gebhart/patrepeval huggingface dataset:
Biosynthesis and Functions of a Melanoid Pigment Produced by Species of the Sporothrix Complex in the Presence of l -Tyrosine (2012)

Sporothrix schenckii is the etiological agent of sporotrichosis, the main subcutaneous mycosis in Latin America. Melanin is an important virulence factor of S. schenckii, which produces dihydroxynaphthalene melanin (DHN-melanin) in conidia and yeast cells. Additionally, l-dihydroxyphenylalanine (l-DOPA) can be used to enhance melanin production on these structures as well as on hyphae. Some fungi are able to synthesize another type of melanoid pigment, called pyomelanin, as a result of tyrosine catabolism. Since there is no information about tyrosine catabolism in Sporothrix spp., we cultured 73 strains, including representatives of newly described Sporothrix species of medical interest, such as S. brasiliensis, S. schenckii, and S. globosa, in minimal medium with tyrosine. All strains but one were able to produce a melanoid pigment with a negative charge in this culture medium after 9 days of incubation. An S. schenckii DHN-melanin mutant strain also produced pigment in the presence of tyrosine. Further analysis showed that pigment production occurs in both the filamentous and yeast phases, and pigment accumulates in supernatants during stationary-phase growth. Notably, sulcotrione inhibits pigment production. Melanin ghosts of wild-type and DHN mutant strains obtained when the fungus was cultured with tyrosine were similar to melanin ghosts yielded in the absence of the precursor, indicating that this melanin does not polymerize on the fungal cell wall. However, pyomelanin-producing fungal cells were more resistant to nitrogen-derived oxidants and to UV light. In conclusion, at least three species of the Sporothrix complex are able to produce pyomelanin in the presence of tyrosine, and this pigment might be involved in virulence.
Defective co‐activator recruitment in osteoclasts from microphthalmia‐oak ridge mutant mice (2009)

The three basic DNA-binding domain mutations of the microphthalmia-associated transcription factor (Mitf), Mitf(mi/mi), Mitf(or/or), and Mitf(wh/wh) affect osteoclast differentiation with variable penetrance while completely impairing melanocyte development. Mitf(or/or) mice exhibit osteopetrosis that improves with age and their osteoclasts form functional multinuclear osteoclasts, raising the question as to why the Mitf(or/or) mutation results in osteopetrosis. Here we show that Mitf(or/or) osteoclasts express normal levels of acid phosphatase 5 (Acp5) mRNA and significantly lower levels of Cathepsin K (Ctsk) mRNA during receptor activator of nuclear factor kappa B (NFkappaB) ligand (RANKL)-mediated differentiation. Studies using chromatin immunoprecipitation (ChIP) analysis indicate that low levels of Mitf(or/or) protein are recruited to the Ctsk promoter. However, enrichment of Mitf-transcriptional co-activators PU.1 and Brahma-related gene 1 (Brg1) are severely impaired at the Ctsk promoter of Mitf(or/or) osteoclast precursors, indicating that defective recruitment of co-activators by the mutant Mitf(or/or) results in impaired Ctsk expression in osteoclasts. Cathepsin K may thus represent a unique class of Mitf-regulated osteoclast-specific genes that are important for osteoclast function.
Effect of multi-micronutrient on yield and quality attributes of the sweet orange (2012)

Field experiment was conducted for two successive years on sweet orange to evaluate the effect of multi-micronutrient on yield and quality attributes of sweet orange grown on Inceptisols of Aurangabad district of Maharashtra, India. The result indicates that the number of fruits per tree increased with the application of balanced dose of NPK along with multi-micronutrient from 426 to 554. Similarly, weight of fruit per tree was ranged from 72.42 kg/tree in control to 143.80 kg/tree in the treatment receiving multi-micronutrients through soil. Productivity was also enhanced from 20.06 to 39.83 t/ha due to application of multi-micronutrients along with recommended NPK. The quality of the fruits in terms of juice, TSS, fruit girth, ascorbic acid content, reducing and non-reducing sugar increased with the application of multi-micronutrient and NPK either applied through soil or fertigation, whereas, acidity of the fruit juice was found highest in untreated control as compared to balance nutrient application.

