gebhart/patrepeval huggingface dataset:
Cross-talk performance comparison among different OXC architectures (2002)

Crosstalk performance of different OXC architectures are compared through simulations and preliminary experiments. We show that a careful OXC design can remove limitation due to imperfect switch (in experimentation a thermo-optical element) operation.
Isolation of cross-reactive monoclonal antibodies against divergent human coronaviruses that delineate a conserved and vulnerable site on the spike protein (2020)

Abstract The coronavirus spike glycoprotein, located on the virion surface, is the key mediator of cell entry. As such, it is an attractive target for the development of protective antibodies and vaccines. Here we describe two human monoclonal antibodies, 1.6C7 and 28D9, that display a remarkable cross-reactivity against distinct species from three Betacoronavirus subgenera, capable of binding the spike proteins of SARS-CoV and SARS-CoV-2, MERS-CoV and the endemic human coronavirus HCoV-OC43. Both antibodies, derived from immunized transgenic mice carrying a human immunoglobulin repertoire, blocked MERS-CoV infection in cells, whereas 28D9 also showed weak cross-neutralizing potential against HCoV-OC43, SARS-CoV and SARS-CoV-2 in a neutralization-sensitive virus pseudotyping system, but not against authentic virus. Both cross-reactive monoclonal antibodies were found to target the stem helix in the spike protein S2 fusion subunit which, in the prefusion conformation of trimeric spike, forms a surface exposed membrane-proximal helical bundle, that is antibody-accessible. We demonstrate that administration of these antibodies in mice protects from a lethal MERS-CoV challenge in both prophylactic and/or therapeutic models. Collectively, these antibodies delineate a conserved, immunogenic and vulnerabe site on the spike protein which spurs the development of broad-range diagnostic, preventive and therapeutic measures against coronaviruses.
Atom Probe Tomography of III-Nitrides Based Semiconducting Devices (2013)

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.
The cryo-EM structure of the SF3b spliceosome complex bound to a splicing modulator reveals a pre-mRNA substrate competitive mechanism of action (2018)

Somatic mutations in spliceosome proteins lead to dysregulated RNA splicing and are observed in a variety of cancers. These genetic aberrations may offer a potential intervention point for targeted therapeutics. SF3B1, part of the U2 small nuclear RNP (snRNP), is targeted by splicing modulators, including E7107, the first to enter clinical trials, and, more recently, H3B-8800. Modulating splicing represents a first-in-class opportunity in drug discovery, and elucidating the structural basis for the mode of action opens up new possibilities for structure-based drug design. Here, we present the cryogenic electron microscopy (cryo-EM) structure of the SF3b subcomplex (SF3B1, SF3B3, PHF5A, and SF3B5) bound to E7107 at 3.95 Å. This structure shows that E7107 binds in the branch point adenosine-binding pocket, forming close contacts with key residues that confer resistance upon mutation: SF3B1<sup>R1074H</sup> and PHF5A<sup>Y36C</sup> The structure suggests a model in which splicing modulators interfere with branch point adenosine recognition and supports a substrate competitive mechanism of action (MOA). Using several related chemical probes, we validate the pose of the compound and support their substrate competitive MOA by comparing their activity against both strong and weak pre-mRNA substrates. Finally, we present functional data and structure-activity relationship (SAR) on the PHF5A<sup>R38C</sup> mutation that sensitizes cells to some chemical probes but not others. Developing small molecule splicing modulators represents a promising therapeutic approach for a variety of diseases, and this work provides a significant step in enabling structure-based drug design for these elaborate natural products. Importantly, this work also demonstrates that the utilization of cryo-EM in drug discovery is coming of age.
Fieser's Reagents for Organic Synthesis, Volume 18 By Tse-Lok Ho (National Chiao Tung University). John Wiley & Sons, Inc.:  New York. 1999. xii + 504 pp. $79.95. ISBN 0-471-24477-5. (1999)

ADVERTISEMENT RETURN TO ISSUEPREVBook ReviewNEXTFieser's Reagents for Organic Synthesis, Volume 18 By Tse-Lok Ho (National Chiao Tung University). John Wiley & Sons, Inc.: New York. 1999. xii + 504 pp. $79.95. ISBN 0-471-24477-5.Amir H. HoveydaView Author Information Boston CollegeCite this: J. Am. Chem. Soc. 1999, 121, 51, 12215Publication Date (Web):October 16, 1999Publication History Published online16 October 1999Published inissue 1 December 1999https://pubs.acs.org/doi/10.1021/ja995703zhttps://doi.org/10.1021/ja995703zbook-reviewACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views109Altmetric-Citations-LEARN 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:Organic synthesis,Reagents Get e-Alerts
Benchmarking 6-DOF Outdoor Visual Localization in Changing Conditions (2017)

