gebhart/patrepeval huggingface dataset:
ADAMTS13 inhibits oxidative stress and ameliorates progressive chronic kidney disease following ischaemia/reperfusion injury (2020)

Acute kidney injury (AKI) reduces the expression of ADAMTS13 that contributes to progressive CKD, microvascular dysfunction, oxidative stress, inhibition of Nrf2 activity and renal histopathological damage. All of which can be alleviated by administration of rhADAMTS13.
Thyrocalcitonin and the Jejunal Absorption of Calcium, Water, and Electrolytes in Normal Subjects (1973)

Jejunal absorption of calcium, water, and electrolytes was measured in 10 normal subjects by the triple-lumen perfusion method. During the control period, water and electrolyte movements were minimal when a bicarbonate-free test solution was infused. By contrast, bicarbonate-containing solutions were readily absorbed in the control period. Intravenous infusion of synthetic salmon calcitonin (SCT) (1 Medical Research Council U/kg wt/h) over 110-120 min resulted in a marked jejunal secretion of water, sodium, potassium, and chloride in 8 of the 10 subjects. This jejunal secretion occurred with both the bicarbonate-free and the bicarbonate-containing test solutions. Calcium absorption was not affected by SCT, and the serum calcium concentration did not fall during SCT infusion. These results suggest that diarrhea in patients with medullary carcinoma of the thyroid may be due to intestinal secretion secondary to high blood concentrations of thyrocalcitonin.
LIGNIN-KMC: A Toolkit for Simulating Lignin Biosynthesis (2019)

Lignin is an abundant biopolymer of phenylpropanoid monomers that is critical for plant structure and function. Based on the abundance of lignin in the biosphere and interest in lignin valorization, a more comprehensive understanding of lignin biosynthesis is imperative. Here we present an open-source software toolkit, LIGNIN-KMC, that combines kinetic Monte Carlo and first-principles calculations of radical coupling events, which enables modeling of lignin biosynthesis in silico. Specifically, lignification is simulated using the Gillespie algorithm with a graph representation of the lignin fragments and with rates derived from density functional theory calculations of individual fragment couplings. Using this approach, we confirm experimental findings regarding the impact of lignification conditions on final polymer structure and identify new features of fundamental interest to plant cell wall biosynthesis including (1) the monolignol supply rate under in planta lignification conditions likely varies as a function of evolutionary stresses; (2) under conditions of low monolignol supply rates, increasing the fraction of sinapyl alcohol increases the depolymerization yield of monomers upon ether bond cleavage; and (3) by including calculated energetics of caffeyl alcohol homopolymers, the model accurately predicts C-lignin structures. These examples not only highlight the robustness of our modeling framework, but also motivate future studies of new lignin types, unexplored monolignol chemistries, and lignin structure predictions, all with an overarching aim of developing a more comprehensive, molecular understanding of native lignin, which, in turn, can advance the biological and chemistry communities interested in this important biopolymer.
Chromopeptides from phycoerythrocyanin. Structure and linkage of the three bilin groups (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChromopeptides from phycoerythrocyanin. Structure and linkage of the three bilin groupsJohn E. Bishop, Henry Rapoport, Alan V. Klotz, Crystal F. Chan, Alexander N. Glazer, Paul Fueglistaller, and Herbert ZuberCite this: J. Am. Chem. Soc. 1987, 109, 3, 875–881Publication Date (Print):February 1, 1987Publication History Published online1 May 2002Published inissue 1 February 1987https://pubs.acs.org/doi/10.1021/ja00237a039https://doi.org/10.1021/ja00237a039research-articleACS PublicationsRequest reuse permissionsArticle Views201Altmetric-Citations69LEARN 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
Chemie: auf zu neuen Zielen – Gedanken zur Zukunft der Chemie (2004)

