gebhart/patrepeval huggingface dataset:
Inhibition of endoplasmic reticulum-to-Golgi traffic by poliovirus protein 3A: genetic and ultrastructural analysis (1997)

Poliovirus protein 3A, only 87 amino acids in length, is a potent inhibitor of protein secretion in mammalian cells, blocking anterograde protein traffic from the endoplasmic reticulum (ER) to the Golgi complex. The function of viral protein 3A in blocking protein secretion is extremely sensitive to mutations near the N terminus of the protein. Deletion of the first 10 amino acids or insertion of a single amino acid between amino acids 15 and 16, a mutation that causes a cold-sensitive defect in poliovirus RNA replication, abrogates the inhibition of protein secretion although wild-type amounts of the mutant proteins are expressed. Immunofluorescence light microscopy and immunoelectron microscopy demonstrate that 3A protein, expressed in the absence of other viral proteins, colocalizes with membranes derived from the ER. The precise topology of 3A with respect to ER membranes is not known, but it is likely to be associated with the cytosolic surface of the ER. Although the glycosylation of 3A in translation extracts has been reported, we show that tunicamycin, under conditions in which glycosylation of cellular proteins is inhibited, has no effect on poliovirus growth. Therefore, glycosylation of 3A plays no functional role in the viral replicative cycle. Electron microscopy reveals that the ER dilates dramatically in the presence of 3A protein. The absence of accumulated vesicles and the swelling of the ER-derived membranes argues that ER-to-Golgi traffic is inhibited at the step of vesicle formation or budding from the ER.
PL and PLE characterization of high current density resonant tunnelling diodes for THz applications (2022)

Low-temperature photoluminescence spectroscopy (PL) and excitation spectroscopy(PLE) are used to characterize and compare high current density resonant tunnelling diodes (RTD) structures. RTD structural characteristics are detected using X-Ray diffraction (XRD) while the electrical characteristics are detected by PL and PLE. Results are used to link the structure electrical properties to the RTD device IV characteristic. We started focusing the attention on the first quasi bound state (e<sub>1</sub>) energy, fundamental for the RTD operation. PL is used to detect the TypeI and Type II QW radiative transitions. The e<sub>1</sub> state is obtained by the difference between the Type I (e<sub>1</sub>–hh<sub>1</sub>) and type II (conduction band–hh<sub>1</sub>) transitions. PLE is consequently used to detect the e2-hh2 transition from which we characterize the energy of the e2 state and its position with respect to the e1 state. Experimental data are confirmed by the RTDs device IV characteristics. We highlight the combination PL and PLE as a powerful, fast, and non-destructive characterization method to link wafer properties and device performance in RTD structures.
CW second harmonic results at 460 GHz of a gyrotron oscillator - for sensitivity enhanced NMR (2006)

We report 460 and 233 GHz CW results of a gyrotron operating at the second electron cyclotron harmonic and fundamental, respectively. A record CW power level of over 8 W has been obtained at 460 GHz in the TE/sub 0,6/ mode with 12.4 kV and 135 mA. The gyrotron has operated under computer control for over an hour with stable power output of better than 1%. Fundamental CW studies at 233 GHz in the TE/sub 2,3/ mode reveal that oscillations start with less than 7 W of beam power below 3.5 kV. The gyrotron will extend sensitivity-enhanced NMR through dynamic nuclear polarization to the highest field ever used, 16.5 T (700 MHz /sup 1/H).
Science Objectives for Flagship-Class Mission Concepts for the Search for Evidence of Life at Enceladus (2022)

