gebhart/patrepeval huggingface dataset:
Global Gene Expression Analysis Reveals a Role for the α1 Integrin in Renal Pathogenesis (2001)

Kidney fibrosis is the hallmark of most types of progressive kidney disease, including the genetic disorder Alport's syndrome. We undertook gene expression analysis in Alport's syndrome mouse kidneys using microchip arrays to characterize the development of fibrosis. In addition to matrix and matrix-remodeling genes, consistent with interstitial fibrosis, macrophage-related genes show elevated expression levels in Alport's syndrome kidneys. Immunohistochemical analysis of kidney sections illustrated that macrophages as well as myofibroblasts accumulate in the tubular interstitium. Deletion of alpha(1) integrin results in decreased accumulation of both myofibroblasts and macrophages in the tubular interstitium in Alport's syndrome mice and delays disease progression. Transforming growth factor beta antagonism, although reducing interstitial fibrosis, does not limit macrophage accumulation in the tubular interstitium and disease progression. In this study, we identified previously overlooked inflammatory events that occur in the tubulointerstitial region. We propose that in addition to the previously suggested role for the alpha(1)beta(1) integrin in mesangial expansion and abnormal laminin deposition, this integrin may be critical for monocyte accumulation that, in turn, may lead directly to renal failure. Our gene expression and immunohistochemical data indicate that macrophage accumulation is dependent on alpha(1) integrin expression on the macrophage cell surface and that anti-alpha(1) integrin strategies may be employed as therapeutics in the treatment of chronic inflammatory and fibrotic diseases.
Radiosynthesis and Preclinical Evaluation of 3′-Aza-2′-[18F]fluorofolic Acid: A Novel PET Radiotracer for Folate Receptor Targeting (2012)

The folate receptor (FR) has been identified as a valuable target for the imaging of cancer and activated macrophages, involved in inflammatory and autoimmune diseases via positron emission tomography (PET). Therefore, conjugates of folic acid have been synthesized by coupling of a radiolabeled prosthetic group to the glutamate part of folic acid (pendent approach). In this work, we present a novel class of folates, where the phenyl ring of folic acid was isosterically replaced by a pyridine moiety for direct labeling with [(18)F]fluoride (integrated approach). 3'-Azafolic acid and its 2'-halogenated derivatives (2'-chloro and 2'-fluoro) were evaluated in vitro to determine their binding affinity. 3'-Aza-2'-[(18)F]fluorofolic acid ([(18)F]6) was obtained, starting from N(2)-acetyl-3'-aza-2'-chlorofolic acid di-tert-butylester (2), in a maximum decay corrected radiochemical yield of about 9% in ≥98% radiochemical purity and high specific activities of 35-127 GBq/μmol. Binding affinity to the FR was high (IC(50) = 0.8 ± 0.2 nM), and the radiotracer was stable in human plasma over 4 h at 37 °C. No degradation or defluorination was detected after incubation of the radiotracer for 1 h at 37 °C with human and murine liver microsomes and human S9-fraction. In vivo PET imaging and biodistribution studies with mice demonstrated a high and specific uptake in FR-positive KB tumor xenografts (12.59 ± 1.77% ID/g, 90 min p.i.). A high and specific accumulation of radioactivity was observed in the kidneys (57.33 ± 8.40% ID/g, 90 min p.i.) and salivary glands (14.09 ± 0.93% ID/g, 90 min p.i.), which are known to express the FR and nonspecific uptake found in the liver (10.31 ± 2.37% ID/g, 90 min p.i.). Preinjection of folic acid resulted in a >85% reduced uptake of [(18)F]6 in FR-positive tissues (xenografts, kidneys, and salivary glands). Furthermore, no radioactive metabolites were detected in the blood, urine, or tumor tissue, 30 min p.i. These characteristics indicate that this new (18)F-labeled 3'-azafolate is an appropriate tool for imaging FR-positive (malignant) tissue.
Molecular Prognostic Markers in Uveal Melanoma: Expression Profiling and Genomic Studies (2008)

