gebhart/patrepeval huggingface dataset:
Inflammation Markers, Adhesion Molecules, and All-Cause and Cardiovascular Mortality in Patients with ESRD (2005)

Inflammation is a major risk factor for mortality and cardiovascular (CV) complications in patients with ESRD. The predictive value of C-reactive protein (CRP) of the main proinflammatory cytokines (IL-1beta, IL-6, IL-18, and TNF-alpha) and of two adhesion molecules (intercellular adhesion molecule-1 and vascular cell adhesion molecule-1) in 217 dialysis patients was compared. Serum IL-6 and CRP added significant prediction power to the multivariate Cox model of all-cause death, and the gain in the prediction power attributable to IL-6 was approximately two times higher than that of CRP. Patients in the third tertiles of serum IL-6 and CRP had a relative risk of all-cause mortality 2.5 and 1.8 times higher than those in the first corresponding tertiles, and there was no statistical difference between these two relative risks. The gain in prediction power associated with TNF-alpha, IL-beta, IL-18, intercellular adhesion molecule-1, and vascular cell adhesion molecule-1 was of small degree (P = NS). Similarly, serum IL-6 added the highest prediction power to the CV death model, and the IL-6 attributable gain was approximately two times higher than that of serum CRP. However, the risk estimate for CV mortality of patients with high serum IL-6 did not differ significantly from that of patients with high serum CRP. IL-6 adds significantly greater predictive power for all-cause and CV death to statistical models based on traditional and nontraditional risk factors in ESRD patients. However, the risk estimate by CRP being reasonably close to that of IL-6, CRP may be a cheap alternative to IL-6 in clinical practice.
Dynamic recruitment of axin by Dishevelled protein assemblies (2007)

Dishevelled (Dvl) proteins are cytoplasmic components of the Wnt signalling pathway, which controls numerous cell fate decisions during animal development. During Wnt signalling, Dvl binds to the intracellular domain of the frizzled transmembrane receptors, and also to axin to block its activity, which results in the activation of beta-catenin and, consequently, in a transcriptional switch. We have previously reported that the DIX domain of mammalian Dvl2 allows it to form dynamic protein assemblies. Here, we show that these Dvl2 assemblies recruit axin, and also casein kinase Iepsilon. Using photobleaching experiments of GFP-tagged Dvl2 and axin to study the dynamics of their interaction, we found that the recruitment of axin-GFP by Dvl2 assemblies is accompanied by a striking acceleration of the dynamic properties of axin-GFP. We also show that the interaction between Dvl2 and axin remains highly dynamic even after Wnt-induced relocation to the plasma membrane. We discuss how the recruitment of casein kinase Iepsilon by Dvl2 assemblies might impact on the recruitment of axin to the plasma membrane during Wnt signalling.
Molecular Basis of 9G4 B Cell Autoreactivity in Human Systemic Lupus Erythematosus (2013)

9G4(+) IgG Abs expand in systemic lupus erythematosus (SLE) in a disease-specific fashion and react with different lupus Ags including B cell Ags and apoptotic cells. Their shared use of VH4-34 represents a unique system to understand the molecular basis of lupus autoreactivity. In this study, a large panel of recombinant 9G4(+) mAbs from single naive and memory cells was generated and tested against B cells, apoptotic cells, and other Ags. Mutagenesis eliminated the framework-1 hydrophobic patch (HP) responsible for the 9G4 idiotype. The expression of the HP in unselected VH4-34 cells was assessed by deep sequencing. We found that 9G4 Abs recognize several Ags following two distinct structural patterns. B cell binding is dependent on the HP, whereas anti-nuclear Abs, apoptotic cells, and dsDNA binding are HP independent and correlate with positively charged H chain third CDR. The majority of mutated VH4-34 memory cells retain the HP, thereby suggesting selection by Ags that require this germline structure. Our findings show that the germline-encoded HP is compulsory for the anti-B cell reactivity largely associated with 9G4 Abs in SLE but is not required for reactivity against apoptotic cells, dsDNA, chromatin, anti-nuclear Abs, or cardiolipin. Given that the lupus memory compartment contains a majority of HP(+) VH4-34 cells but decreased B cell reactivity, additional HP-dependent Ags must participate in the selection of this compartment. This study represents the first analysis, to our knowledge, of VH-restricted autoreactive B cells specifically expanded in SLE and provides the foundation to understand the antigenic forces at play in this disease.
DSAC — Differentiable RANSAC for Camera Localization (2017)

