gebhart/patrepeval huggingface dataset:
Lipid Profiles of Canine Invasive Transitional Cell Carcinoma of the Urinary Bladder and Adjacent Normal Tissue by Desorption Electrospray Ionization Imaging Mass Spectrometry (2009)

Desorption electrospray ionization mass spectrometry (DESI-MS) was used in an imaging mode to interrogate the lipid profiles of thin tissue sections of canine spontaneous invasive transitional cell carcinoma of the urinary bladder (a model of human invasive bladder cancer) as well as adjacent normal tissue from four different dogs. The glycerophospholipids and sphingolipids that appear as intense signals in both the negative ion and positive ion modes were identified by tandem mass spectrometry product ion scans using collision-induced dissociation. Differences in the relative distributions of the lipid species were present between the tumor and adjacent normal tissue in both the negative and positive ion modes. DESI-MS images showing the spatial distributions of particular glycerophospholipids, sphinoglipids, and free fatty acids in both the negative and positive ion modes were compared to serial tissue sections that were stained with hematoxylin and eosin (H&E). Increased absolute and relative intensities for at least five different glycerophospholipids and three free fatty acids in the negative ion mode and at least four different lipid species in the positive ion mode were seen in the tumor region of the samples in all four dogs. In addition, one sphingolipid species exhibited increased signal intensity in the positive ion mode in normal tissue relative to the diseased tissue. Principal component analysis was also used to generate unsupervised statistical images from the negative ion mode data, and these images are in excellent agreement with the DESI images obtained from the selected ions and also the H&E-stained tissue.
Volumetric model determination of the tibia based on 2D radiographs using a 2D/3D database (2001)

We present a new concept with mathematical background for the construction of a three-dimensional (3D) volumetric model of the human tibia based on two conventional orthogonal two-dimensional (2D) radiographic images. This approach is supported by a computer database containing a collection of 80 2D/3D image data sets of individual cadaveric tibiae. For each of these tibiae, the database contains digitized 2D orthogonal radiographic images in both anterior and lateral views, and the corresponding 3D CT data obtained by computerized tomography. To obtain a 3D model of a tibia for a given patient, shape matching is performed. The computer finds the most similar tibia to the patient's tibia among the 2D radiographic images in the database by applying a matching process. To improve accuracy, a 2D image warping procedure can be applied on the slices of the selected bone prior to 3D reconstruction. The warping process is controlled by the contour data of the two orthogonal views. We found that the 3D model thus achieved was useful for virtual preoperative planning and for simulation of the internal fixation of long bones.
Next century challenges (1999)

Article Free Access Share on Next century challenges: scalable coordination in sensor networks Authors: Deborah Estrin USC/Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA USC/Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CAView Profile , Ramesh Govindan USC/Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA USC/Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CAView Profile , John Heidemann USC/Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA USC/Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CAView Profile , Satish Kumar USC/Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA USC/Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CAView Profile Authors Info & Claims MobiCom '99: Proceedings of the 5th annual ACM/IEEE international conference on Mobile computing and networkingAugust 1999 Pages 263–270https://doi.org/10.1145/313451.313556Published:01 August 1999Publication History 1,787citation7,746DownloadsMetricsTotal Citations1,787Total Downloads7,746Last 12 Months255Last 6 weeks29 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
A parallel MPEG-2 video encoder with look-ahead rate control (2002)

We describe a parallel implementation of a MPEG-2 compliant, constant bit rate video encoder on a shared memory system. The emphasis is on techniques for obtaining compressed video with picture quality superior to that of commercially available real-time hardware encoders. We propose a novel scheme for bit allocation and rate control. The most remarkable aspect of this scheme is the analysis of future frames in order to determine bit allocation for the current frame. This analysis includes use of preliminary motion estimation, masking factor computation, and coding regions of future frames to model their coding complexity. To the best of our knowledge, this is the first instance of an MPEG encoder which integrates a detailed analysis of future frames in the bit-allocation/rate-control mechanism.
VGLUTs in Peripheral Neurons and the Spinal Cord: Time for a Review (2013)

