gebhart/patrepeval huggingface dataset:
Capturing True Workload Dependency of BTI-induced Degradation in CPU Components (2016)

Atomistic-based approaches accurately model Bias Temperature Instability phenomena, but they suffer from prolonged execution times, preventing their seamless integration in system-level analysis flows. In this paper we present a comprehensive flow that combines the accuracy of Capture Emission Time (CET) maps with the efficiency of the Compact Digital Waveform (CDW) representation. That way, we capture the true workload-dependent BTI-induced degradation of selected CPU components. First, we show that existing works that assume constant stress patterns fail to account for workload dependency leading to fundamental estimation errors. Second, we evaluate the impact of different real workloads on selected CPU sub-blocks from a commercial processor design. To the best of our knowledge, this is the first work that combines atomistic property and true workload-dependency for variability analysis.
Multimodality optical coherence tomography based tethered capsule endomicroscopy for upper gastrointestinal tract imaging (2021)

We introduce two multimodal extensions of our optical coherence tomography (OCT) based tethered capsule endomicroscopy (TCE) platform, tailored towards an enhanced clinical applicability for upper gastrointestinal tract imaging. The first extension presented – white light (RGB)-OCT-based TCE – provides both, true-color visualization of the tissue surface and depth-resolved sub-surface OCT imaging, co-registered in time and space. The second extension presented – fluorescence (FL)-OCT-based TCE – enables the addition of tissue specific molecular contrast. We present compact, modular, easily portable, plug-and-play system designs for both extensions, as well as imaging results in swine esophagus, in vivo.
Chromosome 15 trisomy in spontaneous and carcinogen‐induced murine lymphomas of B‐cell origin (1981)

G-banding analyses of 14 independently derived B-cell lymphomas showed the frequent occurrence of chromosome 15 trisomy. It was present in seven of nine spontaneous B-cell lymphomas, but in company with other trisomies, monosomies and marker chromosomes. In five carcinogen-induced primary B-cell leukemias, trisomy 15 was the dominating change. Taken together with the previously demonstrated importance of chromosome 15 trisomy for T-cell leukemogenesis and of the 12;15 translocation in plasmacytogenesis in the mouse, it appears likely that the distal part of chromosome 15 carries a cluster of genes, perhaps a supergene region, that may play an important role in the differentiation and/or the normal responsiveness of various lymphoreticular cell types to growth control.
Vibration-Induced Loosening Performance of Preloaded Threaded Fasteners (2010)

In an effort to establish a theoretical outline of a criterion for preventing the vibration-induced loosening of preloaded threaded fasteners, this paper provides an experimental and analytical insight into the effect of the initial bolt preload and the excitation amplitude on the self loosening performance of cap screw fastener. A nonlinear model is used for predicting the clamp load loss caused by the vibration-induced loosening of cap screw fasteners under cyclic transverse loading. Experimental verification was conducted on the twisting torque variation and the effect of the preload level and transverse displacement amplitude. Comparison of the experimental and analytical results on the clamp load loss with the number of cycles verifies that the proposed model accurately predicts self-loosening performance.
Abstract 5248: Quantum dot multiplexing of prognostic marker and stem cell marker expression in colorectal cancer circulating tumor cells (2011)

