gebhart/patrepeval huggingface dataset:
Induction of Endothelial PAS Domain Protein-1 by Hypoxia: Characterization and Comparison With Hypoxia-Inducible Factor-1α (1998)

Hypoxia results in adaptive changes in the transcription of a range of genes including erythropoietin. An important mediator is hypoxia-inducible factor-1 (HIF-1), a DNA binding complex shown to contain at least two basic helix-loop-helix PAS-domain (bHLH-PAS) proteins, HIF-1alpha and aryl hydrocarbon nuclear receptor translocator (ARNT). In response to hypoxia, HIF-1alpha is activated and accumulates rapidly in the cell. Endothelial PAS domain protein 1 (EPAS-1) is a recently identified bHLH-PAS protein with 48% identity to HIF-1alpha, raising the question of its role in responses to hypoxia. We developed specific antibodies and studied expression and regulation of EPAS-1 mRNA and protein across a range of human cell lines. EPAS-1 was widely expressed, and strongly induced by hypoxia at the level of protein but not mRNA. Comparison of the effect of a range of activating and inhibitory stimuli showed striking similarities in the EPAS-1 and HIF-1alpha responses. Although major differences were observed in the abundance of EPAS-1 and HIF-1alpha in different cell types, differences in the inducible response were subtle with EPAS-1 protein being slightly more evident in normoxic and mildly hypoxic cells. Functional studies in a mutant cell line (Ka13) expressing neither HIF-1alpha nor EPAS-1 confirmed that both proteins interact with hypoxically responsive targets, but suggest target specificity with greater EPAS-1 transactivation (relative to HIF-1alpha transactivation) of the VEGF promoter than the LDH-A promoter.
Geometry of multi-layer freeform structures for architecture (2007)

The geometric challenges in the architectural design of freeform shapes come mainly from the physical realization of beams and nodes. We approach them via the concept of parallel meshes, and present methods of computation and optimization. We discuss planar faces, beams of controlled height, node geometry, and multilayer constructions. Beams of constant height are achieved with the new type of edge offset meshes. Mesh parallelism is also the main ingredient in a novel discrete theory of curvatures. These methods are applied to the construction of quadrilateral, pentagonal and hexagonal meshes, discrete minimal surfaces, discrete constant mean curvature surfaces, and their geometric transforms. We show how to design geometrically optimal shapes, and how to find a meaningful meshing and beam layout for existing shapes. © 2007 ACM.
Granulin–Epithelin Precursor Overexpression Promotes Growth and Invasion of Hepatocellular Carcinoma (2004)

GEP is an important factor for HCC growth, invasion, and metastasis. GEP has the potential to serve as a tumor marker and therapeutic target.
Evolution of neovascularization in mice with overexpression of vascular endothelial growth factor in photoreceptors. (1998)

These data support the feasibility of using rhodopsin-VEGF transgenic mice to study tissue-specific aspects of NV in the retina and to test antiangiogenic agents for inhibition of intraretinal and subretinal NV.
Development and Evaluation of Fluorogenic TaqMan Reverse Transcriptase PCR Assays for Detection of Dengue Virus Types 1 to 4 (2004)

The fluorogenic TaqMan reverse transcriptase PCR (RT-PCR) assay was developed for detecting each of the dengue virus (DV) types 1 to 4. DV genome was detected in all the 35 serum samples from confirmed dengue cases by the TaqMan RT-PCR, although it was not detected in 13 and 21% by conventional type-specific and cross-reactive RT-PCR, respectively.
The involvement of calcium phosphates in biological mineralization and demineralization processes (1992)

Abstract
SEPP: Software Installation and Sharing System (1998)

SEPP is an application installation, sharing and packaging solution for large, decentrally managed Unix environments. SEPP can be used without making modifications to the organizational structure of the participants’ servers. It provides consistent application setup, documentation, wrapper scripts and usage logging as well as version concurrency and clean software removal. This paper first gives an overview of products already available in this field and then goes on describing SEPP.
Performance of a random OFDMA system for mobile communications (2002)

