gebhart/patrepeval huggingface dataset:
Polycystin-1 maturation requires polycystin-2 in a dose-dependent manner (2015)

Autosomal dominant polycystic kidney disease (ADPKD) is a common inherited nephropathy responsible for 4%-10% of end-stage renal disease cases. Mutations in the genes encoding polycystin-1 (PC1, PKD1) or polycystin-2 (PC2, PKD2) cause ADPKD, and PKD1 mutations are associated with more severe renal disease. PC1 has been shown to form a complex with PC2, and the severity of PKD1-mediated disease is associated with the level of the mature PC1 glycoform. Here, we demonstrated that PC1 and PC2 first interact in the ER before PC1 cleavage at the GPS/GAIN site and determined that PC2 acts as an essential chaperone for PC1 maturation and surface localization. The chaperone function of PC2 was dependent on the presence of the distal coiled-coil domain and was disrupted by pathogenic missense mutations. In Pkd2-/- mice, complete loss of PC2 prevented PC1 maturation. In Pkd2 heterozygotes, the 50% PC2 reduction resulted in a nonequimolar reduction (20%-25%) of the mature PC1 glycoform. Interbreeding between various Pkd1 and Pkd2 models revealed that animals with reduced levels of functional PC1 and PC2 in the kidney exhibited severe, rapidly progressive disease, illustrating the importance of complexing of these proteins for function. Our results indicate that PC2 regulates PC1 maturation; therefore, mature PC1 levels are a determinant of disease severity in PKD2 as well as PKD1.
An Inferring Semantic System Based on Relational Models for Mobile Robotics (2015)

Nowadays, there are many robots with the ability to move along its environment and they need a navigation system. In the semantic navigation paradigm, the ability to reason and to infer new knowledge is required. In this work a relational database is presented and proposed. This database allows to manage and to raise queries of semantic information from any environment in which a mobile robot would perform a semantic navigation, providing advantages such as conceptual simplicity and a fast method for switching between semantic environments, being unnecessary redefine new rules. In this paper, a target topological level is obtained from a semantic level destination.
Fkh1 and Fkh2 associate with Sir2 to control CLB2 transcription under normal and oxidative stress conditions (2013)

The Forkhead (Fkh) box family of transcription factors is evolutionary conserved from yeast to higher eukaryotes and its members are involved in many physiological processes including metabolism, DNA repair, cell cycle, stress resistance, apoptosis, and aging. In budding yeast, four Fkh transcription factors were identified, namely Fkh1, Fkh2, Fhl1, and Hcm1, which are implicated in chromatin silencing, cell cycle regulation, and stress response. These factors impinge transcriptional regulation during cell cycle progression, and histone deacetylases (HDACs) play an essential role in this process, e.g., the nuclear localization of Hcm1 depends on Sir2 activity, whereas Sin3/Rpd3 silence cell cycle specific gene transcription in G2/M phase. However, a direct involvement of Sir2 in Fkh1/Fkh2-dependent regulation of target genes is at present unknown. Here, we show that Fkh1 and Fkh2 associate with Sir2 in G1 and M phase, and that Fkh1/Fkh2-mediated activation of reporter genes is antagonized by Sir2. We further report that Sir2 overexpression strongly affects cell growth in an Fkh1/Fkh2-dependent manner. In addition, Sir2 regulates the expression of the mitotic cyclin Clb2 through Fkh1/Fkh2-mediated binding to the CLB2 promoter in G1 and M phase. We finally demonstrate that Sir2 is also enriched at the CLB2 promoter under stress conditions, and that the nuclear localization of Sir2 is dependent on Fkh1 and Fkh2. Taken together, our results show a functional interplay between Fkh1/Fkh2 and Sir2 suggesting a novel mechanism of cell cycle repression. Thus, in budding yeast, not only the regulation of G2/M gene expression but also the protective response against stress could be directly coordinated by Fkh1 and Fkh2.
Inhibition of in vivo tumor growth by the <i>beta</i> chemokine, TCA3. (1994)