<i>Cassini</i> revealed that Saturn's Moon Enceladus hosts a subsurface ocean that meets the accepted criteria for habitability with bio-essential elements and compounds, liquid water, and energy sources available in the environment. Whether these conditions are sufficiently abundant and collocated to support life remains unknown and cannot be determined from <i>Cassini</i> data. However, thanks to the plume of oceanic material emanating from Enceladus' south pole, a new mission to Enceladus could search for evidence of life without having to descend through kilometers of ice. In this article, we outline the science motivations for such a successor to <i>Cassini</i>, choosing the primary science goal to be determining whether Enceladus is inhabited and assuming a resource level equivalent to NASA's Flagship-class missions. We selected a set of potential biosignature measurements that are complementary and orthogonal to build a robust case for any life detection result. This result would be further informed by quantifications of the habitability of the environment through geochemical and geophysical investigations into the ocean and ice shell crust. This study demonstrates that Enceladus' plume offers an unparalleled opportunity for <i>in situ</i> exploration of an Ocean World and that the planetary science and astrobiology community is well equipped to take full advantage of it in the coming decades.
Correction to: The pathogenic intestinal spirochaete Brachyspira pilosicoli forms a diverse recombinant species demonstrating some local clustering of related strains and potential for zoonotic spread (2019)

The article published in 2013 [1] described the use of the available Brachyspira multilocus sequence typing (MLST) scheme [2] to characterize the population structure of the intestinal spirochete Brachyspira pilosicoli . It used sequences of seven loci that were amplified from 131 strains that had been isolated from different geographical origins and species.
Preisach modeling of piezoceramic and shape memory alloy hysteresis (2002)

Smart materials such as piezoceramics and shape memory alloys (SMAs) exhibit significant hysteresis and in order to estimate the effect on open and closed loop control a suitable model is needed. One promising candidate is the Preisach independent domain hysteresis model that is characterized by the congruent minor loop and wiping out properties. Comparable minor loop and decaying oscillation test data for a multi-sheet piezoceramic actuator (made of lead zirconate titanate) attached to a flexible beam are presented and are seen to be very consistent with the two Preisach model properties. The commanded parameter is the sheet transverse electric field while the measured parameter is an approximately colocated strain induced in the beam. Equivalent data for a Nitinol SMA wire muscle, attached to the same beam, are also presented. The input and output parameters are the SMA current and a beam strain respectfully. The minor loop and wiping out evidence is less strong than that of the piezoceramic case, but encouraging. In all experiments the quasi-steady state responses were generated in order to avoid exciting beam flexible modes which would complicate the analysis.
KeyPose: Multi-View 3D Labeling and Keypoint Estimation for Transparent Objects (2020)

Estimating the 3D pose of desktop objects is crucial for applications such as robotic manipulation. Many existing approaches to this problem require a depth map of the object for both training and prediction, which restricts them to opaque, lambertian objects that produce good returns in an RGBD sensor. In this paper we forgo using a depth sensor in favor of raw stereo input. We address two problems: first, we establish an easy method for capturing and labeling 3D keypoints on desktop objects with an RGB camera; and second, we develop a deep neural network, called KeyPose, that learns to accurately predict object poses using 3D keypoints, from stereo input, and works even for transparent objects. To evaluate the performance of our method, we create a dataset of 15 clear objects in five classes, with 48K 3D-keypoint labeled images. We train both instance and category models, and show generalization to new textures, poses, and objects. KeyPose surpasses state-of-the-art performance in 3D pose estimation on this dataset by factors of 1.5 to 3.5, even in cases where the competing method is provided with ground-truth depth. Stereo input is essential for this performance as it improves results compared to using monocular input by a factor of 2. We will release a public version of the data capture and labeling pipeline, the transparent object database, and the KeyPose models and evaluation code. Project website: https://sites.google.com/corp/view/keypose.
Pathology image-based lung cancer subtyping using deeplearning features and cell-density maps (2020)

In this paper, we propose a patch-based system to classify non-small cell lung cancer (NSCLC) diagnostic whole slide images (WSIs) into two major histopathological subtypes: adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC). Classifying patients accurately is important for prognosis and therapy decisions. The proposed system was trained and tested on 876 subtyped NSCLC gigapixel-resolution diagnostic WSIs from 805 patients &#x2013; 664 in the training set and 141 in the test set. The algorithm has modules for: 1) auto-generated tumor/non-tumor masking using a trained residual neural network (ResNet34), 2) cell-density map generation (based on color deconvolution, local drain segmentation, and watershed transformation), 3) patch-level feature extraction using a pre-trained ResNet34, 4) a tower of linear SVMs for different cell ranges, and 5) a majority voting module for aggregating subtype predictions in unseen testing WSIs. The proposed system was trained and tested on several WSI magnifications ranging from x4 to x40 with a best ROC AUC of 0.95 and an accuracy of 0.86 in test samples. This fully-automated histopathology subtyping method outperforms similar published state-of-the-art methods for diagnostic WSIs.
Design of Low Loss Directional Couplers for High Q Integrated Resonators (2014)

