gebhart/patrepeval huggingface dataset:
Highly Efficient and Photostable Photosensitizer Based on BODIPY Chromophore (2005)

Photosensitizers are reagents that produce reactive oxygen species upon light illumination and are commonly used to study oxidative stress or for photodynamic therapy. There are many available photosensitizers, but most have limitations, such as low photostability, structural instability, or a limited usable range of solvent conditions. Here, we describe a novel photosensitizer scaffold (2I-BDP) based on the unique characteristics of the BODIPY chromophore (i.e., high extinction coefficient, high photostability, and insensitivity to solvent environment). 2I-BDP shows stronger near-infrared singlet oxygen luminescence emission and higher photostability than the well-known photosensitizer, Rose Bengal. Unlike other photosensitizers, this scaffold is widely applicable under various conditions, including lipophilic and aqueous environments. HeLa cells loaded with 2I-BDP could be photosensitized by light illumination, demonstrating that 2I-BDP is potentially useful as a reagent for cell photosensitization, oxidative stress studies, or PDT.
In Vivo Optical Microendoscopy for Imaging Cells Lying Deep within Live Tissue (2012)

Although in vivo microscopy has been pivotal in enabling studies of neuronal structure and function in the intact mammalian brain, conventional intravital microscopy has generally been limited to superficial brain areas such as the olfactory bulb, the neocortex, or the cerebellar cortex. For imaging cells in deeper areas, this article discusses in vivo optical microendoscopy using gradient refractive index (GRIN) microlenses that can be inserted into tissue. Our general methodology is broadly applicable to many deep brain regions and areas of the body. Microendoscopes are available in a wide variety of optical designs, allowing imaging across a range of spatial scales and with spatial resolution that can now closely approach that offered by standard water-immersion microscope objectives. The incorporation of microendoscope probes into portable miniaturized microscopes allows imaging in freely behaving animals. When combined with the broad sets of available fluorescent markers, animal preparations, and genetically modified mice, microendoscopic methods enable sophisticated experimental designs for probing how cellular characteristics may underlie or reflect animal behavior and life experience, in healthy animals and animal models of disease.
Using GIS to Predict Corn Yields in Colombia (2008)

Crop yield prediction can play an important role in developing the agriculture sector in Colombia. Remote sensing and GIS have proven to be an effective mechanism for this purpose in developed economies. This project created a proof-of-concept application for the Colombian Ministry of Agriculture and other related governmental institutions. The project used existing methodologies including the classification of satellite imagery, interpolation of climate data into continuous surfaces, the extraction of Normalized Difference Vegetation Index, and the computation of multiple linear regressions. ESRI ArcGIS provided the interface, software, tools and functions to build the application, and to integrate and automate the application‟s functionalities.
Identification of a <i>ras</i> -Activated Enhancer in the Mouse Osteopontin Promoter and Its Interaction with a Putative ETS-Related Transcription Factor Whose Activity Correlates with the Metastatic Potential of the Cell (1995)

The role of RAS in transducing signals from an activated receptor into altered gene expression is becoming clear, though some links in the chain are still missing. Cells possessing activated RAS express higher levels of osteopontin (OPN), an alpha v beta 3 integrin-binding secreted phosphoprotein implicated in a number of developmental, physiological, and pathological processes. We report that in T24 H-ras-transformed NIH 3T3 cells enhanced transcription contributes to the increased expression of OPN. Transient transfection studies, DNA-protein binding assays, and methylation protection experiments have identified a novel ras-activated enhancer, distinct from known ras response elements, that appears responsible for part of the increase in OPN transcription in cells with an activated RAS. In electrophoretic mobility shift assays, the protein-binding motif GGAGGCAGG was found to be essential for the formation of several complexes, one of which (complex A) was generated at elevated levels by cell lines that are metastatic. Southwestern blotting and UV light cross-linking studies indicated the presence of several proteins able to interact with this sequence. The proteins that form these complexes have molecular masses estimated at approximately 16, 28, 32, 45, 80, and 100 kDa. Because the approximately 16-kDa protein was responsible for complex A formation, we have designated it MATF for metastasis-associated transcription factor. The GGANNNAGG motif is also found in some other promoters, suggesting that they may be similarly controlled by MATF.
An Extension of the Sender Domain Authentication DKIM (2008)