TCA3 is a proinflammatory murine glycoprotein that shares structural features with cytokines of the beta chemokine family and is a chemoattractant for neutrophils and monocytes. To assess the in vivo functions of TCA3, the cDNA was expressed in two mouse myeloma cell lines. Although the transfected and control cells had similar growth rates in vitro, TCA3-expressing tumors demonstrated impaired growth in both normal and immunodeficient mice. Histologic evaluation of the injection sites demonstrated that TCA3 expression resulted in an early neutrophil and monocyte infiltrate accompanied by tumor necrosis. There was complete regression of the TCA3-transfected tumor in some immunocompetent syngeneic mice. The TCA3-transfected cells induced specific and long-lasting immunity in mice that showed complete tumor regression; these animals were resistant to challenge with nontransfected tumor cells. In contrast, priming with irradiated tumor cells provided little protection against challenge with nontransfected tumor, which indicates that TCA3 specifically augments tumor immunogenicity. Mixing TCA3-transfected cells with normal tumor cells causes retarded growth of the normal tumor cells provided the latter are injected into the same site. Furthermore, direct in situ injection of soluble rTCA3 early during the course of tumor implantation also inhibits tumor growth. The data suggest that TCA3 may perform two roles in tumor protection: it induces lymphocyte-independent antitumor activity and stimulates tumor-specific immunity. We speculate that TCA3 has natural adjuvant activities that result in augmented immune responses.
Expression of vacuolar H(+)-ATPase in mouse osteoclasts during in vitro differentiation (1992)

Osteoclasts express high levels of a vacuolar H(+)-adenosinetriphosphatase (H(+)-ATPase) on the ruffled membrane which they employ to dissolve bone mineral by acidifying their site of attachment on bone. The factors that control amplification of H(+)-ATPase during osteoclast differentiation are poorly understood. We examined the expression of vacuolar H(+)-ATPase in a cell culture system in which mouse spleen cells can be induced to differentiate into osteoclasts by coculture with a mouse bone marrow stromal cell line. We found that the coculture system produced active osteoclasts, identified as multinucleated cells with staining for tartrate-resistant acid phosphatase activity that formed genuine resorption pits in bone. These cells developed high levels of H(+)-ATPase expression in culture, and omission of dexamethasone or 1 alpha,25-dihydroxyvitamin D3 from the coculture system each partially suppressed the expression of H(+)-ATPase. The results demonstrate that the spleen and PA6 cell coculture system may be useful for investigating the factors that control the induction of H(+)-ATPase amplification that occurs during osteoclast differentiation.
Hybrid treatment of aortic arch aneurysms. (2015)

The advent of thoracic aortic endovascular stent-grafting has drastically changed the management of thoracic aneurysms. In 1991, Volodos and colleagues performed the first hybrid aortic arch repair. The case involved an arch debranching with placement of an endograft in a patient with a previous repair for an aortic coarctation. Since that time, thoracic endografts have largely been incorporated into the treatment of aortic arch disease using hybrid approaches. In this article we will discuss the technical details of both the open and endovascular portion of hybrid aortic arch repairs. We will also review the evidence supporting the use of hybrid operations to repair aortic arch pathology, with a focus on mortality, morbidity and technical success.
One-step Synthesis of 3-(Dialkylamino)indolizines by the Palladium-catalyzed Reaction of α-Bromopyridine, Propargyl Alcohol, and Secondary Amine (1980)

Abstract 3-(Dialkylamino)indolizines were synthesized in one step by the reaction of 2-bromopyridine, propargyl alcohol, and secondary amines in the presence of Pd(PPh3)2Cl2–CuI as a catalyst. 3-(2-Pyridyl)-2-propyn-1-ol and 3-(2-pyridyl)acrylaldehyde were suggested to be intermediates of the reaction. 3-Dialkylamino derivatives of pyrrolo[1,2-a]quinoline, pyrrolo[2,1-a]isoquinoline, and pyrrolo[1,2-b]pyridazine were obtained from the corresponding α-haloazaaromatics in a similar way.
Effect of Structural Modification of Enol−Carboxamide-Type Nonsteroidal Antiinflammatory Drugs on COX-2/COX-1 Selectivity (1997)

