gebhart/patrepeval huggingface dataset:
A New Blocker for the TGF-β Pathway (1999)

For more than a decade, researchers have suspected that two proteins known as Ski and Sno play a role in the unrestrained cell growth that leads to cancer, but because no one was able to determine their role in the cell, they received little attention. Now five separate papers--including one on page
 771
 of this issue--show that Ski and Sno can block one of the cell9s major growth-controlling pathways, the transforming growth factor-b signal. The finding puts the proteins at the center of one of the hottest areas of cell biology and sheds new light on this ubiquitous pathway.
Repulsive guidance molecules (RGMs) and neogenin in bone morphogenetic protein (BMP) signaling (2013)

Bone morphogenetic proteins (BMPs) belong to the transforming growth factor-beta (TGFβ) superfamily. BMPs mediate a highly conserved signal transduction cascade through the type-I and type-II serine/threonine kinase receptors and intracellular Smad proteins, which regulate multiple developmental and homeostatic processes. Mutations in this pathway can cause various diseases in humans, such as skeletal disorders, cardiovascular diseases, and various cancers. Multiple levels of regulation, including extracellular regulation, help to ensure proper spatiotemporal control of BMP signaling in the right cellular context. The family of repulsive guidance molecules (RGMs) and the type-I transmembrane protein neogenin, a paralog of DCC (Deleted in Colorectal Cancer), have been implicated in modulating the BMP pathway. In this review, we discuss the properties and functions of RGM proteins and neogenin, focusing on their roles in the modulation of BMP signal transduction.
EL CASCARÓN DE HUEVO DE AVESTRUZ DE LA SEPULTURA Nº 100 DE VILLARICOS (1997)

Revista especializada en la publicación de trabajos originales de investigación en Prehistoria y Arqueología. Es la publicación periódica más antigua de la UAM. Su enfoque abierto a cualquier temática y época pasada, hasta la más cercana, que sea objeto de la Ciencia arqueológica se abre a una decidida proyección internacional en la que quiere basar su futuro inmediato.
Antigenic and immunogenic properties of cyanogen bromide peptides from gonococcal outer membrane protein IB. Evidence for the existence of a surface-exposed conserved epitope. (1987)

Two distinct species of gonococcal porin proteins exist that differ with regard to surface exposure. Protein IB, expressed by strains of the WII/III serogroup, has both termini buried in the outer membrane, leaving a central region of the molecule exposed at the cell surface. We have attempted to define this region of protein IB in detail by studying the antigenic and immunogenic properties of peptides derived from protein IB. Treatment of gonococcal protein IB (serotype 5) with cyanogen bromide resulted in cleavage of protein IB into three major fragments of Mr of 15,000, 13,000, and 8,000. The location of these peptides in the intact protein was determined by analysis of partial cleavage products. The 8,000 Mr peptide (CB2) was found to be located in the central region of the protein. Chymotrypsin cleavage of protein IB revealed a cleavage site near one of the cyanogen bromide cleavage sites. Trypsin was found to cleave the protein, either in outer membranes complexes (OMC) or in detergent micelles, in the central CB2 fragment. These results suggest that CB2 is a part of the surface-exposed region of protein IB. Immunization of mice with purified protein IB (serotype 5) induced antibodies against all three CB-peptides. Absorption of the sera with homologous OMC resulted in a complete removal of antibodies against CB2, supplying further evidence for its surface-exposed nature. Antibodies against the 13,000 Mr peptide (CB1) could not be absorbed with intact OMC, suggesting that this peptide is buried within the outer membrane. Antisera raised against CB2 of serotype 5 demonstrated a considerable cross-reactivity with heterologous outer membranes. On the contrary, intact OMC induced mainly type-specific antibodies. These data demonstrate the presence of conserved epitopes on the surface-exposed CB2 peptide. These conserved epitopes are generally not very immunogenic when present in intact OMC.
Promise of embedded system with GPU in artificial leg control: Enabling time-frequency feature extraction from electromyography (2009)

Applying electromyographic (EMG) signal pattern recognition to artificial leg control is challenging because leg EMGs are non-stationary. Time-frequency features are suitable for representing non-stationary signals; however, the computational complexity to extract time-frequency features is too high and current embedded systems used for artificial limb control are inadequate for real-time computing. The aim of this study was to quantify the computational speed of a novel embedded system, the Graphic Processor Unit (GPU), on EMG time-frequency feature extraction. The computational time derived from a GPU was compared to that derived from a general purpose CPU. The results indicated that the GPU significantly increased the computational speed. When the size of EMG analysis window was set to 100 ms, the GPU extracted EMG time-frequency features over 50 times faster than the CPU setting. Therefore, high performance GPU shows a great promise for EMG-controlled artificial legs and other medical applications that need high-speed and real-time computation.
A system to read names and addresses on tax forms (1996)

