gebhart/patrepeval huggingface dataset:
Data from Identification of Anti-CA125 Antibody Responses in Ovarian Cancer Patients by a Novel Deep Sequence–Coupled Biopanning Platform (2023)

&lt;div&gt;Abstract&lt;p&gt;High-grade epithelial ovarian cancer kills more women than any other gynecologic cancer and is rarely diagnosed at an early stage. We sought to identify tumor-associated antigens (TAA) as candidate diagnostic and/or immunotherapeutic targets by taking advantage of tumor autoantibody responses in individuals with ovarian cancer. Plasma-derived IgG from a pool of five patients with advanced ovarian cancer was subjected to iterative biopanning using a library of bacteriophage MS2 virus-like particles (MS2-VLPs) displaying diverse short random peptides. After two rounds of biopanning, we analyzed the selectant population of MS2-VLPs by Ion Torrent deep sequencing. One of the top 25 most abundant peptides identified (DISGTNTSRA) had sequence similarity to cancer antigen 125 (CA125/MUC16), a well-known ovarian cancer–associated antigen. Mice immunized with MS2-DISGTNTSRA generated antibodies that cross-reacted with purified soluble CA125 from ovarian cancer cells but not membrane-bound CA125, indicating that the DISGTNTSRA peptide was a CA125/MUC16 peptide mimic of soluble CA125. Preoperative ovarian cancer patient plasma (&lt;i&gt;n&lt;/i&gt; = 100) was assessed for anti-DISGTNTSRA, anti-CA125, and CA125. Patients with normal CA125 (&lt;35 IU/mL) at the time of diagnosis had significantly more antibodies to DISGTNTSRA and to CA125 than those patients who had high CA125 (&gt;35 IU/mL). A statistically significant survival advantage was observed for patients who had either normal CA125 and/or higher concentrations of antibodies to CA125 at the time of diagnosis. These data show the feasibility of using deep sequence–coupled biopanning to identify TAA autoantibody responses from cancer patient plasma and suggest a possible antibody-mediated mechanism for low CA125 plasma concentrations in some ovarian cancer patients. &lt;i&gt;Cancer Immunol Res; 4(2); 157–64. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Andrew W.K.’s I Get Wet (2014)

<JATS1:p>“It’s Time To Party,” the first track off of I Get Wet, opens with a rapid-fire guitar line - nothing fancy, just a couple crunchy power chords to acclimate the ears - repeated twice before a booming bass drum joins in to provide a quarter-note countdown. A faint, swirling effect intensifies with each bass kick and, by the eighth one, the ears have prepped themselves for the metal mayhem they are about to receive. When it all drops, and the joyous onslaught of a hundred guitars is finally realized, you'll have to forgive your ears for being duped into a false sense of security, because it's that second intensified drop a few seconds later - the one where yet more guitars manifest and Andrew W.K. slam-plants his vocal flag by screaming the song's titular line - that really floods the brain with endorphins, serotonin, dopamine, and whatever else formulates invincibility.</JATS1:p> <JATS1:p>Polished to a bright overdubbed-to-oblivion sheen, the party-preaching I Get Wet didn’t capture the zeitgeist of rock at the turn of the century; it captured the timelessness of youth, as energized, awesome, and unapologetically stupid as ever. With insights from friends and unprecedented help from the mythological maniac himself - whose sermon and pop sensibilities continue to polarize - this book chronicles the sound's evolution, uncovers the relevance of Steev Mike, and examines how Andrew W.K.'s inviting, inclusive lyrics create the ultimate shared experience between artist and audience.</JATS1:p>
The Rayleigh method applied to EUV lithography simulation (2003)

In Extreme Ultraviolet lithography, the electromagnetic modeling of the mask allows to determine the influence of the mask structure on the electromagnetic field. That makes it possible for example to analyze the influence of a defect within the multi-layer stack. This paper describes a modeling method of the EUV mask based on the Rayleigh assumptions1. These hypotheses lead to a more restrictive validity domain than rigorous methods like modal methods or Finite Difference Time Domain (FDTD), but is shown in this paper to be usable adapted for EUV mask simulation. Furthermore the simulations are less costly in memory resources and in computing time.
A novel pH-regulated, unusual 603 bp overlapping protein coding gene pop is encoded antisense to ompA in Escherichia coli O157:H7 (EHEC) (2019)