In this paper we consider the uplink performance of an OFDMA (orthogonal frequency division multiple access) system for mobile communications. We describe the random OFDMA system which is based on MC-FDMA (multicarrier FDMA), and where each user has a set of randomly selected subchannels. We also analyze the problem of block synchronization in an OFDM transmission. Then we describe three different system implementations depending on the underlying level of the block synchronization. We define the considered performance criteria and discuss the influence of the different system implementations. Finally, we show some simulation results for the performance of the different system implementations.
Pullulanase of Thermoanaerobacterium thermosulfurigenes EM1 (Clostridium thermosulfurogenes): molecular analysis of the gene, composite structure of the enzyme, and a common model for its attachment to the cell surface (1994)

The complete pullulanase gene (amyB) from Thermoanaerobacterium thermosulfurigenes EM1 was cloned in Escherichia coli, and the nucleotide sequence was determined. The reading frame of amyB consisted of 5,586 bp encoding an exceptionally large enzyme of 205,991 Da. Sequence analysis revealed a composite structure of the pullulanase consisting of catalytic and noncatalytic domains. The N-terminal half of the protein contained a leader peptide of 35 amino acid residues and the catalytic domain, which included the four consensus regions of amylases. Comparison of the consensus regions of several pullulanases suggested that enzymes like pullulanase type II from T. thermosulfurigenes EM1 which hydrolyze alpha-1,4- and alpha-1,6-glycosidic linkages have specific amino acid sequences in the consensus regions. These are different from those of pullulanases type I which only cleave alpha-1,6 linkages. The C-terminal half, which is not necessary for enzymatic function, consisted of at least two different segments. One segment of about 70 kDa contained two copies of a fibronectin type III-like domain and was followed by a linker region rich in glycine, serine, and threonine residues. At the C terminus, we found three repeats of about 50 amino acids which are also present at the N-termini of surface layer (S-layer) proteins of, e.g., Thermus thermophilus and Acetogenium kivui. Since the pullulanase of T. thermosulfurigenes EM1 is known to be cell bound, our results suggest that this segment serves as an S-layer anchor to keep the pullulanase attached to the cell surface. Thus, a general model for the attachment of extracellular enzymes to the cell surface is proposed which assigns the S-layer a new function and might be widespread among bacteria with S-layers. The triplicated S-layer-like segment is present in several enzymes of different bacteria. Upstream of amyB, another open reading frame, coding for a hypothetical protein of 35.6 kDa, was identified. No significant similarity to other sequences available in DNA and protein data bases was found.
Determining therapeutic susceptibility in multiple myeloma by single-cell mass accumulation (2017)

Multiple myeloma (MM) has benefited from significant advancements in treatment that have improved outcomes and reduced morbidity. However, the disease remains incurable and is characterized by high rates of drug resistance and relapse. Consequently, methods to select the most efficacious therapy are of great interest. Here we utilize a functional assay to assess the ex vivo drug sensitivity of single multiple myeloma cells based on measuring their mass accumulation rate (MAR). We show that MAR accurately and rapidly defines therapeutic susceptibility across human multiple myeloma cell lines to a gamut of standard-of-care therapies. Finally, we demonstrate that our MAR assay, without the need for extended culture ex vivo, correctly defines the response of nine patients to standard-of-care drugs according to their clinical diagnoses. This data highlights the MAR assay in both research and clinical applications as a promising tool for predicting therapeutic response using clinical samples.
Inhibition of Cd83 Cell Surface Expression during Dendritic Cell Maturation by Interference with Nuclear Export of Cd83 mRNA (2000)