The sender domain authentication protocol DKIM (domain keys identified mail) attracts much attention, in which the sender domain adds a signature header generated from headers and body of the original email, and the sender domain will be authenticated by a verification of the signature. However, a verification will be failed when headers are changed before it is reached to the receiver. This article proposes to combine DKIM and PIAT, the partial integrity assurance technology, so that the original sender domain authentication will be successful even when headers are changed by a mailing-list domain without generating a signature on the modified email.
Fluorescent Sequence-Specific dsDNA Binding Oligomers (2007)

Sequence-specific detection methods for double-stranded DNA that obviate the need for denaturation would provide a powerful tool for bioorganic chemistry and genetics. As part of a sustained effort to develop sequence-specific fluorescent DNA detection methods, two programmable oligomers have been synthesized which target their respective sequences 5‘-WTACGW-3‘ and 5‘-WGGGGW-3‘ (W = A or T). The two oligomers were found to fluoresce weakly in the absence of DNA but showed significant fluorescence enhancement by the addition of match DNA. The fluorescence is shown to increase in a concentration-dependent manner, and the intensity varies depending on the number of mismatch sites incorporated into the DNA hairpins. This new class of oligomers provides a method to detect DNA sequences without denaturation and in the absence of conjugation to a dye molecule. This is a first step toward sequence-specific DNA-binding molecules containing a fluorescent switch integrated as part of the recognition modules.
WormAssay: A Novel Computer Application for Whole-Plate Motion-based Screening of Macroscopic Parasites (2012)

Lymphatic filariasis is caused by filarial nematode parasites, including Brugia malayi. Adult worms live in the lymphatic system and cause a strong immune reaction that leads to the obstruction of lymph vessels and swelling of the extremities. Chronic disease leads to the painful and disfiguring condition known as elephantiasis. Current drug therapy is effective against the microfilariae (larval stage) of the parasite, but no drugs are effective against the adult worms. One of the major stumbling blocks toward developing effective macrofilaricides to kill the adult worms is the lack of a high throughput screening method for candidate drugs. Current methods utilize systems that measure one well at a time and are time consuming and often expensive. We have developed a low-cost and simple visual imaging system to automate and quantify screening entire plates based on parasite movement. This system can be applied to the study of many macroparasites as well as other macroscopic organisms.
Optimization of low-noise GaAs MESFET's (1980)

This paper presents a device design which is an effective way of reconciling the two conflicting requirements for low-noise GaAs MESFET's. Decreasing the effective value of gate length can be achieved, without penalty of increased gate metallization resistance, by the virtue of a proper gate-recess structure. This effect can be explained by the "effective gate length" concept. The pertinent fabrication techniques and the optimal noise-figure expression are given for an optimized structure with illustrated examples.
Hepatocellular carcinoma-associated mesenchymal stem cells promote hepatocarcinoma progression: Role of the S100A4-miR155-SOCS1-MMP9 axis (2013)

S100A4 secreted from LC-MSCs is involved in the modulation of HCC progression, and may be a potential therapeutic target. (HEPATOLOGY 2013).
Bofors Schnauzer - a biosensor for detection of explosives (1996)

