gebhart/patrepeval huggingface dataset:
Informed Dynamic Scheduling for Belief-Propagation Decoding of LDPC Codes (2007)

Low-density parity-check (LDPC) codes are usually decoded by running an iterative belief-propagation, or message-passing, algorithm over the factor graph of the code. The traditional message-passing schedule consists of updating all the variable nodes in the graph, using the same pre-update information, followed by updating all the check nodes of the graph, again, using the same pre-update information. Recently several studies show that sequential scheduling, in which messages are generated using the latest available information, significantly improves the convergence speed in terms of number of iterations. Sequential scheduling raises the problem of finding the best sequence of message updates. This paper presents practical scheduling strategies that use the value of the messages in the graph to find the next message to be updated. Simulation results show that these informed update sequences require significantly fewer iterations than standard sequential schedules. Furthermore, the paper shows that informed scheduling solves some standard trapping set errors. Therefore, it also outperforms traditional scheduling for a large numbers of iterations. Complexity and implementability issues are also addressed.
Two-photon induced photodecarbonylation reaction of cyclopropenones (2005)

Irradiation of cyclopropenones (1a-c) with 800 nm pulses of ultrafast laser results in a photodecarbonylation reaction via nonresonant two-photon absorption of light.
Mechanism of action of Bacillus thuringiensis var israelensis insecticidal δ‐endotoxin (1983)

Bacillus thuringiensis var israelensis delta-endotoxin protein active against mosquitoes was inactivated by prior incubation with lipids extracted from Aedes albopictus cells. Experiments with lipid dispersions and multilamellar liposomes showed that the toxin binds to phosphatidyl choline, sphingomyelin and phosphatidyl ethanolamine provided these lipids contain unsaturated fatty acids. Phosphatidyl serine binds toxin less efficiently and phosphatidyl inositol, cardiolipin, cerebroside and cholesterol show no affinity for the toxin. The results suggest an insecticidal mechanism in which interaction of toxin with affinity for the toxin. The results suggest an insecticidal mechanism in which interaction of toxin with specific plasma membrane lipids causes a detergent-like rearrangement of the lipids, leading to disruption of membrane integrity and eventual cytolysis.
Hyaluronidase Induction of a WW Domain-containing Oxidoreductase That Enhances Tumor Necrosis Factor Cytotoxicity (2001)

To determine how hyaluronidase increases certain cancer cell sensitivity to tumor necrosis factor (TNF) cytotoxicity, we report here the isolation and characterization of a hyaluronidase-induced murine WW domain-containing oxidoreductase (WOX1). WOX1 is composed of two N-terminal WW domains, a nuclear localization sequence, and a C-terminal alcohol dehydrogenase (ADH) domain. WOX1 is mainly located in the mitochondria, and the mitochondrial targeting sequence was mapped within the ADH domain. Induction of mitochondrial permeability transition by TNF, staurosporine, and atractyloside resulted in WOX1 release from mitochondria and subsequent nuclear translocation. TNF-mediated WOX1 nuclear translocation occurred shortly after that of nuclear factor-kappaB nuclear translocation, whereas both were independent events. WOX1 enhanced TNF cytotoxicity in L929 cells via its WW and ADH domains as determined using stable cell transfectants. In parallel with this observation, WOX1 also enhanced TRADD (TNF receptor-associated death domain protein)-mediated cell death in transient expression experiments. Antisense expression of WOX1 raised TNF resistance in L929 cells. Enhancement of TNF cytotoxicity by WOX1 is due, in part, to its significant down-regulation of the apoptosis inhibitors Bcl-2 and Bcl-x(L) (>85%), but up-regulation of pro-apoptotic p53 ( approximately 200%) by the ADH domain. When overexpressed, the ADH domain mediated apoptosis, probably due to modulation of expression of these proteins. The WW domains failed to modulate the expression of these proteins, but sensitized COS-7 cells to TNF killing and mediated apoptosis in various cancer cells independently of caspases. Transient cotransfection of cells with both p53 and WOX1 induced apoptosis in a synergistic manner. WOX1 colocalizes with p53 in the cytosol and binds to the proline-rich region of p53 via its WW domains. Blocking of WOX1 expression by antisense mRNA abolished p53 apoptosis. Thus, WOX1 is a mitochondrial apoptogenic protein and an essential partner of p53 in cell death.
Engineering and expression of a chimeric transferrin receptor monoclonal antibody for blood–brain barrier delivery in the mouse (2008)