Sind Überlegungen zur Zukunft relevant oder dienen sie nur der Zerstreuung? Regelmäßig werden wichtige Grundüberzeugungen aufgrund wissenschaftlicher Erkenntnisse verworfen, mit oft tiefgreifenden Folgen für die Gesellschaft. Falsche Annahmen lassen sich im Nachhinein leicht ausmachen, aber lassen sie sich auch in der Gegenwart erkennen, und lassen sich aus der Erkenntnis Schlussfolgerungen für die Zukunft ziehen? Dieser Essay diskutiert gesellschaftlich akzeptierte Annahmen und das Potenzial der Naturwissenschaften, sie zu widerlegen.
Insights into the Structure of Comirnaty Covid-19 Vaccine: A Theory on Soft, Partially Bilayer-Covered Nanoparticles with Hydrogen Bond-Stabilized mRNA–Lipid Complexes (2023)

Despite the worldwide success of mRNA-LNP Covid-19 vaccines, the nanoscale structures of these formulations are still poorly understood. To fill this gap, we used a combination of atomic force microscopy (AFM), dynamic light scattering (DLS), transmission electron microscopy (TEM), cryogenic transmission electron microscopy (cryo-TEM), and the determination of the intra-LNP pH gradient to analyze the nanoparticles (NPs) in BNT162b2 (Comirnaty), comparing it with the well-characterized PEGylated liposomal doxorubicin (Doxil). Comirnaty NPs had similar size and envelope lipid composition to Doxil; however, unlike Doxil liposomes, wherein the stable ammonium and pH gradient enables accumulation of <sup>14</sup>C-methylamine in the intraliposomal aqueous phase, Comirnaty LNPs lack such pH gradient in spite of the fact that the pH 4, at which LNPs are prepared, is raised to pH 7.2 after loading of the mRNA. Mechanical manipulation of Comirnaty NPs with AFM revealed soft, compliant structures. The sawtooth-like force transitions seen during cantilever retraction imply that molecular strands, corresponding to mRNA, can be pulled out of NPs, and the process is accompanied by stepwise rupture of mRNA-lipid bonds. Unlike Doxil, cryo-TEM of Comirnaty NPs revealed a granular, solid core enclosed by mono- and bilipid layers. Negative staining TEM shows 2-5 nm electron-dense spots in the LNP's interior that are aligned into strings, semicircles, or labyrinth-like networks, which may imply cross-link-stabilized RNA fragments. The neutral intra-LNP core questions the dominance of ionic interactions holding together this scaffold, raising the possibility of hydrogen bonding between mRNA and the lipids. Such interaction, described previously for another mRNA/lipid complex, is consistent with the steric structure of the ionizable lipid in Comirnaty, ALC-0315, displaying free ═O and -OH groups. It is hypothesized that the latter groups can get into steric positions that enable hydrogen bonding with the nitrogenous bases in the mRNA. These structural features of mRNA-LNP may be important for the vaccine's activities in vivo.
Microfluidic droplet-based PCR instrumentation for high-throughput gene expression profiling and biomarker discovery (2015)

PCR is a common and often indispensable technique used in medical and biological research labs for a variety of applications. Real-time quantitative PCR (RT-qPCR) has become a definitive technique for quantitating differences in gene expression levels between samples. Yet, in spite of this importance, reliable methods to quantitate nucleic acid amounts in a higher throughput remain elusive. In the following paper, a unique design to quantify gene expression levels at the nanoscale in a continuous flow system is presented. Fully automated, high-throughput, low volume amplification of deoxynucleotides (DNA) in a droplet based microfluidic system is described. Unlike some conventional qPCR instrumentation that use integrated fluidic circuits or plate arrays, the instrument performs qPCR in a continuous, micro-droplet flowing process with droplet generation, distinctive reagent mixing, thermal cycling and optical detection platforms all combined on one complete instrument. Detailed experimental profiling of reactions of less than 300 nl total volume is achieved using the platform demonstrating the dynamic range to be 4 order logs and consistent instrument sensitivity. Furthermore, reduced pipetting steps by as much as 90% and a unique degree of hands-free automation makes the analytical possibilities for this instrumentation far reaching. In conclusion, a discussion of the first demonstrations of this approach to perform novel, continuous high-throughput biological screens is presented. The results generated from the instrument, when compared with commercial instrumentation, demonstrate the instrument reliability and robustness to carry out further studies of clinical significance with added throughput and economic benefits.
Correction: Benchmarking of survival outcomes following haematopoietic stem cell transplantation: A review of existing processes and the introduction of an international system from the European Society for Blood and Marrow Transplantation (EBMT) and the Joint Accreditation Committee of ISCT and EBMT (JACIE) (2019)