Visual localization enables autonomous vehicles to navigate in their surroundings and augmented reality applications to link virtual to real worlds. Practical visual localization approaches need to be robust to a wide variety of viewing condition, including day-night changes, as well as weather and seasonal variations, while providing highly accurate 6 degree-of-freedom (6DOF) camera pose estimates. In this paper, we introduce the first benchmark datasets specifically designed for analyzing the impact of such factors on visual localization. Using carefully created ground truth poses for query images taken under a wide variety of conditions, we evaluate the impact of various factors on 6DOF camera pose estimation accuracy through extensive experiments with state-of-the-art localization approaches. Based on our results, we draw conclusions about the difficulty of different conditions, showing that long-term localization is far from solved, and propose promising avenues for future work, including sequence-based localization approaches and the need for better local features. Our benchmark is available at visuallocalization.net.
Perspective: It is time to consider new ways to attack unpesticidable (undruggable) target sites by designing peptide pesticides (2022)

Evolved resistance and regulatory deregistration have severely limited farmers' pesticide options. Many potential new pesticide target sites have been elucidated using targeted gene suppression and mutational tools, but few small molecules could be found that inhibit the target enzymes; the targets were considered 'undruggable'. Some organisms from all biological kingdoms use toxic peptides to ward off or kill enemies, and the agrochemical industry has used a few peptide analogs (glufosinate and bialophos) for field application. Conversely, pharmaceutical scientists have been using three-dimensional target protein structure to discover and synthesize short peptides that bind tightly to the surfaces of, and inhibit previously undruggable targets. New computational tools to quickly elucidate 3-D protein structure from amino acid sequence have just emerged. They replace crystallizing target proteins and performing X-ray crystallography to elucidate 3-D structure. These new tools allow prediction of peptides that will bind to the target proteins. They have further modified such peptides to enhance penetration, translocation and temperature stability. There is reason to assume that the same pioneering techniques can be used to develop peptide pesticides as well as pesticide synergists that act against undruggable targets and have excellent environmental and toxicological profiles. © 2022 Society of Chemical Industry.
Describable Visual Attributes for Face Images (2011)

We introduce the use of describable visual attributes for face images. Describable visual attributes are labels that can be given to an image to describe its appearance. This thesis focuses mostly on images of faces and the attributes used to describe them, although the concepts also apply to other domains. Examples of face attributes include gender, age, jaw shape, nose size, etc. The advantages of an attribute-based representation for vision tasks are manifold: they can be composed to create descriptions at various levels of specificity; they are generalizable, as they can be learned once and then applied to recognize new objects or categories without any further training; and they are efficient, possibly requiring exponentially fewer attributes (and training data) than explicitly naming each category. We show how one can create and label large datasets of real-world images to train classifiers which measure the presence, absence, or degree to which an attribute is expressed in images. These classifiers can then automatically label new images. We demonstrate the current effectiveness and explore the future potential of using attributes for image search, automatic face replacement in images, and face verification, via both human and computational experiments. To aid other researchers in studying these problems, we introduce two new large face datasets, named FaceTracer and PubFig, with labeled attributes and identities, respectively. Finally, we also show the effectiveness of visual attributes in a completely different domain: plant species identification. To this end, we have developed and publicly released the Leafsnap system, which has been downloaded by almost half a million users. The mobile phone application is a flexible electronic field guide with high-quality images of the tree species in the Northeast US. It also gives users instant access to our automatic recognition system, greatly simplifying the identification process.
CLDP Robust Planarization for Geographic Face Routing (2005)

Geographic routing algorithms are attractive for wireless ad hoc networks because they have been shown to scale better than other alternatives they require per-node state independent of network size, dependent only on network density. More recently, geographic routing algorithms have been proposed for use as a routing primitive for static sensor networks, as building blocks for data storage and flexible query processing in sensor networks, and even as a fallback routing mechanism for reduced state routing in the Internet.
Supplementary Figure S1 from Development of Human Anti-Murine T-Cell Receptor Antibodies in Both Responding and Nonresponding Patients Enrolled in TCR Gene Therapy Trials (2023)

&lt;p&gt;Supplementary Figure S1.&lt;/p&gt;
Portable LED-induced autofluorescence spectroscopy for oral cancer diagnosis (2017)