Bofors made an initiative to take a leading position by introducing the Bofors Concept of Demining. The Bofors Concept of Demining comprises concepts for a total system incorporating different technologies that will be the tools for: search and detection of minefields; detection, location and identification of individual mines; destruction of mines; and verification of the work carried out. The crucial item on this agenda is detection, location and identification of individual mines. The overall plan is to build a multisensor system which will be based on in combination: biosensor detectors; ground penetrating radar; and metal detectors. This paper discusses the biosensor which combines microelectronics and micromechanics together with the latest in biotechnology. It works by detecting TNT vapour given off by a mine which is then concentrated into a solvent. A quartz crystal oscillates at a frequency of approximately 8 to 9 MHz. Such a system is very sensitive to changes in the mass of the resonator. Antibodies which are sensitive to TNT are attached on the surface of the oscillator. If the small volume of solvent contains TNT, some of the antibodies will release from the surface of the oscillator. The frequency of the oscillator will then change due to the change in mass. The change in frequency is then detected, and the change of frequency will be in the range of 5 to 25 Hz. If the frequency has changed, the operator will be warned immediately. The system has a sensitivity of less than 10 picogram.
Low complexity carrier recovery for coherent QAM using superscalar parallelization (2010)

We demonstrate the application of superscalar and interleaving hardware parallelization scheme on carrier recovery for coherent optic receivers. The combination of superscalar parallelization with feedback carrier recovery provides performance close to the theoretical limit.
Immunohistochemistry study of human vestibular nerve schwannoma differentiation (2002)

Differentiation of primary human vestibular nerve schwannomas (VS) caused by mutations of the NF2 gene was evaluated by examining the expression patterns of genes that are specifically expressed in different stages of Schwann cell lineage. In schwannoma cells that are not in contact with an axon, the expression levels of the major myelin sheath proteins, such as protein zero glycoprotein (P0), myelin basic protein (MBP), and peripheral myelin protein 22 (PMP22), were greatly reduced. However, high expression levels of nerve growth factor receptor (NGFR), neural cell adhesion molecule (N-CAM), and cell adhesion molecule L1 (L1) were observed. In addition, expression of transcription factors Krox20, Krox24, and SCIP/Oct6 was also detected in the tumor cells. These results suggest that loss of the NF2 gene was responsible for the transformation of the Schwann cells into a neoplastic stage that has a similar genetic profile to the pro-myelinating stage. Finally, the primary human vestibular schwannoma cells failed to be regulated and redifferentiated by a regenerating axon, when the human tumors were transplanted into sciatic nerve of nude rat. These results suggest that the NF2 gene might be involved in the differentiation of Schwann cells.
Metastatic Potential of 21T Human Breast Cancer Cells Depends on Akt/Protein Kinase B Activation (2007)

Most cancer lethality is caused by metastasis. To gain insight into the molecular basis of tumor progression to metastasis, we used the 21T series of human mammary epithelial cells obtained by successive biopsies from one breast cancer patient. The c-erbB2 gene is amplified and overexpressed in each of three 21T tumor lines. The erbB receptor tyrosine kinase-activated phosphatidylinositol 3-kinase/Akt signaling cascade is crucial for the development and maintenance of epithelial cells, and dysregulation of this pathway is frequently associated with cellular transformation and cancer. For Akt to be fully activated, Ser(473) on its COOH terminus needs to be phosphorylated. We detected more Ser(473) Akt phosphorylation in MT cells, derived from a pleural effusion, compared with cells from the primary tumor. This phosphorylation has recently been shown to be catalyzed by mammalian target of rapamycin (mTOR)/rictor kinase. By using genetic and pharmacologic activators and inhibitors, we showed that Ser(473) Akt phosphorylation is more sensitive to mTOR/rictor inhibition in metastatic tumor cells than normal mammary epithelial and primary tumor cells. The mTOR/rictor kinase activity was indispensable for both Ser(473) Akt phosphorylation and migration of metastatic MT2 cells. In addition, a large decrease of protein phosphatase PH domain leucine-rich repeat protein phosphatase (PHLPP) was found, which could be responsible for the overexpression of Ser(473) Akt in MT cells. Our data indicate that these breast cancer cells acquire new vulnerabilities, rictor and PHLPP, which might provide an Achilles' heel for therapeutic intervention of breast cancer metastasis.
The Safety and Efficacy of Parathyroid Hormone (PTH) as a Biological Response Modifier for the Enhancement of Bone Regeneration (2006)

