gebhart/patrepeval huggingface dataset:
Differential Contribution of the <i>Gata1</i> Gene Hematopoietic Enhancer to Erythroid Differentiation (2008)

GATA1 is a key regulator of erythroid cell differentiation. To examine how Gata1 gene expression is regulated in a stage-specific manner, transgenic mouse lines expressing green fluorescent protein (GFP) reporter from the Gata1 locus in a bacterial artificial chromosome (G1BAC-GFP) were prepared. We found that the GFP reporter expression faithfully recapitulated Gata1 gene expression. Using GFP fluorescence in combination with hematopoietic surface markers, we established a purification protocol for two erythroid progenitor fractions, referred to as burst-forming units-erythroid cell-related erythroid progenitor (BREP) and CFU-erythroid cell-related erythroid progenitor (CREP) fractions. We examined the functions of the Gata1 gene hematopoietic enhancer (G1HE) and the highly conserved GATA box in the enhancer core. Both deletion of the G1HE and substitution mutation of the GATA box caused almost complete loss of GFP expression in the BREP fraction, but the CREP stage expression was suppressed only partially, indicating the critical contribution of the GATA box to the BREP stage expression of Gata1. Consistently, targeted deletion of G1HE from the chromosomal Gata1 locus provoked suppressed expression of the Gata1 gene in the BREP fraction, which led to aberrant accumulation of BREP stage hematopoietic progenitor cells. These results demonstrate the physiological significance of the dynamic regulation of Gata1 gene expression in a differentiation stage-specific manner.
Bifunctional Gd<sub>2</sub>O<sub>3</sub>/C Nanoshells for MR Imaging and NIR Therapeutic Applications (2008)

Abstract This paper reports dual function Gd 2 O 3 /C nanoshells for application in MR contrast images and NIR‐triggered killing cancer cells. The nanoshells are prepared using biological gelatin particles as core templates through a two‐step thermal treatment. The surfaces of the nanoshells can be readily modified by poly(styrene‐alt‐maleic acid) (PSMA) polymer to improve their water‐dispersible properties and increase their biocompatibility. The Gd 2 O 3 /C nanoshells show brightened images of kidney cortex and liver in mice, whereas the Gd 2 O 3 /C@PSMA nanoshells show a darkened liver signal. The biodistribution is measured as a function of time and shows that the nanoshells circulate in the vessels and are cleared out gradually from organs. The graphite carbon coated on the Gd 2 O 3 nanoshells displays absorbance in the near‐IR (NIR) region. A large extinction coefficient is obtained, indicating the potential of the nanoshells as photothermal agents. The Gd 2 O 3 /C@PSMA nanoshells conjugated with anti‐epithermal growth factor receptor antibodies are used for targeting and destroying A549 lung cancer cells by means of NIR‐triggered killing capability. Both laser power density and material dose dependence are investigated to evaluate photothermolysis in cancer cells.
Ephus: multipurpose data acquisition software for neuroscience experiments (2010)

Physiological measurements in neuroscience experiments often involve complex stimulus paradigms and multiple data channels. Ephus (http://www.ephus.org) is an open-source software package designed for general-purpose data acquisition and instrument control. Ephus operates as a collection of modular programs, including an ephys program for standard whole-cell recording with single or multiple electrodes in typical electrophysiological experiments, and a mapper program for synaptic circuit mapping experiments involving laser scanning photostimulation based on glutamate uncaging or channelrhodopsin-2 excitation. Custom user functions allow user-extensibility at multiple levels, including on-line analysis and closed-loop experiments, where experimental parameters can be changed based on recently acquired data, such as during in vivo behavioral experiments. Ephus is compatible with a variety of data acquisition and imaging hardware. This paper describes the main features and modules of Ephus and their use in representative experimental applications.
Self-Organized Biological Dynamics and Nonlinear Control (2000)