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
A matched biphasic microstimulator for an implantable retinal prosthetic device (2004)

This paper describes the design and implementation of an implantable microstimulator chip designed for stimulating electrodes in a retinal prosthetic device. The chip is capable of providing biphasic current pulses up to 600 /spl mu/A amplitude to a maximum load of 10 k/spl Omega/ with anodic/cathodic matching of 1.3%. The current source operates at low voltage headroom of 0.5 V by using an active feedback setup. The gain variations for output currents are less than 3%. A 1:8 demultiplexing is used for a stimulus frequency of 50-60 Hz. A variable amplification scheme is implemented to maintain a high resolution throughout the entire stimulus range. The outputs are equipped with charge cancellation mechanism to ensure safety of the tissue. Measurement results of a prototype fabricated in AMI 1.6 /spl mu/m bulk CMOS technology are presented.
857 LAMP1 targeting of the large T antigen of merkel cell polyomavirus elicits potent CD4+ T cell responses and prevents tumor growth (2020)

<h3>Background</h3> The majority of Merkel cell carcinomas (MCC), a rare and highly-aggressive type of neuroendocrine skin cancer, are associated with Merkel cell polyomavirus (MCPyV) infection. MCPyV integrates into the host genome, resulting in expression of a truncated form of the viral large T antigen (LT) in infected cells, and making LT an attractive target for therapeutic cancer vaccines. While induction of tumor-reactive CD8+ T cells is a major goal of cancer therapy, CD4+ T cells provide essential support to CD8+ T cells by promoting their expression of cytotoxic effector molecules and increasing their migratory capacity. Cytokines secreted by CD4+ T cells, such as IFNγ, can also exert desirable effects on the tumor microenvironment. Therefore, we set out to design a cancer vaccine that promotes potent, antigen-specific CD4+ T cell responses to MCPyV-LT. <h3>Methods</h3> To activate antigen-specific CD4+ T cells in vivo, we utilized our nucleic acid platform, UNITE (UNiversal Intracellular Targeted Expression), which fuses a tumor-associated antigen with lysosomal-associated membrane protein 1 (LAMP1). This lysosomal targeting technology results in enhanced antigen presentation and a balanced T cell response. LTS220A, encoding a mutated form of MCPyV-LT that abrogates its pro-oncogenic properties, was introduced into the UNITE platform. LTS220A-UNITE, known as ITI-3000, was administered to female C57BL/6 mice intradermally in the ear with electroporation. <h3>Results</h3> ITI-3000 promoted a potent, antigen-specific CD4+ T cell response to MCPyV-LT. Vaccination with ITI-3000 significantly delayed and slowed growth of B16F10 tumors expressing LTS220A in prophylactic and therapeutic settings, respectively. ITI-3000 induced a favorable tumor microenvironment (TME), including significantly enhanced numbers of CD4+ T cells, CD8+ T cells, NK cells, and NKT cells. Tumor-infiltrating myeloid cells were reduced in frequency in vaccinated mice and polarized towards an anti-tumor phenotype. Cytokine analysis of the TME showed significantly enhanced levels of cytokines associated with anti-tumor immune responses in ITI-3000-vaccinated mice, including IFNγ, TNFα, IL-2, and IL-1β. Additionally, ITI-3000 synergized with PD-1 blockade, further reducing tumor burden and enhancing survival in mice receiving combination therapy. <h3>Conclusions</h3> We find that DNA vaccination with ITI-3000 using the UNITE platform enhances CD4+ T cell responses to MCPyV-LT and results in anti-tumor immune responses in a mouse model of Merkel cell carcinoma. <h3>Ethics Approval</h3> This study was approved by Immunomic Therapeutics’ Institutional Animal Care and Use Committee, protocol number 16-11-002.
Research Challenges and Opportunities in Knowledge Representation (2013)