Uveal Melanomas (UMs) arise from melanocytes. This cell type originates from neural crest cells\nand thereby uveal melanomas share their origin with pheochromocytomas, neuroblastomas,\nparagangliomas and cutaneous melanomas, other tumors that develop from neural crest\noriginating cells. Uveal melanoma is the most common primary tumor in the eye with an\nincidence of approximately 7 per million every year in the Western World. In adults, 80 percent\nof all intraocular tumors are uveal melanomas. The mean age at diagnosis is 60 years. Most uveal\nmelanomas arise in the ciliary body (23%), or the choroid (72%) and a small fraction originates\nin the iris (5%). Predispositions for UM are a light eye color, fair skin color and ability to tan,\nwhich are all related with a fair phenotype. Despite advances in treatment with enucleation, preenucleation\nradiotherapy, stereotactic radiotherapy, brachytherapy, charged particle irradiation,\nthermo therapy and local eye wall resection, the mortality rate has not changed significantly. As\nmany as 50% of all newly diagnosed patients will die from distant metastases, which are mainly\nlocated in the liver.
Formalin-inactivated respiratory syncytial virus vaccine induces antibodies to the fusion glycoprotein that are deficient in fusion-inhibiting activity (1988)

The fusion (F) glycoprotein of respiratory syncytial virus (RSV) induces neutralizing antibodies and antibodies that inhibit fusion of infected cells (FI antibody). It was previously shown that infants and children immunized with Formalin-inactivated RSV 20 years ago developed antibodies that bound to the F glycoprotein but were deficient in neutralizing activity. A reexamination of these sera indicated that they were also deficient in FI activity. Thus, Formalin-inactivated RSV vaccine stimulated an unbalanced immune response in which an unusually large proportion of the induced antibodies were directed against nonprotective epitopes rather than against the epitopes that induce functional antibodies, i.e., neutralizing and FI antibodies. This deficiency in stimulation of functional antibodies probably decreased the protective efficacy of the vaccine and could have contributed to potentiation of disease in the vaccines during subsequent RSV infection.
Computer-generated pen-and-ink illustration (1994)

This paper describes the principles of traditional pen-and-ink illustration, and shows how a great number of them can be implemented as part of an automated rendering system. It introduces “stroke textures,” which can be used for achieving both texture and tone with line drawing. Stroke textures also allow resolution-dependent rendering, in which the choice of strokes used in an illustration is appropriately tied to the resolution of the target medium. We demonstrate these techniques using complex architectural models, including Frank Lloyd Wright's “Robie House.”
Smart identification frameworks for ubiquitous computing applications (2004)

We present our results in the conceptual design and the implementation of ubiquitous computing applications using smart identification technologies. First, we describe such technologies and their potential application areas, followed by an overview of some applications we have developed. Based on the experiences we gained from the development of these systems, we point out design concepts that we find useful for structuring and implementing such applications. Building upon these concepts, we have created two frameworks based on Jini (i.e., distributed Java objects) and Web services to support the development of ubiquitous computing applications that make use of smart identification technology. We describe our prototype frameworks, discuss the underlying concepts and present some lessons learned.
Verifying safety properties using separation and heterogeneous abstractions (2004)

In this paper, we show how separation (decomposing a verification problem into a collection of verification subproblems) can be used to improve the efficiency and precision of verification of safety properties. We present a simple language for specifying separation strategies for decomposing a single verification problem into a set of subproblems. (The strategy specification is distinct from the safety property specification and is specified separately.) We present a general framework of heterogeneous abstraction that allows different parts of the heap to be abstracted using different degrees of precision at different points during the analysis. We show how the goals of separation (i.e., more efficient verification) can be realized by first using a separation strategy to transform (instrument) a verification problem instance (consisting of a safety property specification and an input program), and by then utilizing heterogeneous abstraction during the verification of the transformed verification problem.
Cell‐cycle‐dependent expression of human ornithine decarboxylase (1987)

