gebhart/patrepeval huggingface dataset:
Analogue-based Drug Discovery (2010)

Analogue-based drug discovery , Analogue-based drug discovery , کتابخانه مرکزی دانشگاه علوم پزشکی تهران
Patterns of lymphatic drainage from the skin in patients with melanoma. (2003)

An essential prerequisite for a successful sentinel lymph node biopsy (SLNB) procedure is an accurate map of the pattern of lymphatic drainage from the primary tumor site in each patient. In melanoma patients, mapping requires high-quality lymphoscintigraphy, which can identify the actual lymphatic collecting vessels as they drain into the sentinel lymph nodes. Small-particle radiocolloids are needed to achieve this goal, and imaging protocols must be adapted to ensure that all true sentinel nodes, including those in unexpected locations, are found in every patient. Clinical prediction of lymphatic drainage from the skin is not possible. The old clinical guidelines based on Sappey's lines therefore should be abandoned. Patterns of lymphatic drainage from the skin are highly variable from patient to patient, even from the same area of the skin. Unexpected lymphatic drainage from the skin of the back to sentinel nodes in the triangular intermuscular space and, in some patients, through the posterior body wall to sentinel nodes in the para-aortic, paravertebral, and retroperitoneal areas has been found. Lymphatic drainage from the head and neck frequently involves sentinel nodes in multiple node fields and can occur from the base of the neck up to nodes in the occipital or upper cervical areas or from the scalp down to nodes at the neck base, bypassing many node groups. The sentinel node is not always found in the nearest node field and is best defined as "any lymph node receiving direct lymphatic drainage from a primary tumor site." Lymphatic drainage can occur from the upper limb to sentinel nodes above the axilla. Drainage to the epitrochlear region from the hand and arm as well as to the popliteal region from the foot and leg is more common than was previously thought. Interval nodes, which lie along the course of a lymphatic vessel between a lesion site and a recognized node field, are not uncommon, especially in the trunk. Drainage across the midline of the body is quite common in the trunk and in the head and neck. Micrometastatic disease can be present in any sentinel node regardless of its location, and for the SLNB technique to be accurate, all true sentinel nodes must be biopsied in every patient.
Tough nuts to crack (2013)

Most members of the genus Bifidobacterium are commensals of the human gastrointestinal tract and some strains were shown to exert beneficial effects on their host. Based on these effects and due to their status as GRAS (generally recognized as safe) microorganisms, specific strains of bifidobacteria are marketed as probiotics. Despite their important role in food and dairy industries, the mechanisms responsible for the probiotic effects of bifidobacteria are mostly unknown. Over the last decade, the genomes of a large number of bifidobacteria have been sequenced and analyzed. This has yielded a number of genes and their products that are speculated to contribute to the probiotic effects of bifidobacteria. The gold standard to demonstrate a role for specific genes is the analysis of mutants. At present, only a small number of mutants of bifidobacteria have been generated by targeted mutagenesis. This is owed to the genetic inaccessibility of most strains and a lack of appropriate molecular tools. Successful generation of mutants of bifidobacteria was achieved by various methods including classical suicide vector strategies, increase of transformation efficiencies by methylation of plasmids and the use of temperature-sensitive vectors. In this commentary, we will describe the methods successfully used for mutagenesis of bifidobacteria and discuss their advantages and limitations.
Rationale For Immune-Based Therapies in Merkel Polyomavirus-Positive and -Negative Merkel Cell Carcinomas (2016)

Merkel cell carcinoma (MCC) is a rare but often deadly skin cancer that is typically caused by the Merkel cell polyomavirus (MCPyV). Polyomavirus T-antigen oncoproteins are persistently expressed in virus-positive MCCs (˜80% of cases), while remarkably high numbers of tumor-associated neoantigens are detected in virus-negative MCCs, suggesting that both MCC subsets may be immunogenic. Here we review mechanisms by which these immunogenic tumors evade multiple levels of host immunity. Additionally, we summarize the exciting potential of diverse immune-based approaches to treat MCC. In particular, agents blocking the PD-1 axis have yielded strikingly high response rates in MCC as compared with other solid tumors, highlighting the potential for immune-mediated treatment of this disease.
Using GPS to Measure the Impact of Construction Activities on Rural Interstates (2006)

