gebhart/patrepeval huggingface dataset:
Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation (2020)

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.
Supplementary Figure 2 from Activation of Hematopoietic Stem/Progenitor Cells Promotes Immunosuppression Within the Pre–metastatic Niche (2023)

&lt;p&gt;Analysis of the bone marrow microenvironment and CXCR4 expression on E0771 BCA Tumor cells&lt;/p&gt;
PARP inhibition promotes endothelial‐like traits in melanoma cells and modulates pericyte coverage dynamics during vasculogenic mimicry (2022)

Vasculogenic mimicry (VM) describes the ability of highly aggressive tumor cells to develop pseudovascular structures without the participation of endothelial cells. PARP1 is implicated in the activation of hypoxia-inducible factors, which are crucial in tumor neovascularization. We have explored the role of hypoxia and PARP inhibition in VM. In uveal melanoma xenografts, the PARP inhibitor olaparib improved in vivo pericyte coverage specifically of VM channels. This was concomitant with reduced metastasis in olaparib-treated VM<sup>+</sup> tumors. PARP inhibition and hypoxia modulated melanoma tube formation in vitro, inducing a more sparse and regular tubular architecture. Whole-transcriptome profiling revealed that olaparib treatment under hypoxic conditions modulated the expression of genes implicated in vasculogenesis during tube formation, enhancing the endothelial-like phenotype of VM<sup>+</sup> uveal melanoma cells. PARP inhibition, especially during hypoxia, upregulated PDGFβ, which is essential for pericyte recruitment. Our study indicates that PARP inhibitors may enhance the endothelial characteristics of VM<sup>+</sup> cells, modulate pericyte coverage, and reduce metastatic spread in VM<sup>+</sup> melanoma. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Identification of Hookworm DAF-16/FOXO Response Elements and Direct Gene Targets (2010)

Our results show that Ac-DAF-16 is involved in diverse biological processes throughout hookworm development. Further investigation of these target genes will provide insights into the molecular basis by which Ac-DAF-16 regulates its downstream gene network in hookworm infection.
Unsupervised Medical Image Segmentation Based on the Local Center of Mass (2018)

Image segmentation is a critical step in numerous medical imaging studies, which can be facilitated by automatic computational techniques. Supervised methods, although highly effective, require large training datasets of manually labeled images that are labor-intensive to produce. Unsupervised methods, on the contrary, can be used in the absence of training data to segment new images. We introduce a new approach to unsupervised image segmentation that is based on the computation of the local center of mass. We propose an efficient method to group the pixels of a one-dimensional signal, which we then use in an iterative algorithm for two- and three-dimensional image segmentation. We validate our method on a 2D X-ray image, a 3D abdominal magnetic resonance (MR) image and a dataset of 3D cardiovascular MR images.
Video Coding for Machines with Feature-Based Rate-Distortion Optimization (2020)

Common state-of-the-art video codecs are optimized to deliver a low bitrate by providing a certain quality for the final human observer, which is achieved by rate-distortion optimization (RDO). But, with the steady improvement of neural networks solving computer vision tasks, more and more multimedia data is not observed by humans anymore, but directly analyzed by neural networks. In this paper, we propose a standard-compliant feature-based RDO (FRDO) that is designed to increase the coding performance, when the decoded frame is analyzed by a neural network in a video coding for machine scenario. To that extent, we replace the pixel-based distortion metrics in conventional RDO of VTM-8.0 with distortion metrics calculated in the feature space created by the first layers of a neural network. Throughout several tests with the segmentation network Mask R-CNN and single images from the Cityscapes dataset, we compare the proposed FRDO and its hybrid version HFRDO with different distortion measures in the feature space against the conventional RDO. With HFRDO, up to 5.49% bitrate can be saved compared to the VTM-8.0 implementation in terms of Bjøntegaard Delta Rate and using the weighted average precision as quality metric. Additionally, allowing the encoder to vary the quantization parameter results in coding gains for the proposed HFRDO of up 9.95% compared to conventional VTM.
Evaluation of Conductive Inks for Anti-Counterfeiting Deterrents (2008)