The reading of names and addresses is one of the most complex tasks in automated forms processing. This paper describes an integrated real-time system to read names and addresses on tax forms of the U.S. Internal Revenue Service. The Name and Address Block Reader (NABR) system accepts both machine-printed and hand-printed address block images as input. The application software has two major steps: document analysis (connected component analysis, address block extraction, label detection, hand-print/machine-print discrimination) and document recognition. Document recognition has two nonidentical streams for machine-print and hand-print: the key steps are address parsing, character recognition, word recognition, and postal database lookup. (ZIP+4 and City-State-ZIP files.) System output is a packet containing the results of recognition together with database access status file. Real-time throughput (8500 forms/h) is achieved by employing a loosely coupled multiprocessing architecture where successive input images are distributed to available address recognition processors. The functional architecture, software design, system architecture, and the hardware implementation are described. Performance evaluation on machine-printed and handwritten addresses are presented.
Peripheral Blood Stem Cells for Allogeneic Transplantation: A Review (2001)

Peripheral blood stem cells (PBSCs) have become increasingly popular for use in hematopoietic stem cell transplantation. PBSCs are readily collected by continuous-flow apheresis from patients and healthy donors after the administration of s.c. recombinant colony-stimulating factors with only minimal morbidity and discomfort. Although the precise identification of PBSCs remains elusive, they can be phenotypically identified as a subset of all circulating CD34(+) cells. There are important phenotypic and biologic distinctions between PBSCs and bone marrow (BM)-derived progenitor cells. PBSCs express more lineage-specific antigens but are less metabolically active than their BM-derived counterparts. The use of PBSCs for allogeneic transplantation has been compared to BM in several randomized trials and cohort studies. The use of PBSCs in leukemia, myeloma, non-Hodgkin's lymphoma, and myelodysplasia has resulted in shorter times to neutrophil and platelet engraftment at the expense of increased rates of chronic graft-versus-host disease. The increase in graft-versus-host disease is mainly due to a log-fold increase in donor T cells transferred with the graft. Relapse rates after transplantation may be lower after PBSC transplantation but a convincing survival advantage has not been demonstrated overall. It is possible that a stronger graft-versus-tumor effect may exist with PBSCs when compared with BM although the mechanisms leading to this effect are not clear.
Transcriptional regulation of tubulin gene expression in differentiating trochoblasts during early development of Patella vulgata (1994)

The expression of alpha- and beta-tubulin genes during the early development of the marine mollusk Patella vulgata has been investigated. From the 32-cell stage onwards, an enhanced expression of both alpha- and beta-tubulin mRNAs was detected in the primary trochoblasts. After one additional cleavage, these cells become cleavage-arrested and then form cilia. They are the first cells to differentiate during Patella development. Later, alpha- and beta-tubulin mRNA is also found in the accessory and secondary trochoblasts. Together these three cell-lines form the prototroch, the ciliated locomotory organ of the trochophore larva. The early and abundant expression of tubulin genes precede and accompany cilia formation in the trochoblasts and provides us with an excellent molecular differentiation marker for these cells. Apart from the trochoblasts, tubulin gene expression was also found in other cells at some stages. At the 88-cell stage, elevated tubulin mRNA levels were found around the large nucleus of the mesodermal stem cell 4d. In later stages, tubulin gene expression was detected in the cells that form the flagella of the apical tuft and in the refractive bodies. An alpha-tubulin gene was isolated and characterized. A lacZ fusion gene under control of the 5' upstream region of this tubulin gene was microinjected into embryos at the two-cell stage. The reporter gene product was only detected in the three trochoblast cell-lines at the same time as tubulin genes were expressed in these cells. Reporter gene product was not detected in any other cells. Thus, this 5' upstream region of this alpha-tubulin gene contains all the elements required for the correct spatiotemporal pattern of expression.
High-Accuracy Low-Precision Training (2018)

Low-precision computation is often used to lower the time and energy cost of machine learning, and recently hardware accelerators have been developed to support it. Still, it has been used primarily for inference - not training. Previous low-precision training algorithms suffered from a fundamental tradeoff: as the number of bits of precision is lowered, quantization noise is added to the model, which limits statistical accuracy. To address this issue, we describe a simple low-precision stochastic gradient descent variant called HALP. HALP converges at the same theoretical rate as full-precision algorithms despite the noise introduced by using low precision throughout execution. The key idea is to use SVRG to reduce gradient variance, and to combine this with a novel technique called bit centering to reduce quantization error. We show that on the CPU, HALP can run up to $4 \times$ faster than full-precision SVRG and can match its convergence trajectory. We implemented HALP in TensorQuant, and show that it exceeds the validation performance of plain low-precision SGD on two deep learning tasks.
MATHEMATICAL MODELING OF THE IMPACT OF MALARIA VACCINES ON THE CLINICAL EPIDEMIOLOGY AND NATURAL HISTORY OF PLASMODIUM FALCIPARUM MALARIA: OVERVIEW (2006)