A human ornithine decarboxylase (ODC) gene probe has been isolated from a Jurkat T-cell cDNA expression library, sequenced, and used to analyze ODC mRNA levels in untransformed human lymphocytes and fibroblasts stimulated to proliferate by various mitogens. The partial cDNA sequence is 86% homologous to the mouse ODC cDNA, and Northern blots indicate that the human and mouse mRNA species are similar in size. ODC mRNA is barely detectable in quiescent human T lymphocytes and undetectable in density-arrested W138 fibroblasts. Following stimulation of T-lymphocyte proliferation with phytohemagglutinin, the ODC mRNA level rises to a peak around mid G1 phase and decreases as the cells enter S phase. Serum stimulation of density-arrested fibroblasts results in an elevation of the ODC mRNA level which persists throughout the cell cycle. Epidermal growth factor (20 ng/ml) but not insulin (10 mg/ml) or dexamethasone (55 ng/ml) stimulates ODC expression in quiescent W138 fibroblasts. Southern blots suggest that human cells have a single copy of the ODC gene.
Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks (2006)

We evaluated three methods for integrating clinical and microarray data: decision integration, partial integration and full integration and used them to classify publicly available data on breast cancer patients into a poor and a good prognosis group. The partial integration method is most promising and has an independent test set area under the ROC curve of 0.845. After choosing an operating point the classification performance is better than frequently used indices.
Pilomatricoma of the Head and Neck (2003)

Because preoperative diagnosis of pilomatricoma is usually incorrect, careful clinical examination and a high index of suspicion would result in a more accurate diagnosis. Complete surgical excision is the treatment of choice. Otolaryngologists should consider pilomatricoma in the differential diagnosis of neck masses.
Dynamical Bragg diffraction from crystalline colloidal arrays (1989)

Polystyrene spheres with attached functional groups that ionize in solution repel one another; at sufficiently high sphere concentrations the spheres self-assemble into a crystalline lattice with lattice constants large enough to diffract visible light. We have experimentally and theoretically examined diffraction phenomena from colloidal crystals of polystyrene spheres of diameters between 69 and 127 nm in water. We relate the diffraction bandwidths to the sphere scattering powers in the context of the dynamical diffraction theory and demonstrate the importance of the dynamical theory for predicting the observed diffraction angles, intensities, and bandwidths. We also discuss the mechanism contributing to the diffuse scattering and show the significance of the coherent scattering by lattice phonons.
Optimal Rebuilding of Multiple Erasures in MDS Codes (2016)

Maximum distance separable (MDS) array codes are widely used in storage systems due to their computationally efficient encoding and decoding procedures. An MDS code with r redundancy nodes can correct any r node erasures by accessing (reading) all the remaining information in the surviving nodes. However, in practice, e erasures are a more likely failure event, for some 1 ≤ e <; r. Hence, a natural question is how much information do we need to access in order to rebuild e storage nodes. We define the rebuilding ratio as the fraction of remaining information accessed during the rebuilding of e erasures. In our previous work, we constructed MDS codes, called zigzag codes, that achieve the optimal rebuilding ratio of 1/r for the rebuilding of any systematic node when e = 1; however, all the information needs to be accessed for the rebuilding of the parity node erasure. The (normalized) repair bandwidth is defined as the fraction of information transmitted from the remaining nodes during the rebuilding process. For codes that are not necessarily MDS, Dimakis et al. proposed the regenerating codes framework where any r erasures can be corrected by accessing some of the remaining information, and any e = 1 erasure can be rebuilt from some subsets of surviving nodes with optimal repair bandwidth. In this paper, we present three results on rebuilding of codes: 1) we show a fundamental outer bound on the storage size of the node and the repair bandwidth similar to the regenerating codes framework, and show that zigzag codes achieve the optimal rebuilding ratio of e/r for systematic nodes of MDS codes, for any 1 ≤ e r; 2) we construct systematic codes that achieve optimal rebuilding ratio of 1/r, for any systematic or parity node erasure; and 3) we present error correction algorithms for zigzag codes, and in particular demonstrate how these codes can be corrected beyond their minimum Hamming distances.
Dependence of Enhancer-Mediated Transcription of the Immunoglobulin μ Gene on Nuclear Matrix Attachment Regions (1994)