Meloxicam (5), an NSAID in the enol-carboxamide class, was developed on the basis of its antiinflammatory activity and relative safety in animal models. In subsequent screening in microsomal assays using human COX-1 and COX-2, we discovered that it possessed a selectivity profile for COX-2 superior to piroxicam and other marketed NSAIDs. We therefore embarked on a study of enol-carboxamide type compounds to determine if COX-2 selectivity and potency could be dramatically improved by structural modification. Substitution at the 6- and 7-positions of the 4-oxo-1,2-benzothiazine-3-carboxamide, alteration of the N-methyl substituent, and amide modification were all examined. In addition we explored several related systems including the isomeric 3-oxo-1,2-benzothiazine-4-carboxamides, thienothiazines, indolothizines, benzothienothiazines, naphthothiazines, and 1,3- and 1,4-dioxoisoquinolines. While a few examples were found with greater potency in the COX-2 assay, no compound tested had a better COX-2/COX-1 selectivity profile than that of 5.
SWIFT: A Dynamical Model of Saccade Generation During Reading. (2005)

Mathematical models have become an important tool for understanding the control of eye movements during reading. Main goals of the development of the SWIFT model (R. Engbert, A. Longtin, & R. Kliegl, 2002) were to investigate the possibility of spatially distributed processing and to implement a general mechanism for all types of eye movements observed in reading experiments. The authors present an advanced version of SWIFT that integrates properties of the oculomotor system and effects of word recognition to explain many of the experimental phenomena faced in reading research. They propose new procedures for the estimation of model parameters and for the test of the model's performance. They also present a mathematical analysis of the dynamics of the SWIFT model. Finally, within this framework, they present an analysis of the transition from parallel to serial processing.
Note on the soluble sugars of sorghum. (1980)

Sorghum (Sorghum bicolor (L.) Moench) is a major food crop\nranking fifth in world grain production. It is an important source of calories and protein for a large segment of the human population in the semiarid tropics. Although information on proteins, amino acids, and starch content of sorghum is avaialable (Rooney 1973)...
Video Frame Segmentation Using Competitive Contours (2005)

Publication in the conference proceedings of EUSIPCO, Antalya, Turkey, 2005
Introduction to the Theory and Practice of Econometrics (1989)

This book interweaves inferential approaches and theory and practice in econometrics. Basic statistical and linear algebra concepts are introduced as they are needed to give life to the statistical model under study. Most econometric applications start with a tentative theory or hypothesis a sample of data and the goal of learning something about the phenomena under study from the limited set of observations. Therefore a sample of data that may be used to investigate a particular economic hypothesis is presented to motivate the analysis of each of the statistical models presented. This linkage between the economic process that is thought to have generated the data and a particular statistical model is a unifying theme throughout the book. It progresses from the special case of investigating the possibilities for determining the location and scale parameters for a population from a sample of observations to investigating a complex simultaneous system of structural equations under general stochastic assumptions. To ensure that the reader understands the basic concepts and conclusions as they relate to linear statistical models simple special case models are evaluated and then the analysis is repeated for the general case. The 1st half of book gives the student a solid introduction to the formulation and use of linear statistical models. The 2nd half introduces the student to the econometric problems that arise when it is taken into account that economic data are stochastic dynamic and simultaneous and that the optimal statistical procedure sometimes changes as we change the statistical model the amount and type of information used and the measure of performance.
Synthesis and Characterization of Some Novel Dendritic Architectures Bearing Chalcone at the Periphery Through Click Approach (2009)

Synthesis of 1,2,3-triazole-based dendritic architectures bearing a chalcone unit at the surface group has been achieved through a click reaction by the convergent synthetic strategy, in which tri- and tetra-azide were used as core units.
LEADING YOUR COMPANY TO THE NEXT LEVEL (2014)