Oral cancer is a serious and growing problem in many developing and developed countries. To improve the cancer screening procedure, we developed a portable light-emitting-diode (LED)-induced autofluorescence (LIAF) imager that contains two wavelength LED excitation light sources and multiple filters to capture ex vivo oral tissue autofluorescence images. Compared with conventional means of oral cancer diagnosis, the LIAF imager is a handier, faster, and more highly reliable solution. The compact design with a tiny probe allows clinicians to easily observe autofluorescence images of hidden areas located in concave deep oral cavities. The ex vivo trials conducted in Taiwan present the design and prototype of the portable LIAF imager used for analyzing 31 patients with 221 measurement points. Using the normalized factor of normal tissues under the excitation source with 365 nm of the central wavelength and without the bandpass filter, the results revealed that the sensitivity was larger than 84%, the specificity was not smaller than over 76%, the accuracy was about 80%, and the area under curve of the receiver operating characteristic (ROC) was achieved at about 87%, respectively. The fact shows the LIAF spectroscopy has the possibilities of ex vivo diagnosis and noninvasive examinations for oral cancer.
DSServe - Data Science using Serverless (2022)

AI Applications uses various data science tools such as Jupyter notebook to prescribe a series of steps, commonly referred as workflow, for building AI Solutions. The steps in workflow can be as simple as loading the data from remote storage, visualize the data for better understanding or conducting data quality study, or it can be as complex as generating features for modeling, best model discovery processes, etc. Clearly, different steps of the data science workflow has varying requirement of compute resources. Moreover, the execution of steps in workflow are Adhoc and Subjective. With wider availability of various Serverless technology, in this paper, we demonstrate a generalized framework that can be used to provide on demand scale out capability for the Data Science Workflow. In particular, we selected the most common AI operation, namely Automatic Model Selection, as an example to demonstrate benefits of serverless computing. We conducted a detailed experimental results using IBM Code Engine technology to validate the benefits of our proposed approach.
Supplementary Table 3 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma (2023)

&lt;p&gt;XLSX file - 585KB, miRNA microarray data from 5 pairs of CRCs and 2 pairs of adenomas.&lt;/p&gt;
Antimicrobial Peptides Secreted From Human Cryopreserved Viable Amniotic Membrane Contribute to its Antibacterial Activity (2017)

Chronic wounds remain a large problem in the field of medicine and are often associated with risk of infection and amputation. Recently, a commercially available human cryopreserved viable amniotic membrane (hCVAM) has been shown to effectively promote wound closure and reduce wound-related infections. A sprevious study indicates that hCVAM can inhibit the growth of bacteria associated with chronic wounds. In the present study, we investigated the mechanism of hCVAM antimicrobial activity. Our data demonstrate that antimicrobial activities against common pathogens in chronic wounds such as P.aeruginosa, S.aureus and Methicillin-resistant S.aureus (MRSA) are mediated via the secretion of soluble factors by viable cells in hCVAM and that these factors are proteins in nature. Further, we show that genes for antimicrobial peptides (AMPs) including human beta-defensins (HBDs) are expressed by hCVAM and that expression levels positively correlate with antimicrobial activity of hCVAM. At the protein level, our data indicate that HBD2 and HBD3 are secreted by hCVAM and directly contribute to its activity against P. aeruginosa. These data provide evidence that soluble factors including AMPs are hCVAM antimicrobial agents and are consistent with a role for AMPs in mediating antimicrobial properties of the membrane.
107-Gb/s full-ETDM transmission over field installed fiber using vestigial sideband modulation (2007)

107-Gb/s full-ETDM transmission is shown over a 160-km field installed fiber link. A high tolerance towards narrowband optical filtering is demonstrated using vestigial sideband modulation to minimize the spectral width.
Constrained Maximum Correntropy Adaptive Filtering (2016)

Constrained adaptive filtering algorithms inculding constrained least mean square (CLMS), constrained affine projection (CAP) and constrained recursive least squares (CRLS) have been extensively studied in many applications. Most existing constrained adaptive filtering algorithms are developed under mean square error (MSE) criterion, which is an ideal optimality criterion under Gaussian noises. This assumption however fails to model the behavior of non-Gaussian noises found in practice. Motivated by the robustness and simplicity of maximum correntropy criterion (MCC) in non-Gaussian impulsive noises, this paper proposes a new adaptive filtering algorithm called constrained maximum correntropy criterion (CMCC). Specifically, CMCC incorporates a linear constraint into a MCC filter to solve a constrained optimization problem explicitly. The proposed adaptive filtering algorithm is easy to implement and has low computational complexity, and in terms of convergence accuracy (say lower mean square deviation) and stability, can significantly outperform those MSE based constrained adaptive algorithms in presence of heavy-tailed impulsive noises. Additionally, the mean square convergence behaviors are studied under energy conservation relation, and a sufficient condition to ensure the mean square convergence and the steady-state mean square deviation (MSD) of the proposed algorithm are obtained. Simulation results confirm the theoretical predictions under both Gaussian and non- Gaussian noises, and demonstrate the excellent performance of the novel algorithm by comparing it with other conventional methods.
Designing response surface model-based run-by-run controllers: a worst case approach (1996)