Transcription of the immunoglobulin mu heavy chain locus is regulated by an intronic enhancer that is flanked on both sides by nuclear matrix attachment regions (MARs). These MARs have now been shown to be essential for transcription of a rearranged mu gene in transgenic B lymphocytes, but they were not required in stably transfected tissue culture cells. Normal rates of transcriptional initiation at a variable region promoter and the formation of an extended deoxyribonuclease I (DNase I)--sensitive chromatin domain were dependent on MARs, although DNase I hypersensitivity at the enhancer was detected in the absence of MARs. Thus, transcriptional activation of the mu gene during normal lymphoid development requires a synergistic collaboration between the enhancer and flanking MARs.
Fast Hybrid Algorithms for PET Image Reconstruction (2006)

We describe a hybrid approach to iterative PET image reconstruction in which we combine three algorithms: preconditioned conjugate gradient (PCG), ordered subsets separable paraboloidal surrogate (OSSPS), and emission reconstruction incremental optimization transfer (ERIOT). These algorithms exhibit quite different convergence behavior, e.g. the initial convergence of OSSPS is fast but it soon enters a limit cycle. Conversely, initial convergence of PCG is slow compared to OSSPS and ERIOT but its asymptotic behavior is the fastest. The hybrid approach estimates convergence behavior for each method by fitting an exponential to the objective function as a function of iteration number and switches between the algorithms to optimize the convergence behavior throughout the iterations. This hybrid approach is compared to each of the component algorithms in application to simulated PET data demonstrating a reduction of at least 50% in iterations required for effective convergence compared to use of PCG alone.
Inflammation Imaging (2005)

Acute and chronic lung diseases are almost invariably associated with some degree of inflammation. Cells that evolved as an effective mechanism to counter infection and heal lung tissue may, in some circumstances, themselves be partially responsible for the pathogenesis of chronic lung disease that leads to irreversible lung damage and loss of lung function. Although standard measurements of lung function can document the progression of disease, the contributions of the numerous interacting elements to the process are difficult to measure in life. The use of molecular imaging techniques allows the different components of the inflammatory response to be monitored in situ in humans. In particular, positron emission tomography of selected markers targeted to specific cells and biochemical pathways can provide accurate measurements of disease activity, enabling a better understanding of inflammatory processes at all stages of disease. The practicability of sequential measurements allows one to monitor the natural history of different lung diseases. More importantly, imaging provides a unique tool for quantification of the modulation of discrete and specific aspects of inflammatory lung disease by targeted interventions. This should facilitate the development of new treatment strategies with better specificity for key elements of each disease.
Thinking person's guide to OS/2 2.1 (1993)

From the Publisher:
Contains easy-to-follow steps to master OS/2, explaining the basics and dynamic capabilities of the OS/2 2.1 graphical user interface, the Workplace Shell. Photographs of actual screens guide readers through this new and intuitive system illustrating how to reach information quickly and easily. Packed with examples and samples, it contains everything necessary to run applications on the OS/2 desktop.
Frontiers, Opportunities, and Challenges in Biochemical and Chemical Catalysis of CO2 Fixation (2013)

Two major energy-related problems confront the world in the&#13;\nnext 50 years. First, increased worldwide competition for&#13;\ngradually depleting fossil fuel reserves (derived from past&#13;\nphotosynthesis) will lead to higher costs, both monetarily and politically. Second, atmospheric CO_2 levels are at their highest recorded level since records began. Further increases are predicted to produce large and uncontrollable impacts on the world climate. These projected impacts extend beyond climate to ocean acidification, because the ocean is a major sink for atmospheric CO2.1 Providing a future energy supply that is secure and CO_2-neutral will require switching to nonfossil energy sources such as wind, solar, nuclear, and geothermal energy and developing methods for transforming the energy produced by these new sources into forms that can be stored, transported, and used upon demand.
Tightly-coupled monocular visual-inertial fusion for autonomous flight of rotorcraft MAVs (2015)

There have been increasing interests in the robotics community in building smaller and more agile autonomous micro aerial vehicles (MAVs). In particular, the monocular visual-inertial system (VINS) that consists of only a camera and an inertial measurement unit (IMU) forms a great minimum sensor suite due to its superior size, weight, and power (SWaP) characteristics. In this paper, we present a tightly-coupled nonlinear optimization-based monocular VINS estimator for autonomous rotorcraft MAVs. Our estimator allows the MAV to execute trajectories at 2 m/s with roll and pitch angles up to 30 degrees. We present extensive statistical analysis to verify the performance of our approach in different environments with varying flight speeds.
Early Identification of Refractory Epilepsy (2000)