We present a low loss directional coupler study for Si3N4 ultra-high Q resonators. Through tapering of the resonator-bus gap, we demonstrate record-high integrated waveguide coupled intrinsic quality factor (Qint) values of 81 million.
Bodenhausen, Geoffrey: Traveling through the World of Magnetic Resonance in the 1970s (2007)

The sections in this article are
ChemInform Abstract: Carbohydrate Transition State Mimics. Part 1. Synthesis of Imidazolo‐Piperidinopentoses as Nagstatine Analogues. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Nanowire based flexible electrode array with pedot film for neural recordings (2015)

The electrode-tissue interface plays an important role in neural recordings. Here, we designed and fabricated a flexible electrode array with nanowire structures and poly(3,4-ethylenedioxythiophene) PEDOT on the flexible substrate. ZnO nanowires were used as a nano pillar structure, which increases effective surface area drastically, to decrease electrode impedance. Furthermore, ZnO nanowires was coated with PEDOT to enhance both biocompatibility and charge transfer characteristics. Flexible electrode array with nanowires and PEDOT shows a higher signal-to-noise ratio (SNR).
Sulfonate N‐Heterocyclic Carbene–Copper Complexes: Uniquely Effective Catalysts for Enantioselective Synthesis of C−C, C−B, C−H, and C−Si Bonds (2020)

Abstract A copper‐based complex that contains a sulfonate N‐heterocyclic carbene ligand was first reported 15 years ago. Since then, these organometallic entities have proven to be uniquely effective in catalyzing an assortment of enantioselective transformations, including allylic substitutions, conjugate additions, proto‐boryl additions to alkenes, boryl and silyl substitutions, hydride‐allyl additions to alkenyl boronates, and additions of boron‐containing allyl moieties to N‐H ketimines. In this review article, we detail the shortcomings in the state‐of‐the‐art that fueled the development of this air stable ligand class, members of which can be prepared on multigram scale. For each reaction type, when relevant, the prior art at the time of the advance involving sulfonate NHC‐Cu catalysts and/or subsequent key developments are briefly analyzed, and the relevance of the advance to efficient and enantioselective total or formal synthesis of biologically active molecules is underscored. Mechanistic analysis of the structural attributes of sulfonate NHC‐Cu catalysts that are responsible for their ability to facilitate transformations with high efficiency as well as regio‐ and enantioselectivity are detailed. This review contains several formerly undisclosed methodological advances and mechanistic analyses, the latter of which constitute a revision of previously reported proposals.
Alkylation of Cyclododecanone with Allyl Acetate in the Presence of Solid Radical Initiators (2018)

The radical alkylation of cyclododecanone (CDD) with allyl acetate (AlAc) yielding 2‐[3‐(acetyloxy)propyl] cyclododecanone (CDDPA) in the presence of different inorganic radical initiators was investigated. The most useful initiator among other inorganic metal oxides was found to be CuO. The molar ratio of CDD and AlAc was varied between 10:1 and 3:1. CuO was characterized by using different analytical methods, such as N 2 adsorption, powder X‐ray diffraction, temperature‐programmed reduction, scanning electron microscopy, and X‐ray photoelectron spectroscopy. The reaction was performed in a batch system, by adding all the reactants at once, and in a semibatch procedure by dosing AlAc over the whole time of the experiment. Different parameters that affected the selectivity of CDDPA were studied, such as the ratio of CDD/AlAc, reaction time, surface of CuO initiator, and reaction temperature. The best result was obtained with 21 % conversion of CDD and 77 % selectivity to CDDPA at a final molar ratio of CDD/AlAc = 4:1 in the semibatch procedure.
Does the Performance of LDPC Codes Depend on the Channel? (2006)