RANSAC is an important algorithm in robust optimization and a central building block for many computer vision applications. In recent years, traditionally hand-crafted pipelines have been replaced by deep learning pipelines, which can be trained in an end-to-end fashion. However, RANSAC has so far not been used as part of such deep learning pipelines, because its hypothesis selection procedure is non-differentiable. In this work, we present two different ways to overcome this limitation. The most promising approach is inspired by reinforcement learning, namely to replace the deterministic hypothesis selection by a probabilistic selection for which we can derive the expected loss w.r.t. to all learnable parameters. We call this approach DSAC, the differentiable counterpart of RANSAC. We apply DSAC to the problem of camera localization, where deep learning has so far failed to improve on traditional approaches. We demonstrate that by directly minimizing the expected loss of the output camera poses, robustly estimated by RANSAC, we achieve an increase in accuracy. In the future, any deep learning pipeline can use DSAC as a robust optimization component.
Metascheduling for continuous media (1993)

Next-generation distributed systems will support continuous media (digital audio and video) in the same framework as other data. Many applications that use continuous media need guaranteed end-to-end performance (bounds on throughput and delay). To reliably support these requirements, system components such as CPU schedulers, networks, and file systems must offer performance guarantees. A metascheduler coordinates these components, negotiating end-to-end guarantees on behalf of clients. The CM-resource model , described in this paper, provides a basis for such a metascheduler. It defines a workload parameterization, an abstract interface to resources, and an algorithm for reserving multiple resources. The model uses an economic approach to dividing end-to-end delay, and it allows system components to “work ahead,” improving the performance of nonreal-time workload.
Pulmonary gene and microRNA expression changes in mice exposed to benzo(a)pyrene by oral gavage (2011)

Exposure to the environmental mutagen benzo(a)pyrene (BaP) alters the expression of AHR-responsive genes as well as genes involved in other pathways. We recently reported that exposure of adult mice to BaP resulted in a robust transcriptome response in the liver, but this was accompanied by a complete lack of change in microRNA (miRNA) expression. Since BaP exposure does not result in hepatocarcinogenicity, but does cause lung cancer, in the present study we examine the pulmonary mRNA and miRNA responses to BaP in the same mice. Adult male B6C3F1 mice were exposed to 150 and 300 mg/kg BaP by oral gavage for three consecutive days and sacrificed 4h after the last exposure. Serum clinical chemistry was performed for both the doses to assess the general toxicity of BaP; a modest decrease in serum inorganic phosphorous was observed at both the doses. A small decrease in serum glucose following 150 mg/kg and alkaline phosphatase following 300 mg/kg BaP was observed. BaP-DNA adduct levels in whole lung and liver tissues were assessed by (32)P post labelling and similar dose dependent increases were observed for lung and liver. Using DNA microarrays, pulmonary mRNA and miRNA expressions were analysed. Over 1000 genes were statistically differentially expressed (p<0.05). The perturbed pathways included oxidative stress, xenobiotic metabolism, cell proliferation, cell cycle, B and T-cell receptor signalling and primary immunodeficiency signalling pathways. Analysis of miRNA profiles revealed downregulation of miR-150, miR-142-5p, miR-122 and upregulation of miR-34c, miR-34b-5p and miR-29b. These miRNAs are involved in the biological processes, immune response, cell proliferation and cell cycle, which are the main pathways affected at the mRNA level. Thus, miRNAs are more responsive to BaP in lungs than in liver, and are likely to be involved in the regulation of the pulmonary responses to BaP exposure.
Conditional Lethal Amber Mutations in Essential Escherichia coli Genes (2004)