	 

	Key words: Multi-micronutrient, sweet orange, NPK, quality of fruit.
Isolation of triploid and tetraploid olive (Olea europaea L.) plants from mixoploid cv. ‘Frantoio’ and ‘Leccino’ mutants by in vivo and in vitro selection (1996)

Abstract This paper reports a procedure for isolating triploid and tetraploid olive plants, which have not been produced before either artificially or in nature. These polyploids were isolated from two mixoploid somatic mutants obtained earlier by treating Trantoio' and ‘Leccino’ plantlets with gamma radiation. The mixoploid mutants exhibit increased thickness of leaf, stem and root tissues, short internodes, a modified leaf lamina shape and a strong resistance to Spilocaea oleagina (Cast.) Hugh. In addition, they produce a mixture of normal drupes and some abnormally large ones, almost twice normal size. The variation in the nuclear DNA content of the mixoploid mutants is closely correlated with variation in their pollen size, crop capacity and the production of large fruit. Triploid genotypes with 69 chromosomes were isolated by germinating the seeds of these large fruits, collected from both the mixoploid mutants. Tetraploid plantlets, with 92 chromosomes, were obtained from cv. ‘Frantoio’ by selecting in vitro , during several proliferation phases, the shoots with obvate leaf shape which occurred among the shoots with normal lanceolate or intermediate leaf shape.
Nano-Ablation of Inorganic Materials Using Laser Plasma Soft X-rays at around 10 nm (2006)

We have investigated the direct nanomachining of inorganic materials using laser plasma soft X-rays (LPSXs). LPSXs were generated by the irradiation of Ta targets with Q-switched 532 nm Nd:YAG laser light at an energy density of ∼104 J/cm2. Under this condition, Ta plasma emits soft X-rays at around 10 nm. The LPSXs were focused on the surfaces of inorganic materials, using an ellipsoidal mirror that we desined so as to focus LPSXs at around 10 nm efficiently. We found that synthetic quartz glass, fused silica, Pyrex, LiF, CaF2, Al2O3, and LiNbO3 can be machined. Typically, silica glass is ablated at 47 nm/shot, and it has a surface roughness less than 10 nm after 10 shots. To demonstrate lateral resolution, we fabricated a WSi contact mask with 200-nm-pitch line-and-space patterns on quartz glass. After soft X-ray irradiation, trench structures with a width of 70 nm were clearly observed.
Prototyping 1,4-butanediol (BDO) biosynthesis pathway in a cell-free transcription-translation (TX-TL) system (2015)

Abstract Current methods for assembling metabolic pathways require a process of repeated trial and error and have a long design-build-test cycle. Further, it remains a challenge to precisely tune enzyme expression levels for maximizing target metabolite production. Recently it was shown that a cell-free transcriptional-translation system (TX-TL) can be used to rapidly prototype novel complex biocircuits as well as metabolic pathways. TX-TL systems allow protein expression from multiple DNA pieces, opening up the possibility of modulating concentrations of DNA encoding individual pathway enzymes and testing the related effect on metabolite production. In this work, we demonstrate TX-TL as a platform for exploring the design space of metabolic pathways using a 1,4-BDO biosynthesis pathway as an example. Using TX-TL, we verified enzyme expression and enzyme activity and identified the conversion of 4-hydroxybutyrate to downstream metabolites as a limiting step of the 1,4-BDO pathway. We further tested combinations of various enzyme expression levels and found increasing downstream enzyme expression levels improved 1,4-BDO production.
Revisit of View-Oriented Parallel Programming (2007)

Traditional parallel programming styles have many problems which hinder the development of parallel applications. The message passing style can be too complex for many programmers. While shared memory based parallel programming is relatively easy, it requires programmers to guarantee there is no data race in programs by using mutually exclusive locks. Data race conditions are generally difficult to debug and difficult to prevent as well. The view-oriented parallel programming (VOPP) is a novel shared-memory-based programming style. It removes the burden of guaranteeing data race free from the programmers. With the VOPP approach, shared data objects in a parallel program are divided into views according to the memory access pattern of the parallel algorithm. Data race is not an issue in VOPP, since mutual exclusion is automatically done by the underlying system when a view is accessed. The programmer only needs to synchronize the access of views using synchronization primitives like barriers. By removing data races of view access, VOPP makes it easier to code and less difficult to debug programs. It provides potential performance advantages on multi-core systems as well as cluster computers. It will also provide useful information for efficient implementation of transactional memory.
Media Frames of the Ontario Safe Streets Act: assessing the moral panic model (2011)