In this letter, we discuss the performance of low-density parity-check (LDPC) codes on memoryless channels. Using a recently proposed analysis technique based on extrinsic information transfer (EXIT) charts, we present an interpretation of the known fact that the bit-error rate (BER) performance of an ensemble of LDPC codes shows little dependence on the specific memoryless channel. This result has been partially observed in the literature for symmetric channels and is here extended to asymmetric channels. We conjecture and demonstrate that the performance of an ensemble of LDPC codes depends primarily and solely on the mutual information (MI) between the input and the output of the channel. As a validation of this conjecture, we compare the performance of a few LDPC codes with various rates for five representative memoryless (both symmetric and asymmetric) channels, obtaining results in excellent agreement with the EXIT chart-based prediction
216-49: Application Of Cardiac Resynchronization Therapy Differs In The USA Compared TO Outside USA- The International ADVANCE CRT REGISTRY (2016)

Introduction: Cardiac resynchronization therapy (CRT) is used worldwide to treat heart failure (HF) patients (pts). However, accumulating evidence points to certain subgroups that may benefit more, and others less, from CRT prescribed according to international guidelines. Moreover, access to different technologies (eg defibrillator vs pacemaker CRT platforms) and leads (eg. multipolar) may exhibit regional differences. Whether these factors influence implant decisions in the USA vs outside USA (OUS) practice is unknown. Methods: ADVANCE-CRT aims to elucidate non-responder care in clinical practice settings worldwide (40 US and 27 OUS centres). Enrollment data were used to characterize baseline differences between 1105 USA and 362 OUS pts (N: India 198, China 44, Korea 35, Japan 33, Columbia 25, Brazil 19, and Argentina 8). Results: USA and OUS CRT pts did not differ in gender distribution (68% male), and percentage of subjects with NYHA Class III heart failure, diabetes, and antiarrhythmic drug treatment (21%). OUS pts were more likely to have LBBB, QRS >150 ms, non-ischemic cardiomyopathy, and poorer LV function. Also, OUS pts were younger (62.9 ±11.1 vs 69.5 ± 11.2 years, p < 0.0001) and included a smaller percentage of pts on guideline directed medical therapy. In contrast, USA pts were more obese, likely to have milder HF, AF and a smoking history. In the USA, the left ventricular (LV) lead was more likely to be a quadripolar LV lead implanted in the lateral location (p < 0.0001). In contrast, in OUS pts, LV leads tended to be bipolar and sited posterolaterally (p <0.0001). CRT defibrillator was used more than CRT pacemaker in both USA and OUS, but the proportion was higher in USA (p < 0.001). Conclusion: Despite a common set of guidelines for CRT practice, CRT candidates and CRT systems used differ significantly between the USA and OUS.
Target Discovery of Selective Non-Small-Cell Lung Cancer Toxins Reveals Inhibitors of Mitochondrial Complex I (2019)

Selective toxicity among cancer cells of the same lineage is a hallmark of targeted therapies. As such, identifying compounds that impair proliferation of a subset of non-small-cell lung cancer (NSCLC) cell lines represents one strategy to discover new drugs for lung cancer. Previously, phenotypic screens of 202 103 compounds led to the identification of 208 selective NSCLC toxins ( McMillan , E. A. , <i>Cell</i> , 2018 , 173 , 864 ). The mechanism of action for the majority of these compounds remains unknown. Here, we discovered the target for a series of quinazoline diones (QDC) that demonstrate selective toxicity among 96 NSCLC lines. Using photoreactive probes, we found that the QDC binds to both mitochondrial complex I of the electron transport chain and hydroxyacyl CoA dehydrogenase subunit alpha (HADHA), which catalyzes long-chain fatty acid oxidation. Inhibition of complex I is the on-target activity for QDC, while binding to HADHA is off-target. The sensitivity profile of the QDC across NSCLC lines correlated with the sensitivity profiles of six additional structurally distinct compounds. The antiproliferative activity of these compounds is also the consequence of binding to mitochondrial complex I, reflecting significant structural diversity among complex I inhibitors. Small molecules targeting complex I are currently in clinical development for the treatment of cancer. Our results highlight complex I as a target in NSCLC and report structurally diverse scaffolds that inhibit complex I.
Low-complexity digital encoding strategies for wireless sensor networks (2002)