Vesicular glutamate transporters (VGLUTs) are key molecules for the incorporation of glutamate in synaptic vesicles across the nervous system, and since their discovery in the early 1990s, research on these transporters has been intense and productive. This review will focus on several aspects of VGLUTs research on neurons in the periphery and the spinal cord. Firstly, it will begin with a historical account on the evolution of the morphological analysis of glutamatergic systems and the pivotal role played by the discovery of VGLUTs. Secondly, and in order to provide an appropriate framework, there will be a synthetic description of the neuroanatomy and neurochemistry of peripheral neurons and the spinal cord. This will be followed by a succinct description of the current knowledge on the expression of VGLUTs in peripheral sensory and autonomic neurons and neurons in the spinal cord. Finally, this review will address the modulation of VGLUTs expression after nerve and tissue insult, their physiological relevance in relation to sensation, pain, and neuroprotection, and their potential pharmacological usefulness.
A selective undo mechanism for graphical user interfaces based on command objects (1994)

It is important to provide a recovery operation for applications with a graphical user interface. A restricted linear undo mechanism can conveniently be implemented using object-oriented techniques. Although linear undo provides an arbitrarily long history, it is not possible to undo isolated commands from the history without undoing all following commands. Various undo models have been proposed to overcome this limitation, but they all ignore the problem that in graphical user interfaces a previous user action might not have a sensible interpretation in another state. Selective undo introduced here can undo isolated commands by copying them into the current state “ if that is meaningful.” Furthermore, the semantics of selective undo are argued to be more natural for the user, because the mechanism only looks at the command to undo and the current state and does not depend on the history in between. The user interface for selective undo can also be implemented generically. Such a generic implementation is able to provide a consistent recovery mechanism in arbitrary applications.
Culturing of Retinal Pigment Epithelium Cells (2009)

The retinal pigment epithelium (RPE) is a monolayer of cells adjacent to the photoreceptors of the retina. It plays a crucial role in maintaining photoreceptor health and survival. Degeneration or dysfunction of the RPE can lead to photoreceptor degeneration and as a consequence to visual impairment. The most common diseased state of the RPE becomes manifest in age-related macular degeneration, an increasing cause of blindness in the elderly. RPE cells are therefore of great interest to researchers working in the field of tissue engineering and cell transplantation. In fact, studies in animal models have proven that the transplantation of RPE cells can delay the course of photoreceptor degenerative diseases. Although first attempts to transplant RPE cells into the subretinal space in human individuals suffering from age-related macular degeneration were less successful, RPE cell transplantation is still favored as a future therapeutic option, and much work is done to develop and design cell transplants. Cell banking is a prerequisite to have well-differentiated and characterized cells at hand when needed for research purposes, but also for therapeutic approaches. In this chapter the authors will describe methods to isolate, culture and preserve adult human RPE cells for the purpose of RPE cell banking.
Deletion of the selection cassette, but not cis-acting elements, in targeted Flk1-lacZ allele reveals Flk1 expression in multipotent mesodermal progenitors (2005)

Flk1, the gene encoding the vascular endothelial growth factor receptor 2 (VEGFR-2), is a well-known marker for vascular and hematopoietic progenitors and is indispensable for normal hematopoiesis and vasculogenesis. Here we show that Flk1 expression in the early mouse embryo marks a broad spectrum of mesodermal progenitors exiting the primitive streak as well as later mesodermal cell types including some cardiomyocytes, portions of the somites, and all extraembryonic mesoderm cells. These findings made use of an Flk1-lacZ knock-in allele in which the neomycin selection cassette was removed, which resulted in full replication of the endogenous expression of Flk1. Targeted deletion of a region in intron 1 that has been proposed to direct endothelial expression produced no alteration in either endothelial or broader mesodermal expression of the Flk1-lacZ allele. Examination of lacZ expression in homozygotes for the Flk1lacZ neo-out allele revealed that lacZ-expressing mesodermal cells persisted in nonvascular regions. Thus, Flk1 expression marks progenitors with broad mesodermal potential but is not absolutely required for the development of all mesodermal lineages in which it is expressed.
Solution Structure and Conformational Changes of the Streptomyces Chitin-Binding Protein (CHB1) (2000)