This paper presents a framework for carrying out run-by-run (RbR) control via a deterministic worst-case approach. In particular the RbR controller developed tries to minimize the worst-case performance of the plant. This yields a methodology for handling uncertainty. A consequence of using the deterministic approach is that we no longer need any assumptions on the statistics of the noise. Rather, what we require is that the noise be bounded. Thus, we can also deal with non-Gaussian and correlated noise. We provide results comparing the performance of the controller to a recursive least squares (RLS) based controller.
Supplementary Figure 4 from Chronic Myelogenous Leukemia– Initiating Cells Require Polycomb Group Protein EZH2 (2023)

&lt;p&gt;Gene expression analysis.&lt;/p&gt;
Hg(1‐x)CdxTe from short to long wave infrared on Si substrates grown by MBE (2010)

Abstract In this paper, we show the power of using molecular beam epitaxy (MBE) for the growth of the mercury cadmium telluride (HgCdTe) system. Abrupt composition profiles, changes in doping levels, or switching doping types are easily performed. It is shown that high quality material is achieved with Hg (1‐ x ) Cd x Te grown by MBE from a cadmium mole fraction of x =0.15 to x =0.72. Doping elements incorporation as low as 10 15 cm ‐3 for both n‐type and p‐type material as well as high incorporation levels &gt;10 18 cm ‐3 for both carrier types were achieved. Secondary ion mass spectrometry (SIMS) data, x‐ray data, Hall data, the influence of doping incorporation with cadmium content and growth rate, etch pit density (EPD), composition uniformity determined from Fourier transform infrared (FTIR) transmission spectroscopy, and surface defect maps from low to high x values are presented to illustrate the versatility and quality of HgCdTe material grown by MBE. (© 2010 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Interpolated Background Subtraction Method For Coronary Stenosis Quantification (1988)

The determination of percent stenosis of coronary arteries is an important task in medicine. In this paper we discuss three different algorithms which can be used in conjunction with videodensitometry to measure this quantity. These algorithms may be used in subtracting the background under a vessel segment thus eliminating the need for a preinjection mask. Mathematical details of the algorithms and experimental results are presented.
Embedded RSFQ Pseudorandom Binary Sequence Generator for Multichannel High-Speed Digital Data Link Testing and Synchronization (2017)

As the digital data links for superconducting circuits advance and higher data throughput per channel becomes possible, timing margins shrink and data integrity becomes a major challenge. Particular interest for multichannel applications is establishing the high-quality data link to interface with subsequent electronics. In this paper, we focus on integration of an on-chip pseudorandom binary sequence (PRBS) generator into a superconducting analog-to-digital converter (ADC) design to facilitate link stability evaluation and automated interchannel synchronization. PRBS generator and the ADC use a common clock source. An on-chip deserializer/demux, which includes the output drivers, is driven by a set of data sources depending on switch selections on-chip. The outputs are connected to a field-programmable gate array (FPGA) at room temperature, which hosts the developed interface circuitry for data reception, data integrity evaluation, and the synchronization mechanism. The integrated circuit (IC) that combines ADC and PRBS7 generator circuit was designed for the HYPRES 4.5 kA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> four-layer standard fabrication process and features four deserialized outputs. A second similar IC was designed comprising an ADC frontend as well as a PRBS15 generator and was fabricated in the MIT-LL 10 kA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> process. The implemented alignment engine that bonds the individual channels into a single data link was proven up to 10 Gbps while taking 1-2 μs to complete the alignment. We built chip-to-FPGA data links, comprising the on-chip driver and room-temperature interface amplifier, up to 14 Gbps using FPGA serial-link GTY transceiver. Successful data transport from an ADC using multiple parallel data links to an FPGA upon completion of the channel bonding was demonstrated.
[From cell therapy to organ regeneration therapy: generation of functional organs from pluripotent stem cells]. (2011)

Current stem cell therapy mainly targets diseases that can be treated by cell transplantation. The complexity of organogenesis hinders in vitro generation of organs derived from patient's pluripotent stem cells (PSCs), an ultimate goal of regenerative medicine. To address this issue, we attempted in vivo generation of PSC-derived pancreas using Pdx1(-/-) blastocysts(pancreatogenesis-disabled) and blastocyst complementation technique. When wild type rat PSCs were injected into mouse Pdx1(-/-) blastocysts, defective cells were totally replaced and pancreas was formed almost entirely by injected rat PSC derived cells. Chimeric mice of Pdx1(-/-) genotype survived to adulthood without any sign of diabetes. Generation of organs using blastocyst complementation in vivo provides a new strategy for understanding organogenesis and a novel approach for organ supply.