gebhart/patrepeval huggingface dataset:
Analysis of Underivatized Amino Acids and Their d/l-Enantiomers by Sheathless Capillary Electrophoresis/Electrospray Ionization-Mass Spectrometry (2003)

Capillary electrophoresis/electrospray ionization-mass spectrometry (CE/ESI-MS) was applied to the analysis of underivatized amino acids and the separation of their d/l-enantiomers. Under full-scan mode, all standard protein amino acids were separated and detected at low-femtomole levels using a 130-cm-long, 20-μm-i.d., 150-μm-o.d. underivatized fused-silica capillary with 1 M formic acid as the background electrolyte. The CE/ESI-MS technique was also applied to the separation of l-arginine from l-canavanine (a close analogue of arginine where the terminal methylene linked to the guanidine group of arginine is replaced by an oxygen atom) in a complex mixture containing all standard protein amino acids. The utility of CE/ESI-MS in the analysis of real-world samples was demonstrated by the identification of two metabolic diseases (PKU and tyrosinemia) through blood analysis with minimal sample preparation. In addition, the on-line separation of 11 underivatized l-amino acids from their d-enantiomers was achieved by using a 30 mM solution of (+)-(18-crown-6)-2,3,11,12-tetracarboxylic acid as the background electrolyte.
Microscope-Integrated Intraoperative Ultrahigh-Speed Swept-Source Optical Coherence Tomography for Widefield Retinal and Anterior Segment Imaging (2018)

BACKGROUND AND OBJECTIVE: To demonstrate the feasibility of retinal and anterior segment intraoperative widefield imaging using an ultrahigh-speed, swept-source optical coherence tomography (SS-OCT) surgical microscope attachment. PATIENTS AND METHODS: A prototype post-objective SS-OCT using a 1,050-nm wavelength, 400 kHz A-scan rate, vertical cavity surface-emitting laser (VCSEL) light source was integrated to a commercial ophthalmic surgical microscope after the objective. Each widefield OCT data set was acquired in 3 seconds (1,000 × 1,000 A-scans, 12 × 12 mm² for retina and 10 × 10 mm² for anterior segment). RESULTS: Intraoperative SS-OCT was performed in 20 eyes of 20 patients. In six of seven membrane peels and five of seven rhegmatogenous retinal detachment repair surgeries, widefield retinal imaging enabled evaluation pre- and post-operatively. In all seven cataract cases, anterior imaging evaluated the integrity of the posterior lens capsule. CONCLUSIONS: Ultrahigh-speed SS-OCT enables widefield intraoperative viewing in the posterior and anterior eye. Widefield imaging visualizes ocular structures and pathology without requiring OCT realignment.
Solution-Grown Rubrene Crystals as Radiation Detecting Devices (2017)

There has been increased interest in organic semiconductors over the last decade because of their unique properties. Of these, 5, 6, 11, 12-tetraphenylnaphthacene (rubrene) has generated the most interest because of its high charge carrier mobility. In this work, large single crystals with a volume of ~1 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> were grown from solution by a temperature reduction technique. The faceted crystals had flat surfaces and cm-scale, visually defect-free areas suitable for physical characterization. X-ray diffraction analysis indicates that solvent does not incorporate into the crystals and photoluminescence spectra are consistent with pristine, high-crystallinity rubrene. Furthermore, the response curve to pulsed optical illumination indicates that the solution grown crystals are of similar quality to those grown by physical vapor transport, albeit larger. The good quality of these crystals in combination with the improvement of electrical contacts by application of conductive polymer on the graphite electrodes have led to the clear observation of alpha particles with these rubrene detectors. Preliminary results with a <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">252</sup> Cf source generate a small signal with the rubrene detector and may demonstrate that rubrene can also be used for detecting high-energy neutrons.
Numerical modelling and image reconstruction in diffuse optical tomography (2009)

