gebhart/patrepeval huggingface dataset:
Ripplocations provide a new mechanism for the deformation of phyllosilicates in the lithosphere (2019)

Deformation in Earth's lithosphere is localised in narrow, high-strain zones. Phyllosilicates, strongly anisotropic layered minerals, are abundant in these rocks, where they accommodate much of the strain and play a significant role in inhibiting or triggering earthquakes. Until now it was understood that phyllosilicates could deform only by dislocation glide along layers and could not accommodate large strains without cracking and dilation. Here we show that a new class of atomic-scale defects, known as ripplocations, explain the development of layer-normal strain without brittle damage. We use high-resolution transmission electron microscopy (TEM) to resolve nano-scale bending characteristic of ripplocations in the phyllosilicate mineral biotite. We demonstrate that conjugate delamination arrays are the result of elastic strain energy release due to the accumulation of layer-normal strain in ripplocations. This work provides the missing mechanism necessary to understand phyllosilicate deformation, with important rheological implications for phyllosilicate bearing seismogenic faults and subduction zones.
The ΦPA3 Phage Nucleus is Enclosed by a Self-Assembling, 2D Crystalline Lattice (2022)

Abstract A growing number of jumbo bacteriophages, with genomes exceeding 200 kb, have been found to establish a Phage Nucleus—a micron-scale, proteinaceous structure encompassing the replicating phage DNA. Bacteriophage and host proteins associated with replication and transcription are concentrated inside the Phage Nucleus while nucleotide synthesis, translation, and numerous other host and exogenous proteins are effectively excluded, including CRISPR-Cas and restriction endonuclease host defense systems. Here, we show that fragments of the Phage Nucleus isolated from ΦPA3 infected Pseudomonas aeruginosa cells form a square lattice and demonstrate that the recombinantly purified primary Phage Nuclear Enclosure (PhuN) protein spontaneously assembles into sheets also constructed from a square lattice which we resolve to 3.8 Å by cryo-EM. Our structure reveals that the flexible termini and large loops mediate adaptable inter-tetramer contacts that drive shell assembly into a C2-symmetric lattice. While the interfaces between subunits are mostly well packed, two of the interfaces are open, forming clear channels that likely have important functional implications for the transport of proteins, mRNA and small molecules.
Conversion of a C-20-deoxy-C21, steroid, 5-pregnen-3beta-ol, into testosterone by rat testicular microsomes. (1976)

5-[7ALPHA-3H] Pregnen-3beta-ol, a C-20-deoxy analog of pregnenolone, was synthesized and tested as a substrate for the enzyme system occurring in testes that cleaves the side chain of C21 steroids between C-17 and C-20. This C-20-deoxy C21 steroid was incubated with a microsomal preparation obtained from rat testis and was converted into testosterone in 5% yield. Another C-20-deoxy analog of pregnenolone, 5,20-pregnadien-3beta-ol, was not converted into testosterone by this enzyme system. The significance of this finding for the natural processes by which pregnenolone is converted by the same subcellular fraction into the male sex hormone is examined in the light of the hypothesis that intermediates involved in steroidogenesis are transient, reactive complexes of the appropriate reactants (steroids, oxygen, etc.) with specific enzymes.
Pelvic imaging with phased‐array coils: Quantitative assessment of signal‐to‐noise ratio improvement (1992)

The signal-to-noise ratios (S/Ns) of two different pelvic magnetic resonance (MR) imaging phased arrays were compared with that of the body coil. Each array consisted of two coils placed anteriorly and two posteriorly, oriented transversely in one array and longitudinally in the other. S/N measurements were obtained in an adjustable water-filled phantom that stimulated the shape and radio-frequency loading effects of various-size patients. Depending on the simulated anterior-posterior thickness of the patient, the S/N produced by the longitudinal array ranged from 2.3 to 3.1 times higher than that of the body coil. The S/N of the transverse array was 3.1 to 3.4 times higher. The increased coil sensitivity permits imaging with shorter acquisition times, smaller fields of view, finer resolution, and/or thinner sections. Two examples in patients demonstrate the enhanced imaging capability of the phased arrays.
Hiding Data in Plain Sight: Undetectable Wireless Communications Through Pseudo-Noise Asymmetric Shift Keying (2019)

