blood brain barrier, represents an attractive novel approach. Material and METHODS Surgical tissues from 23 patients were implanted into the brains of NOD/SCID mice (1x105 cells/mouse) to develop patient-derived orthotopic xenograft (PDOX) models. Analysis of histology, gene expression (RNAseq), tumor growth was performed and compared with the patient tumors during subtransplantations (up to 5 passages). Anti-tumor activities of SVV-001 were examined in vitro in primary monolayer cultures, 3D neurospheres and purified glioma stem cells derived from 13 PDOX models; and its therapeutic efficacy validated in vivo in PDOX models through single i.v. injection (1x1011 viral particle) alone and in combination with fractionated (2 Gy/day x 5 days) radiation. Changes of animal survival times were analyzed together with viral infection, cell proliferation and DNA damage. RESULTS PDOX formation was confirmed in 17/23 (73.9%) GBMs. They replicated key histopathological features and diffuse invasion of the patient tumors. RNAseq identified the differentially expressed genes and subclassified PDOX models into proneural, classic and mesenchymal groups. SVV-001 killed primary monolayer cultures (4/13 models) and neurosphere (7/13 models) and putative glioma stem cells (CD133+ and/or CD15+ cells) in vitro, infected PDOX tumors without harming normal brain cells in vivo and significantly prolonged survival times in 2/2 models. Combination with radiation showed a trend in further prolonging animal survival times through enhanced DNA damages by SVV-001. CONCLUSION A panel of 17 clinically relevant and molecularly annotated PDOX modes of GBM is developed. The strong anti-tumor activities of SVV-001 in vitro and in vivo in GBM models provided experimental rational that support the initiation of clinical trials in GBM patients.
Mitigative techniques for ground-water contamination associated with severe nuclear accidents. Analysis of generic site conditions. Volume 1 (1985)

The Pacific Northwest Laboratory evaluated the feasibility of using ground-water contaminant mitigation techniques to control radionuclide migration following a severe commercial nuclear power reactor accident. The two types of severe commercial reactor accidents investigated are: (1) containment basemat penetration of core melt debris which slowly cools and leaches radionuclides to the subsurface environment, and (2) containment basemat penetration of sump water without full penetration of the core mass. Six generic hydrogeologic site classifications were developed from an evaluation of reported data pertaining to the hydrogeologic properties of all existing and proposed commercial reactor sites. One-dimensional radionuclide transport analyses were conducted on each of the individual reactor sites to determine the generic characteristics of a radionuclide discharge to an accessible environment. Ground-water contaminant mitigation techniques that may be suitable, depending on specific site and accident conditions, for severe power plant accidents were identified and evaluated. Feasible mitigative techniques and associated constraints on feasibility were determined for each of the six hydrogeologic site classifications. Three case studies were conducted at power plant sites located along the Texas Gulf Coast and the Ohio River. Mitigative strategies were evaluated for their impact on contaminant transport. Results show that the techniques evaluated significantly increased ground-watermore » travel times and reduced contaminant migration rates.« less