The development of diffuse optical tomography as a functional imaging modality has relied largely on the use of model-based image reconstruction. The recovery of optical parameters from boundary measurements of light propagation within tissue is inherently a difficult one, because the problem is nonlinear, ill-posed and ill-conditioned. Additionally, although the measured near-infrared signals of light transmission through tissue provide high imaging contrast, the reconstructed images suffer from poor spatial resolution due to the diffuse propagation of light in biological tissue. The application of model-based image reconstruction is reviewed in this paper, together with a numerical modelling approach to light propagation in tissue as well as generalized image reconstruction using boundary data. A comprehensive review and details of the basis for using spatial and structural prior information are also discussed, whereby the use of spectral and dual-modality systems can improve contrast and spatial resolution.
Efficient document rendering with enhanced run length encoding (2006)

Document imaging and transmission systems (typically MFPs) require both effective and efficient image rendering methods that support standard data formats for a variety of document types, and allow for real time implementation. Since most conventional raster formats (e. g. TIFF, PDF, JPEG) are designed for use with either black and white text, or continuous-tone images, more specialized rendering methods are often required for representing mixed content documents. The baseline TIFF format supports a few binary compression options: PackBits, CCITT G3 and G4. Conventionally, halftoning algorithms, such as error diffusion, can be used to create a binary representation of a document image in the TIFF format. However, PackBits, CCITT G3 and G4 compression generally do not produce desired compression on halftone images. In this paper, we propose an efficient error diffusion algorithm optimized for PackBits compression. This method, which we refer to as POED (PackBits optimized error diffusion), is a form of threshold modulation error diffusion which takes advantage of the byte-oriented run length structure of PackBits compression by encouraging repetition of bytes in the resulting binary image. To maintain the sharpness of text, a binary segmentation algorithm is provided to switch off the adaptive error diffusion procedure and switch on the Floyd Steinberg error diffusion procedure in text regions. The POED method with PackBits compression yields higher compression ratios than the conventional error diffusion method, while maintaining desirable visual quality with low computational and memory requirements. We show experimental results to compare our method with the Floyd Steinberg error diffusion method.
Jalangi: a selective record-replay and dynamic analysis framework for JavaScript (2013)

JavaScript is widely used for writing client-side web applications and is getting increasingly popular for writing mobile applications. However, unlike C, C++, and Java, there are not that many tools available for analysis and testing of JavaScript applications. In this paper, we present a simple yet powerful framework, called Jalangi, for writing heavy-weight dynamic analyses. Our framework incorporates two key techniques: 1) selective record-replay, a technique which enables to record and to faithfully replay a user-selected part of the program, and 2) shadow values and shadow execution, which enables easy implementation of heavy-weight dynamic analyses. Our implementation makes no special assumption about JavaScript, which makes it applicable to real-world JavaScript programs running on multiple platforms. We have implemented concolic testing, an analysis to track origins of nulls and undefined, a simple form of taint analysis, an analysis to detect likely type inconsistencies, and an object allocation profiler in Jalangi. Our evaluation of Jalangi on the SunSpider benchmark suite and on five web applications shows that Jalangi has an average slowdown of 26X during recording and 30X slowdown during replay and analysis. The slowdowns are comparable with slowdowns reported for similar tools, such as PIN and Valgrind for x86 binaries. We believe that the techniques proposed in this paper are applicable to other dynamic languages.
The Consideration of Different Aspects of Design of Eccentric Bracing Frames (EBF) according to AISC-Seismic Provisions (2006)

IMAC
A 38.6-fJ/Conv.-Step Inverter-Based Continuous-Time Bandpass ΔΣ ADC in 28 nm Using Asynchronous SAR Quantizer (2021)

We propose a self-biased inverter-based amplifier for realizing a high-speed low-power second-order single-loop continuous-time bandpass delta-sigma modulator (CT-BP- ΔΣM). The design is amenable to nanoscale CMOS and exploits a single self-biased pseudo-differential inverter with a positive feedback to replace conventional op-amps used in an integrator configuration. The modulator also uses a 5-bit asynchronous successive approximation register (ASAR) quantizer. With a 30 MHz bandwidth at 400 MS/s sampling rate and 100 MHz intermediate frequency (IF), the modulator achieves 61 dB dynamic range (DR) and 58 dB SNDR while consuming 2.5 mW from a 1V supply. The core area in 28 nm LP CMOS is 0.04 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . A 38.6 fJ/conv.-step figure of merit is achieved.
Figures S1-S10 from HER2-Overexpressing Breast Cancers Amplify FGFR Signaling upon Acquisition of Resistance to Dual Therapeutic Blockade of HER2 (2023)