The presence of construction work zones on interstates impacts the traveling conditions encountered by motorists. These changes not only affect the traveling public, but also the workers that perform the construction. The impacts of the work being performed also tend to cause queuing. In addition, these periods of construction operations have been linked to an increase in the number of accidents and fatalities that involve road-users and construction crews. A research project was undertaken to evaluate possible options to improve the safety of construction work zones on interstates in the state of Indiana. One component of this project dealt with the use of the Global Positioning System (GPS) to collect traffic data and to relate the traveling conditions encountered with the differing construction activities taking place. This paper describes the GPS study conducted in three different rural work zones on Interstate 65 in Indiana. Multiple runs were conducted at each location to analyze the impact of traveling conditions to changes in lane restrictions during construction periods on traveling conditions.
An improved gas kick detection method based on continuous Doppler ultrasonic wave in deep water drilling (2017)

Gas kick detection is an essential part of safe well control process in deep water drilling. The conventional gas kick detection methods are based on the drilling mud flow velocity measured near the well mouth which often results in a high probability of delay. For deep water drilling, the gas kick detection method based on non-intrusive detection at mud line is one of the most commonly used methods with low cost and strong timeliness. In this article, the reflection model of continuous Doppler ultrasonic wave in multiphase fluid was analyzed and an improved gas kick detection method at mud line was proposed. The proposed method gives a comprehensive judgment on gas kick state based on continuous Doppler shift frequency (multiphase flow velocity), amplitude, and spectral shape. Experimental results on water and 1 . 1 g/cm 3 oil-based drilling mud demonstrated that the proposed method can detect early gas kick with over 3% void fraction effectively and measure multiphase flow velocity accurately under the steady flow state, showing a relative error smaller than 10%.
Virucidal Effect of Stimulated Eosinophils on Human Immunodeficiency Virus Type 1 (1996)

Eosinophils, when stimulated, release a variety of agents that can be toxic to ingested or extracellular targets. Among these systems is one that consists of eosinophil peroxidase (EPO), H2O2, and a halide. We report here that phorbol myristate acetate (PMA)-stimulated human eosinophils are virucidal to HIV-1 in a chloride-containing medium. When the eosinophil concentration is decreased to a level at which the virucidal effect is incomplete, the addition of bromide or iodide restored complete virucidal activity. The virucidal effect of eosinophils, PMA, and bromide under these conditions is inhibited by the peroxidase inhibitor azide and catalase, but not heated catalase or superoxide dismutase, implicating the EPO-H2O2-halide system. Purified EPO when combined with H2O2 in a chloride-containing medium is virucidal to HIV-1. When the EPO concentration is suboptimal, virucidal activity is increased by bromide, iodide, and, in this instance, thiocyanate and the virucidal activity of the bromide-supplemented system is inhibited by azide and catalase. Our findings, together with the demonstration that eosinophils express CD4 on their surface and, under some circumstances, can be productively infected with HIV-1, raise the possibility that biological oxidants formed by eosinophils can influence the pathogenesis of HIV-1 infection by their toxicity to eosinophil-associated or extracellular virus.
XML to RDF Conversion: A Generic Approach (2008)

The role of metadata is gaining importance due to today's growth of multimedia content. Currently, XML is the standard for data interchange. However, as XML Schemas do not express semantics but rather the document structure, there is a lack of semantic interoperability regarding current (XML-based) metadata standards. By using semantic Web technologies, ontologies can be created to describe the semantics of a particular metadata format. A problem is that the existing XML data (compliant with a particul.ar metadata format) cannot be used by an ontology, implying the need for a conversion of XML data to RDF instances. In this paper, a generic approach is proposed for the transformation of XML data into RDF instances in an ontology-dependent way. By means of a mapping document, the link is described between an XML Schema (describing the structure of particular XML data) and an OWL ontology. Our approach is illustrated by applying it to the DIG35 specification, which is an XML-based metadata standard for the description of digital images.
Generative Models from the perspective of Continual Learning (2019)

Which generative model is the most suitablefor Continual Learning? This paper aims at evaluating andcomparing generative models on disjoint sequential imagegeneration tasks. We investigate how several models learn andforget, considering various strategies: rehearsal, regularization,generative replay and fine-tuning. We used two quantitativemetrics to estimate the generation quality and memory ability.We experiment with sequential tasks on three commonly usedbenchmarks for Continual Learning (MNIST, Fashion MNISTand CIFAR10). We found that among all models, the originalGAN performs best and among Continual Learning strategies,generative replay outperforms all other methods. Even ifwe found satisfactory combinations on MNIST and FashionMNIST, training generative models sequentially on CIFAR10is particularly instable, and remains a challenge. Our code isavailable online.
A Wavelet-Based Sprite Codec (2004)