Undetectable wireless transmissions are fundamental to avoid eavesdroppers or censorship by authoritarian governments. To address this issue, wireless steganography “hides” covert information inside primary information by slightly modifying the transmitted waveform such that primary information will still be decodable, while covert information will be seen as noise by agnostic receivers. Since the addition of covert information inevitably decreases the SNR of the primary transmission, a key challenge in wireless steganography is to mathematically analyze and optimize the impact of the covert channel on the primary channel as a function of different channel conditions. Another core issue is to make sure that the covert channel is almost undetectable by eavesdroppers. Existing approaches are protocol-specific and thus their performance cannot be assessed and optimized in general scenarios. To address this research gap, we notice that existing wireless technologies rely on phase-keying modulations (e.g., BPSK, QPSK) that in most cases do not use the channel up to its Shannon capacity. Therefore, the residual capacity can be leveraged to implement a wireless system based on a pseudo-noise asymmetric shift keying (PN-ASK) modulation, where covert symbols are mapped by shifting the amplitude of primary symbols. This way, covert information will be undetectable, since a receiver expecting phase-modulated symbols will see their shift in amplitude as an effect of channel/path loss degradation. Through rigorous mathematical analysis, we first investigate the SER of PN-ASK as a function of the channel; then, we find the optimal PN-ASK parameters that optimize primary and covert throughput under different channel condition. We evaluate the throughput performance and undetectability of PN-ASK through extensive simulations and on an experimental testbed based on USRP N210 software-defined radios. Results indicate that PN-ASK improves the throughput by more than 8x with respect to prior art. Finally, we demonstrate through experiments that PN-ASK is able to transmit covert data on top of IEEE 802.11g frames, which are correctly decoded by an off-the-shelf laptop WiFi card without any hardware modifications.
564 Single-cell transcriptomic analysis of immune compartments following combination immunotherapy treatment in poorly immunogenic tumors (2021)

<h3>Background</h3> A major goal in cancer immunology is to rationally design combination therapies that lead to a higher response rate, especially for poorly immunogenic tumors that do not respond to immune checkpoint blockade therapy alone. We previously developed a combination therapeutic strategy, termed AIPV, consisting of a tumor-targeting antibody, a recombinant interleukin-2 with an extended half-life, an anti-PD-1 antibody, and a T cell vaccine [1]. The full AIPV therapy can eradicate large, aggressive, poorly immunogenic tumors in multiple mouse tumor models. However, the exact cellular and molecular pathways involved in such an effective response remain poorly understood. <h3>Methods</h3> In this study, we used single-cell RNA-sequencing to define the detailed cellular and molecular changes in tumors and tumor-draining lymph nodes following the full AIPV therapy or a less effective sub-combination therapy in mice with poorly immunogenic B16F10 tumors. <h3>Results</h3> Using our approach, we were able to uncover T cells, NK cells, neutrophils, macrophages/monocytes, classical dendritic cells, and plasmacytoid dendritic cells in tumors. We observed profound remodeling of every immune cell type following the effective therapeutic treatment. In particular, we found that classical dendritic cells take up tumor antigens, become activated, and migrate to draining lymph nodes following the AIPV therapy, but not following the less effective IPV therapy. We characterized the transcriptomic changes of these dendritic cells and found that they over-express molecules involved in antigen uptake. <h3>Conclusions</h3> Our study comprehensively characterized a system that can overcome resistance to immune checkpoint blockade therapy, paving a cellular and molecular roadmap for immune-based therapeutic strategies that offer clinical benefits for poorly immunogenic tumors. <h3>References</h3> Moynihan KD, Opel CF, Szeto GL, Tzeng A, Zhu EF, Engreitz JM, et al. Eradication of large established tumors in mice by combination immunotherapy that engages innate and adaptive immune responses. Nat Med. 2016;22: 1402–1410. <h3>Ethics Approval</h3> All mouse experiments were reviewed and approved by the Koch Institute and Broad Institute Animal Care and Use Committee (IACUC) (ID 0222-08-18).
Spiderweb Nanomechanical Resonators via Bayesian Optimization: Inspired by Nature and Guided by Machine Learning (Adv. Mater. 3/2022) (2022)

Nanomechanical Resonators In article number 2106248, Miguel A. Bessa, Richard A. Norte, and co-workers report the design of a nature-inspired spiderweb sensor using artificial intelligence and discover a novel vibration mechanism. The device's world-class performance is verified experimentally, opening avenues toward ultrasensitive detection of fundamental forces and quantum technologies operating at room temperature.
Figure S2 from Shifts in the Fecal Microbiota Associated with Adenomatous Polyps (2023)