&lt;p&gt;'Fig. S1. LTR tumors maintain resistance following serial transplantation. Fig. S2. Expression of ABC transporters is not altered in LTR tumors. Fig. S3. LTR tumor-derived cell lines are sensitive to high concentrations of lapatinib + trastuzumab in vitro. Fig. S4. Identification of FGF3/4/19 amplification in an LTR tumor. Fig. S5. The combination of FGFR1 and HER2 inhibitors induces apoptosis in 11q13-amplified HER2+ cell lines. Fig. S6. Treatment with lucitanib reverses alterations in tumor microenvironment in LTR xenografts. Fig. S7. The FGFR1 inhibitor AZD4547 reverses resistance to L+T. Fig. S8. Amplification of FGF pathway genes co-occurs with ERBB2 amplification in a subset of human breast cancers. Fig. S9. CONSORT Diagram for the FinHer trial. Fig. S10. Flow diagram for samples from the NeoALTTO trial.'&lt;/p&gt;
Straight-Line Dual-Polarization PSK Transmitter with Polarization Differential Modulation (2020)

Coherent transceivers are now regarded as promising candidates for upgrading the current 400Gigabit Ethernet (400GbE) transceivers to 800G. However, due to the complicated structure of a dual-polarization IQ modulator (DP-IQM) with its bulky polarization-beam splitter/comber (PBS/PBC), the increase in the transmitter size and cost is inevitable. In this paper, we propose a compact PBS/PBC-free transmitter structure with a straight-line configuration. By using the concept of polarization differential modulation, the proposed transmitter is capable of generating a DP phase-shift-keyed (DP-PSK) signal, which makes it directly applicable to the current coherent systems. A detailed analysis of the system performance reveals that the imperfect equalization and the bandwidth limitation at the receiver are the dominant penalty factors. Although such a penalty is usually unacceptable in long-haul applications, the proposed transmitter can be attractive due to its significant simplicity and compactness for short-reach applications, where the cost and the footprint are the primary concerns.
Supplementary Figure 2 from Autotaxin and LPA<sub>1</sub> and LPA<sub>5</sub> Receptors Exert Disparate Functions in Tumor Cells versus the Host Tissue Microenvironment in Melanoma Invasion and Metastasis (2023)

&lt;p&gt;Supplementary Figure 2. LPA1-5 receptor profiling in whole lung tissue isolated from WT, LPA1-, LPA2- and LPA5KO mice, respectively using quantitative real-time PCR. Data are expressed as mean {plus minus} SEM (n = 3 mice).&lt;/p&gt;
The Amyloid-Reactive Monoclonal Anitbody 11-1F4 Binds a Cryptic Epitope on Fibrils and Partially Denatured Immunoglobulin Light Chains and Inhibits Fibrillogenesis (2004)

We have previously reported [1] that a murine mAb, designated 11-1F4, prepared against a human Vκ4 fibrils (LEN), reacted specifically with AL amyloid, regardless of the VL subgroup of the protein. In order to determine the molecular bases of this interaction, we have utilized a europium-linked immunoabsorbent assay (EuLISA) to measure the interaction of mAb 11-1F4 with light chain-related proteins. These studies show that this antibody does not recognize native κ and λ chains but, rather, binds with nanomolar affinity to proteins that have been partially denatured, i.e., when coated onto plastic wells used in the assay. EuLISA of peptides derived from proteolytic cleavage of the Vκ4 immunogen revealed that the cryptic epitope was located in a region encompassing the first 59 amino acids. Through epitope mapping of synthetic peptides, this site was placed more precisely within the first (N-terminal) 22 residues that comprise the first framework region (FRI) of Ig light chains, and especially involves those located between positions 1 and 4. Additionally, our finding that mAb11-1F4 inhibited at sub-equimolar concentrations de novo Vl fibrillogenesis suggests that interaction of this antibody with a partially unfolded amyloidogenic intermediate may act to stabilize the molecule and/or sterically inhibit fibril formation. The discovery that mAb 11-1F4 can prevent fibrillogenesis, as well as accelerate amyloidolysis, has provided new information on its immunoreactivity and therapeutic potential for patients with primary (AL) amyloidosis.
Abstract 1541: Secondary mutations in ALK and resistance to ALK kinase inhibitors (2011)