The International Standards Organization (ISO) has proposed a family of standards for compression of image and video sequences, including the JPEG, MPEG-1, and MPEG-2. The latest MPEG-4 standard has many new dimensions to coding and manipulation of visual content. A video sequence usually contains a background object and many foreground objects. Portions of this background may not be visible in certain frames due to the occlusion of the foreground objects or camera motion. MPEG-4 introduces the novel concepts of video object planes (VOPs) and Sprites. A VOP is a visual representation of real world objects with shapes that need not be rectangular. Sprite is a large image composed of pixels belonging to a video object visible throughout a video segment. Since a sprite contains all parts of the background that were at least visible once, it can be used for direct reconstruction of the background VOP. Sprite reconstruction is dependent on the mode in which it is transmitted. In the static sprite mode, the entire sprite is decoded as an Intra VOP before decoding the individual VOPs. Since sprites consist of the information needed to display multiple frames of a video sequence, they are typically much larger than a single frame of video. Therefore, a static sprite can be considered as a large static image. In this paper, a novel solution to address the problem of spatial scalability has been proposed, where the sprite is encoded in discrete wavelet transform (DWT). A lifting kernel method of DWT implementation has been used for encoding and decoding sprites. Modifying the existing lifting scheme while maintaining it to be shape-adaptive results in a reduced complexity. The proposed scheme has the advantages of: 1) avoiding the need for any extensions to image or tile border pixels and is hence superior to the discrete cosine transform-based low latency scheme (used in the current MPEG-4 verification model) and 2) mapping the in place computed wavelet coefficients into a zero-tree structure without actually rearranging them, thereby saving allocation of additional memory. The proposed solutions provide efficient implementation of the sprite decoder, making possible a VLSI realization with a reduced real estate.
Dimeric RFX Proteins Contribute to the Activity and Lineage Specificity of the Interleukin-5 Receptor α Promoter through Activation and Repression Domains (1999)

Interleukin-5 (IL-5) plays a central role in the differentiation, proliferation, and functional activation of eosinophils. The specific action of IL-5 on eosinophils and hematopoietically related basophils is regulated by the restricted expression of IL-5 receptor alpha (IL-5Ralpha), a subunit of high-affinity IL-5R, on these cells. We have previously identified an enhancer-like cis element in the IL-5Ralpha promoter that is important for both full promoter function and lineage-specific activity. Here, we demonstrate by yeast one-hybrid screening that RFX2 protein specifically binds to this cis element. RFX2 belongs to the RFX DNA-binding protein family, the biological role of which remains obscure. Using an electrophoretic mobility shift assay, we further show that RFX1, RFX2, and RFX3 homodimers and heterodimers specifically bind to the cis element of the IL-5Ralpha promoter. The mRNA expression of RFX1, RFX2, and RFX3 was detected ubiquitously, but in transient-transfection assays, multimerized RFX binding sites in front of a basal promoter efficiently functioned in a tissue- and lineage-specific manner. To further investigate RFX functions on transcription, full-length and deletion mutants of RFX1 were targeted to DNA through fusion to the GAL4 DNA binding domain. Tissue- and lineage-specific transcriptional activation with the full-length RFX1 fusion plasmid on a reporter controlled by GAL4 binding sites was observed. Distinct activation and repression domains within the RFX1 protein were further mapped. Our findings suggest that RFX proteins are transcription factors that contribute to the activity and lineage specificity of the IL-5Ralpha promoter by directly binding to a target cis element and cooperating with other tissue- and lineage-specific cofactors.
Toughening of polybenzoxazine by alloying with urethane prepolymer and flexible epoxy: A comparative study (2005)

Abstract The toughness of polybenzoxazine can effectively be improved by alloying with isophorone diisocyanate (IPDI)‐based urethane prepolymers (PU) or with flexible epoxy (EPO732). The experimental results, i.e., flexural testing and dynamic mechanical analysis, reveal that the toughness of the alloys of the rigid polybenzoxazine and the PU or the EPO732 systematically increases with the amount of either toughener, due to the addition of more flexible molecular segments in the polymer hybrids. The curing temperature of the benzoxazine resin (bisphenol A‐aniline type [BA‐a]) at about 225°C shifts to a higher value when the fraction of BA‐a in either alloy decreases. Interestingly, the enhancement in the glass transition temperature (T g ) of BA‐a/PU alloys is clearly observed, i.e., T g of the BA‐a/PU alloys are significantly higher (T g beyond 200°C) than those of the parent resins, i.e., 165°C for BA‐a and −70°C for PU. However, this characteristic is not observed in the BA‐a/EPO732 alloy systems. The enhanced T g of the BA‐a/PU alloy at a 70/30 mass ratio is found to be 220°C, while that of BA‐a/EPO732 at the same mass ratio is observed to be only 95°C, which further decreases as the content of epoxy fraction increases. Furthermore, the degradation temperature based on 5% weight loss in the thermogravimetric analyzer (TGA) thermograms of the BA‐a/PU alloys is found to improve with the presence of the PU, though the opposite trend is observed in the BA‐a/EPO732 systems. The char yield of both alloy systems is steadily enhanced with the increased benzoxazine content because the char yield of the polybenzoxazine is inherently higher than that of the two tougheners. Therefore, the polybenzoxazine alloys with the IPDI‐based urethane prepolymer, e.g., the 70/30 BA‐a/PU, are a promising system for a tough, high thermal stability polymeric network, suitable for both bulk and composite matrix applications. POLYM. ENG. SCI. 45:288–296, 2005. © 2005 Society of Plastics Engineers.
A cost-effective architecture for 8×8 two-dimensional DCT/IDCT using direct method (1997)