Abstract Antisense transcription is well known in bacteria. However, translation of antisense RNAs is typically not considered, as the implied overlapping coding at a DNA locus is assumed to be highly improbable. Therefore, such overlapping genes are systematically excluded in prokaryotic genome annotation. Here we report an exceptional 603 bp long open reading frame completely embedded in antisense to the gene of the outer membrane protein ompA . Ribosomal profiling revealed translation of the mRNA and the protein was detected in Western blots. A σ 70 promoter, transcription start site, Shine-Dalgarno motif and rho-independent terminator were experimentally validated. A pH-dependent phenotype conferred by the protein was shown in competitive overexpression growth experiments of a translationally arrested mutant versus wild type. We designate this novel gene pop ( p H-regulated o verlapping p rotein-coding gene). Increasing evidence based on ribosome-profiling indicates translation of antisense RNA, suggesting that more overlapping genes of unknown function may exist in bacteria.
The effect of specialized multimedia collections on web searching (2004)

Multimedia Web searching is a significant information activity for many people. Major Web search engines are critical resources in people's efforts to locate relevant online multimedia information. It is therefore important that we understand how searchers are utilizing these Web information systems in their quest to retrieve multimedia information to design effective Web systems in support of these information needs. In this paper, we report the results of a research study evaluating the effect of separate multimedia Web collections on individual searching behavior. The AltaVista search engine has an extensive multimedia collection and uses tabs to search specific collections. The motivating questions for this research are: (1) What are the characteristics of multimedia searching on AltaVista? and (2) What are the effects on Web searching of separate multimedia collections? The results of our research show that multimedia searching is complex relative to general Web searching. Searching specific multimedia collections has reduced the complexity of audio searching, but it has not had the same effect for image and video searching. Query length and Boolean usage rates are much higher for image searching, compared to general Web searching. We discuss the implications of the research findings for the design, development and evaluation of Web multimedia retrieval systems.
MODEL-BASED ULTRASONIC INSPECTION TECHNIQUE DEVELOPMENT AND EVALUATION (2008)

Traditionally, ultrasonic inspection methods are developed using extensive lab measurements. This approach provides limited insight in the interaction of waves with artificial and realistic defects. However, for a thorough insight in the factors that determine the reliability it is necessary to understand the wave field inside the object of inspection. Therefore, we propose the usage of advanced numerical simulation tools which visualize the full‐elastic wave field. This way a connection can be made between the recorded signal and the wave field inside the test object. These insights improve the performance of an inspection method and reduce time spent on experimental validation.
Iron Homeostasis andTrypanosoma bruceiAssociated Immunopathogenicity Development: A Battle/Quest for Iron (2015)

African trypanosomosis is a chronic debilitating disease affecting the health and economic well-being of developing countries. The immune response during African trypanosome infection consisting of a strong proinflammatory M1-type activation of the myeloid phagocyte system (MYPS) results in iron deprivation for these extracellular parasites. Yet, the persistence of M1-type MYPS activation causes the development of anemia (anemia of chronic disease, ACD) as a most prominent pathological parameter in the mammalian host, due to enhanced erythrophagocytosis and retention of iron within the MYPS thereby depriving iron for erythropoiesis. In this review we give an overview of how parasites acquire iron from the host and how iron modulation of the host MYPS affects trypanosomosis-associated anemia development. Finally, we also discuss different strategies at the level of both the host and the parasite that can/might be used to modulate iron availability during African trypanosome infections.
Smartphone-based fluorescence imager for PpIX-based PDT treatment planning: System design and initial results (2019)