The growing impact of nonlinear science on biology and medicine is fundamentally changing our view of living organisms and disease processes. This book introduces the application to biomedicine of a broad range of interdisciplinary concepts from nonlinear dynamics, such as self-organization, complexity, coherence, stochastic resonance, fractals and chaos. It comprises 18 chapters written by leading figures in the field and covers experimental and theoretical research, as well as the emerging technological possibilities such as nonlinear control techniques for treating pathological biodynamics, including heart arrhythmias and epilepsy. This book will attract the interest of professionals and students from a wide range of disciplines, including physicists, chemists, biologists, sensory physiologists and medical researchers such as cardiologists, neurologists and biomedical engineers.
Estimating locations and coverage areas of mobile network cells based on crowdsourced data (2013)

Mobile network operators usually keep the data about their mobile network topology very secret. However, having this data, many sophisticated and innovative applications could be realized. Today's smartphones provide the means to measure cell data with which the mobile network topology of different operators can be approximately derived by applying various position estimation algorithms. These approaches deliver different results in terms of distance to the real positions of base stations and positions calculated by Google. In this paper, we analyze and evaluate state-of-the-art approaches for estimating base station positions out of crowdsourced data and integrate the most suitable methode(s) into the OpenMobileNetwork, which is an open-source initiative for publishing mobile network data using the semantic principles of Linked Data. The results show that the grid-based approach provides the best estimates for base station positions when compared with their real locations.
Early Renal Pathophysiology in an Acute Model of Cyclosporine Nephrotoxicity in Rats (1987)

We have recently described a rat model of acute cyclosporine nephrotoxicity characterized by rapid onset of reproducible mild to moderate renal failure. In the present studies, we have examined early pathophysiologic events and morphologic changes in this model. Following acute intraperitoneal administration of 60 mg/kg of parenteral cyclosporine, renal blood flow (RBF) fell 24% from baseline. Intraperitoneal administration of an oral cyclosporine preparation (60 mg/kg) also reduced RBF (25%), as did administration of an equivalent volume of parenteral cremophore (23%). Renal vascular resistance (RVR) increased significantly in all these groups. In contrast, intraperitoneal administration of mineral oil or olive oil oral vehicle produced no significant change in RBF (4% fall from baseline), and RVR actually decreased in these control animals. Following 2 daily doses of these agents, RBF remained significantly lower in rats given parenteral cyclosporine (5.10 mL/min vs 8.54 mL/min in cremophore rats and 7.28 mL/min in oil control rats) and renal vascular resistance remained high. Systemic blood pressure was also significantly lower in cyclosporine-treated rats at 2 days, and GFR was depressed. Morphologic studies revealed a correlation at 2 days between tubular vacuolation and renal blood flow and renal vascular resistance in cyclosporine-treated rats.
Senescence, Apoptosis or Autophagy? (2008)

Many features of aging result from the incapacity of cells to adapt to stress conditions. When damage accumulates irreversibly, mitotic cells from renewable tissues rely on either of two mechanisms to avoid replication. They can permanently arrest the cell cycle (cellular senescence) or trigger cell death programs. Apoptosis (self-killing) is the best-described form of programmed cell death, but autophagy (self-eating), which is a lysosomal degradation pathway essential for homeostasis, reportedly contributes to cell death as well. Unlike mitotic cells, postmitotic cells like neurons or cardiomyocytes cannot become senescent since they are already terminally differentiated. The fate of these cells entirely depends on their ability to cope with stress. Autophagy then operates as a major homeostatic mechanism to eliminate damaged organelles, long-lived or aberrant proteins and superfluous portions of the cytoplasm. In this mini-review, we briefly summarize the molecular networks that allow damaged cells either to adapt to stress or to engage in programmed-cell-death pathways.
A framework for similarity recognition of CAD models (2016)