Abstract Circulating tumor cells (CTCs) reflect disease burden in metastatic colorectal cancer (mCRC) and show reduced numbers in patients who are responding to chemotherapy. Current analysis is limited to counting CTCs and little additional marker analysis. We sought to develop methodology to allow multiplexing of marker detection in individual CTCs to assess tumor cell heterogeneity and to gain insight into relationships of prognostic and therapy response markers. This ongoing study is evaluating expression of up to 8 markers in a single CTC by a multispectral multiplex imaging technique using nano-particle type quantum dot (Q-Dot) dyes. We hypothesize that CTCs that are extremely rare (∼ 1 in 10 million RBCs) in the blood of cancer patients play an important role in metastasis. In view of the small number of such cells in the blood of mCRC patients (prognostication based on &amp;lt;3 versus &amp;gt;3 CTCs/7.5 ml of blood) there is a need to derive more molecular correlations from single CTCs. We designed a clinical protocol to collect blood from mCRC patients receiving chemotherapy with the intent to evaluate multiplexed molecular marker expression in CTCs in responders versus non-responders using the FDA-approved Veridex CellSearch technology. We are evaluating CD26, CD133, EGFR, Ki 67, p27, c-Myc, ALDH1, Bcl-Xl, Mcl-1, phosho-Akt, phospho-ERK, TRAIL receptors, IAPs, and p53 using antibodies conjugated to different Q-Dots. Ongoing studies include prognostic marker, stem cell marker, and cell proliferation/death response marker analysis in human tumor xenografts of HCT116, p53-null HCT116, DLD1, SW620, and SW480. Initial profiling of tumor cell lines revealed that mutant p53 and KRAS-expressing SW620 derived from a patient with mCRC has CD26 and CD133 expression including a sub-population of tumor cells that co-express these two stem cell markers. HCT116 showed positive EGFR, CD26, but little or no CD133 expression. We are evaluating correlations between the primary tumors in mice as compared to the CTCs in mice and similar experiments are part of the clinical protocol. The studies should unravel the complexity of CTC heterogeneity, and define informative subsets of markers that can be routinely included in studies to assess prognosis and response to therapy. The ease with which CTCs can be isolated makes these studies of comparisons with primary tumors critical in order to establish and validate new methods for assessing tumor behavior and response to therapy in the clinic through this CTC “liquid biopsy” technique. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5248. doi:10.1158/1538-7445.AM2011-5248
Supplementary Figure 2 from An Oncogenic Role for <i>ETV1</i> in Melanoma (2023)

Supplementary Figure 2 from An Oncogenic Role for &lt;i&gt;ETV1&lt;/i&gt; in Melanoma
Simple and efficient GPU accelerated topology optimisation: Codes and applications (2023)

This work presents topology optimisation implementations for linear elastic compliance minimisation in three dimensions, accelerated using Graphics Processing Units (GPUs). Three different open-source implementations are presented for linear problems. Two implementations use GPU acceleration, based on either OpenMP 4.5 or the Futhark language to implement the hardware acceleration. Both GPU implementations are based on high level GPU frameworks, and hence, avoid the need for expertise knowledge of e.g. CUDA or OpenCL. The third implementation is a vectorised and multi-threaded CPU code, which is included for reference purposes. It is shown that both GPU accelerated codes are able to solve large-scale topology optimisation problems with 65.5 million elements in approximately 2 h using a single GPU, while the reference implementation takes approximately 3 h and 10 min using 48 CPU cores. Furthermore, it is shown that it is possible to solve nonlinear topology optimisation problems using GPU acceleration, demonstrated by a nonlinear end-compliance optimisation with finite strains and a Neo-Hookean material model discretised by 1 million elements.
An automatic decision threshold control circuit for WDM-PON based on the wavelength-locked F-P LDs (2008)

We propose and demonstrate a simple decision threshold control circuit. By employing this method, we demonstrate a feasibility of WDM-PON at 1.25 Gb/s per channel with 100 GHz spacing based on the wavelength-locked F-P LDs.
All-Optical, Photonic Band Gap Modulation in Azobenzene Liquid Crystal Doped Cholesterics (Preprint) (2006)

Cholesteric liquid crystals doped with high clearing temperature azobenzene liquid crystals are shown to possess large, fast, and reversible dynamic photosensitive features. Selective wavelengths shifts approaching 400 nm are reported and depending on the host cholesteric liquid crystal, both red-shifted and blue-shifted wavelength changes can be induced. The photoinduced states of these material systems are shown to be stable for long periods of time upon removal of the radiation source, completely reversible, and dynamically fast. These phototunable features were demonstrated using both CW and nanosecond laser beams. The latter was used to change the selective reflection wavelength from blue to green with a single nanosecond pulse and the ability to write information into these films using these processes were demonstrated.
Amyloid-type Protein Aggregation and Prion-like Properties of Amyloids (2021)