&lt;p&gt;Supplementary Figure 2. Heat map of significantly predictive taxa. Hierarchical clustering is based on the Euclidean distance of log proportion, complete linkage. The left cluster is enriched in adenoma samples (P=0.1, Fisher's exact test).&lt;/p&gt;
Towards Upscaling of La5.5WO11.25−δ Manufacture for Plasma Spraying-Thin Film Coated Hydrogen Permeable Membranes (2020)

Lanthanum tungstate (La<sub>6</sub>WO<sub>12</sub>) is a promising material for the development of hydrogen separation membranes, proton ceramic electrolyzer cells and protonic ceramic fuel cells due to its interesting transport properties and stability under different operation conditions. In order to improve the hydrogen transport through the La<sub>6</sub>WO<sub>12</sub> membranes, thin membranes should be manufactured. This work is based on the industrial production of La<sub>5.5</sub>WO<sub>11.25-δ</sub> (LWO) powder by spray drying and the manufacturing of thin membranes by low-pressure plasma spraying (LPPS-TF) technique. LPPS-TF allows the production of dense thin films of high quality in an industrial scale. The powders produced by spray drying were morphological and electrochemically characterized. Hydrogen permeation fluxes of a membrane manufactured with these powders were evaluated and fluxes are similar to those reported previously for LWO powder produced in the lab scale. Finally, the transport properties of LWO thin films deposited on Al<sub>2</sub>O<sub>3</sub> indicate that LPPS-TF produces high-quality LWO films with potential for integration in different applications.
WISDOM (2009)

We demonstrate an information credibility analysis system called WISDOM. The purpose of WISDOM is to evaluate the credibility of information available on the Web from multiple viewpoints. WISDOM considers the following to be the source of information credibility: information contents, information senders, and information appearances. We aim at analyzing and organizing these measures on the basis of semantics-oriented natural language processing (NLP) techniques.
Conidia of Erysiphe trifoliorum attempt penetration twice during a two-step germination process on non-host barley leaves and an artificial hydrophobic surface (2011)

In the present study, using a high-fidelity digital microscope, we observed the sequence of appressorial development on the germ tubes of a powdery mildew fungus isolated from red clover leaves. Based on its morphological characteristics and rDNA internal transcribed spacer (ITS) sequences, the fungus was identified as Erysiphe trifoliorum, and one of its isolates, designated as KRCP-4N, was used in this work. The conidial germination of isolate KRCP-4N was studied on host (red clover) and non-host (barley) leaves, as well as on an artificial hydrophobic membrane (Parafilm). More than 90% of conidia germinated synchronously and developed dichotomous appressoria (symmetrical double-headed appressoria) on all substrata used. On host leaves, all appressorium-forming conidia developed hyphae (colonyforming hyphae) from conidial bodies without extending germ tubes from the tips of the appressoria. On non-host leaves and on Parafilm-covered glass slides, however, all conidia extended germ tubes from one side of dichotomous appressoria (two-step germination). In addition to the dichotomous appressoria, we detected a few conidia that produced hooked appressoria and extended germ tubes from the tip of the appressorium. Penetration attempts by KRCP-4N conidia on barley leaves were impeded by papillae formed at penetration sites beneath these two types of appressorium. From these results, we conclude that the “two-step germination” of E. trifoliorum KRCP-4N conidia is the result of an unsuccessful penetration attempt, causing diversity in appressorial shape.
Synthesis and characterization of new highly organosoluble poly(etherimide)s derived from 1,1‐bis{4‐[4‐(3,4‐dicarboxyphenoxy)phenyl]‐4‐phenylcyclohexane} dianhydride (2002)