The essential genes of microorganisms encode biological functions important for survival and thus tend to be of high scientific interest. Drugs that interfere with essential functions are likely to be interesting candidates for antimicrobials. However, these genes are hard to study genetically because knockout mutations in them are by definition inviable. We recently described a conditional mutation system in Escherichia coli that uses a plasmid to produce an amber suppressor tRNA regulated by the arabinose promoter. This suppressor was used here in the construction of amber mutations in seven essential E. coli genes. Amber stop codons were introduced as "tagalong" mutations in the flanking DNA of a downstream antibiotic resistance marker by lambda red recombination. The drug marker was removed by expression of I-SceI meganuclease, leaving a markerless mutation. We demonstrate the method with the genes frr, gcpE, lpxC, map, murA, ppa, and rpsA. We were unable to isolate an amber mutation in ftsZ. Kinetics of cell death and morphological changes were measured following removal of arabinose. As expected given the wide range of cellular mechanisms represented, different mutants showed widely different death curves. All of the mutations were bactericidal except the mutation in gcpE, which was bacteriostatic. The strain carrying an amber mutation in murA was by far the most sensitive, showing rapid killing in nonpermissive medium. The MurA protein is critical for peptidoglycan synthesis and is the target for the antibiotic fosfomycin. Such experiments may inexpensively provide valuable information for the identification and prioritization of targets for antibiotic development.
Does the Immune System See Tumors as Foreign or Self? (2003)

Given the vast number of genetic and epigenetic changes associated with carcinogenesis, it is clear that tumors express many neoantigens. A central question in cancer immunology is whether recognition of tumor antigens by the immune system leads to activation (i.e., surveillance) or tolerance. Paradoxically, while strong evidence exists that specific immune surveillance systems operate at early stages of tumorigenesis, established tumors primarily induce immune tolerance. A unifying hypothesis posits that the fundamental processes of cancer progression, namely tissue invasion and metastasis, are inherently proinflammatory and thus activating for innate and adaptive antitumor immunity. To elude immune surveillance, tumors must develop mechanisms that block the elaboration and sensing of proinflammatory danger signals, thereby shifting the balance from activation to tolerance induction. Elucidation of these mechanisms provides new strategies for cancer immunotherapy.
The Effect of Inflammation on the Utilization of Erythrocyte and Transferrin Bound Radioiron for Red Cell Production (1957)

By EMIL #{149}J. FREIIIEICH, AARON )sILLLER, CH iitI I s P. EMERSON ANI) JOSEPH F’. Ross I NFECTION ANI) INFLA\IMATI()N have been shown to inipair the ability of the 1)Omie mnarrow to respomid to in(reased deniands for re(l cell production. Following acute or chronic blood loss, inflalnmuation slows the rate of hemoglobin productiomi;tm iii pernicious amiemia patiemits umidergoing adequate vitaniimi B-12 therapy, infection slows the rate of recovery;2 in patients with hemolytic anemias, inflammnation can depress hemiioglobin product ion amid rc’stilt in hypophastic crises.3 ‘ \Vhile inflammnatioii does depress hemnogbobimi produl(tion, the niechamiism by which this occurs is not known. Inflammation also produces marked chamiges imi iron miietabolism. A decrease imiserumn iromi comicentration is a comistant findimig.5 The miiechamiism of the hypoferremia and its role imi the bomie miiarrow depression is not clearly umiderstood.
A flip-chip-packaged 1.8V 28dBm class-AB power amplifier with shielded concentric transformers in 32nm SoC CMOS (2011)

As CMOS technology continues to scale for SoC applications, significant challenges to implement a monolithic linear high-power amplifier have emerged. This results from the low breakdown voltage of transistors, high on-chip passive loss on a conductive substrate, stringent bump-pattern constraints and thermal dissipation requirements of flip-chip packages. Most fully-integrated linear CMOS PAs reported to date were either fabricated on a relatively mature process (65nm or above) in a wire-bonded die with relatively high supply voltage (3.3V), or exhibited low power efficiency when backed-off. In many cases, digital pre-distortion was implemented to improve linearity and efficiency. We present a 1.8V single-chip CMOS PA with 21dBm average output power and 16% PAE while meeting -25dB EVM for 64-QAM OFDM signal without digital pre-distortion linearization in 32nm SoC CMOS on a flip-chip package. This per formance is enabled by: 1) On-chip shielded concentric transformers with power-splitting/combining structures to fit the design within the bump pattern constraint and thermal dissipation requirement of an SoC flip-chip package and to enhance power handling capability; 2) Minimum phase distortion by opti mized inter-stage power matching allowed by the high fmax of the minimum channel-length device.
Evaluation of Constitutive Viral Promoters in Transgenic Soybean Roots and Nodules (2008)