This review will focus on the process of amyloid-type protein aggregation. Amyloid fibrils are an important hallmark of protein misfolding diseases and therefore have been investigated for decades. Only recently, however, atomic or near-atomic resolution structures have been elucidated from various in vitro and ex vivo obtained fibrils. In parallel, the process of fibril formation has been studied in vitro under highly artificial but comparatively reproducible conditions. The review starts with a summary of what is known and speculated from artificial in vitro amyloid-type protein aggregation experiments. A partially hypothetic fibril selection model will be described that may be suitable to explain why amyloid fibrils look the way they do, in particular, why at least all so far reported high resolution cryo-electron microscopy obtained fibril structures are in register, parallel, cross-β-sheet fibrils that mostly consist of two protofilaments twisted around each other. An intrinsic feature of the model is the prion-like nature of all amyloid assemblies. Transferring the model from the in vitro point of view to the in vivo situation is not straightforward, highly hypothetic, and leaves many open questions that need to be addressed in the future.
Evidence for the Circulation and Inter-Hemispheric Movement of the H14 Subtype Influenza A Virus (2013)

Three H14 influenza A virus (IAV) isolates recovered in 2010 during routine virus surveillance along the Mississippi Migratory Bird Flyway in Wisconsin, U.S.A. raised questions about the natural history of these rare viruses. These were the first H14 IAV isolates recovered in the Western Hemisphere and the only H14 IAV isolates recovered since the original four isolates in 1982 in Asia. Full length genomic sequencing of the 2010 H14 isolates demonstrated the hemagglutinin (HA) gene from the 1982 and 2010 H14 isolates showed 89.6% nucleotide and 95.6% amino acid similarity and phylogenetic analysis of these viruses placed them with strong support within the H14 subtype lineage. The level of genomic divergence observed between the 1982 and 2010 viruses provides evidence that the H14 HA segment was circulating undetected in hosts and was not maintained in environmental stasis. Further, the evolutionary relationship observed between 1982 H14 and the closely related H4 subtype HA segments were similar to contemporary comparisons suggesting limited adaptive divergence between these sister subtypes. The nonstructural (NS) segment of one 2010 isolate was placed in a NS clade isolated infrequently over the last several decades that includes the NS segment from a previously reported 1982 H14 isolate indicating the existence of an unidentified pool of genomic diversity. An additional neuraminidase reassortment event indicated a recent inter-hemispheric gene flow from Asia into the center of North America. These results demonstrate temporal and spatial gaps in the understanding of IAV natural history. Additionally, the reassortment history of these viruses raises concern for the inter-continental spread of IAVs and the efficacy of current IAV surveillance efforts in detecting genomic diversity of viruses circulating in wild birds.
Abstract 3818: CTC profiling: Integration of biomarker analysis with current Veridex CellSearch technology (2011)

Abstract The presence and number of circulating tumor cells (CTCs) in the blood of cancer patients is predictive of clinical outcome. To date only the CellSearch system by Veridex has been FDA approved for use in breast, prostate and colon cancer (cc). However, a limited number of biomarkers are examined in the CellSearch system. In the case of colorectal cancer, cytokeratin (CK) and epithelial cell adhesion molecule (EpCAM) expression is used to identify cells as CTCs. Additional analysis of other biomarkers by Cheshire technology is provided as fee for service and only uses the current fluorescent channels utilized by the CellSearch Analyzer. Our aim is to greatly enhance the number of biomarkers that can be tested in an economic and efficient manner and integrating the analysis into the existing CellSearch isolation and analytic platform. We combined Nuance multispectral imaging with quantum dot technology to expand the biomarkers analysis. Quantum dots (QD) have the advantage that they can be excited in the UV wavelengths while emitting across the visible spectrum. Only DAPI in the original CellSearch panel of reagents is excited in this range and its emission does not overlap with the QDs. This allows us to visualize additional biomarkers without interfering with CellSearch CTC analysis. Antibodies against a panel of known biomarkers were labeled with quantum dots. Each antibody was verified by standard immunofluorescence in appropriate tissue culture lines before quantum dot labeling. Antibody labeling and titration was confirmed on tissue culture cell lines before adding it to the panel of CTC staining reagents. To model multiplexing assays, blood is spiked with a known number of cells from appropriate cancer cell lines. Following standard CTC isolation and enumeration, cells are retained in the MagNest and allowed to dry. Cells are then stained with our biomarker panel. Currently 8 quantum dots are commercially available for simultaneous analysis. Our panel of biomarkers is under revision, but includes phospho-AKT, Ki-67, CD26, CD133 and EGFR. We are expanding the panel to include markers for death pathway signaling including Mcl-1, Bcl-XL, Flip, TRAIL, and death receptors. Separate panels are also being developed for breast cancer. Additional panels can include markers for sensitivity to chemotherapeutic reagents (TS, DPD, PTHFR, GSTP1, ERCC1, ERCC2, UGT1A1, BRAF), cell proliferation, known tumor susceptibility genes or tumor markers (APC, p53, HER2, PSA, IGF1-R) or probes for specific signal transduction pathways (NFκB, Wnt). Analysis of samples from patients undergoing chemotherapy -/+ targeted therapy is underway to evaluate the status of the stem cell, prognostic markers and cell death determinants in individual CTCs as a function of time. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3818. doi:10.1158/1538-7445.AM2011-3818
Open systems (2012)