Modern intelligent systems in every area of science rely critically on knowledge representation and reasoning (KR). The techniques and methods developed by the researchers in knowledge representation and reasoning are key drivers of innovation in computer science; they have led to significant advances in practical applications in a wide range of areas from natural-­‐language processing to robotics to software engineering. Emerging fields such as the semantic web, computational biology, social computing, and many others rely on and contribute to advances in knowledge representation. As the era of “Big Data” evolves, scientists in a broad range of disciplines are increasingly relying on knowledge representation to analyze, aggregate, and process the vast amounts of data and knowledge that today’s computational methods generate. We convened the Workshop on Research Challenges and Opportunities of Knowledge Representation in order to take stock in the past decade of KR research, to analyze where the major challenges are, to identify new opportunities where novel KR research can have major impact, and to determine how we can improve KR education as part of the core Computer Science curriculum. The main outcome of the workshop is a set of recommendations both for KR research and for policy-­‐ makers to enable major advancements that will have broad impact in science, technology, and education.
Low coherence digital holographic tomography (2003)

Low coherence digital holographic microscopy (LCDHM) is a new 3D imaging technique combining the advantages of digital holographic microscopy with those of reduced coherence interferometry. This gives the possibility to perform tomography of 3D objects while maintaining the excellent performances of DHM. A tomographic depth resolution of 11 µm has been achieved as a proof of principle. Images of the epithelial cells of the porcine cornea are presented.
Successive Decode-and-Forward Relaying with Reconfigurable Intelligent Surfaces (2021)

The key advantage of successive relaying (SR) networks is their ability to mimic the full-duplex (FD) operation with half-duplex (HD) relays. However, the main challenge that comes with such schemes is the associated inter-relay interference (IRI). In this work, we propose a reconfigurable intelligent surface (RIS)-enhanced SR network, where one RIS is deployed near each of the two relay nodes to provide spatial suppression of IRI, and to maximize the gain of desired signals. The resultant max-min optimization problem with joint phase-shift design for both RISs is first tackled via the semidefinite programming (SDP) approach. Then, a lower-complexity solution suitable for real-time implementation is proposed based on particle swarm optimization (PSO). Numerical results demonstrate that even relatively small RISs can provide significant gains in achievable rates of SR networks, and the proposed PSO scheme can achieve a near optimal performance.
Experiences from on-site dielectric spectroscopy measurements on power transformers (2004)

Electromyographic investigations into the function of the two individual heads of the lateral pterygoid muscle in normal persons are compared with patients suffering the pain of temporomandibular joint dysfunction and those with painless clicks. The results indicate that the lower head of the lateral pterygoid muscle, normally active only when depressing, protruding and deviating the mandible, becomes active on closing and clenching in patients suffering pain. Patients with painless clicks behave as normals. These results are discussed and a theory is presented which suggests that temporomandibular joint dysfunction has a simple pathological basis.
Abruptly focusing X-waves: Nondiffracting waves with localized disruptions (2019)

We present a family of electromagnetic wavepackets with nondiffracting behavior for most of their propagation, but are capable of extremely strong focusing behavior at specified locations, enhancing their peak intensity by over 200 times. © 2019 The Author(s)
Effect of Chlorite Clay-Mineral Dissolution on the Improved Oil Recovery From Sandstone Rocks During Diethylenetriaminepentaacetic Acid Chelating-Agent Flooding (2018)