Abstract A designer is mainly supported by two essential factors in design decisions. These two factors are intelligence and experience aiding the designer by predicting the interconnection between the required design parameters. Through classification of product data and similarity recognition between new and existing designs, it is partially possible to replace the required experience for an inexperienced designer. Given this context, the current paper addresses a framework for recognition and flexible retrieval of similar models in product design. The idea is to establish an infrastructure for transferring design as well as the required PLM (Product Lifecycle Management) know-how to the design phase of product development in order to reduce the design time. Furthermore, such a method can be applied as a brainstorming method for a new and creative product development as well. The proposed framework has been tested and benchmarked while showing promising results. Highlights Developing a knowledge-based framework to assist the designer in design decisions. Opitz feature recognition and code generation from STEP for data standardization. An efficient similarity recognition algorithm to retrieve models from database.
Head, Eye, and Hand Patterns for Driver Activity Recognition (2014)

In this paper, a multiview, multimodal vision framework is proposed in order to characterize driver activity based on head, eye, and hand cues. Leveraging the three types of cues allows for a richer description of the driver's state and for improved activity detection performance. First, regions of interest are extracted from two videos, one observing the driver's hands and one the driver's head. Next, hand location hypotheses are generated and integrated with a head pose and facial landmark module in order to classify driver activity into three states: wheel region interaction with two hands on the wheel, gear region activity, or instrument cluster region activity. The method is evaluated on a video dataset captured in on-road settings.
[Prokaryotic DNA methyltransferases: the structure and the mechanism of interaction with DNA]. (2003)

The review considers current views on the function of DNA methyltransferases (MTases) that belong to prokaryotic type II restriction-modification systems. A commonly accepted classification of MTases is described along with their primary and tertiary structures and molecular mechanisms of their specific interaction with DNA (including methylation). MTase inhibitors are also considered. Special emphasis is placed on the flipping of the target heterocyclic base out of the double helix and on the methods employed in its analysis. Base flipping is a fundamentally new type of DNA conformational changes and is also of importance in the case of other DNA-operating enzymes. MTases show unique sequence homology, and are similar in structure of functional centers and in the mechanism of methylation. These data contribute to the understanding of the general biological significance of methylation, since prokaryotic and eukaryotic MTases are structurally and functionally similar.
Prostanoid receptor EP1 and Cox-2 in injured human nerves and a rat model of nerve injury: a time-course study (2006)

Different stages of infiltration and activation of macrophages may be observed in the peripheral and central nervous system following peripheral nerve injury. EP1 receptor level increase in sensory neurones, and macrophage infiltration, appears to precede increased Cox-2 expression by macrophages. However, other methods for detecting Cox-2 levels and activity are required. EP1 antagonists may show therapeutic effects in acute and chronic neuropathic pain, in addition to inflammatory pain.
Enhancing Frac-Pack Evaluations With Directional and Spectral Gamma Ray Measurements (1997)

Abstract The effectiveness of frac-pack operations can be easily monitored by using radioactive tracers. The fluid and solid components of materials placed downhole can be tagged with different gamma-ray-emitting isotopes. After the pumping operations have been completed, specialized gamma ray logging sondes can be run in the well to establish the precise locations of the tagged materials. Directional gamma ray measurements determine the azimuthal placement distributions. Gamma ray spectral energy measurements allow the contributions of individual isotopes to be separated so that the vertical extent and radial displacement efficiency of the individual components pumped can be established. This technology can be used to evaluate frac-packs and most other downhole placement operations. The knowledge of where materials are actually placed during downhole pumping operations provides unique diagnostic information. This allows subsequent operations to be improved and made more effective as necessary. This paper reports on frac-pack operations in the shallow, unconsolidated sands of the Duri field in Indonesia. Gamma ray spectroscopy and directional gamma ray logs were run in several wells as part of a study to determine frac-pack performance. The gamma ray directional logs show a number of significant asymmetries where sand was apparently placed on one side of the wellbore. There was some evidence of "ballooning" in several zones where the frac-pack pushed the formation sand away from the borehole. The gamma ray spectroscopy logs offered supporting evidence which was confirmed by additional laboratory analysis. The interpretation of all the gamma ray log results confirmed the frac-pack operations. The log results also provided evidence regarding the detailed manner in which the frac-pack was placed and gave rise to some adjustments to enhance frac-pack procedures. This project demonstrated that frac-pack technology resulted in increased oil production and utilization of frac-pack operations will continue. However, maintenance requirements were not reduced as much as desired because of proppant flowback. Methods for further reducing costs are being investigated.
Two-Stage Light-Gas Gun Installation for Hypervelocity Impact Studies (1973)