Abstract A new bulky pendent bis(ether anhydride), 1,1‐bis[4‐(4‐dicarboxyphenoxy)phenyl]‐4‐phenylcyclohexane dianhydride, was prepared in three steps, starting from the nitrodisplacement of 1,1‐bis(4‐hydroxyphenyl)‐4‐phenylcyclohexane with 4‐nitrophthalonitrile to form bis(ether dinitrile), followed by alkaline hydrolysis of the bis(ether dinitrile) and subsequent dehydration of the resulting bis(ether diacid). A series of new poly(ether imide)s were prepared from the bis(ether anhydride) with various diamines by a conventional two‐stage synthesis including polyaddition and subsequent chemical cyclodehydration. The resulting poly(ether imide)s had inherent viscosities of 0.50–0.73 dL g −1 . The gel permeation chromatography measurements revealed that the polymers had number‐average and weight‐average molecular weights of up to 57,000 and 130,000, respectively. All the polymers showed typical amorphous diffraction patterns. All of the poly(ether imide)s showed excellent solubility in comparison with the other polyimides derived from adamantane, norbornane, cyclododecane, and methanohexahydroindane and were readily dissolved in various solvents such as N ‐methyl‐2‐pyrrolidinone, N,N ‐dimethylacetamide (DMAc), N,N ‐dimethylformamide, pyridine, cyclohexanone, tetrahydrofuran, and even chloroform. These polymers had glass‐transition temperatures of 226–255 °C. Most of the polymers could be dissolved in chloroform in as high as a 30 wt % concentration. Thermogravimetric analysis showed that all polymers were stable up to 450 °C, with 10% weight losses recorded from 458 to 497 °C in nitrogen. These transparent, tough, and flexible polymer films could be obtained by solution casting from DMAc solutions. These polymer films had tensile strengths of 79–103 MPa and tensile moduli of 1.5–2.1 GPa. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2066–2074, 2002
Supplementary Figure 2 from FLT3 Ligand Enhances the Cancer Therapeutic Potency of Naked RNA Vaccines (2023)

&lt;p&gt;PDF file - 1.37 MB&lt;/p&gt;
Seasonal Fluctuation of Flavonol Glycosides in Epimedium Species (1989)

The seasonal fluctuation of flavonol glycosides in the leaves of Epimedium grandiflorum var. thunbergianum, E. cremeum and E. sempervirens (Berberidaceae) was investigated. The total content of glycosides was shown in the highest quantity at the flowering time, and as the leaves mature it has become stable amount with a little decrease. The suitable period for the harvest of Epimedium leaves was concluded to be two or three months after the flowering time.
Development of Patient Evacuation Resource Classification System (PERC) Using Systems Engineering to Assist Hospital Evacuations in a Disaster (2020)

The aim of this study was the development of a decision-support tool capable of identifying the most appropriate transportation and local area coalition bed space (resources) for patient evacuations during a crisis. Introduction of the new concept of dichotomous tables and how they are incorporated into the Patient Evacuation Resource Classification (PERC) system. The methods used were Systems Engineering fundamentals to conduct a requirements analysis of the process, develop a new construct guided by functional analysis, design an evidence-based model that accurately identifies patient resource requirements translatable to resource capabilities, and create a prototype for a proof of concept. Research resulted in the PERC system prototype. The PERC system prototype created by this research allows for system testing under a Solomon four-group design simulation with the participation of leading medical, emergency response, academic, consulting industry, and logistics professionals from the Washington, DC, metropolitan area.
INVESTIGATING THE OPTIMAL VIRTUAL REALITY TRAINING STRATEGY: A RANDOMIZED CONTROLLED TRIAL COMPARING SPACED VERSUS MASSED TRAINING IN THE DIRECT ANTERIOR APPROACH FOR TOTAL HIP ARTHROPLASTY (2023)

Evidence supporting the use of virtual reality (VR) training in orthopaedic procedures is rapidly growing. However, the impact of the timing of delivery of this training is yet to be tested. We aimed to investigate whether spaced VR training is more effective than massed VR training. 24 medical students with no hip arthroplasty experience were randomised to learning the direct anterior approach total hip arthroplasty using the same VR simulation, training either once-weekly or once-daily for four sessions. Participants underwent a baseline physical world assessment on a saw bone pelvis. The VR program recorded procedural errors, time, assistive prompts required and hand path length across four sessions. The VR and physical world assessments were repeated at one-week, one-month, and 3 months after the last training session. Baseline characteristics between the groups were comparable (p &gt; 0.05). The daily group demonstrated faster skills acquisition, reducing the median ± IQR number of procedural errors from 68 ± 67.05 (session one) to 7 ± 9.75 (session four), compared to the weekly group's improvement from 63 ± 27 (session one) to 13 ± 15.75 (session four), p &lt; 0.001. The weekly group error count plateaued remaining at 14 ± 6.75 at one-week, 16.50 ± 16.25 at one-month and 26.45 ± 22 at 3-months, p &lt; 0.05. However, the daily group showed poorer retention with error counts rising to 16 ± 12.25 at one-week, 17.50 ± 23 at one-month and 41.45 ± 26 at 3-months, p&lt;0.01. A similar effect was noted for the number of assistive prompts required, procedural time and hand path length. In the real-world assessment, both groups significantly improved their acetabular component positioning accuracy, and these improvements were equally maintained (p&lt;0.01). Daily VR training facilitates faster skills acquisition; however weekly practice has superior skills retention.
Development of Flapping Robot with Self-Takeoff from The Ground Capability (2021)