Low-complexity schemes for digital encoding of a noise-corrupted signal and associated signal estimators are presented. This problem arises in wireless distributed sensor networks where an environmental signal of interest is to be estimated at a central site from low-bandwidth digitized information received from collections of remote sensors. We show that the use of a properly designed and often easily implemented additive control input before signal quantization can significantly enhance overall system performance. In particular, efficient estimators can be constructed and used with optimized pseudo-noise, deterministic, and feedback-based control inputs, resulting in a hierarchy of practical systems with very attractive performance-complexity characteristics.
Reliably determining data leakage in the presence of strong attackers (2016)

We address the problem of determining what data has been leaked from a system after its recovery from a successful attack. This is a forensic process which is relevant to give a better understanding of the impact of a data breach, but more importantly it is becoming mandatory according to the recent developments of data breach notification laws. Existing work in this domain has discussed methods to create digital evidence that could be used to determine data leakage, however most of them fail to secure the evidence against malicious adversaries or use strong assumptions such as trusted hardware. In some limited cases, data can be processed in the encrypted domain which, although being computationally expensive, can ensure that nothing leaks to an attacker, thereby making the leakage determination trivial. Otherwise, victims are left with the only option of considering all data to be leaked.
Front Matter: Volume 7422 (2009)

This PDF file contains the front matter associated with SPIE Proceedings volume 7422, including the Title Page, Copyright information, Table of Contents, Introduction, and the Conference Committee listing.
Effects of Single Dose Administration of MD-1100 on Safety, Tolerability, Exposure, and Stool Consistency in Healthy Subjects (2005)

Purpose: MD-1100, a Guanylate Cyclase-C agonist that acts on the intestinal epithelium, is a novel agent that acts in animal models to promote intestinal secretion and transit and additionally reduces intestinal visceral pain. These pharmacological actions are ideal attributes for the treatment of IBS-C. In an effort to better understand the potential utility of MD-1100 for treating G.I. disorders, we have begun to characterize its safety, tolerability, exposure, and pharmacodynamics in healthy male and post-menopausal female subjects. Methods: A placebo-controlled, double-blind, randomized, single oral ascending dose (30 to 3000 micrograms) study was performed with 30 healthy subjects. Subjects were assessed for safety, tolerability, MD-1100 systemic exposure, and pharmacodynamics. One of the tools we utilized to assess the pharmacodynamic activity of MD-1100 to stimulate intestinal transit was the Bristol Stool Form Scale (BSFS) with increases in the scale (1–7) reflecting a decrease in stool consistency. Results: We observed no SAEs during this study, and the pattern of AEs between placebo and MD-1100 treated subjects was similar with the exception of the intended pharmacodynamic actions from an agent that promotes secretion and transit. MD-1100 was well tolerated at all dose levels and, as anticipated for this luminally acting compound, we were unable to detect any systemic exposure of MD-1100. MD-1100 elicited an increase in the BSFS post-dose, reflecting a decrease in stool consistency. We also observed other indications of G.I. activity post-dosing of MD-1100, including an apparent increase in stool weight. Conclusions: In this single-dose Phase 1 study, MD-1100 was well tolerated across the dose range studied (30–3000 micrograms). As expected for an agent that was designed to act in the intestine with minimal oral absorption, MD-1100 appears to possess G.I. pharmacodynamic activity in healthy subjects with no detectable levels of systemic exposure. To date, the preclinical and clinical data strongly support the potential of MD-1100 for the treatment of G.I. conditions, including IBS-C. In addition to the single dose study described here, a multiple ascending dose study of MD-1100 in 48 healthy subjects has recently completed enrollment. We anticipate advancing MD-1100 further into clinical development with the objective of evaluating whether MD-1100 will act to treat the pain, bloating, and constipation associated with IBS-C.