Protein therapeutics may be delivered across the blood-brain barrier (BBB) by genetic fusion to a BBB molecular Trojan horse. The latter is an endogenous peptide or a peptidomimetic monoclonal antibody (MAb) against a BBB receptor, such as the insulin receptor or the transferrin receptor (TfR). Fusion proteins have been engineered with the MAb against the human insulin receptor (HIR). However, the HIRMAb is not active against the rodent insulin receptor, and cannot be used for drug delivery across the mouse BBB. The rat 8D3 MAb against the mouse TfR is active as a drug delivery system in the mouse, and the present studies describe the cloning and sequencing of the variable region of the heavy chain (VH) and light chain (VL) of the rat 8D3 TfRMAb. The VH and VL were fused to the constant region of mouse IgG1 heavy chain and mouse kappa light chain, respectively, to produce a new chimeric TfRMAb. The chimeric TfRMAb was expressed in COS cells following dual transfection with the heavy and light chain expression plasmids, and was purified by protein G affinity chromatography. The affinity of the chimeric TfRMAb for the murine TfR was equal to the 8D3 MAb using a radio-receptor assay and mouse fibroblasts. The chimeric TfRMAb was radio-labeled and injected into mice for a pharmacokinetics study of the clearance of the chimeric TfRMAb. The chimeric TfRMAb was rapidly taken up by mouse brain in vivo at a level comparable to the rat 8D3 MAb. In summary, these studies describe the genetic engineering, expression, and validation of a chimeric TfRMAb with high activity for the mouse TfR, which can be used in future engineering of therapeutic fusion proteins for BBB drug delivery in the mouse.
Optical coherence tomography-based corneal power measurement and intraocular lens power calculation following laser vision correction (an American Ophthalmological Society thesis). (2013)

The predictive accuracy of OCT-based IOL power calculation was better than Haigis-L and Shammas-PL formulas in eyes after laser vision correction.
Improvements in Cloning Efficiencies May Be Possible by Increasing Uniformity in Recipient Oocytes and Donor Cells (2003)

The low efficiency of somatic cell cloning is the major obstacle to widespread use of this technology. Incomplete nuclear reprogramming following the transfer of donor nuclei into recipient oocytes has been implicated as a primary reason for the low efficiency of the cloning procedure. The mechanisms and factors that affect the progression of the nuclear reprogramming process have not been completely elucidated, but the identification of these factors and their subsequent manipulation would increase cloning efficiency. At present, many groups are studying donor nucleus reprogramming. Here, we present an approach in which the efficiency of producing viable offspring is improved by selecting recipient oocytes and donor cells that will produce cloned embryos with functionally reprogrammed nuclei. This approach will produce information useful in future studies aimed at further deciphering the nuclear reprogramming process.
On the Evolutionary Conservation of the Cell Death Pathway: Mitochondrial Release of an Apoptosis-inducing Factor duringDictyostelium discoideumCell Death (2001)

Mitochondria play a pivotal role in apoptosis in multicellular organisms by releasing apoptogenic factors such as cytochrome c that activate the caspases effector pathway, and apoptosis-inducing factor (AIF) that is involved in a caspase-independent cell death pathway. Here we report that cell death in the single-celled organism Dictyostelium discoideum involves early disruption of mitochondrial transmembrane potential (DeltaPsim) that precedes the induction of several apoptosis-like features, including exposure of the phosphatidyl residues at the external surface of the plasma membrane, an intense vacuolization, a fragmentation of DNA into large fragments, an autophagy, and the release of apoptotic corpses that are engulfed by neighboring cells. We have cloned a Dictyostelium homolog of mammalian AIF that is localized into mitochondria and is translocated from the mitochondria to the cytoplasm and the nucleus after the onset of cell death. Cytoplasmic extracts from dying Dictyostelium cells trigger the breakdown of isolated mammalian and Dictyostelium nuclei in a cell-free system, and this process is inhibited by a polyclonal antibody specific for Dictyostelium discoideum apoptosis-inducing factor (DdAIF), suggesting that DdAIF is involved in DNA degradation during Dictyostelium cell death. Our findings indicate that the cell death pathway in Dictyostelium involves mitochondria and an AIF homolog, suggesting the evolutionary conservation of at least part of the cell death pathway in unicellular and multicellular organisms.
In Vivo Protective Effect of Tumour Necrosis Factor Against Experimental Infection with Herpes Simplex Virus Type 1 (1991)