When using security printing for product protection, deploying magnetic or conductive inks can increase the number of ways in which the printed information on a package or label can be authenticated. This approach is commonly used with bank checks, where the routing and account numbers are printed at the bottom of the check in MICR (magnetic ink character recognition) ink and can be authenticated both visually using OCR (optical character recognition) and magnetically via an electronic check reader. As improved conductive inks are developed for use in inkjet printing, additional approaches may be deployed in which two or more methods can be used to authenticate printed information.In this paper we examine the print quality of MICR ink and a new silver-based conductive ink. We use the 2D DataMatrix bar code as a test vehicle for verifying print quality. We also implement structural pre-compensation to increase the range of module sizes which authenticate. We then examine the feasibility and difficulty of counterfeiting a personal bank check and discuss the issues surrounding authentication approaches.
draft-irtf-cfrg-bls-signature-00.txt (2019)

BLS is a digital signature scheme with compression properties. With a
given set of signatures (signature_1, ..., signature_n) anyone can
produce a compressed signature signature_compressed. The same is true
for a set of secret keys or public keys, while keeping the connection
between sets (i.e., a compressed public key is associated to its
compressed secret key). Furthermore, the BLS signature scheme is
deterministic, non-malleable, and efficient. Its simplicity and
cryptographic properties allows it to be useful in a variety of use-
cases, specifically when minimal storage space or bandwidth are
required.
Quasilinear control approach to wind farm power control (2013)

Quasilinear Control (QLC) is a set of methods for analysis and design of systems with nonlinear actuators and sensors. The approach of QLC is based on the method of stochastic linearization, which replaces each nonlinearity with an equivalent gain and bias. In this paper, we apply QLC for controller design of a wind farm with multiple wind turbines. These turbines are modeled by a linear plant preceded by an asymmetric saturation nonlinearity, which accounts for limited availability of wind. It is shown, using numerical simulations, that the controllers obtained via QLC perform significantly better in a broad range of regimes as compared to those designed in our earlier work by ignoring the saturations.
Secnidazole Is a Promising Imidazole Mitigator of Serratia marcescens Virulence (2021)

<i>Serratia marcescens</i> is an opportunistic pathogen that causes diverse nosocomial infections. <i>S. marcescens</i> has developed considerable resistance to different antibiotics and is equipped with an armory of virulence factors. These virulence factors are regulated in <i>S. marcescens</i> by an intercellular communication system termed quorum sensing (QS). Targeting bacterial virulence and QS is an interesting approach to mitigating bacterial pathogenesis and overcoming the development of resistance to antimicrobials. In this study, we aimed to evaluate the anti-virulence activities of secnidazole on a clinical isolate of <i>S. marcescens</i>. The effects of secnidazole at sub-inhibitory concentrations (sub-MICs) on virulence factors, swarming motility, biofilm formation, proteases, hemolysin activity, and prodigiosin production were evaluated in vitro. Secnidazole's protective activity against <i>S. marcescens</i> pathogenesis was assessed in vivo in mice. Furthermore, a molecular docking study was conducted to evaluate the binding ability of secnidazole to the <i>S. marcescens</i> SmaR QS receptor. Our findings showed that secnidazole at sub-MICs significantly reduced <i>S. marcescens</i> virulence factor production in vitro and diminished its pathogenesis in mice. The <i>insilico</i> docking study revealed a great ability of secnidazole to competitively hinder the binding of the autoinducer to the SmaR QS receptor. In conclusion, secnidazole is a promising anti-virulence agent that may be used to control infections caused by <i>S. marcescens</i>.
Single‐Site vs. Cluster Catalysis in High Temperature Oxidations (2021)

Abstract The behavior of single Pt atoms and small Pt clusters was investigated for high‐temperature oxidations. The high stability of these molecular sites in CHA is a key to intrinsic structure–performance descriptions of elemental steps such as O 2 dissociation, and subsequent oxidation catalysis. Subtle changes in the atomic structure of Pt are responsible for drastic changes in performance driven by specific gas/metal/support interactions. Whereas single Pt atoms and Pt clusters (&gt; ca. 1 nm) are unable to activate, scramble, and desorb two O 2 molecules at moderate T (200 °C), clusters &lt;1 nm do so catalytically, but undergo oxidative fragmentation. Oxidation of alkanes at high T is attributed to stable single Pt atoms, and the C‐H cleavage is inferred to be rate‐determining and less sensitive to changes in metal nuclearity compared to its effect on O 2 scrambling. In contrast, when combustion involves CO, catalysis is dominated by metal clusters, not single Pt atoms.
Hexazirconium‐ and Hexahafnium‐Containing Tungstoarsenates(III) and Their Oxidation Catalysis Properties (2010)