This paper assesses the “moral panic” framework of Stanley Cohen with reference to panhandling and squeegeeing in Ontario. There are four general tenets of the moral panic model, three of which can be said to have been documented in the case of panhandling in Ontario: a recognized threat (panhandling), a rise in public concern, and punitive control mechanisms established to eliminate the threat. This paper argues that the fourth tenet, a stereotypical presentation of the moral threat to the social order, has not been systematically analyzed, and therefore that is the task of this paper. Specifically, this paper examines the framing used by the mainstream print media in Ontario to construct the panhandling/squeegeeing problem. Articles and letters­ to the­ editor were sampled from two mainstream Ontario newspapers, the Toronto Star and the Ottawa Citizen, to examine the mainstream media’s framing of panhandling and squeegee cleaning.&#x0D; This sample was taken between 1995 and 2005, a timeframe which revolves around the implementation of the Ontario Safe Streets Act 2000, which is recognized as the punitive control mechanism designed to eliminate the threat of panhandling. The findings of this paper lead to the conclusion that panhandling in Ontario during the implementation of the Ontario Safe Streets Act does not constitute a classic moral panic by virtue of the role the media played. However, the evidence that punitive control mechanisms were established absent the support of the mainstream media suggests that a deeper understanding of the role of mainstream media as well as political interests is required with respect to framing moral panics.
Carbohydrate Coatings via Aryldiazonium Chemistry for Surface Biomimicry (2013)

Carbohydrates are extremely important biomolecules and their immobilization onto solid surfaces is of interest for the development of new biomimetic materials and of new methods for understanding processes in glycobiology. We have developed an efficient surface modification methodology for the functionalization of a range of materials with biologically active carbohydrates based on aryldiazonium chemistry. We describe the synthesis and characterization of carbohydrate reagents, which were subsequently employed for the one-step, solution-based modification of carbon, metals, and alloys with monosaccharides. We used a combination of spectroscopic and nanogravimetric methods to characterize the structure of the carbohydrate layers; we report an average surface coverage of 7.8 × 10–10 mol cm–2 under our experimental conditions. Concanavalin A, a mannose-binding lectin, and Peanut Agglutinin, a galactose-binding lectin, were found to bind from solution to their respective monosaccharide binding partners immobilized at the surface. This result suggests that the spontaneous chemisorption of aryldiazonium monosaccharide precursors leads to the formation of monosaccharide layers that retain the biological recognition specificity of the parent carbohydrate molecule. Finally, we carried out measurements using fluorescently labeled Bovine Serum Albumin (BSA) and found that these carbohydrate coatings reduce unspecific adsorption of this protein at carbon surfaces. These results suggest that aryldiazonium-derived carbohydrate coatings may offer a promising strategy for preventing undesirable protein accumulation onto surfaces.
LIN28B is over-expressed in specific subtypes of pediatric leukemia and regulates lncRNA H19 (2016)

LIN28B is over-expressed in specific subtypes of pediatric leukemia and regulates lncRNA H19
Spatial resolution and spectral information content of proton NMR spectroscopic imaging of tumour metabolism. (1996)

The value of metabolic proton NMR spectroscopic imaging to detect and classify tumours increases with the spatial resolution and the information content of the spectra. Several factors influencing these quantities are discussed.
Detection of early changes in lung cell cytology by flow-systems analysis techniques. Progress report, July 1--December 31, 1977 (1978)