The efficiency of beta-glucuronidase (GUS) expression was evaluated with five viral promoters to identify the most suitable promoter or promoters for use in soybean hairy roots, including applications to study the symbiotic interaction with Bradyrhizobium japonicum. Levels of GUS activity were fluorimetrically and histochemically assayed when the GUS (uidA) gene was driven by the Cauliflower mosaic virus (CaMV) 35S promoter and enhanced 35S (E35S) promoter, the Cassava vein mosaic virus (CsVMV) promoter, the Figwort mosaic virus (FMV) promoter, and the Strawberry vein banding virus (SVBV2) promoter. We demonstrate that GUS activity was highest when driven by the FMV promoter and that the promoter activity of 35S and SVBV2 was significantly lower than that of the CsVMV and E35S promoters when tested in soybean hairy roots. In mature soybean root nodules, strong GUS activity was evident when the FMV, 35S, and CsVMV promoters were used. These results indicate that the FMV promoter facilitates the strong expression of target genes in soybean hairy roots and root nodules.
Error probability of bit-interleaved coded modulation using the Gaussian approximation (2004)

This paper presents a very accurate and simple to compute approximation to the perfor- mance of bit-interleaved coded modulation (BICM) systems. The proposed method is based on approxi- mating the binary-input continuous-output equivalent BICM channel by a binary-input AWGN (BI-AWGN) channel with scaled SNR. The scaling factor can be easily computed numerically and depends on the ac- tual channel SNR and on the modulation signal set and binary labeling. The key is that very good ap- proximation results when the Bhattacharyya param- eter is used to estimate the variance of the under- lying Gaussian channel. Under such approximation, we can use all bounding techniques known for binary codes in Gaussian channels. In particular, we use the union and the tangential-sphere bounds and we ap- ply such results to both convolutional and turbo-like codes. The proposed method represents a simple yet powerful tool for estimating the error probability of finite-length turbo-like codes with BICM.
A facile one-step synthesis of delta 1,4-3-keto bile acid esters by iodoxybenzene and benzeneselenic anhydride. (1988)

A facile one-step conversion of stereoisomeric methyl 3-hydroxycholanoates to 1,4-dien-3-one, by treatment in boiling toluene with iodoxybenzene catalyzed by benzeneselenic anhydride, is described. The direct oxidation-dehydrogenation at C-3 is applicable to other cholanoates (hyodeoxycholic, chenodeoxycholic, ursodeoxycholic, deoxycholic, and cholic) when the hydroxyl groups at C-6, C-7, or C-12 are protected. Without protection at C-6 and C-7, the products from hyodeoxycholic, chenodeoxycholic, ursodeoxycholic, and cholic esters are complex mixtures, whereas, methyl deoxycholate yields the 1,4-dien-3,12-dione cleanly.
Changes in mitochondrial membrane potential during oxidative stress-induced apoptosis in PC12 cells (1997)

We examined the effects of various types of oxidative stress on cell survival and on mitochondrial membrane potential (delta psi m) in PC12 cells transfected with BCL-2. Several types of oxidative stress such as exposure to hydrogen peroxide, 13-L-hydroperoxylinoleic acid, and xanthine + xanthine oxidase triggered apoptotic nuclear condensation and DNA fragmentation in normal PC12 cells. These types of oxidative stress induced significant increases in level of reactive oxygen species (ROS) before cell death. By contrast, BCL-2 prevented the apoptosis induced by these oxidative stresses. However, BCL-2 did not reduce ROS levels, indicating that it functions downstream of ROS generation. We measured delta psi m as a potential target of ROS during oxidative stress-induced cell death. Hydrogen peroxide, 13-L-hydroperoxylinoleic acid, and xanthine + xanthine oxidase induced a significant loss of delta psi m simultaneously with cell death. BCL-2 prevented the decrease in delta psi m as well as apoptosis induced by oxidative stress. These observations suggest that the oxidative stress triggers apoptosis associated with both increased generation of ROS and decreases in level of delta psi m and that BCL-2 prevents cell death as well as delta psi m but not ROS production.
The Fap1 fimbrial adhesin is a glycoprotein: antibodies specific for the glycan moiety block the adhesion of Streptococcus parasanguis in an in vitro tooth model (2002)