Six of the best! Two Zr6- and Hf6-containing tungstoarsenates(III) [M6O4(OH)4(H2O)2(CH3COO)5(AsW9O33)2]11− (M=Zr, Hf) have been synthesized and structurally characterized in solution and in the solid state, and both species are highly active in H2O2-based selective oxidations. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Comparative anatomy and evolution of the gastrotrich muscular system (2002)

Gastrotrichs figure prominently in metazoan phylogeny because they share a suite of complex morphological characteristics with several other members of the Bilateria. But their microscopic size, cryptic interstitial habitat, and lack of fossil record have exacerbated the usual barriers to phylogenetic analysis. To arrive at a better understanding of gastrotrich systematics and evolution, cladistic analyses and detailed studies of the muscular system were performed. A fluorescent F-actin stain was applied to whole mounts of 26 species of Gastrotricha to characterize the musculature. Muscle patterns were mapped, their functions inferred, and the direction of evolution hypothesized for several families. The musculature of all gastrotrichs is arranged as a series of circular, helicoidal, and longitudinal bands around the digestive tract. Circular muscles are generally present in splanchnic and somatic positions. Helicoidal muscles in 50--60° angles are present on the pharynx and intestine of most species. Longitudinal muscles are arranged radially around the digestive tract in dorsal, lateral, ventral and ventrolateral positions. Extraordinary muscle orientations are present in several species. In macrodasyidan gastrotrichs, the musculature of Dactylopodola baltica (Dactylopodolidae) is considered to be closest to the ground pattern of the phylum and consists of the following: splanchnic circular muscles on the pharynx and intestine, longitudinal muscles in dorsal, lateral, ventral and ventrolateral positions, pharyngeal and intestinal helicoidal muscles, and somatic circular muscles. Within the Chaetonotida, species of Neodasys and Xenotrichula have the most plesiomorphic muscle topologies. Muscle patterns are similar to macrodasyidans though several muscle orientations have become reduced (splanchnic and somatic circular muscles), are the result of evolutionary modification to existing muscles (incomplete splanchnic and somatic circular muscles, dorsoventral muscles) or evolved independently (the branched Ruckenhautmuskel). This study relied on a phylogenetic perspective to delineate the origin of specific muscle patterns in gastrotrichs and allow for the separation of phyletic heritage from adaptation. Several species from both orders possess muscle patterns that can be regarded as apomorphic and may therefore serve as taxonomic characters. Closer scrutiny of these species may reveal the underlying selective processes that led to the origin and maintenance of novel muscle orientations in gastrotrichs.
Challenges in vaccinology (1996)

The science of vaccinology, i.e. the induction of immune responses for the prevention and treatment of infectious and chronic diseases, will lead to better understanding of the immune mechanisms involved and technological ways to trigger these. This article describes the current situation with respect to the large-scale application of microbial vaccines and describes the various components of the adaptive immune system, the effector and memory B, CD4+ and CD8+ T cells. New vaccine technologies such as antigen delivery, adjuvants, synthetic constructs, nucleic acid vaccines, live vectors and mucosal immunization are described. Possibilities for the improvement of existing vaccines and the development of new vaccines are noted.
Study on Full Digital Beamforming for HAPS Backhaul System with Base Station On-board Using 38 GHz Band Frequency (2021)