Abstract Background: The anaplastic lymphoma kinase (ALK) inhibitor crizotinib is clinically effective in cancer patients whose tumors harbor ALK translocations. However, drug resistance will ultimately develop in most if not all patients. We studied drug resistance mechanisms using both in vitro models and analyses from tumors of patients that had developed crizotinib resistance. Methods and Results: We identified a secondary mutation in ALK, F1174L, as one cause of crizotinib resistance in a patient with an inflammatory myofibroblastic tumor (IMT) harbouring a RANBP2-ALK translocation who progressed while crizotinib therapy. When present in cis with an ALK translocation, this mutation (also detected in neuroblastomas) causes an increase in ALK phosphorylation, cell growth and downstream signaling. Furthermore, the F1174L mutation inhibits crizotinib mediated downregulation of ALK signaling and blocks apoptosis in RANBP2-ALK Ba/F3 cells. We also evaluated the impact of mutations in the ALK gatekeeper residue (L1196) and engineered all possible gatekeeper mutations resulting from a single nucleotide change into the background of EML4-ALK. Three of the mutations (L1196M, L1196Q and L1196V) in the background of EML4-ALK led to IL-3 independent growth. Furthermore the EML4-ALK L1196M mutant resulted in a greater baseline ALK phosphorylation, cell growth and downstream signaling compared to EML4-ALK alone. A chemically distinct ALK inhibitor, TAE684, or the HSP90 inhibitor 17-AAG are both effective in models harbouring the F1174L or the L1196M ALK mutations. Conclusions: We identify secondary mutations in ALK that confer crizotinib resistance. In addition, we identify therapeutic strategies, alternative ALK inhibitors or HSP90 inhibitors that may be clinically effective in patients that have developed crizotinib resistance. Understanding the mechanistic basis of drug resistance is necessary in order to develop effective clinical treatments for patients with ALK-translocated cancers. 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 1541. doi:10.1158/1538-7445.AM2011-1541
DeepVideoMVS: Multi-View Stereo on Video with Recurrent Spatio-Temporal\n Fusion (2020)

We propose an online multi-view depth prediction approach on posed video\nstreams, where the scene geometry information computed in the previous time\nsteps is propagated to the current time step in an efficient and geometrically\nplausible way. The backbone of our approach is a real-time capable, lightweight\nencoder-decoder that relies on cost volumes computed from pairs of images. We\nextend it by placing a ConvLSTM cell at the bottleneck layer, which compresses\nan arbitrary amount of past information in its states. The novelty lies in\npropagating the hidden state of the cell by accounting for the viewpoint\nchanges between time steps. At a given time step, we warp the previous hidden\nstate into the current camera plane using the previous depth prediction. Our\nextension brings only a small overhead of computation time and memory\nconsumption, while improving the depth predictions significantly. As a result,\nwe outperform the existing state-of-the-art multi-view stereo methods on most\nof the evaluated metrics in hundreds of indoor scenes while maintaining a\nreal-time performance. Code available:\nhttps://github.com/ardaduz/deep-video-mvs\n
Heterocycle-Activated Aromatic Nucleophilic Substitution of AB2 Poly(aryl ether phenylquinoxaline) Monomers. 3 (1996)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTHeterocycle-Activated Aromatic Nucleophilic Substitution of AB2 Poly(aryl ether phenylquinoxaline) Monomers. 3S. Srinivasan, R. Twieg, J. L. Hedrick, and C. J. HawkerView Author Information IBM Research Division, Almaden Research Center, 650 Harry Road, San Jose, California 95120-6099Cite this: Macromolecules 1996, 29, 26, 8543–8545Publication Date (Web):December 16, 1996Publication History Received1 July 1996Revised16 September 1996Published online16 December 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ma960939yhttps://doi.org/10.1021/ma960939ybrief-reportACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views400Altmetric-Citations41LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Ethers,Monomers,Polymerization,Polymers,Solvents Get e-Alerts
Data Parallel Multi‐GPU Path Tracing using Ray Queue Cycling (2023)