This report summarizes ongoing experiments to develop cytological and biochemical indicators for measuring damage to respiratory tract cells exposed by inhalation of environmental toxic agents. The specific goal of this project is to apply flow cytometric methods to analyze and detect changes in lung epithelium as a function of exposure to toxic agents such as those associated with the production of synthetic fuels from oil shale and coal. The objectives during the past 6 months were to complete modifications to the multiparameter cell separator by adding a krypton laser with an output capability of specific wavelengths ranging from the uv to the ir; analyze and separate lung cells based on their DNA content; evaluate some new fluorescent DNA and protein stains; and treat hamster lung cells with proteolytic enzymes for increasing cell yield. Future experiments will involve the continued analysis and characterization of exfoliated lung cells based primarily on cellular DNA content, protein, morphological features, and specific enzyme activities; quantitation of macrophage activity; exposure of hamsters to toxic agents such as oil shale particulates and ozone; and continued analysis of cells based on DNA content. As this new technology becomes adapted to analyzing respiratory tract cells, the measurement of physical and biochemical cell properties as a function of exposure to toxic agents will be increased. This analytical approach is designed to assist in the establishment of guidelines for estimating risks to exposed humans.
Acute lysis pneumopathy after chemotherapy for acute myelomonocytic leukemia with abnormal marrow eosinophils (1992)

Acute respiratory failure developed in two patients with hyperleukocytic acute myelomonocytic leukemia with abnormal marrow eosinophils within 1 to 3 days after the beginning of high-dose induction chemotherapy. The presence of moderate pulmonary leukostasis before chemotherapy initiation, the simultaneous occurrence of an acute tumor lysis syndrome, the lack of evidence of any other cause of respiratory distress, and the clinical evolution lead the authors to attribute pulmonary injury to lysis of resident leukemic cells. The responsibility of eosinophilic cellular constituents for the diffuse alveolar damage is discussed.
Ballistic- and quantum-conductor carbon nanotubes: A reference experiment put to the test (2014)

Using the liquid metal contact method for in-situ electron transport measurements in TEM, this paper revisits the question of whether carbon nanotubes (CNTs) are diffusive or ballistic conductors. It challenges previous conclusions of many ex-situ measurements that CNTs support ballistic transport and quantum conductance. It also suggests three reasons that possibly led to false positive results in the previous measurements.
Synthesis of New Dihydroindeno[1,2-c]isoquinoline and Indenoisoquinolinium Chloride Topoisomerase I Inhibitors Having High in Vivo Anticancer Activity in the Hollow Fiber Animal Model (2001)

A number of novel dihydroindenoisoquinolines and indenoisoquinolinium salts were synthesized and examined for cytotoxicity in cancer cell cultures and for inhibition of topoisomerase I (top1). The top1-mediated DNA cleavage patterns produced in the presence of several of the new analogues were also investigated, and a few of the more potent compounds were examined for activity in hollow fiber animal models. Very cytotoxic dihydroindenoisoquinoline and isoquinolinium salts were obtained with mean graph midpoints (MGMs) for growth inhibition in the low submicromolar range. Two of the new dihydroindenoisoquinolines were found to be weaker top1 inhibitors than the lead compound 1, while two of the indenoisoquinolinium salts were more potent. The top1-mediated DNA cleavage patterns of the indenoisoquinolines examined were found to be similar to each other but different from that of camptothecin. Several of the more potent indenoisoquinolines displayed promising anticancer activities in hollow fiber animal models.
Cytomegalovirus-specific cytolytic T-cell lines and clones generated against adenovirus-pp65-infected dendritic cells (2001)

Cytomegalovirus (CMV) infection is a serious complication of allogeneic bone marrow transplantation (BMT). CMV disease can usually be prevented by passive immunization with donor-derived CMV-pp65-specific T-cell clones if provided early post-BMT. The classic method of generating CMV-specific T-cell clones requires donor-derived fibroblast lines infected with CMV as stimulators, thus limiting the availability of CMV immunotherapy to those patients for whom a donor skin biopsy can be obtained 6 to 8 weeks pretransplantation. To overcome this limitation we have used monocyte-derived dendritic cells (DCs) to induce donor anti-CMV cytotoxic T lymphocytes (CTLs). Matured, adeno-pp65-infected DCs were added at day 0 and at day 7 of a 2-week culture of donor peripheral blood mononuclear cells. DC-primed cultures were compared with cultures stimulated in an identical fashion with CMV-infected fibroblasts or with adeno-pp65-infected freshly isolated blood monocytes. Specific killing of CMV-infected fibroblasts was detected in all except the culture stimulated with pp65-infected monocytes. DCs infected after maturation elicited greater CTL activity than did DCs matured after infection. A series of 5 CD8+ clones from a fibroblast-stimulated culture and 7 CD8+ clones from a mature-DC-stimulated culture derived from a single HLA-A*0201+ individual were characterized. All 12 clones lysed autologous CMV-infected fibroblasts. All except 1 clone from the CMV-infected fibroblast arm (fibroblast arm) lysed vaccinia-pp65-infected B-lymphoblastoid cell lines (BLCLs); none lysed vaccinia-pp150-infected or noninfected BLCLs. Ten of 10 CD8+ clones tested were restricted by HLA-A*0201. Seven of the 12 clones were Vbeta6+ (2 from the fibroblast arm and 5 from the DC arm) with an identical Vbeta6.1-J1.4 sequence. Three clones from the fibroblast arm and 5 clones from the DC arm recognized the pp65 peptide NLVPMVATV (amino acids [aa], 495-503). These data show that CMV-specific T-cell clones with similar restriction patterns, T cell-receptor usage, and specificity can be generated using monocyte-derived pp65-infected-DC or CMV-infected-fibroblast stimulators. This approach should broaden the applicability of CMV-specific T-cell immunotherapy to a wider spectrum of patients by reducing the time required to generate CMV-specific T-cell clones.
On the reuse of past optimal queries (1995)