Among the various transform techniques for image compression, the discrete cosine transform (DCT) is the most popular and effective one in practical image and video coding applications, such as high-definition television (HDTV). We develop a novel 8/spl times/8 two-dimensional (2-D) discrete cosine transform/inverse discrete cosine transform (DCT/IDCT) architecture based on the direct 2-D approach and the rotation technique. The computational complexity is reduced by taking advantage of the special attribute of a complex number. Both the parallel and the folded architectures are proposed. Unlike other approaches, the proposed architecture is regular and economically allowable for VLSI implementation. Compared to the row-column method, less internal wordlength is needed in order to meet the error requirement of IDCT, and the throughput of the proposed architecture can achieve two times that of the row-column method with 30% hardware increased.
Mechanistic Aspects of Polynaphthalimide Synthesis from NMR Analysis (2009)

The mechanism of the polycondensation reaction leading to naphthalimide polymers has been investigated using a model compound. In complement to 19 F-NMR analysis, 1 H- and 13 C-NMR spectroscopies were used to identify the intermediate compound. It was concluded that there was no evidence for the formation of an isoimide, but the formation of an amide—acid intermediate was clearly demonstrated.
A dairy producer's view of respiratory disease (2009)

Respiratory disease is a significant economic burden for United States dairies. Although there has been quality research, there is a need to translate the academic findings to the dairy barn. In particular, there is a need to implement solutions in the context of the economic ramifications of disease management. Plans to combat respiratory disease need to be simple, implemented incrementally and require low 'management energy'. If respiratory disease is prevented at an early age, this will ensure the greatest chance that the animals will reach their full genetic potential to produce.
Long-term biocompatibility of a miniature stimulator implanted in feline hind limb muscles (1998)

Chronic foreign-body responses and muscular changes were examined following the implantation of active miniature stimulators into the hind limb muscles of cats for periods of up to three months. The radio-frequency (RF)-powered stimulators were injected into muscles through a 12-gauge hypodermic needle. The tissue responses around the active stimulators were compared histologically to those provoked by passive devices, broken glass, silicone tubing, polyester suture material coated with polybutylate, and two of the internal components of the stimulator (ferrite, integrated circuit chip). Active and passive stimulators produced similar, benign foreign-body reactions that resulted in an essentially identical fibrous capsule over time. The responses were similar to those produced by the internal components and the suture material, and were more modest than those produced by the broken glass. The capsule did not appear to interfere with the functionality of active devices because thresholds measured during the post-implantation survival period did not change significantly over time. Unexpectedly, the severity of the reaction differed significantly amongst the various target muscles. Medial gastrocnemius exhibited the most severe response, whereas tibialis anterior had the least reaction.
An annotation-based API for supporting runtime code annotation reading (2017)

Code annotations are the core of the main APIs and frameworks for enterprise development, and are widely used on several applications. However, despite these APIs and frameworks made advanced uses of annotations, the language API for annotation reading is far from their needs. In particular, annotation reading is still a relatively complex task, that can consume a lot of development time and that can couple the framework internal structure to its annotations. This paper proposes an annotation-based API to retrieve metadata from code annotations and populate an instance with meta-information ready to be used by the framework. The proposed API is based on best practices and approaches for metadata definition documented on patterns, and has been implemented by a framework named Esfinge Metadata. We evaluated the approach by refactoring an existing framework to use it through Esfinge Metadata. The original and the refactored versions are compared using several code assessment techniques, such as software metrics, and bad smells detection, followed by a qualitative analysis based on source code inspection. As a result, the case study revealed that the usage of the proposed API can reduce the coupling between the metadata reading code and the annotations.