Extreme coverage extension is one of its requirements and use cases in beyond 5G and 6G era. HAPS (high-altitude platform station) has drawn attention because of its characteristics to stay at a fixed location of an altitude of about 20 km, typically forming a coverage area with a cell radius of more than 50 km on the ground and having much lower latency than LEO with a one-way propagation time of about 0.1 ms. This paper treats a HAPS backhaul system using the millimeter wave band (38 GHz band) with base station on-board. In this target system, huge number of antenna array elements for beamforming is needed to compensate free space loss in 38 GHz band, and full digital beamforming is desired to connect multiple ground stations for feeder and service links and at the same time. Since digital beamforming needs analog circuit for each antenna array element, it leads to high power consumption. Phase coherency calibration is needed for every array antenna element to achieve good beamforming performance, and real-time calibration to directly measure in-band characteristics in 38 GHz band is desired in a circumstance of very low temperature and very low atmospheric pressure at stratosphere. It is technically challenging because of huge number of array antenna element. For these technical issues, we propose power reduction by low resolution ADC/DAC with dithering by utilizing beamforming gain and real-time phase coherency calibration to directly measure in-band characteristics in 38 GHz band without interrupting to transmit main signal by superimposing known spread spectrum signal with low power level. Computer simulation shows that when the target of phase error is $\sigma$ = 1 degree (i.e., SNR = 35 dB) or less with 5 bits of DAC input, calibration for 2 polarization (vertical and horizontal) and 1024 antenna elements can be done every 4 seconds.
Fluoroolefins. II. Isomerization of .beta.-substituted perfluoroolefins. Kinetic vs. equilibrium control (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFluoroolefins. II. Isomerization of .beta.-substituted perfluoroolefins. Kinetic vs. equilibrium controlDonald J. Burton and Frank E. HerkesCite this: J. Org. Chem. 1968, 33, 5, 1854–1860Publication Date (Print):May 1, 1968Publication History Published online1 May 2002Published inissue 1 May 1968https://pubs.acs.org/doi/10.1021/jo01269a033https://doi.org/10.1021/jo01269a033research-articleACS PublicationsRequest reuse permissionsArticle Views197Altmetric-Citations28LEARN 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 Get e-Alerts
A model and compilation strategy for out-of-core data parallel programs (1995)

It is widely acknowledged in high-performance computing circles that parallel input/output needs substantial improvement in order to make scalable computers truly usable. We present a data storage model that allows processors independent access to their own data and a corresponding compilation strategy that integrates data-parallel computation with data distribution for out-of-core problems. Our results compare several communication methods and I/O optimizations using two out-of-core problems, Jacobi iteration and LU factorization.
The Standard Map Machine (1989)

Abstract : The Standard Map Machine (SMM) is designed as an answer to the intensive computational requirements involved in the study of chaotic behavior in nonlinear systems. The high-speed and high-precision performance of this computer is due to its simple architecture specialized to the numerical computations required of nonlinear systems. This report will discuss the design and implementation of this special-purpose machine. (JHD)
Balanced octave-tunable absorptive bandstop filter (2018)

This paper presents, for the first time, a balanced octave-tunable absorptive bandstop filter. The balanced (differential) operation is realized by coupling two transmission lines with an opposite polarity to each of two high-Q tunable Substrate Integrated Waveguide (SIW) cavity resonators. The filter is based on the 90 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sup> hybrid-coupler absorptive bandstop filter topology enabling high levels of rejection over a wide tuning range. Both simulated and measured results are shown. The total size of the proposed filter is 0.39λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> × 0.36λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> (λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> at 1.57 GHz), and it is tunable from 1.57-3.18 GHz with 102% tuning range. Over the full range, the measured 10-dB fractional bandwidth ranges from 1-2.4%, and the attenuation level is better than 47 dB.
Surface treatments and coatings to maintain fresh‐cut mango quality in storage (2010)

This study with repeated experiments showed that calcium ascorbate with citric acid and N-acetyl-L-cysteine maintained cut mango slices attractiveness in storage by keeping light color in both varieties. The addition of a polysaccharide coating did not consistently improve quality.
Stereoselective Synthesis and Biological Profile of All Stereoisomers of Lactam Analogues of Strigolactones GR24 and GR18 (2023)

Abstract Strigolactones (SLs) are signaling molecules involved in plant development and governing interactions with soil microorganisms in the rhizosphere as well as the germination of parasitic weeds. Developing their use in Crop Protection is a promising approach to a sustainable agriculture by mitigating biotic and abiotic stresses. Recently, a new class of lactam analogues of SL has emerged, namely strigolactams, displaying outstanding potency to induce the germination of parasitic weed O. cumana as well as enhanced chemical and soil stability. Herein, we describe the stereoselective synthesis of GR24 and GR18 lactams harnessing the chemistry of chiral keteniminium (KI) salts, in particular the unprecedented reactivity of chloro‐substituted KI, supported by DFT calculations. We disclose subsequently the biological activity on corn of the 32 stereopure strigolactams prepared, highlighting the crucial influence of stereochemistry and lactam substitution, rationalized by docking analyses. Finally, we performed stability studies in soil, which reveal that stereoisomers display very different half‐lives, reflecting the significant impact of stereochemistry on degradation kinetics.
Postoperative pain due to an occult spinal infection: A case report (2021)

The development of postoperative lower back pain and/or lumbar radicular pain can be a sign of a spinal infection. A thorough clinical and laboratory work-up is essential in the preoperative evaluation of patients with spinal pain.