Cohen believes that one of today's most pressing problems is the need for companies to differentiate themselves from the competition. This may seem straightforward but it is not. He is the leader of a Mexico‐based shipping company, with many larger multinational companies as his competitors. He uses personalized service, backed by strong, conscientious leadership, as his differentiator. He outlines five principles: (1) Get Serious About Leading, (2) Provide Unequaled Service, (3) Unleash Happiness, (4) Maintain a Start‐up Mentality, and (5) Get Your Team to Play As One. “If you don't keep raising the bar,” Cohen writes, “the company will stagnate.”
Expression of N-cadherin in esophageal squamous cell carcinoma and silencing expression of N-cadherin using RNA interference on invasiveness of EC9706 cells. (2009)

Down-regulation of E-cadherin and up-regulation of N-cadherin may be involved in the genesis of ESCC. Silencing N-cadherin using RNA interference could inhibit the invasiveness of EC9706 cells in vitro.
Microfabricated PDMS multichannel emitter for electrospray ionization mass spectrometry (2001)

A novel microfabricated multichannel emitter for electrospray ionization mass spectrometry (ESI-MS) was implemented with polydimethylsiloxane (PDMS) using a soft lithography technique. The emitters are formed as electrospray tips along a thin membrane on the edge of the device with channels of 100 microm x 30 microm dimensions. The electrospray performance of the PDMS emitters for a single channel device and a four channel device interfaced with a time-of-flight mass spectrometer was evaluated for detecting the molecular weight of reference peptides (angiotensin I and bradykinin). The emitters were durable at the flow rate of 1-20 microL min(-1) for more than 30 h of continuous electrospray with limit of detection of 1 microM (S/N 18). This microfabrication method for a PDMS multichannel emitter as an integral part of a microfluidic device will facilitate development of more complex microfluidic analysis systems using ESI-MS.
Crosstalk between ACE inhibitors, B2 kinin receptor and nitric oxide in endothelial cells (2001)

The endothelium is an important target organ of angiotensin converting enzyme (ACE) inhibitors. Within these monolayered cells establishing the interface between blood and vasculature, a complex signal transduction machinery is the basis for a major role of ACE inhibition in the regulation of vascular homoestasis. This chapter will focus on the endothelial aspects of ACE-inhibition, on its interaction with components of the kallikrein-kinin system.
660 nm In0.5Ga0.5P light-emitting diodes on Si substrates (1988)

In0.5Ga0.5P light-emitting diodes (LED’s) that operate in the 660 nm region were fabricated on Si substrates using GaAs buffer layers. InGaP layers were grown by metalorganic-chloride vapor phase epitaxy (MO-chloride VPE), and GaAs layers were grown by metalorganic vapor phase epitaxy (MOVPE) at atmospheric pressure. Red color emission was clearly seen under room light at 20 mA dc injection. The LED operation was stable at 5 kA/cm2 despite the high dislocation density of around 107 cm−2 .
Anthropogenic emissions of methane in the United States (2013)

This study quantitatively estimates the spatial distribution of anthropogenic methane sources in the United States by combining comprehensive atmospheric methane observations, extensive spatial datasets, and a high-resolution atmospheric transport model. Results show that current inventories from the US Environmental Protection Agency (EPA) and the Emissions Database for Global Atmospheric Research underestimate methane emissions nationally by a factor of ∼1.5 and ∼1.7, respectively. Our study indicates that emissions due to ruminants and manure are up to twice the magnitude of existing inventories. In addition, the discrepancy in methane source estimates is particularly pronounced in the south-central United States, where we find total emissions are ∼2.7 times greater than in most inventories and account for 24 ± 3% of national emissions. The spatial patterns of our emission fluxes and observed methane-propane correlations indicate that fossil fuel extraction and refining are major contributors (45 ± 13%) in the south-central United States. This result suggests that regional methane emissions due to fossil fuel extraction and processing could be 4.9 ± 2.6 times larger than in EDGAR, the most comprehensive global methane inventory. These results cast doubt on the US EPA's recent decision to downscale its estimate of national natural gas emissions by 25-30%. Overall, we conclude that methane emissions associated with both the animal husbandry and fossil fuel industries have larger greenhouse gas impacts than indicated by existing inventories.
Reflective Optics for Obtaining Prescribed Irradiative Distributions from Collimated Sources (1974)