Dendritic cells (DCs), nature's adjuvant, must mature to sensitize T cells. However, although the maturation process is essential, it is not yet fully understood at the molecular level. In this study, we investigated the course of expression of the unique hypusine-containing protein eukaryotic initiation factor 5A (eIF-5A), which is part of a particular RNA nuclear export pathway, during in vitro generation of human DCs. We show that eIF-5A expression is significantly upregulated during DC maturation. Furthermore, an inhibitor of the hypusine modification, GC7 (N(1)-guanyl-1, 7-diaminoheptane), prevents CD83 surface expression by apparently interfering with nucleocytoplasmic translocation of the CD83 mRNA and, importantly, significantly inhibits DC-mediated T lymphocyte activation. The data presented suggest that CD83 mRNA is transported from the nucleus to the cytoplasm via a specific nuclear export pathway and that hypusine formation appears to be essential for the maturation of functional DCs. Therefore, pharmacological interference with hypusine formation may provide a new possibility to modulate DC function.
Conjugated Polymer Photovoltaic Cells (2004)

Conjugated polymers are attractive semiconductors for photovoltaic cells because they are strong absorbers and can be deposited on flexible substrates at low cost. Cells made with a single polymer and two electrodes tend to be inefficient because the photogenerated excitons are usually not split by the built-in electric field, which arises from differences in the electrode work functions. The efficiency can be increased by splitting the excitons at an interface between two semiconductors with offset energy levels. Power conversion efficiencies of almost 4% have been achieved by blending polymers with electron-accepting materials such as C60 derivatives, cadmium selenide, and titanium dioxide. We predict that efficiencies higher than 10% can be achieved by optimizing the cell's architecture to promote efficient exciton splitting and charge transport and by reducing the band gap of the polymer so that a larger fraction of the solar spectrum can be absorbed.
Identification of nucleated red blood cells in maternal circulation: A second step in screening for fetal aneuploidies and pregnancy complications (2006)

Determining the number of NRBCs in maternal circulation could represent an additional screening step for fetal aneuploidies, as long as the anemic status of the mother is taken into consideration. However, more cases with abnormal Doppler results must be investigated before this test is used for in the prediction of pregnancy complications.
Scalability study on a capacitorless 1T-DRAM from single-gate PD-SOI to double-gate FinDRAM (2005)

This paper describes both operation principle and scalability of a capacitor-less 1T-DRAM, and proposes a new concept about extending the use of 1T-DRAM to gate lengths of less than 50 nm. Superior characteristics such as long retention time and large sense margin even for gate lengths around 50 nm can be obtained with a double-gate fully depleted FinFET DRAM. Considering capacity, speed, power, and structural complexity of embedded memory, the capacitor-less 1T-DRAM has the possibility of playing the leading part among other memories.
Efficient Adenoviral Vector Transduction of Human Hematopoietic SCID-Repopulating and Long-Term Culture-Initiating Cells (2000)

This article presents our studies on the adenoviral transduction efficiency, level of transgene expression, cell cycle status, and multilineage reconstitution ability of human CD34+ hematopoietic cells transduced under proliferating and survival growth conditions. Bone marrow and umbilical cord blood CD34+ cells were cultured in serum-free medium under survival conditions with thrombopoietin (Tpo) alone, or under proliferating conditions with Tpo, c-Kit ligand (KL), and Flt3 ligand (FL). Adenoviral vectors carrying the enhanced green fluorescent protein (EGFP) gene under the control of the PGK-1 promoter were used to transduce CD34+ cells. Approximately 10% of CD34+ cells were EGFP+ under both culture conditions. In contrast, up to 50% of CD34+CD38- cells were EGFP+, whereas a maximum of 8% of CD34+CD38(high) cells were EGFP+ (p < 0.001). Both colony-forming unit cells (CFU-C) and 5-week long-term culture-initiating cells (LTC-ICs) were efficiently transduced. Under survival conditions, a substantial fraction of transduced CD34+ cells remained quiescent. The nondividing CD34+EGFP+ cells contained LTC-ICs capable of reconstituting longterm culture for as long as 10 weeks. CD34+EGFP+ cells also retained the ability to engraft and multilineage-reconstitute NOD/SCID mice. These observations demonstrate that primitive human hematopoietic progenitor cells can be efficiently transduced by adenoviral vectors.
Regulation and Immunolocalization of Acyl-Coenzyme A:Cholesterol Acyltransferase in Mammalian Cells as Studied with Specific Antibodies (1995)