The shape and overall dimensions of the recently discovered Streptomyces alpha-chitin-binding protein, CHB1, were investigated by synchrotron radiation X-ray solution scattering. The radius of gyration and the maximum size of CHB1 were determined to be 1.75 +/- 0.03 nm and 6.0 +/- 0.2 nm, respectively. Using two independent ab initio approaches the low-resolution shape of the protein was found to consist of two domains, an elongated main globule with a length of about 4 nm and a foot-like domain of about 2 nm width. The structural and functional properties of CHB1 depend strongly on the presence of disulfide bonds; upon their reduction, the protein loses its affinity to chitin.
Isolating web programs in modern browser architectures (2009)

Many of today's web sites contain substantial amounts of client-side code, and consequently, they act more like programs than simple documents. This creates robustness and performance challenges for web browsers. To give users a robust and responsive platform, the browser must identify program boundaries and provide isolation between them.
Rational design of nascent metalloenzymes (2000)

Understanding the early genesis of new enzymatic functions is one of the challenges in protein design, mechanistic enzymology, and molecular evolution. We have experimentally mimicked starting points in this process by introducing primitive iron and oxygen binding sites at various locations in thioredoxin, a small protein lacking metal centers, by using computational design. These rudimentary active sites show emerging enzymatic activities that select to varying degrees between different oxygen chemistries. Even within these nascent enzymes, mechanisms by which different reactions are controlled can be discerned. These involve both stabilizing and destabilizing interactions imposed on the metal center by the surrounding protein matrix.
Signal Recovery From Random Measurements Via Orthogonal Matching Pursuit (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> This paper demonstrates theoretically and empirically that a greedy algorithm called Orthogonal Matching Pursuit (OMP) can reliably recover a signal with <emphasis><formula formulatype="inline"><tex>$m$</tex></formula></emphasis> nonzero entries in dimension <emphasis><formula formulatype="inline"><tex>$d$</tex> </formula></emphasis> given <emphasis><formula formulatype="inline"><tex>$ {\rm O}(m \ln d)$</tex></formula></emphasis> random linear measurements of that signal. This is a massive improvement over previous results, which require <emphasis><formula formulatype="inline"><tex>${\rm O}(m^{2})$</tex></formula></emphasis> measurements. The new results for OMP are comparable with recent results for another approach called Basis Pursuit (BP). In some settings, the OMP algorithm is faster and easier to implement, so it is an attractive alternative to BP for signal recovery problems. </para>
Synthesis and Evaluation of Pregnane Derivatives as Inhibitors of Human Testicular 17α-Hydroxylase/C17,20-Lyase, (1996)

The pregnene derivatives with modifications at the 17,20-side chain and D-ring were synthesized and evaluated as inhibitors of human testicular 17 alpha-hydroxylase/C17,20-lyase. The results demonstrate that compounds which have 20-substituents with moderate to strong dipole properties, such as 20-oxime (3, 20), 20 beta-ol (24, 30), and 20 beta-carboxaldehyde (27), are potent inhibitors of this enzyme complex. The 20-substituents with hydrophobic property were devoid of inhibitory activity, e.g., the dimethylhydrazones 8 and 9. The 16-ene together with 20-oxime (20) showed the most potent inhibition of this enzyme complex, whereas 17(20)-ene modification as in 17(20)-ene-20-carbonitrile (14) did not increase activity in comparison to the 20 beta-carbonitrile (16). The bioisotere of 27 with 20-aza (19) also reduced the inhibitory activity. The results showed that isomeric configurations at the 20-position of some steroidal compounds are important factors which influence the potency of the inhibition significantly (e.g., 20 beta-ols 24 and 30 were 3-5-fold more potent than 20 alpha-ols 23 and 29). As expected, some compounds based on the pregn-5-en-3 beta-ol skeleton, which is similar to the natural substrate of human testicular 17 alpha-hydroxylase/C17,20-lyase in A- and B-rings, showed more potent inhibition than similar compounds which are based on the pregn-4-en-3-one skeleton (e.g., 23-25 compared to 29-31). These results suggest that A- and B-rings make significant contributions to the binding of these steroidal compounds to the 17 alpha-hydroxylase and C17,20-lyase. In comparison to ketoconazole, a nonsteroidal inhibitor of 17 alpha-hydroxylase and C17,20-lyase which has been used in the treatment of prostatic cancer, the steroidal compounds 20, 24, and 27 demonstrate more potent inhibition for this enzyme complex. These inhibitors warrant further investigation in biological systems. The structural features of these compounds may serve as leads in the design of new inhibitors.
The induction of hapten-specific T cell tolerance by using hapten-modified lymphoid cells. I. Characteristics of tolerance induction. (1976)