Streptococcus parasanguis is a primary colonizer of the tooth surface and plays a pivotal role in the formation of dental plaque. The fimbriae of S. parasanguis are important in mediating adhesion to saliva-coated hydroxylapatite (SHA), an in vitro tooth adhesion model. The Fap1 adhesin has been identified as the major fimbrial subunit, and recent studies suggest that Fap1 is a glycoprotein. Monosaccharide analysis of Fap1 purified from the culture supernatant of S. parasanguis indicated the presence of rhamnose, glucose, galactose, N-acetylglucosamine and N-acetylgalactosamine. A glycopeptide moiety was isolated from a pronase digest of Fap1 and purified by immunoaffinity chromatography. The monosaccharide composition of the purified glycopeptide was similar to that of the intact molecule. The functionality of the glycan moiety was determined using monoclonal antibodies (MAbs) specific for the intact Fap1 glycoprotein. These antibodies were grouped into two categories based on their ability to block adhesion of S. parasanguis to SHA and their corresponding specificity for either protein or glycan epitopes of the Fap1 protein. 'Non-blocking' MAb epitopes were mapped to unique protein sequences in the N-terminus of the Fap1 protein using non-glycosylated recombinant Fap1 proteins (rFap1 and drFap1) expressed in Escherichia coli. In contrast, the 'blocking' antibodies did not bind to the recombinant Fap1 proteins, and were effectively competed by the binding to the purified glycopeptide. These data suggest that the 'blocking' antibodies are specific for the glycan moiety and that the adhesion of S. parasanguis is mediated by sugar residues associated with Fap1.
Integrating Off-Board Cameras and Vehicle On-Board Localization for Pedestrian Safety (2013)

Situational awareness for industrial vehicles is crucial to ensure safety of personnel and equipment. While human drivers and onboard sensors are able to detect obstacles and pedestrians within line-of-sight, in complex environments, initially occluded or obscured dynamic objects can unpredictably enter the path of a vehicle. We propose a system that integrates a vision-based offboard pedestrian tracking subsystem with an onboard localization and navigation subsystem. This combination enables warnings to be communicated and effectively extends the vehicle controller's field of view to include areas that would otherwise be blind spots. A simple flashing light interface in the vehicle cabin provides a clear and intuitive interface to alert drivers of potential collisions. Alternatively, the system can be also applied to vehicles that have autonomous navigation capabilities, in which case, instead of alert lights, the vehicle is halted or redirected. We implemented and tested the proposed solution on an automated industrial vehicle under autonomous operation and on a human-driven vehicle in a full-scale production facility, over a period of four months.
Translation of Research Evidence From Animals to Humans (2006)

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Semiconductor Nanoparticles in Contact:  Quenching of the Photoluminescence from Silicon Nanocrystals by WO3 Nanoparticles Suspended in Solution (1998)

Weblike aggregates of Si nanocrystals and tungsten oxide nanoparticles are produced by a laser vaporization controlled condensation technique. XRD, FTIR, and Raman results confirm that the Si nanoparticles have a diamond-like crystalline structure and WO3 nanoparticles exhibit a monoclinic crystalline structure. Due to the quantum size effect, the band gaps of Si nanocrystals and WO3 nanoparticles shift to higher energies by 0.68 and 0.55 eV, respectively, from the bulk values. The red emission of Si nanocrystals is quenched by adding successive amounts of the WO3 nanoparticles to Si nanoparticles suspended in a methanol solution. The quenching follows Stern−Volmer kinetics and the quenching rate constants are 14.1 × 106 and 3.2 × 106 (Ms)-1 for WO3 and W2O5, respectively. The quenching mechanism is explained by an electron transfer from the CB of the Si to the CB of the WO3 nanoparticles.