Acyl-coenzyme A:cholesterol acyltransferase (ACAT) catalyzes the formation of intracellular cholesterol esters in various tissues. We recently reported the cloning and expression of human macrophage ACAT cDNA. In the current study, we report the production of specific polyclonal antibodies against ACAT by immunizing rabbits with the recombinant fusion protein composed of glutathione S-transferase and the first 131 amino acids of ACAT protein. Immunoblot analysis showed that the antibodies cross-reacted with a 50-kDa protein band from a variety of human cell lines. These antibodies immunodepleted more than 90% of detergent-solubilized ACAT activities from six different human cell types, demonstrating that the 50-kDa protein is the major ACAT catalytic component in these cells. In multiple human tissues examined, the antibodies recognized protein bands with various molecular weights. These antibodies also cross-reacted with the ACAT protein in Chinese hamster ovary cells. Immunoblot analysis showed that the ACAT protein contents in human fibroblast cells, HepG2 cells, or Chinese hamster ovary cells were not affected by sterol in the medium, demonstrating that the main mechanism for sterol-dependent regulation of ACAT activity in these cells is not change in ACAT protein content. As revealed by indirect immunofluorescent microscopy, the ACAT protein in tissue culture cells was located in the endoplasmic reticulum. This finding, along with earlier studies, suggests that cholesterol concentration in the endoplasmic reticulum may be the major determinant for regulating ACAT activity in the intact cells.
Incorporating long-range consistency in CNN-based texture generation (2016)

Gatys et al. (2015) showed that pair-wise products of features in a convolutional network are a very effective representation of image textures. We propose a simple modification to that representation which makes it possible to incorporate long-range structure into image generation, and to render images that satisfy various symmetry constraints. We show how this can greatly improve rendering of regular textures and of images that contain other kinds of symmetric structure. We also present applications to inpainting and season transfer.
Implementation of adaptive critic-based neurocontrollers for turbogenerators in a multimachine power system (2003)

This paper presents the design and practical hardware implementation of optimal neurocontrollers that replace the conventional automatic voltage regulator (AVR) and the turbine governor of turbogenerators on multimachine power systems. The neurocontroller design uses a powerful technique of the adaptive critic design (ACD) family called dual heuristic programming (DHP). The DHP neurocontrollers' training and testing are implemented on the Innovative Integration M67 card consisting of the TMS320C6701 processor. The measured results show that the DHP neurocontrollers are robust and their performance does not degrade unlike the conventional controllers even when a power system stabilizer (PSS) is included, for changes in system operating conditions and configurations. This paper also shows that it is possible to design and implement optimal neurocontrollers for multiple turbogenerators in real time, without having to do continually online training of the neural networks, thus avoiding risks of instability.
Expression of G protein-coupled receptors and related proteins in HEK293, AtT20, BV2, and N18 cell lines as revealed by microarray analysis (2011)

This study provides researchers an easily accessible mRNA profile of the endogenous signaling repertoire that these four cell lines possess. This will assist in choosing the most appropriate cell line for studying GPCRs and related signaling proteins. It also provides a better understanding of the potential interactions between GPCRs and those signaling proteins.
An Angle-Based Approach to Two-Dimensional Mesh Smoothing. (2000)

We present an effective and easy-to-implement angle-based smoothing scheme for triangular, quadrilateral and tri-quad mixed meshes. For each mesh node our algorithm compares all the pairs of adjacent angles incident to the node and adjusts these angles so that they become equal in the case of a triangular mesh and a quadrilateral mesh, or they form the ideal ratio in the case of a tri-quad mixed mesh. The size and shape quality of the mesh after this smoothing algorithm is much better than that after Laplacian smoothing. The proposed method is superior to Laplacian smoothing by reducing the risk of generating inverted elements and increasing the uniformity of element sizes. The computational cost of our smoothing method is yet much lower than optimization-based smoothing. To prove the effectiveness of this algorithm, we compared errors in approximating a given analytical surface by a set of bi-linear patches corresponding to a mesh with Laplacian smoothing and a mesh with the proposed smoothing method. The experiments show that a mesh smoothed with our method has roughly 20 % less approximation error.
Lignocellulosic Biomass Pretreatment Using AFEX (2009)