Birds are agile in locomotion and able to move quickly and easily from one place to another. When a bird is on the ground, and a threat approaches, the bird will fly away and escape. An ornithopter robot provides advantages in energy saving, maneuverability, and crash safety. Most flapping robots require an operator or assistance to take off. The goal of this study is to enable self-takeoff from the ground. The developed robot can generate thrust to its body by exceeding its own weight using a simple flapping mechanism and lightweight design. The result of the takeoff experiment showed that the ornithopter robot was able to self-takeoff from the ground without assistance.
Practical Force-Motion Models for Sliding Manipulation (1996)

The goal of this article is to develop practical descriptions of the relationship between forces and motions in sliding manipu lation. We begin by reviewing the limit surface, a concept from the mechanics of sliding bodies that uses kinematic analysis to find the force and moment required to produce any given sliding motion. Next we provide experimental results showing that the limit surface only approximates the actual force-motion relationship. Then we look at other approximations that can be used to provide a simplified model useful in control, planning, and simulation of manipulation. These approximations include square pyramids, cones, ellipsoids, and ellipsoids with facets removed. Different approximations may be most appropriate, depending on the required computational speed and accuracy and the need to produce conservative results.
Architectural Effects on Acid Reaction-Diffusion Kinetics in Molecular Glass Photoresists (2010)

Understanding acid reaction-diffusion kinetics is crucial for controlling the lithographic performance of chemically amplified photoresists. In this work, we study how the molecular architectures of positive-tone chemically amplified molecular glass resists affect the acid reaction-diffusion kinetics during the post-expose bake (PEB) or annealing step. We compare the acid reaction-diffusion kinetics of a common photoacid generator in molecular glass resists with chemical similarity to poly(4-hydroxystyrene), and that are designed with branched and ring architectures. In situ Fourier transform infrared (FTIR) spectroscopy methods are used to measure reaction rate, acid trapping behavior, and acid diffusivity as a function of PEB temperature. We find that the acid reaction-diffusion kinetics in molecular glass resists is correlated to the film molar density that in turn depends on the architecture of the molecular glass molecules. These results allow modeling of the latent image formation in molecular glass resists that is critical for pattern feature resolution and line edge roughness. A comparison between experimentally measured and theoretically predicted diffusion lengths in one molecular glass resist system was made. Because little is understood of the fundamentals of acid diffusion in this class of molecular glass resists, this paper provides critical insight into the molecular design of next-generation photoresists for high-resolution lithography.
Continuous Fluorescence from Single Colloidal Semiconductor Nanocrystals (2008)

We have synthesized CdZnSe/ZnSe nanocrystals that on the single molecule level exhibit complete suppression of fluorescence blinking, extremely short radiative lifetimes, and multiple emission peaks. Possible mechanisms for these unique optical properties will be discussed.
Enhancing the open circuit voltage of dye sensitized solar cells by surface engineering of silica particles in a gel electrolyte (2013)

We prepared a quasi-solid electrolyte for dye-sensitized solar cells (DSSCs) that consist of ionic liquid and modified silica particles. Commercial bare silica F5 particles and modified silica F5 by NH2 and NH3+ groups were prepared, and fully characterized. The best photovoltaic performance was observed using the NH2 modified silica particles giving an open circuit voltage (Voc) of 815 mV, a short-circuit current (Jsc) of 11.23 mA cm−2, and a fill factor (FF) of 0.75 corresponding to an overall power conversion efficiency of 7.04% at 100 mW cm−2 AM 1.5. The modification of the silica particles by NH2 groups increases the Voc of DSSCs by around 60 mV compared to pure ionic liquid electrolyte based DSSCs.