Abstract We propose a novel approach to data‐parallel path tracing on single‐node/multi‐GPU hardware that builds on ray forwarding, but which aims—above all else—at generality and practicability. We do this by avoiding any attempts at reducing the number of traces or forward operations performed, and instead focus on always using all GPUs' aggregate compute and bandwidth to effectively trace each ray on every GPU. We show that—counter‐intuitively—this is both feasible and desirable; and that when run on typical data‐center/cloud hardware, the resulting framework not only achieves good performance and scalability, but also comes with significantly fewer limitations, assumptions, or preprocessing requirements than existing techniques.
Modeling the Effectiveness of Diverters for Matrix Acidizing Based on Filter Cake Characteristics (2018)

Abstract During acidizing treatments in carbonate reservoirs, a degradable diversion system (DDS) is commonly applied to achieve a more uniform distribution of acid along the wellbore. The effectiveness of a DDS strongly depends on the permeability of the filter cake, which is formed by diverter materials that accumulate inside perforation tunnels or on the rock face. A new DDS with a lower filter cake permeability than a conventional DDS is presented, along with a study based on an acidizing model to show the effect of fiber cake permeability on acid diversion. An existing acidizing model was applied as a tool to evaluate the diversion effect of a DDS. The model was created by considering fluid flow in the wellbore, fluid distribution among reservoir zones, and predicted wormhole propagation inside the formation. The model also has the capability to simulate the formation of filter cake, either inside perforation tunnels or on the rock face, and redistribute the fluid flow accordingly. To fully understand the role of filter cake permeability on the effectiveness of a DDS, simulation cases were established for both a conventional DDS and the newly-introduced, low permeability DDS. The reservoir permeability contrasts among zones was also varied to understand the applicable range of a given DDS. The DDS effectiveness can be evaluated by comparing the simulated bottomhole pressure response and the acid injection rate into each zone. The simulation results indicate that the low permeability DDS is significantly more effective than the traditional DDS. In all cases, the use of the low permeability DDS predicts a larger pressure response resulting from the temporary blocking of high permeability zones as well as better acid injectivity in low permeability zones. Based on the flow rate distribution, the effect of filter cake permeability is clearly observed up to a permeability contrast of 50 between reservoir zones. By providing a better flow to low permeability reservoir zones, the new DDS demonstrates better diversion performance than the traditional DDS; this results in a more successful acidizing treatment, especially when the permeability contrast of the reservoir zones is high.
Systemic, Ocular and Genetic Risk Factors for Age-related Macular Degeneration and Polypoidal Choroidal Vasculopathy in Singaporeans (2017)

To examine the association of systemic, ocular and genetic risk factors in neovascular age-related macular degeneration (nAMD) in a large cohort of Asian patients, and to further compare risk factors between those with typical AMD and polypoidal choroidal vasculoapthy (PCV) subtypes. We recruited 456 cases and 1,824 controls matched for age, gender and ethnicity. Data on systemic and ocular risk factors were collected on questionnaires. In a subgroup of subjects, we included genetic data on four AMD-associated single nucleotide polymorphisms (SNPs). Risk factors for nAMD and subtypes were analyzed. Systemic risk factors for nAMD included older age, male gender, higher BMI and higher HDL-cholesterol. Ocular risk factors included pseudophakic and shorter axial length. Risk factors common to both typical AMD and PCV subtypes included age, BMI and HDL-cholesterol. Shorter axial length was only associated with PCV, while male gender and pseudophakia were only associated with typical AMD. In the subgroup with genotype data, ARMS2 rs10490924 and CFH rs800292 were associated with nAMD. None of the risk factors were significantly different between PCV and typical AMD. Systemic, ocular and genetic risk factors were largely similar for typical AMD and PCV subtypes in this Asian population based in Singapore.