C57BL/6 mice, which differ genetically from other strains by their resistance to herpes simplex virus type 1 (HSV-1) infection, were inoculated intraperitoneally with different doses of tumour necrosis factor alpha (TNF-alpha). Mice pretreated with 100 ng, or even 10 ng, of TNF-alpha showed prolonged survival compared to control mice that were infected with 10(7) p.f.u. of HSV-1. Significant protection was observed in mice injected 4 or 8 h prior to or after HSV-1 inoculation, respectively. Protection was also observed when mice which differed at their H-2 locus were treated with TNF-alpha after infection with HSV-1. Interferon could not be detected in the sera of mice at different time points after infection with HSV-1 or injection of TNF-alpha and there was no enhanced interferon titre in mice treated with both TNF-alpha and HSV-I, suggesting some interferon-independent protection. However, mice treated with TNF-alpha showed a marked activation of natural killer (NK) cells compared to untreated control mice or mice that were treated with HSV-1 alone. To test whether enhanced NK cell activity is responsible for TNF-alpha-induced protection, mice were injected with the NK cell-specific antibody anti-asialo Gm-1. In this experimental protocol the survival rate was almost unaffected, indicating that the observed protection was not due to activation of NK cells and that TNF-alpha is involved in the regulation of antiviral mechanisms other than the activation of interferons. Although additional production of interferon induced by TNF-alpha cannot be excluded, an antiviral effect of TNF-alpha on the course of HSV-1 infection may be postulated from our data.
Pulse Transit Time and Blood Pressure During Cardiopulmonary Exercise Tests (2014)

Pulse transit time (PTT), the interval between ventricular electrical activity and peripheral pulse wave, is assumed to be a surrogate marker for blood pressure (BP) changes. The objective of this study was to analyze PTT and its relation to BP during cardiopulmonary exercise tests (CPET). In 20 patients (mean age 51+/-18.4 years), ECG and finger-photoplethysmography were continuously recorded during routine CPETs. PTT was calculated for each R-wave in the ECG and the steepest slope of the corresponding upstroke in the plethysmogram. For each subject, linear and non-linear regression models were used to assess the relation between PTT and upper-arm oscillometric BP in 9 predefined measuring points including measurements at rest, during exercise and during recovery. Mean systolic BP (sBP) and PTT at rest were 128 mm Hg and 366 ms respectively, 197 mm Hg and 289 ms under maximum exercise, and 128 mm Hg and 371 ms during recovery. Linear regression showed a significant, strong negative correlation between PTT and sBP. The correlation between PTT and diastolic BP was rather weak. Bland-Altman plots of sBP values estimated by the regression functions revealed slightly better limits of agreements for the non-linear model (-10.9 to 10.9 mm Hg) than for the linear model (-13.2 to 13.1 mm Hg). These results indicate that PTT is a good potential surrogate measure for sBP during exercise and could easily be implemented in CPET as an additional parameter of cardiovascular reactivity. A non-linear approach might be more effective in estimating BP than linear regression.
Show me the substrates: modulation of host cell function by type IV secretion systems (2003)

Evidence for the involvement of type IV protein secretion systems in bacterial virulence is accumulating. Many of the substrate proteins secreted by type IV systems either hijack or interfere with specific host cell pathways. These substrates can be injected directly into host cells via the type IV apparatus or are secreted by the type IV machinery in a state that allows them to gain access to cellular targets without the further assistance of the type IV system. Arguably, the protein substrates of most type IV secretion systems remain undiscovered. Here, we review the activities of known type IV substrates and discuss the putative roles of unidentified substrates.
The Use of Vacuum-Assisted Closure Therapy for the Treatment of Lower-Extremity Wounds with Exposed Bone (2001)