Although cellulose is the most abundant organic molecule, its susceptibility to hydrolysis is restricted due to the rigid lignin and hemicellulose protection surrounding the cellulose micro fibrils. Therefore, an effective pretreatment is necessary to liberate the cellulose from the lignin-hemicellulose seal and also reduce cellulosic crystallinity. Some of the available pretreatment techniques include acid hydrolysis, steam explosion, ammonia fiber expansion (AFEX), alkaline wet oxidation, and hot water pretreatment. Besides reducing lignocellulosic recalcitrance, an ideal pretreatment must also minimize formation of degradation products that inhibit subsequent hydrolysis and fermentation. AFEX is an important pretreatment technology that utilizes both physical (high temperature and pressure) and chemical (ammonia) processes to achieve effective pretreatment. Besides increasing the surface accessibility for hydrolysis, AFEX promotes cellulose decrystallization and partial hemicellulose depolymerization and reduces the lignin recalcitrance in the treated biomass. Theoretical glucose yield upon optimal enzymatic hydrolysis on AFEX-treated corn stover is approximately 98%. Furthermore, AFEX offers several unique advantages over other pretreatments, which include near complete recovery of the pretreatment chemical (ammonia), nutrient addition for microbial growth through the remaining ammonia on pretreated biomass, and not requiring a washing step during the process which facilitates high solid loading hydrolysis. This chapter provides a detailed practical procedure to perform AFEX, design the reactor, determine the mass balances, and conduct the process safely.
A Bovine Albumin Peptide as a Possible Trigger of Insulin-Dependent Diabetes Mellitus (1992)

Patients with insulin-dependent diabetes mellitus have immunity to cow's-milk albumin, with antibodies to an albumin peptide that are capable of reacting with a beta-cell--specific surface protein. Such antibodies could participate in the development of islet dysfunction.
Effects of advanced selection methods on sperm quality and ART outcome: a systematic review (2011)

While some of the advanced sperm selection methods are of value in specific clinical ART settings, others are in need of further evaluation. More clinical studies on safety and efficacy are needed before the implementation of advanced sperm selection methods could be universally recommended in ART.
Integrative Omics, Pharmacoproteomics, and Human Body Fluids (2008)

Proteomics of human body fluids for pharmaceutical applications covers a broad spectrum of technologies. A major challenge is the integration of data from various omics technologies: proteomics, genomics, and metabolomics. Applications relevant to the pharmaceutical industry include diagnostics, drug discovery, and drug development. Special features of these applications are that they are done on a large commercial scale. Currently, sample volumes require large-scale separation prior to analysis by mass spectrometry. Several new technologies, particularly those on the nanoscale, are refining this process and reducing the volume of samples required as well as expense. Refinements of technologies for fluid proteomics, including microfluidics and nanobiotechnology, for detection of biomarkers have applications in clinical diagnostics as well as drug discovery. Analysis of body fluids by metabolomic technologies may uncover biomarkers of drug toxicity that may help in avoiding clinical trials for such drugs, which are then discontinued after considerable expense. Finally, by facilitating the integration of diagnostics with therapeutics, these technologies will allow the development of personalized medicine.
Prescribing Patterns of Oral Antineoplastic Therapies Observed in the Treatment of Patients With Advanced Prostate Cancer Between 2012 and 2014: Results of an Oncology EMR Analysis (2016)

This EMR study is among the first to present evidence of US physician practice prescribing patterns regarding initiation of oral antineoplastic agents and use of subsequent therapies in patients with advanced prostate cancer.