an optimal query with respect to a particular information need. Since obtaining an optimal query is an expensive process, the need for mechanisms to save and reuse past optimal queries for future queries is obvions.
Transfer learning of gaits on a quadrupedal robot (2015)

Learning new gaits for compliant robots is a challenging multi-dimensional optimization task. Furthermore, to ensure optimal performance, the optimization process must be repeated for every variation in the environment, for example for every change in inclination of the terrain. This is unfortunately not possible using current approaches, since the time required for the optimization is simply too high. Hence, a sub-optimal gait is often used. The goal in this manuscript is to reduce the learning time of a particle swarm algorithm, such that the robot’s gaits can be optimized over a wide variety of terrains. To facilitate this, we use transfer learning by sharing knowledge about gaits between the different environments. Our findings indicate that using transfer learning new robust gaits can be discovered faster compared to traditional methods that learn a gait for each environment independently.
Synthesis of Sparse Planar Arrays Using Modified Real Genetic Algorithm (2007)

In array design, the positions of sparse array elements is an important concern for optimal performance in terms of its ability to achieve minimum peak sidelobe level (SLL). This paper proposes a modified real genetic algorithm (MGA) based on resetting of chromosome for the element position optimization of sparse planar arrays with rectangular boundary. And here the multiple optimization constraints include the number of elements, the aperture and the minimum element spacing. By simplifying the space between the elements from the actual distance to Chebychev distance, the MGA searches a smaller solution space by means of indirect description of individual, and it can avoid infeasible solution during the optimization process by two novel genetic operators. Finally, the simulation results confirming the great efficiency and the robustness of the proposed method are shown in this paper
Contrasting compressibility trends in layered structures Ag(tcm) and Ni(CN)2 (2014)

Ag(tcm) (tcm = tricyanomethanide) and Ni(CN)2 are layered structures. Both these materials exhibit area negative thermal expansion (area-NTE) due to 'rippling' of the layers - a displacement pattern that causes the interlayer separation to increase and the effective layer area to decrease (Fig. 1a). We have shown that Ag(tcm) shows negative area compressibility (NAC) under hydrostatic pressure. The latter can be attributed to the rippling phenomenon: when hydrostatic pressure is applied, the effective layer area increases (Fig. 1a). On the contrary, Ni(CN)2 shows shows positive linear compressibility in all directions, albeit much more strongly along the stacking axis than in any direction parallel to the square-grid sheets. This is attributed to transverse phonon modes within the Ni(CN)2 sheets, which can be visualised as 'tilting' of the rigid unit modes (RUMs) (Fig. 1b). A discussion of relating such behaviour to the Grüneisen parameters is undertaken in this study.
Ridge waveguide as a near-field optical source (2003)

We investigate the feasibility of using a ridge waveguide at optical frequencies as a near-field optical transducer, using the finite difference time domain method. The complete electromagnetic field picture of the ridge waveguide, in the absence and presence of the irradiated medium, is presented. A power efficiency of 7% and an optical spot with full width half maximum of 50 nm×80 nm is obtained in the medium. We show that impedance considerations play a major role in the transducer-medium optical coupling.