BALB/c mice were made tolerant to the T cell-dependent phenomenon of contact sensitivity to DNFB by i.v. injection of syngeneic lymphoid cells which had been previously modified with DNFB in vitro. The highly efficient unresponsiveness, as measured by ear challenge and in vitro antigen-induced cell proliferation, was shown to follow dose-response kinetics both in vivo and in vitro and to be exquisitely specific for the DNP moiety. The kinetics of tolerance induction were shown to be very rapid and had been previously shown to be long lasting. Unresponsiveness was more efficient when the hapten-modified cells were introduced by the i.v. route and tolerance could be increased by repeated injection of tolerogen. The tolerance could be transferred to normal syngeneic recipients by spleen and/or lymph node cells from tolerant donors. A wide variety of hapten-modified lymphoid cells, including mixed cell populations and enriched populations of T cells, B cells, and macrophages, were capable of inducing tolerance. The unresponsiveness was dependent merely on the association of DNP to the lymphoid membrane proteins and not upon the viability of the hapten-modified cells. These experiments support the hypothesis that in hapten-specific T cell sensitivity, as exemplified by contact sensitivity to DNFB, specific T cell tolerance in actively induced by hapten on self-membrane. In other hapten-specific antibody-forming systems, tolerance appears to be most readily induced by hapten on soluble self protein or on a nonimmunogeneic carrier.
The synthesis of ribonucleotide‐5′‐(5‐Iodoindol‐3‐ol) and (4‐methylcoumarin‐7‐ol) esters for the histochemical demonstration of nucleases (1970)

Abstract The syntheses of ribonucleotide‐5′ monoesters with 5‐iodoindol‐3‐ol and 5′‐uridylic acid and 5′‐adenylic acid monoesters with 4‐methylcoumarin‐7‐ol has been accomplished by the reaction of phosphorodichloridates with various 2′,3′‐ O ‐isopropylidene ribonucleosides, followed by hydrolysis and anion exchange chromatography.
QUANTITATIVE STUDIES OF THE GROWTH OF MOUSE EMBRYO CELLS IN CULTURE AND THEIR DEVELOPMENT INTO ESTABLISHED LINES (1963)

Disaggregated mouse embryo cells, grown in monolayers, underwent a progressive decline in growth rate upon successive transfer, the rapidity of the decline depending, among other things, on the inoculation density. Nevertheless, nearly all cultures developed into established lines within 3 months of culture. The first sign of the emergence of an established line was the ability of the cells to maintain a constant or rising potential growth rate. This occurred while the cultures were morphologically unchanged. The growth rate continued to increase until it equaled or exceeded that of the original culture. The early established cells showed an increasing metabolic autonomy, as indicated by decreasing dependence on cell-to-cell feeding. It is suggested that the process of establishment involves an alteration in cell permeability properties. Chromosome studies indicated that the cells responsible for the upturn in growth rate were diploid, but later the population shifted to the tetraploid range, often very rapidly. Still later, marker chromosomes appeared. Different lines acquired different properties, depending on the culture conditions employed; one line developed which is extremely sensitive to contact inhibition.
Objective Responses in Patients with Malignant Melanoma or Renal Cell Cancer in Early Clinical Studies Do Not Predict Regulatory Approval (2005)

For cytotoxic agents, although overall objective response rates reliably predict subsequent marketing approval, isolated responses in melanoma and renal cell carcinoma are not predictive.
Sperm Motility Is Dependent on a Unique Isoform of the Na,K-ATPase (2000)