Lower-extremity wounds with exposed tendon, bone, or orthopedic hardware present a difficult treatment challenge. In this series of patients, subatmospheric pressure therapy was applied to such lower-extremity wounds. Seventy-five patients with lower-extremity wounds, most of which were the result of trauma, were selected for this study. Dressings made of sterile open-cell foam with embedded fenestrated tubing were contoured to the wound size and placed into the wound. The site was covered with an adhesive plastic sheet. The sheet was placed beneath any external fixation devices, or the fixation device was enclosed within the sheet. The tubing was connected to the vacuum-assisted closure pump. Continuous subatmospheric suction pressure (125 mmHg) was applied to the wound site. The wounds were inspected and the dressings were changed every 48 hours.Vacuum-assisted closure therapy greatly reduced the amount of tissue edema, diminishing the circumference of the extremity and thus decreasing the surface area of the wound. Profuse granulation tissue formed rapidly, covering bone and hardware. The wounds were closed primarily and covered with split-thickness skin grafts, or a regional flap was rotated into the granulating bed to fill the defect. Successful coverage was obtained without complication in 71 of 75 patients. Wounds have been stable from 6 months up to 6 years.
A common ancestry for multiple catalytic antibodies generated against a single transition-state analog. (1994)

Immunization with a single haptenic transition-state analog generates a few catalytic antibodies among the dozens of antibodies capable of binding the hapten. The diversity of the immune response has raised some fundamental issues, such as How do catalytic and noncatalytic antibodies differ on a structural basis? To address this issue, the variable region primary sequences of 11 antibodies (including 6 catalytic and 5 noncatalytic antibodies) elicited against a single haptenic transition-state analog were deduced from cDNA sequences. Cluster analyses using phylogenetic trees constructed by the neighbor-joining method have revealed that the amino acid sequences of noncatalytic antibodies bear no relationship to one another, while the catalytic antibodies share significant structural identity. Furthermore, no catalytic antibodies possessing amino acid sequences with high homology to those of noncatalytic antibodies were detected. Five catalytic antibodies examined showed 89-95% and 74-84% sequence homologies in the complete light- and heavy-chain variable regions, respectively. Thus, it seems likely that the catalytic antibodies elicited against a single hapten use the canonical set of variable region genes. Interestingly, one catalytic antibody showed only limited sequence similarity to the other catalytic antibodies and was found to exhibit a distinctly different substrate specificity. From the broad range of their binding constants to the hapten, it is unlikely that highly homologous catalytic antibodies are generated as a result of simple high-affinity choices. These results emphasize the utility of rationally designed transition-state analogs for the induction of antibody molecules with catalytic activity.
On Manipulating Z-Polyhedra Using a Canonical Representation (1997)

Z-polyhedra are intersections of polyhedra and integral lattices. They arise in the domain of automatic parallelization and VLSI array synthesis. In this paper, we address the problem of computation on Z-polyhedra. We introduce a canonical representation for Z-polyhedra which allows one to perform comparisons and transformations of Z-polyhedra with the help of a computational kernel on polyhedra.
High T C superconductors—composite wire fabrication (1987)

Commercially useful, bulk superconductors typically require stabilization using a normal metal cladding for reasons of electrical, thermal, and mechanical protection and, in general, need to be drawn into fine fibers and wound into a magnet configuration. The recent discovery of high-TC superconductor materials such as Ba2YCu3O7 stimulated worldwide interest in the subject, however, with much concern about fabricability of such brittle ceramic materials into desirable fine wire geometry. In this letter, we report preliminary success in the fabrication of fine-wire, composite superconductors consisting of a high-conductivity normal metal shell such as Ag or Cu/Ni/Au and a superconducting core of Ba2YCu3O7 oxide. The wire is would into a coil, and then heat treated to produce the desired chemistry in a dense structure. The resistivity of the composite wire is measured to be zero at ≊90 K (in zero field) with a zero-field critical density of ≊175 A/cm2. Microscopy and x-ray analysis show that the superconducting core is continuous, and retains phase composition after wire drawing and heat treatment. These results demonstrate the feasibility of producing superconducting ceramic composite wire, although the practical applications must await the resolution of many practical problems and reliability issues.
Impact of SSRI Therapy on Risk of Conversion From Mild Cognitive Impairment to Alzheimer’s Dementia in Individuals With Previous Depression (2017)