Abstract : The report describes a constant base pressure two-stage light-gas gun system installed at North Carolina State University at Raleigh for studying hypervelocity impact phenomena. The gun uses helium gas as propellant and can produce velocities up to 20,000 feet per second. A description of the problems encountered in developing the experimental facility and solutions developed to meet these problems are presented. The components which were designed by the authors include target support, breech support, gas deflector, impact chamber extension, piston and projectile. These components are unique to this installation and have facilitated target alignment, optical measurements and firing the gun.
PROMOTER ACTION IN REACTIONS OF OXIDATION CONCOMITANT WITH THE CATALYTIC DECOMPOSITION OF HYDROGEN PEROXIDE.<sup>1,2</sup> I. THE OXIDATION OF HYDRAZINE (1930)

ADVERTISEMENT RETURN TO ISSUEArticleNEXTPROMOTER ACTION IN REACTIONS OF OXIDATION CONCOMITANT WITH THE CATALYTIC DECOMPOSITION OF HYDROGEN PEROXIDE.1,2 I. THE OXIDATION OF HYDRAZINEDonald P. GrahamCite this: J. Am. Chem. Soc. 1930, 52, 8, 3035–3045Publication Date (Print):August 1, 1930Publication History Published online1 May 2002Published inissue 1 August 1930https://pubs.acs.org/doi/10.1021/ja01371a001https://doi.org/10.1021/ja01371a001research-articleACS PublicationsRequest reuse permissionsArticle Views102Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Waypoint-based Topology Inference (2020)

Traditional network topology inference aims at reconstructing the routing trees rooted at each probing source from end-to-end measurements. However, due to emerging technologies such as network function virtualization, software defined networking, and segment routing, many modern networks are capable of supporting generalized forwarding that can create complex routing topologies different from routing trees. In this work, we take a first step towards closing this gap by proposing methods to infer the routing topology (referred to as 1-1-N topology) from a single source to multiple destinations, where routes may be required to traverse a given waypoint. We first thoroughly study the special case of 1-1-2 topologies, showing that even this seemingly simple case is highly nontrivial with 36 possibilities. We then demonstrate how the solution to the special case can be used as building blocks to infer 1-1-N topologies. The inferred topology is proved to be equivalent to the ground truth up to splitting/combining edges in the same category.
Stereotyped B-cell receptors in one-third of chronic lymphocytic leukemia: a molecular classification with implications for targeted therapies (2012)

Mounting evidence indicates that grouping of chronic lymphocytic leukemia (CLL) into distinct subsets with stereotyped BCRs is functionally and prognostically relevant. However, several issues need revisiting, including the criteria for identification of BCR stereotypy and its actual frequency as well as the identification of "CLL-biased" features in BCR Ig stereotypes. To this end, we examined 7596 Ig VH (IGHV-IGHD-IGHJ) sequences from 7424 CLL patients, 3 times the size of the largest published series, with an updated version of our purpose-built clustering algorithm. We document that CLL may be subdivided into 2 distinct categories: one with stereotyped and the other with nonstereotyped BCRs, at an approximate ratio of 1:2, and provide evidence suggesting a different ontogeny for these 2 categories. We also show that subset-defining sequence patterns in CLL differ from those underlying BCR stereotypy in other B-cell malignancies. Notably, 19 major subsets contained from 20 to 213 sequences each, collectively accounting for 943 sequences or one-eighth of the cohort. Hence, this compartmentalized examination of VH sequences may pave the way toward a molecular classification of CLL with implications for targeted therapeutic interventions, applicable to a significant number of patients assigned to the same subset.
Cytotoxic Flavanones of<i> Schizolaena hystrix </i>from the Madagascar Rainforest (2005)