We report a major project to develop integrated mathematical models for predicting the epidemiologic and economic effects of malaria vaccines both at the individual and population level. The project has developed models of the within-host dynamics of Plasmodium falciparum that have been fitted to parasite density profiles from malaria therapy patients, and simulations of P. falciparum epidemiology fitted to field malariologic datasets from a large ensemble of settings across Africa. The models provide a unique platform for predicting both the short- and long-term effects of malaria vaccines on the burden of disease, allowing for the temporal dynamics of effects on immunity and transmission. We discuss how the models can be used to obtain robust cost-effectiveness estimates for a wide range of malaria vaccines and vaccination delivery strategies in different eco-epidemiologic settings. This paper outlines for a non-mathematical audience the approach we have taken and its underlying rationale.
PRISM III (1996)

PRISM III resulted in several improvements over the original PRISM. Reassessment of physiologic variables and their ranges, better age adjustment for selected variables, and additional risk factors resulted in a mortality risk model that is more accurate and discriminates better. The large number of diverse ICUs in the database indicates PRISM III is more likely to be representative of United States units.
Mathematical Foundations for Manufacturing (1987)

For the field of manufacturing to become a science, it is necessary to develop general mathematical descriptions for the analysis and synthesis of manufacturing systems. Standard analytic models, as used extensively in the past, are ineffective for describing the general manufacturing situation due to their inability to deal with discontinuous and nonlinear phenomena. These limitations are transcended by algebraic models based on set structures. Set-theoretic and algebraic structures may be used to (1) express with precision a variety of important qualitative concepts such as hierarchies, (2) provide a uniform framework for more specialized theories such as automata theory and control theory, and (3) provide the groundwork for quantitative theories. By building on the results of other fields such as automata theory and computability theory, algebraic structures may be used as a general mathematical tool for studying the nature and limits of manufacturing systems. This paper shows how manufacturing systems may be modeled as automatons, and demonstrates the utility of this approach by discussing a number of theorems concerning the nature of manufacturing systems. In addition symbolic logic is used to formalize the Design Axioms, a set of generalized decision rules for design. The application of symbolic logic allows for the precise formulation of the Axioms and facilitates their interpretation in a logical programming language such as Prolog. Consequently, it is now possible to develop a consultive expert system for axiomatic design.
Light‐Activated RNA Interference (2005)

Light-controlled gene expression: Cellular mRNA levels that are regulated by the RNA interference pathway can now be controlled with light. The modification of small interfering RNA (siRNA) with photolabile moieties can partially or fully block RNA interference, depending on the extent of siRNA modification. Upon irradiation, siRNA is released (see picture). Now in its active state, it is able to suppress target gene expression. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z461458_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Protection against fatal Klebsiella pneumoniae burn wound sepsis by passive transfer of anticapsular polysaccharide (1984)

Klebsiella pneumoniae KP1-0 capsular polysaccharide (PS) was isolated from culture supernatants by coprecipitation with N-cetyl-N,N,N-trimethylammonium bromide. PS was composed primarily of carbohydrate and contained less than 1% (wt/wt) protein and nucleic acids. The protective capacity of passively transferred anti-PS was evaluated in a murine burn wound sepsis model. Anti-PS antibody was found to offer high levels of protection (P less than or equal to 0.02) against a low challenge dose of K. pneumoniae KP1-0. The 50% lethal dose for mice which received anti-PS antibody was increased from 10- to 40-fold over that for mice which received normal rabbit serum. Anti-PS antibody was found to be most effective at reducing mortality when administered before the challenge. In experiments designed to monitor the course of the infection, anti-PS was found to both delay the onset of bacteremia and reduce bacterial counts in the blood. Optimal protection against fatal burn wound sepsis was obtained by the use of a combined antibiotic and passive antibody therapy regimen.
View morphing (1996)

Article View morphing Share on Authors: Steven M. Seitz Department of Computer Sciences, University of Wisconsin--Madison, 1210 W. Dayton St., Madison WI Department of Computer Sciences, University of Wisconsin--Madison, 1210 W. Dayton St., Madison WIView Profile , Charles R. Dyer Department of Computer Sciences, University of Wisconsin--Madison, 1210 W. Dayton St., Madison WI Department of Computer Sciences, University of Wisconsin--Madison, 1210 W. Dayton St., Madison WIView Profile Authors Info & Claims SIGGRAPH '96: Proceedings of the 23rd annual conference on Computer graphics and interactive techniquesAugust 1996 Pages 21–30https://doi.org/10.1145/237170.237196Online:01 August 1996Publication History 471citation3,015DownloadsMetricsTotal Citations471Total Downloads3,015Last 12 Months115Last 6 weeks4 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 SiteGet Access
Structure of the kainate receptor subunit GluR6 agonist-binding domain complexed with domoic acid (2005)