Long-term SSRI treatment may delay progression from MCI to Alzheimer's dementia.
Mycobacterium tuberculosis –specific CD8+ T Cells Preferentially Recognize Heavily Infected Cells (2003)

Both CD4+ and CD8+ T cells are important for successful immunity to tuberculosis and have redundant effector functions, such as cytolysis and release of potent antimycobacterial cytokines such as interferon-gamma and tumor necrosis factor-alpha. We hypothesized that CD8+ T cells play a unique role in host defense to Mycobacterium tuberculosis infection as well. Possibilities include preferential and/or enhanced release of granular constituents and/or preferential recognition of heavily infected cells. Utilizing human, Mycobacterium tuberculosis-specific, CD4+ and CD8+ T cell clones, we demonstrate that, after recognition of antigen-presenting cells displaying peptide antigen, CD4+ T cells preferentially release interferon-gamma, whereas CD8+ T cells preferentially lyse antigen-presenting cells. Furthermore, utilizing dendritic cells infected with Mycobacterium tuberculosis expressing green fluorescent protein, we show that CD8+ T cells preferentially recognize heavily infected cells that constitute the minority of infected cells. These data support the hypothesis that the central role of CD8+ T cells in the control of infection with Mycobacterium tuberculosis may be that of surveillance; in essence, recognition of cells in which the containment of Mycobacterium tuberculosis is no longer effective.
Scene change detection algorithm for MPEG video sequence (2002)

A new scene change detection algorithm is developed for MPEG encoded video sequences. The proposed method is very simple that it only requires the bit-rate information at macroblock level as well as the number of various motion-predicted blocks for detection. Those information can be extracted easily from the encoded bit-stream without decompression. Simulation results on different sequences show that the proposed algorithm is effective for detecting abrupt scene changes in MPEG video.
NKT cells: Potential targets for autoimmune disease therapy? (2002)

NKT cells represent a unique T cell lineage that recognize glycolipid antigens in the context of the non-classical MHC class I molecule CD1d. NKT cells are potent producers of immunoregulatory cytokines, and have been implicated in several different autoimmune diseases in mice and humans, including Type 1 diabetes, experimental autoimmune encephalomyelitis--a mouse model for multiple sclerosis, systemic lupus erythematosus, and scleroderma. This review will cover the evidence for an involvement for NKT cells in these autoimmune diseases, and discuss the potential for therapeutic manipulation of these cells as a means of preventing autoimmune disease in the clinic.
c-Myc enhances protein synthesis and cell size during B lymphocyte development (1999)

Members of the myc family of nuclear protooncogenes play roles in cell proliferation, differentiation, and apoptosis. Moreover, inappropriate expression of c-myc genes contributes to the development of many types of cancers, including B cell lymphomas in humans. Although Myc proteins have been shown to function as transcription factors, their immediate effects on the cell have not been well defined. Here we have utilized a murine model of lymphomagenesis (Emu-myc mice) to show that constitutive expression of a c-myc transgene under control of the Ig heavy-chain enhancer (Emu) results in an increase in cell size of normal pretransformed B lymphocytes at all stages of B cell development. Furthermore, we show that c-Myc-induced growth occurs independently of cell cycle phase and correlates with an increase in protein synthesis. These results suggest that Myc may normally function by coordinating expression of growth-related genes in response to mitogenic signals. Deregulated c-myc expression may predispose to cancer by enhancing cell growth to levels required for unrestrained cell division.
Current‐induced switching in spin‐valve structures (2007)

Abstract Spin transfer between conduction electrons and local magnetic moments can switch spin valves between different magnetic configurations. In some conditions, however, the spin torque can induce magnetic switching to stationary precessional modes. In this paper we consider current‐induced magnetic switching in nanopillar spin valves including two thin magnetic films separated by a nonmagnetic layer, and in molecular‐based spin valves. In the former case the spin torque is calculated from the macroscopic spin diffusion equations, while in the latter one we use quantum description based on the Fermi golden rule. (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement (2010)

The multiple genome alignments generated by our software provide a platform for comparative genomic and population genomic studies. Free, open-source software implementing the described genome alignment approach is available from http://gel.ahabs.wisc.edu/mauve.