Patients who have many seizures before therapy or who have an inadequate response to initial treatment with antiepileptic drugs are likely to have refractory epilepsy.
Studies on Antiseptics for Foodstuff. LXXII. : Studies on Diphenyl Ether Derivatives, Biphenyl Derivatives and Dibenzofuran Derivatives as a Preservative for Sake (1971)

Antibacterial tests against Bacillus saprogenes, which causes putrefaction of Sake, were carried out on 22 kinds of diphenyl ether series compounds, two kinds of dibenzofuran series compounds, and four kinds of biphenyl series compounds. In diphenyl ether series compounds, four compounds having a hydroxyl group in one benzene ring and a methyl in the other benzene ring, such as 2-hydroxy-2'-methyldiphenyl ether and 4-hydroxy-4'-methyldiphenyl ether, and a compound with a formyl and a hydroxyl in the same benzene ring, such as 4-formyl-2-hydroxydiphenyl ether, had antibacterial power 4-8 times that of salicylic acid and 2-4 times that of butyl p-hydroxybenzoate. Substitution of the methyl group with carboxyl lowered the antibacterial activity. In biphenyl derivatives, 2, 2'- and 4, 4'-dihydroxybiphenyl had antibacterial activity 8 times that of salicylic acid and 4 times that of butyl p-hydroxybenzoate. Increasing number of the hydroxyl group lowered the antibacterial activity. In dibenzofuran compounds, 3, 7-dihydroxydibenzofuran had twice the antibacterial activity of salicylic acid and about comparable to butyl p-hydroxybenzoate. 3, 7-Dihydroxy-1, 9-dimethyldibenzofuran increased the antibacterial activity to 8 times that of salicylic acid and 4 times that of butyl p-hydroxybenzoate, showing that increase of methyl groups resulted in stronger antibacterial activity.
Production of Epoxides from α,β-Halohydrins by Flavobacterium sp (1983)

The relative activity of Flavobacterium whole cells on the enzymatic synthesis of epoxides from alpha,beta-chlorohydrins, -bromohydrins, and -iodohydrins is described.
3D Display Systems Hardware Research at Sharp Laboratories of Europe : an update (1999)

New three dimensional (3d) displays exploiting patterned retardation elements (i) external and (ii) internal to the LCD are discussed. The fabrication of a 13.8 diagonal patterned retardation element from reactive mesogen, which co-operates with a polariser to form a parallax barrier, is described. An electrically switching LC cell demonstration incorporating a polariser and retarder array inside the LC cell itself has been fabricated and results are presented.
The WNT/Beta-catenin pathway in melanoma (2006)

The Wnt/beta-catenin pathway is involved in various cellular activities--including determination, proliferation, migration and differentiation--in embryonic development and adult homeostasis. The deregulation or constitutive activation of the Wnt/beta-catenin pathway may lead to cancer formation. This review focuses on the role of the Wnt/beta-catenin canonical signaling pathway in the melanocyte lineage, and more specifically, in melanoma. Several components of the Wnt/beta-catenin pathway, such as APC, ICAT, LEF1 and beta-catenin are modified in melanoma tumors and cell lines, leading to activation of this signaling. A hallmark of the activation of this pathway is the presence of beta-catenin in the nucleus. Indeed, beta-catenin is found in about 30% of human melanoma nuclei, indicating a potentially specific role for this signaling pathway in this aggressive type of cancer. Beta-catenin can induce ubiquitous genes such as myc or cyclinD1, cell lineage-restricted genes such as Brn2 and melanocyte-specific genes such as Mitf-M and Dct. The Mitf-M and Brn-2 genes encode transcription factors. Mitf plays a critical role in melanocyte survival, proliferation and differentiation. Brn-2 is involved in melanoma proliferation. Determining how the Wnt/beta-catenin signaling pathway, alone or with other pathways, orchestrates the induction of target genes involved in a diverse range of activities represents a major challenge in research into melanoma formation and tumor progression.