All of the examples in the previous two chapters were closed systems. The ultimate state of closed, chemically reacting systems is chemical equilibrium. Living systems are characterized by mass and energy flows across their boundaries that keep them away from equilibrium. We now discuss open systems, which allow molecules to enter and leave. Open systems ultimately reach a steady state that is often close to a homeostatic state of interest.
ChemInform Abstract: PHOTOCHEMISTRY OF AMINOKETONES. VIII. DIASTEREOSELECTIVE SYNTHESIS OF 3‐HYDROXYPROLINES (1985)

Abstract Die Photocyclisierung der N‐(2‐Benzoyl‐alkyl)‐glycinester (I) erfolgt in einem 80:20‐Gemisch von Cyclohexan und Benzol regio‐ und diastereoselektiv unter Bildung der Hydroxyprolin‐Derivate (II), während in Ether als Lösungsmittel neben geringeren (II)‐Ausb. kleinere bis beträchtliche Mengen von Cyclopropanolen (III) entstehen.
New Evidence for Precursor Species in the Formation of MFI Zeolite in the Tetrapropylammonium Hydroxide−Tetraethyl Orthosilicate−Water System (2002)

Tetraethyl orthosilicate was hydrolyzed and polymerized in concentrated aqueous tetrapropylammonium (TPA) hydroxide solution at 0 and 10 °C and room temperature. The formation of silicate oligomers involved in the TPA-mediated self-assembly process of colloidal Silicalite-1 was investigated using 29Si NMR. A pentacyclic dodecamer with four edge-sharing five-rings on a four-ring was detected as a new intermediate in the formation of Silicalite-1 zeolite. The formation of this pentacyclic dodecamer with a curved inner hydrophobic silicon dioxide surface is a new example of the structure-directing action of TPA. The temperature was found to be a key parameter with respect to the transformation of the intermediates with 11 and 12 Si atoms. At 0 and 10 °C, the tetracyclic undecamer having three five-rings on a four-ring was converted into the pentacyclic dodecamer by insertion of one additional silicate unit. At these low temperatures, it slowly underwent an intramolecular condensation and formation of capped double five-ring not leading to Silicalite-1 formation. At room temperature, three pentacyclic dodecamers rapidly condensed into the Silicalite-1 precursor. The involvement of the pentacyclic dodecamer in the self-assembly process offers an explanation for the absence of systematically missing T-sites in colloidal Silicalite-1.
Fast and efficient search for MPEG-4 video using adjacent pixel intensity difference quantization histogram feature (2010)

In this paper, a fast search algorithm for MPEG-4 video clips from video database is proposed. An adjacent pixel intensity difference quantization (APIDQ) histogram is utilized as the feature vector of VOP (video object plane), which had been reliably applied to human face recognition previously. Instead of fully decompressed video sequence, partially decoded data, namely DC sequence of the video object are extracted from the video sequence. Combined with active search, a temporal pruning algorithm, fast and robust video search can be realized. The proposed search algorithm has been evaluated by total 15 hours of video contained of TV programs such as drama, talk, news, etc. to search for given 200 MPEG-4 video clips which each length is 15 seconds. Experimental results show the proposed algorithm can detect the similar video clip in merely 80ms, and Equal Error Rate (ERR) of 2 % in drama and news categories are achieved, which are more accurately and robust than conventional fast video search algorithm.
Sensitivity Study of Fuel Cost in Extended Burnup BWR Core (1984)