Bioassay-guided fractionation of an ethanol extract of a Madagascar collection of Schizolaena hystrix afforded three new flavanones, schizolaenone A (1), schizolaenone B (2), and 4'-O-methylbonannione A (3), as well as three known flavanones, nymphaeol A, bonannione A, and macarangaflavanone B, and the flavanol bonanniol A. The structures of compounds 1-3 were determined by various one- and two-dimensional NMR techniques. All of the isolates were tested for cytotoxicity against the A2780 human ovarian cancer cell line. Nymphaeol A (IC(50) = 5.5 microg/mL) exhibited the greatest cytotoxicity, while the other flavanones were found to be only weakly active.
Regulation of the Biosynthesis and Degradation of Starch (1982)

INTRODUCTION . REGULATION OF STARCH SYNTHESIS IN ALGAE, CYANOBACTERIA, AND LEAVES . . ...... . . . In vivo Evidence Strongly Suggesting that the [3-P-glycerate]l[P,] Regulates Leaf Starch Synthesis . Regulation of ADPglucose Pyrophosphorylase from Nonchlorophyllous Plant Tissue . Native and Subunit Molecular Weight of the ADPglucose Pyrophosphorylase ....... . SYNTHESIS OF STARCH FROM SUCROSE IN RESERVE TiSSUES . Properties of Sucrose Synthase . . SYNTHESIS OF SUCROSE IN PLANTS . Properties and Regulation of Sucrose-P Synthase . Sucrose-6-Phosphate Phosphatase . Localization of Sucrose Synthesis and Questions Concerning Partition of Photosynthetic Carbon Between Sucrose and Starch . DEGRADATION OF STARCH . Localization of Starch Degradative Enzymes in Leaves. . Properties of Leaf Amylases . Properties of the Spinach Leaf Phosphorylases . Pathway of Starch Degradation in Leaves . Regulation of the Leaf Starch Degradative Enzymes .
Analysis of Mice Containing a Targeted Deletion of β-Globin Locus Control Region 5′ Hypersensitive Site 3 (1996)

To examine the function of murine beta-globin locus region (LCR) 5' hypersensitive site 3 (HS3) in its native chromosomal context, we deleted this site from the mouse germ line by using homologous recombination techniques. Previous experiments with human 5' HS3 in transgenic models suggested that this site independently contains at least 50% of total LCR activity and that it interacts preferentially with the human gamma-globin genes in embryonic erythroid cells. However, in this study, we demonstrate that deletion of murine 5' HS3 reduces expression of the linked embryonic epsilon y- and beta H 1-globin genes only minimally in yolk sac-derived erythroid cells and reduces output of the linked adult beta (beta major plus beta minor) globin genes by approximately 30% in adult erythrocytes. When the selectable marker PGK-neo cassette was left within the HS3 region of the LCR, a much more severe phenotype was observed at all developmental stages, suggesting that PGK-neo interferes with LCR activity when it is retained within the LCR. Collectively, these results suggest that murine 5' HS3 is not required for globin gene switching; importantly, however, it is required for approximately 30% of the total LCR activity associated with adult beta-globin gene expression in adult erythrocytes.
Synthesis and examination of antimicrobial properties of aminomethylated derivatives C6–C7 of alicyclic diols (2009)

Synthesis of C6–C7 alicyclic diols was studied by a catalytic oxidation of cyclohexene, norbornene and their methyl derivatives in the presence of heterogenized molybdenum-containing catalysts. By a triple condensation of the diols with formaldehyde and secondary amines a synthesis of their aminomethylated derivatives with various substituents at nitrogen atom was examined. Antimicrobial properties of the synthesized amino alcohols in M-10 oil as additives with fungicidal and bactericidal activities were studied.