We report the crystal structure of the glycosylated ligand-binding (S1S2) domain of the kainate receptor subunit GluR6, in complex with the agonist domoate. The structure shows the expected overall homology with AMPA and NMDA receptor subunit structures but reveals an unexpected binding mode for the side chain of domoate, in which contact is made to the larger lobe only (lobe I). In common with the AMPA receptor subunit GluR2, the GluR6 S1S2 domain associates as a dimer, with many of the interdimer contacts being conserved. Subtle differences in these contacts provide a structural explanation for why GluR2 L483Y and GluR3 L507Y are nondesensitizing, but GluR6, which has a tyrosine at that site, is not. The structure incorporates native glycosylation, which has not previously been described for ionotropic glutamate receptors. The position of the sugars near the subunit interface rules out their direct involvement in subunit association but leaves open the possibility of indirect modulation. Finally, we observed several tetrameric assemblies that satisfy topological constraints with respect to connection to the receptor pore, and which are therefore candidates for the native quaternary structure.
Quinoxalines XV. Convenient Synthesis and Structural Study of Pyrazolo[1,5-a]quinoxalines (2009)

A series of aryloxymethylquinoxaline oximes, hitherto unknown and synthesized from the corresponding aldehydes, afforded in only one step pyrazolo[1,5-a]quinoxalines in the presence of acetic anhydride at high temperatures. A formal [3,5]-sigmatropic rearrangement was proposed as the mechanistic rationale for this unprecedented transformation. Saponification with potassium hydroxide furnished the free phenol derivatives which were studied by NMR spectroscopy and accompanying theoretical DFT calculations, establishing intramolecular hydrogen bonding and the spatial magnetic properties. Additionally, mass spectrometric fragmentation was investigated by B/E-linked scans and collision-induced dissociation experiments. The fragmentation pattern devoted a new gas phase rearrangement process, which proved to be unique and characteristic for pyrazolo[1,5-a]quinoxalines.
New insights into the metabolic regulation of insulin action and insulin resistance: role of glucose and amino acids (1991)

In primary cultured adipocytes, metabolic substrates such as glucose and amino acids have profound effects on modulating insulin's stimulatory actions on glucose uptake and protein synthesis. Insights into how substrates modulate insulin action were recently obtained when we discovered that the routing of incoming glucose through the hexosamine biosynthesis pathway leads to a refractory state over a period of several hours in which the ability of insulin to stimulate glucose uptake is severely impaired--a state known as insulin resistance. Glutamine:fructose-6-phosphate amidotransferase was found to play a central role in the development of insulin resistance as this enzyme catalyzes the first and rate-limiting step in the formation of hexosamine products. Collectively, these results are consistent with the idea that the hexosamine biosynthesis pathway serves as a glucose sensor coupled to a negative feedback system that can limit the extent of glucose uptake in response to hyperglycemic and hyperinsulinemic conditions.
Major histocompatibility class I presentation of soluble antigen facilitated by Mycobacterium tuberculosis infection. (1996)

Cell-mediated immune responses are essential for protection against many intracellular pathogens. For Mycobacterium tuberculosis (MTB), protection requires the activity of T cells that recognize antigens presented in the context of both major histocompatibility complex (MHC) class II and I molecules. Since MHC class I presentation generally requires antigen to be localized to the cytoplasmic compartment of antigen-presenting cells, it remains unclear how pathogens that reside primarily within endocytic vesicles of infected macrophages, such as MTB, can elicit specific MHC class I-restricted T cells. A mechanism is described for virulent MTB that allows soluble antigens ordinarily unable to enter the cytoplasm, such as ovalbumin, to be presented through the MHC class I pathway to T cells. The mechanism is selective for MHC class I presentation, since MTB infection inhibited MHC class II presentation of ovalbumin. The MHC class I presentation requires the tubercle bacilli to be viable, and it is dependent upon the transporter associated with antigen processing (TAP), which translocates antigenic peptides from the cytoplasm into the endoplasmic reticulum. The process is mimicked by Listeria monocytogenes and soluble listeriolysin, a pore-forming hemolysin derived from it, suggesting that virulent MTB may have evolved a comparable mechanism that allows molecules in a vacuolar compartment to enter the cytoplasmic presentation pathway for the generation of protective MHC class I-restricted T cells.
The Developing Market for Medical Robotics (2006)

This paper discusses the developing market for medical robotics. It first describes some of the dynamics and market drivers in health care, and then provides an outline of the areas of consideration when developing a commercial medical robot. The paper also offers three case studies of robotic systems that have been commercialized. Finally, it summarizes some of the key ingredients to be considered for the commercialization process.