The Na,K-ATPase, a member of the P-type ATPases, is composed of two subunits, alpha and beta, and is responsible for translocating Na(+) out of the cell and K(+) into the cell using the energy of hydrolysis of one molecule of ATP. The electrochemical gradient it generates is necessary for many cellular functions, including establishment of the plasma membrane potential and transport of sugars and ions in and out of the cell. Families of isoforms for both the alpha and beta subunits have been identified, and specific functional roles for individual isoforms are just beginning to emerge. The alpha4 isoform is the most recently identified Na, K-ATPase alpha isoform, and its expression has been found only in testis. Here we show that expression of the alpha4 isoform in testis is localized to spermatozoa and that inhibition of this isoform alone eliminates sperm motility. These data describe for the first time a biological function for the alpha4 isoform of the Na,K-ATPase, revealing a critical role for this isoform in sperm motility.
The process of counterfactual thinking after decision-making: Evidence from an ERP study (2010)

Counterfactual thinking occurs when an individual experiences thoughts that ignore what has happened in the past, and generates a hypothesis which comparing “what is” with “what might have been”. Counterfactual thinking can be classified into upward and downward counterfactual thinking based on the direction of the comparison involved. The present study used an event-related potential (ERP) recording protocol with high temporal resolution to measure neurophysiological activity while participants performed a simple gambling task in which the feedback mode was manipulated (partial and complete feedback). Our results showed that both the amplitudes of FRN (feedback-related Negativity) and P300 enhanced during reflected upward counterfactual thinking processes, while only the FRN reflected downward counterfactual thinking. Moreover, dipole analysis indicated that the dipole was located in the anterior cingulate cortex (ACC). This suggests that the FRN and P300 are both sensitive to counterfactual thinking, and that the ACC may be an important neural structure in the modulation of counterfactual thinking.
NHC-Based Self-Assembled Monolayers on Solid Gold Substrates (2011)

Thin films of 1,3-diethylbenzimidazol-2-ylidene (BIEt) were fabricated from THF solution on solid gold substrates and characterised by high-resolution X-ray photoelectron and near-edge X-ray absorption fine structure spectroscopy. The surface-analytical data are in accord with the formation of self-assembled monolayers of BIEt molecules exhibiting an approximately vertical orientation on the substrate. The crystal structure of (BIEt)(2) was also determined.
Aryl Hydrocarbon Receptor Repressor and TiPARP (ARTD14) Use Similar, but also Distinct Mechanisms to Repress Aryl Hydrocarbon Receptor Signaling (2014)

The aryl hydrocarbon receptor (AHR) regulates the toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). The AHR repressor (AHRR) is an AHR target gene and functions as a ligand-induced repressor of AHR; however, its mechanism of inhibition is controversial. Recently, we reported that TCDD-inducible poly (ADP-ribose) polymerase (TiPARP; ARTD14) also acts as a repressor of AHR, representing a new player in the mechanism of AHR action. Here we compared the ability of AHRR- and TiPARP-mediated inhibition of AHR activity. TCDD increased AHRR mRNA levels and recruitment of AHRR to cytochrome P450 1A1 (CYP1A1) in MCF7 cells. Knockdown of TiPARP, but not AHRR, increased TCDD-induced CYP1A1 mRNA and AHR protein levels. Similarly, immortalized TiPARP(-/-) mouse embryonic fibroblasts (MEFs) and AHRR(-/-) MEFs exhibited enhanced AHR transactivation. However, unlike TiPARP(-/-) MEFs, AHRR(-/-) MEFs did not exhibit increased AHR protein levels. Overexpression of TiPARP in AHRR(-/-) MEFs or AHRRΔ8, the active isoform of AHRR, in TiPARP(-/-) MEFs reduced TCDD-induced CYP1A1 mRNA levels, suggesting that they independently repress AHR. GFP-AHRRΔ8 and GFP-TiPARP expressed as small diffuse nuclear foci in MCF7 and HuH7 cells. GFP-AHRRΔ8_Δ1-49, which lacks its putative nuclear localization signal, localized to both the nucleus and the cytoplasm, while the GFP-AHRRΔ8_Δ1-100 mutant localized predominantly in large cytoplasmic foci. Neither GFP-AHRRΔ8_Δ1-49 nor GFP-AHRRΔ8_Δ1-100 repressed AHR. Taken together, AHRR and TiPARP repress AHR transactivation by similar, but also different mechanisms.