Osteoporosis is characterized by low bone mineral density and deterioration in the microarchitecture of bone that increases its fracture vulnerability. The mainstay of therapy for osteoporosis is anti-resorptive in mechanism. Parathyroid hormone (PTH) is the most recently approved anabolic agent for osteoporosis. The mechanism of PTH's skeleton anabolic action is composite involving pathways linked to common signalling peptides that affect gene osteoblast transcription. A number of animal studies and clinical trials have demonstrated that intermittent PTH administration induces anabolic effects on both cancellous and cortical bone, enhances bone mass and increases mechanical bone strength, increasing spine and hip bone mineral density and reducing fragility fractures. Preclinical studies investigating the effect of PTH on fracture healing show an increase in bone density and strength indicating an enhancement of this biological cascade. Preclinical and clinical safety assessments have revealed little evidence of toxic effects and there have been few reports of adverse events related to their use. An increase in osteosarcoma in rats probably is not prognostic of an equivalent possibility in humans. In summary, parathyroid hormone is a major advance in the treatment of osteoporosis. Additional studies addressing long-term clinical safety are needed. However the current evidence is very promising.
Regulation of C4 Gene Expression in Developing Amaranth Leaves (1992)

Immunofluorescence microscopy and in situ hybridization were used to examine the expression of genes encoding C4 photosynthetic enzymes during early leaf development in the C4 dicotyledonous grain plant amaranth. During early developmental stages, the chloroplast-encoded large subunit and nuclear-encoded small subunit genes of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCase) were expressed in both bundle sheath and mesophyll cells in a C3-type pattern. The RuBPCase proteins and mRNAs became specifically localized to bundle sheath cells in the characteristic C4-type pattern as the leaves continued to expand and develop. Changes in the localization of the RuBPCase proteins corresponded closely with changes in the localization of their mRNAs, indicating that the cell-specific expression of genes encoding RuBPCase is controlled, at least in part, at the level of transcript accumulation. Genes encoding pyruvate orthophosphate dikinase were expressed specifically in mesophyll cells at all developmental stages examined. Immunolocalization with antibodies raised against phosphoenolpyruvate carboxylase (PEPCase) showed that this enzyme is present only in leaf mesophyll cells, even though RNA sequences with homology to PEPCase gene sequences were present in both bundle sheath and mesophyll cells. These results suggest that the regulation of genes encoding PEPCase in amaranth is complex and could involve the differential expression of divergent PEPCase genes or possibly regulation at the post-transcriptional level.
Association rules for Web data mining in WHOWEDA (2002)

The authors discuss association rules which can be discovered from Web data. The association rules are discussed within the scope of our WHOWEDA (warehouse of Web data) project. WHOWEDA is supported by a Web data model and a set of algebraic operators. The Web data model allows a uniform and integrated view of Web data gathered using a user's query graph. A user's query graph describes the query by example (what the user perceives as the query) and the Web coupling query gathers instances of such a query graph from the Web and stores them in the form of subgraphs (called Web tuples) in a Web table. We discuss association rules within this domain. An association rule defines an association between the nodes and links attributes of Web tuples within a Web table. There are two different classes of association rules that can be developed from data in a Web table. There are two different classes of association rules that can be developed from data in a Web table. Node-to-node associations are those rules that relate the content (defined by metadata attributes) between two or more nodes within a Web tuple. Link associations are rules that show the connectivity of different URLs. Distinguishing the two types of associations provides a view of the structure of the Web data. The goal of performing Web association mining on Web data is to better organize searching patterns through hyperlinked documents.
Comparison of fusion methods for the infrared and color visible images (2009)