In clinical delivery of PDT, in-situ measurement of PpIX concentration is rarely done, and yet point-probe measurements have shown extreme heterogeneity exists between patients and between lesions. Direct measurements of PpIX can provide guidance in PDT, informing critical decisions about treatment time and retreatment or further skin preparation. In this work, we present a smartphone-based fluorescence imaging system to map PpIX concentration onto a 2D image for the use in PDT treatment optimization. The hand-held system utilizes a custom application on an iPhone 6s in conjunction with a 3D-printed measurement base containing custom miniaturized light source and electronics and filter system. The prototype has been produced and tested in phantoms and in pre-clinical evaluation. Intralipid phantom measurements detected clinicallyrelevant concentrations of PpIX within the 0.05&mu;M - 4&mu;M range. Preclinical tests on mice showed the ability to detect PpIX concentration for topically applied ALA within 20-30 minute incubation. These results showcase the viability of the system to map pixel intensities to PpIX concentrations and perform in-vivo detection within a clinically relevant timeframe. Clinical trials are in preparation with results expected in the next few months.
Cryptococci at the brain gate: break and enter or use a Trojan horse? (2010)

The mechanism by which Cryptococcus neoformans invades the central nervous system is fundamental for understanding pathogenesis because cryptococcosis commonly presents as meningoencephalitis. There is evidence for both direct invasion of the endothelial cells lining the brain vasculature and a "Trojan horse" mechanism whereby cryptococci enter the central nervous system after macrophage ingestion. However, in this issue of the JCI, Shi et al. use intravital microscopy to reveal that brain invasion by C. neoformans follows a capillary microembolic event. They find that after suddenly stopping in brain capillaries, cryptococci cross into the central nervous system in a process that is urease dependent, requires viability, and involves cellular deformation. This observation provides evidence for direct brain invasion by C. neoformans, but a consideration of all the currently available evidence suggests a role for both direct and phagocyte-associated invasion. Hence, the remarkable neurotropism of C. neoformans may have more than one mechanism.
A chemical process engineering look at digital concrete processes: critical step design, inline mixing, and scaleup (2022)

Digital concrete processes are a series of unit operations, similar to a chemical engineering process, each subject to their own rheological and other performance requirements, such as homogeneity, etc. In this article we examine the concrete extrusion 3D-printing process from this standpoint, first decomposing it into individual unit operations. We examine the role that residence time distributions play in the overall process, and then analyze how large scale printing to structural heights could be performed continuously. We then focus on the critical step of secondary (inline) mixing just before extrusion from the standpoint of mixing processes in the chemical processing industries. This unit operation is then analyzed in the context of scaleup to larger print areas and larger flowrates, finding that increase in viscosity plays a major role in power requirements and printhead mass. Further research questions are then raised based on these analyses.
Characteristics of prosthetic vision in rats with subretinal flat and pillar electrode arrays (2019)

While being helpful for treating a complete loss of sight, current prosthetic technologies are insufficient for addressing the leading cause of untreatable visual impairment-AMD. Subretinal photovoltaic arrays may provide sufficient visual acuity for restoration of central vision in patients blinded by AMD.
Computer-aided gleason grading of prostate cancer histopathological images using texton forests (2010)

The Gleason score is the single most important prognostic indicator for prostate cancer candidates and plays a significant role in treatment planning. Histopathological imaging of prostate tissue samples provides the gold standard for obtaining the Gleason score, but the manual assignment of Gleason grades is a labor-intensive and error-prone process. We have developed a texture classification system for automatic and reproducible Gleason grading. Our system characterizes the texture in images belonging to a tumor grade by clustering extracted filter responses at each pixel into textons (basic texture elements). We have used random forests to cluster the filter responses into textons followed by the spatial pyramid match kernel in conjunction with an SVM classifier. We have demonstrated the efficacy of our system in distinguishing between Gleason grades 3 and 4.
Direct Transistor-level Layout for Digital Blocks (2005)

Cell-based design methodologies have dominated layout generation of digital circuits. Unfortunately, the growing demands for transparent process portability, increased performance, and low-level devic
Calcineurin potentiates activation of the granulocyte-macrophage colony-stimulating factor gene in T cells: involvement of the conserved lymphokine element 0. (1994)

Granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin-2 (IL-2) are produced by stimulation with phorbol-12-myristate acetate (PMA) and calcium ionophore (A23187) in human T cell leukemia Jurkat cells. The expression of GM-CSF and IL-2 is inhibited by immunosuppressive drugs such as cyclosporin A (CsA) and FK506. Earlier studies on the IL-2 gene expression showed that overexpression of calcineurin (CN), a Ca2+/calmodulin-dependent protein phosphatase, can stimulate transcription from the IL-2 promoter through the NF-AT-binding site. In this study, we obtained evidence that transfection of the cDNAs for CN A (catalytic) and CN B (regulatory) subunits also augments transcription from the GM-CSF promoter and recovers the transcription inhibited by CsA. The constitutively active type of the CN A subunit, which lacks the auto-inhibitory and calmodulin-binding domains, acts in synergy with PMA to activate transcription from the GM-CSF promoter. We also found that the active CN partially replaces calcium ionophore in synergy with PMA to induce expression of endogenous GM-CSF and IL-2. By multimerizing the regulatory elements of the GM-CSF promoter, we found that one of the target sites for the CN action is the conserved lymphokine element 0 (CLE0), located at positions between -54 and -40. Mobility shift assays showed that the CLE0 sequence has an AP1-binding site and is associated with an NF-AT-like factor, termed NF-CLE0 gamma. NF-CLE0 gamma binding is induced by PMA/A23187 and is inhibited by treatment with CsA. These results suggest that CN is involved in the coordinated induction of the GM-CSF and IL-2 genes and that the CLE0 sequence of the GM-CSF gene is a functional analogue of the NF-AT-binding site in the IL-2 promoter, which mediates signals downstream of T cell activation.
Comparison of genotype clustering tools with rare variants (2014)

The GenoSNP clustering tool could not be run straight "out of the box" with the HumanExome BeadChip, as modification of hard coded parameters was necessary to achieve optimal performance. Overall, GenCall marginally outperformed the other tools for the HumanExome BeadChip. The use of experimental replicates provided a valuable quality control tool for genotyping projects with rare variants.
Molecular parts and genetic circuits for metabolic engineering of microorganisms (2018)

Microbial conversion of biomass into value-added biochemicals is a highly sustainable process compared to petroleum-based production. In this regard, microorganisms have been engineered via simple overexpression or deletion of metabolic genes to facilitate the production. However, the producer microorganisms require complex regulatory circuits to maximize productivity and performance. To address this issue, diverse genetic circuits have been developed that allow cells to minimize their metabolic burden, overcome metabolic imbalances and respond to a dynamically changing environment. In this review, we briefly explain the basic strategy for constructing genetic circuits by assembling molecular parts such as input, operation and output modules. Next, we describe recent applications of the circuits in the metabolic engineering of microorganisms to improve biochemical production. Beyond those achievements, genetic circuits will facilitate more innovative approaches to future strain development through mining and engineering new genetic elements and improving the complexity of genetic circuit design.
Hypertensive retinopathy (2013)

These findings indicate that the simplified classification of hypertensive retinopathy is both reliable and repeatable. The advantage of the simplified method over the KWB system in correlating retinal microvascular signs to incident cardiovascular risk supports its adoption in clinical practice.
Identification of Antigenic Proteins from Lichtheimia corymbifera for Farmer’s Lung Disease Diagnosis (2016)

The use of recombinant antigens has been shown to improve both the sensitivity and the standardization of the serological diagnosis of Farmer's lung disease (FLD). The aim of this study was to complete the panel of recombinant antigens available for FLD serodiagnosis with antigens of Lichtheimia corymbifera, known to be involved in FLD. L. corymbifera proteins were thus separated by 2D electrophoresis and subjected to western blotting with sera from 7 patients with FLD and 9 healthy exposed controls (HEC). FLD-associated immunoreactive proteins were identified by mass spectrometry based on a protein database specifically created for this study and subsequently produced as recombinant antigens. The ability of recombinant antigens to discriminate patients with FLD from controls was assessed by ELISA performed with sera from FLD patients (n = 41) and controls (n = 43) recruited from five university hospital pneumology departments of France and Switzerland. Forty-one FLD-associated immunoreactive proteins from L. corymbifera were identified. Six of them were produced as recombinant antigens. With a sensitivity and specificity of 81.4 and 77.3% respectively, dihydrolipoyl dehydrogenase was the most effective antigen for discriminating FLD patients from HEC. ELISA performed with the putative proteasome subunit alpha type as an antigen was especially specific (88.6%) and could thus be used for FLD confirmation. The production of recombinant antigens from L. corymbifera represents an additional step towards the development of a standardized ELISA kit for FLD diagnosis.
A systematic methodology for the application of data transfer and storage optimizing code transformations for power consumption and execution time reduction in realizations of multimedia algorithms on programmable processors (2002)