The differential equations are derived for reflective optical surfaces in systems that give prescribed spatial irradiation from collimated sources. The equations are derived for axisymmetric configurations assuming specular reflective surfaces. The formulation considers general source radiant emittance distributions, general receiver shapes, and receiver irradiation distributions. The formulation of the differential equations is effected through the vector formulation of ray-trace equations for the systems, formulation of differential radiant energy balance equations, and appropriate differentiation of the ray-trace equations. The differential equations are derived for two configurations.
Tumor Antigen Epitopes Interpreted by the Immune System as Self or Abnormal-Self Differentially Affect Cancer Vaccine Responses (2010)

Epitope selection is an important consideration in the design of cancer vaccines, but factors affecting selection are not fully understood. We compared the immune responses to peptides and glycopeptides from the common human tumor antigen MUC1, a mucin that is coated with O-linked carbohydrates in its variable number of tandem repeats (VNTR) region. MUC1 expressed on tumor cells is characteristically underglycosylated, creating peptide and glycopeptide neoepitopes that are recognized by the immune system. The response to VNTR peptides is weaker in MUC1-transgenic mice (MUC1-Tg mice) than in wild-type (WT) mice, whereas the response to VNTR glycopeptides is equally strong in the two strains. Thus, glycopeptides seem to be recognized as foreign, whereas peptides, although immunogenic, are perceived as self. To explore this further, we generated MUC1 peptide- and glycopeptide-specific T-cell receptor transgenic mice and studied the function of their CD4 T cells when adoptively transferred into MUC1-Tg or WT mice. Peptide-specific T-cell precursors were not centrally deleted in MUC1-Tg mice and did not acquire a T regulatory phenotype. However, their response to the cognate peptide was reduced in MUC1-Tg mice compared with WT mice. In contrast, glycopeptide-specific CD4 T cells responded equally well in the two hosts and, when simultaneously activated, also enhanced the peptide-specific T-cell responses. Our data show that the immune system differentially recognizes various epitopes of tumor-associated antigens either as self or as foreign, and this controls the strength of antitumor immunity. This represents an important consideration for designing safe and effective cancer vaccines.
Modeling Asthma in Mice (2010)

Clinical reports of areas of damaged airway epithelium associated with shed epithelial cells in bronchoalveolar lavage fluid, aberrant epithelial repair processes, and altered cytokine and growth factor release have highlighted some fundamental differences between the airway epithelium in individuals with and without asthma. However, the consequences of these epithelial changes are not clearly defined, and may be difficult to assess in the clinic. In this Review, we answer the two questions. (1) What in vivo models and methods have been used to inform us about airway epithelium damage, repair, and immune responses? Our response focuses on genetic influences as well as allergen exposure, environmental/chemical, and mechanical models. (2) How can we improve on existing mouse models to understand changes in airway epithelium biology in asthma? In answering the second question, we include exciting recent studies that have combined multiple exposure methods and/or epithelium-centric outcome measurements. By addressing these two questions, we propose that future interrogation of epithelial responses of both existing and nascent mouse models may provide greater understanding of the mechanisms underlying airway inflammation and remodeling in asthma with hope of generating novel therapeutic targets.
Detection of Colorectal Cancer in Circulating Cell-Free DNA by Methylated CpG Tandem Amplification and Sequencing (2019)

MCTA-Seq is a promising method for the noninvasive detection of CRC.
The Push-Me Pull-You of T Cell Activation (2001)

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Visualization-specific compression of large volume data (2002)

When interactive real-time applications are developed with very large volume data, the use of lossy compression is often inevitable. Lossy compression schemes generally encode data without consideration of the purpose of visualization that is actually performed, which often results in inefficient compression. In this paper, we present a new method for classifying voxels according to their importance in visualization, and assigning appropriate weights to them. The associated weight information can be combined with lossy compression schemes to reduce the visual degradation of reconstructed images, resulting in higher compression rates and visual fidelity. Test results demonstrate that the proposed technique improves both the amount of compression and the quality of visualization significantly.