Image fusion involves merging two or more images in such a way as to retain the most desirable characteristics of each. When a color visible image is fused with infrared image, the desired result is a color image with natural color appearance and full information. In this paper, three image fusion algorithms based on discrete wavelet transform (DWT), dual-tree complex wavelet transform (DT-CWT) with image enhancement and bidimensional empirical model decomposition (BEMD) are compared for the infrared and color visible images. A novel image quality metric is proposed to evaluating the performance of image fusion algorithms. This measurement is defined for comparative performance analysis and is used on the output of fusion algorithms that have been applied to a set of infrared and color visible band imagery.
Microscale Heat and Mass Transfer of Vascular and Intracellular Freezing in the Liver (1993)

A set of heat and mass transfer equations is developed to predict vascular as well as intracellular ice formation during freezing in liver tissue. A modified Krogh unit with vascular and cellular compartments is used. In the model intracellular ice formation is predicted by a probability integral with functional dependence on cell compartment volume, temperature, and time. Finite difference computer simulations qualitatively predict the amount and location of vascular and intracellular ice, the temperature distribution in the tissue, and the position of the partial and total freezing interfaces at any time.
A Non-linear Multi-criteria Programming Approach for Determining County Emergency Medical Service Ambulance Allocations (1989)

In this paper an integer, non-linear mathematical programming model is developed to allocate emergency medical service (EMS) ambulances to sectors within a county in order to meet a government-mandated response-time criterion. However, in addition to the response-time criterion, the model also reflects criteria for budget and work-load, and, since ambulance response is best described within the context of a queueing system, several of the model system constraints are based on queueing formulations adapted to a mathematical programming format. The model is developed and demonstrated within the context of an example of a county encompassing rural, urban and mixed sectors which exhibit different demand and geographic characteristics. The example model is solved using an integer, non-linear goal-programming technique. The solution results provide ambulance allocations to sectors within the county, the probability of an ambulance exceeding a prespecified response time, and the utilization factor for ambulances per sector.
ChemInform Abstract: A SIMPLE PREPARATION OF 5‐OXO‐4,5‐DIHYDRO‐1,3‐OXAZOLES (OXAZOLONES) (1979)

Abstract Die Umsetzung von N‐Acylaminosäuren (I) mit dem löslichen Carbodiimid (II) in Methylen‐Chlorid bei 0°C führt in guten Ausbeuten zu chemisch und optisch reinen Oxazolonen(III).
High-Throughput Methods for Combinatorial Drug Discovery (2013)

A more nuanced approach to drug design is to use multiple drugs in combination to target interacting or complementary pathways. Drug combination treatments have shown higher efficacy, fewer side effects, and less toxicity compared to single-drug treatment. In this Review, we focus on the use of high-throughput biological measurements (genetics, transcripts, and chemogenetic interactions) and the computational methods they necessitate to further combinatorial drug design (CDD). We highlight the state-of-the-art analytical methods, including network analysis, integrative informatics, and dynamic molecular modeling, that have been used successfully in CDD. Finally, we present an exhaustive list of the publicly available data and methodological resources available to the community. Such next-generation technologies that enable the measurement of millions of cellular data points simultaneously may usher in a new paradigm in drug discovery, where medicine is viewed as a system of interacting genes and pathways rather than the result of an individual protein or gene.
A model of the <i>lac</i> repressor–operator complex based on physical and genetic data (1991)

Computer graphics were used to build a molecular model of the complex of Lac repressor and lac operator. The model is based (a) on the NMR data of the Kaptein group [Boelens, R., Lamerichs, R. M. J. N., Rullmann, J. A. C., van Boom, J. H. & Kaptein, R. (1988) Protein Sequence Data Anal. 1, 487-498] and (b) on our genetic and biochemical data including specificity changes [Lehming, N., Sartorius, J., Kisters-Woike, B., von Wilcken-Bergmann, B. & Müller-Hill, B. (1990) EMBO J. 9, 615-621]. Effects of amino acid exchanges in the recognition helix could be predicted by the model and were subsequently tested and confirmed by genetic experiments. Comparison of the modelled lac complex with the known crystallographic structures of several helix-turn-helix DNA complexes reveals striking similarities and suggests rules which govern the recognition between particular amino acid side chains and particular base pairs in these systems.