Summary Sandstone oil reservoirs consist of different clay minerals, such as kaolinite, illite, and chlorite. While these clay minerals can highly affect oil recovery from sandstone oil reservoirs, no attention has been given to investigating the effects of clay minerals during such oil recovery, and no solution has been introduced to alleviate the effects. In this study, and for the first time, the effect of chlorite clay-mineral content on the improved oil recovery (IOR) from different sandstone rock samples was investigated. A new solution was proposed to eliminate the effect of chlorite on the oil recovery from sandstone rocks. Different sandstone cores were used, such as Berea (BSS), Bandera (BND), Kentucky (KSS), and Scioto (SCS) sandstone rocks with different clay minerals. ζ-potential measurements were used to investigate the surface charge of the different clays and different sandstone rocks with different fluids. Fluids such as seawater (SW), low-salinity water (LSW), fresh water, and chelating agents were used. Diethylenetriaminepentaacetic acid (DTPA) chelating agent was introduced to mitigate the chlorite effect on oil recovery from sandstone rocks. The wettability was evaluated using contact-angle measurements and the Amott test for different solutions and different rocks in the presence of actual crude oil. Coreflooding experiments were conducted using these fluids with different sandstone rocks to identify the effect of chlorite on the oil recovery. Coreflooding experiments showed that sandstone cores with high chlorite content yielded the lowest oil recovery when SW and LSW were used. The effect of chlorite on the oil recovery from the two sandstone rocks was minimized with 3 wt% DTPA chelating agent. More oil was recovered in the case of DTPA because of the iron chelation from chlorite. ζ-potential showed that sandstone with high chlorite content has a surface charge close to zero in the case of SW and fresh water. In addition, contact-angle measurements showed that samples with high chlorite content have less water-wetness, which will reduce oil recovery. Contact-angle measurements on chlorite sheets showed that chlorite is oil-wet compared with mica at the same conditions. The addition of high-pH DTPA chelating agent sequestered the iron from the chlorite clay minerals and changed the surface charge to very high negative value, and the contact angle confirmed that the rock changed to water-wet after adding the chelating agent. The Amott index showed that adding DTPA increased the water-wetness for SCS that contains 4 wt% chlorite.
Optical observations of layer ordering in helial smectic A∗ liquid crystals (1993)

Abstract We report the first optical microscopic observation of characteristic textures and the associated layer ordering in a recently discovered, helical smectic A* phase on a multiple domain substrate. The experimental results are quite unusual but consistent with a mean-field model of the twisted grain boundary phase.
Regulation of Neuronal Oxidative and Nitrosative Stress by Endogenous Protective Pathways and Disease Processes (2010)

Oxidative/nitrosative stress contributes to the etiology of many neurological disorders in the developing and aged/mature central nervous system, including acute trauma such as ischemia and hyperoxia, as well as chronic diseases such as Alzheimer's and Parkinson's diseases. In addition to the accumulation of nonspecific oxidative damage, it is becoming clear that pathological conditions lead to the oxidative/nitrosative modification of specific proteins, including those involved in apoptosis, proteolysis, and protein (mis)folding. Several disorders, including stroke and Parkinson's disease, are associated with inactivating modifications of antioxidant enzymes themselves, thus compromising antioxidant defenses. Conversely, neuroprotective pathways, such as neurotrophin- and synaptic activity-induced signals, can upregulate key antioxidant systems, potentially contributing to the cytoprotective actions of adaptive stress responses following exercise or calorie-restriction. On the flip-side, hypofunction of these pathways is associated with the death of developing neurons. An increased knowledge of how neuronal antioxidant systems are controlled in health and disease is unearthing therapeutic targets in several disorders. Moreover, the emerging importance of master regulators of antioxidant defenses such as nuclear factor-erythroid 2-related factor 2 (Nrf2) and peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α) is revealing ways through which intrinsic defenses may be manipulated to combat oxidative/nitrosative stress. Such approaches offer an alternative strategy to classical antioxidant interventions based on the administration of free radical scavengers and spin-traps.
Mechanical Pretreatment of Lead Based Alloy Anode for Zinc Electrowinning (2012)

This chapter contains sections titled: Introduction Test Method Results and Discussion Conclusions Acknowledgments
Factors Affecting Perceptual Threshold in Argus II Retinal Prosthesis Subjects (2013)

Reported Argus II clinical study results are in good agreement with prior in vitro and in vivo studies, and support the development of higher-density systems that employ smaller diameter electrodes. (clinicaltrials.gov identifier: NCT00407602).
Detection of Barrett’s neoplasia with a near-infrared fluorescent heterodimeric peptide (2022)

This "first-in-human" clinical study demonstrates the feasibility of detection of early Barrett's neoplasia using a NIR-labeled peptide heterodimer.
Special issue on robot and human interactive communication (2019)

We are pleased to announce the special issue on Robot and Human Interactive Communication 2020. The first special issue was published in 2019 to celebrate the promotion of the IEEE International Sy...