A systematic methodology for the reduction of the power consumption and the execution time in realizations of multimedia applications on programmable processors is proposed. The methodology is mainly based on the application of data transfer and storage optimizing code transformations to a high-level description of the target algorithm. Application of the code transformations according to the proposed order moves the main part of the memory accesses from the large background memories (lying possibly off-chip) to smaller ones (on-chip) or even to foreground storage. Data cache performance is improved as well. In this way the power consumption in the data memory hierarchy of the target processor and in the related interconnect, which forms a significant part of the total power budget of the system, is significantly reduced. Execution time and the power consumption due to instruction storage and transfers are reduced as well after the application of the proposed methodology. Experimental results from real-life applications prove the effectiveness of the proposed methodology.
Faster minimum weight subgraph algorithms (2006)

In this dissertation we consider combinatorial optimization problems. In particular, we concentrate on algorithms that find subgraphs of a given graph of minimum weight that have a certain specified structure. 
First, we consider the problem of finding a minimum weight 2-edge-connected spanning subgraph of a given 2-edge-connected graph. For this problem we provide a linear-time exact algorithm for weighted graphs of bounded treewidth, a linear-time PTAS for unweighted planar graphs, and a PTAS for weighted planar graphs. 
Furthermore, we design algorithms for the b-edge dominating set problem. We improve upon an existing 8/3-approximation for general weighted graphs, prove limitations of previously used methods, and give linear-time algorithms for this problem on trees.
Laser Folded Antenna (2018)

A new hands-free approach to antenna fabrication is presented here, with laser folding used to fabricate a prototype 94.5 GHz end-fed longitudinal shunt slot array (EFLSSA) antenna. Laser cutting and folding was demonstrated for creation of 3D metal antennas as a low cost, rapidly iterated alternative to machining techniques such as electro-discharge machining (EDM) and die forming. The technique used is based on a low cost and power 1064nm marking laser. All cutting and folding is done completely remotely using the laser itself from a blank sheet of metal foil. The demonstrated waveguide slots are cut to sub-micron precision, and modelling of the resulting structure is also presented.
Metallocene derivatives of early transition elements. Part 4. Synthesis and crystal structures of a series of zirconocene(IV) halides [Zr(η-C5H4SiMe3)2X2](X = Cl or Br) and [Zr{η-C5H3(SiMe3)2-1,3}2X2](XF, Br, or I) (1987)

A series of zirconocene(IV) halides, [Zr(η-C5H4SiMe3)2X2][X = Cl (1) or Br (2)] and [Zr{η-C5H3(SiMe3)2-1,3}2X2][X = F (3), Br (4), I (5), or Cl (6)], has been prepared, either by (i) substitutive procedures from ZrCl4[involving the following ligand exchanges: Cl–/C5H4SiMe3–, Cl–/C5H3(SiMe3)2–, Cl–/Br–, Cl–/l–, or Cl–/NMe2– followed by NMe2–/F–], or (ii), for complexes (3), (5), or (6), by oxidative addition to [Zr{η-C5H3(SiMe3)2-1,3}2(CO)2]. The only νasym(ZrX2) vibration to be assigned with confidence is for X = F at 563 cm–1; 1H and 13C n.m.r. data are unexceptional. X-Ray structure determinations of complexes (1)–(5) have been carried out. Their molecular symmetry is close to 2, or crystallographically imposed 2 in (3), with the stereochemistry about the metal centre best described as distorted tetrahedral. The angle X–Zr–X is 93.70(7), 94.2(1), 100.5(3), 100.25(5), and 100.37(4)° for the halides (1)–(5), respectively; and the corresponding centroid–Zr–centroid angles are 129.1, 128.2, 131.4, 131.4, and 131.8°. Metal–halogen distances in (1)[2.505(2) and 2.476(2)Å] and (3)[2.212(6]Å are significantly longer than in the parent zirconocene(IV) halides [Zr(η-C5H5)2X2](cf. 2.44 Å for X = Cl and 1.98 Å for X = F) as are [by ca. 0.04 Å(average)] the metal–centroid distances in (3)–(5).