A sensitivity study on the fuel cost of an extended burnup BWR core has been carried out on the basis of a realistic model of discharge burnup extension. Full power operating length in months in a refueling cycle and the number of refueling batches are chosen as independent variables in the model to describe extended burnup cores of various types. The reference core for the sensitivity study adopts 9-month full power operation and 4-batch refueling scheme. The difference in the plant cost between the extended burnup core and the reference core, which is referred to as plant capacity factor (PCF) credit, is estimated and combined with the fuel cost to calculate the fuel cost with PCF credit. The results show that the fuel cost with PCF credit decreases for the extended burnup core with stretched operating length as the burnup extends in cases of constant non-operating length in a cycle, and that it may increase for the extended burnup core with decreased batch number in cases of constant plant capacity factor. It is also suggested that the cost minimum combination of the independent variables can be found to a given discharge burnup for the extended burnup core with decreased batch number in an intermediate case between these two extreme cases. Extended burnup cores with fixed batch number tend to have a lower natural uranium requirement, but larger separative work requirement. The economic break-even condition for the extended burnup core with decreased batch number is discussed based on the fraction of fixed part in the non-operating length, which is insensitive to the cycle length stretch-out.
O riso no Realismo português (2017)

In diesem Beitrag legen wir die Ansicht zugrunde, dass die substantiell bedeutendste kritische Auseinandersetzung mit dem Lachen und der Satire in der portugiesischen Literatur in den Texten von Eça de Queirós und Ramalho Ortigão zu finden ist (die auch satirische Texte in fiktionaler und journalistischer Prosa verfasst haben). Aus ihren Schriften lässt sich eine Poetik ableiten, die eher didaktisch als normativ orientiert ist, ähnlich einer Abhandlung zur Soziologie der portugiesischen Satire für ein großes Publikum. Eça und Ramalho Ortigão zufolge muss sich die Satire an universellen Vorbildern von Rabelais bis Boileau orientieren. Bei der Suche nach den Gesetzmäßigkeiten einer ethisch begründeten Satire und bei ihren Bemühungen zu ihrer Verbreitung erkannten sie jedoch auch die Gefahren, die den Übertreibungen der Satiriker innewohnen. Sie verwiesen dabei in hellsichtiger Weise sowohl auf die satirischen Eigenschaften der Erhebung und Sublimation, als auch auf die der Satire als Fluch.
Molecular determinants of μ-conotoxin KIIIA interaction with the human voltage-gated sodium channel NaV1.7 (2023)

The voltage-gated sodium (Na<sub>V</sub>) channel subtype Na<sub>V</sub>1.7 plays a critical role in pain signaling, making it an important drug target. Here we studied the molecular interactions between μ-Conotoxin KIIIA (KIIIA) and the human Na<sub>V</sub>1.7 channel (hNa<sub>V</sub>1.7). We developed a structural model of hNa<sub>V</sub>1.7 using Rosetta computational modeling and performed <i>in silico</i> docking of KIIIA using RosettaDock to predict residues forming specific pairwise contacts between KIIIA and hNa<sub>V</sub>1.7. We experimentally validated these contacts using mutant cycle analysis. Comparison between our KIIIA-hNa<sub>V</sub>1.7 model and the cryo-EM structure of KIIIA-hNa<sub>V</sub>1.2 revealed key similarities and differences between Na<sub>V</sub> channel subtypes with potential implications for the molecular mechanism of toxin block. The accuracy of our integrative approach, combining structural data with computational modeling, experimental validation, and molecular dynamics simulations, suggests that Rosetta structural predictions will be useful for rational design of novel biologics targeting specific Na<sub>V</sub> channels.
Synthesis and complete NMR characterization of methacrylateendcapped poly(ortho-esters) (2007)

Abstract In this paper a synthesis method for low molecular weight poly(orthoesters) with photo crosslinkable methacrylate endgroups is presented. Using this procedure, the molecular weight could be controlled and the desired endgroup functionality was introduced in a single reaction step. The detailed characterization of the molecular structure of bismethacrylate endcapped poly(ortho-esters) using NMR affords a re-evaluation of previous assignments reported for similar poly(ortho-ester) polymers. In addition, the use of diffusion filtered 1D 1 H NMR spectroscopy as a simple but effective analysis tool that allows to distinguish resonance contributions from impurities and low molecular weight compounds, most probably the result of degradation, from those of the full size polymer, is demonstrated.