gebhart/patrepeval huggingface dataset:
A conserved immune trajectory of recovery in hospitalized COVID-19 patients (2022)

Abstract Many studies have provided insights into the immune response to COVID-19; however, little is known about the immunological changes and immune signaling occurring during COVID-19 resolution. Individual heterogeneity and variable disease resolution timelines obscure unifying immune characteristics. Here, we collected and profiled &gt;200 longitudinal peripheral blood samples from patients hospitalized with COVID-19, with other respiratory infections, and healthy individuals, using mass cytometry to measure immune cells and signaling states at single cell resolution. COVID-19 patients showed a unique immune composition and an early, coordinated and elevated immune cell signaling profile, which correlated with early hospital discharge. Intra-patient time course analysis tied to clinically relevant events of recovery revealed a conserved set of immunological processes that accompany, and are unique to, disease resolution and discharge. This immunological process, together with additional changes in CD4 regulatory T cells and basophils, accompanies recovery from respiratory failure and is associated with better clinical outcomes at the time of admission. Our work elucidates the biological timeline of immune recovery from COVID-19 and provides insights into the fundamental processes of COVID-19 resolution in hospitalized patients.
DEVELOPING PLANT REGENERATION SYSTEMS FOR IN VITRO CONSERVATION OF MANDARIN (CITRUS RETICULATA) AND PUMMELO (CITRUS MAXIMA) (2005)

ISHS International Symposium on Harnessing the Potential of Horticulture in the Asian-Pacific Region DEVELOPING PLANT REGENERATION SYSTEMS FOR IN VITRO CONSERVATION OF MANDARIN (CITRUS RETICULATA) AND PUMMELO (CITRUS MAXIMA)
Evaluating the Effect of Applying the FDA Definition of Whole Grains to Health Claims for Risk Reduction of Cardiovascular Disease and Diabetes (2009)

The U.S. Food and Drug Administration (FDA) defines whole grains as consisting of the intact, ground, cracked or flaked fruit of the grains whose principal components‐the starchy endosperm, germ and bran‐are present in the same relative proportions as they exist in the intact grain. We evaluated the effect of applying the FDA definition of whole grains on the strength of scientific evidence in support of claims for risk reduction of cardiovascular disease (CVD) and diabetes. We concluded that using the FDA definition for whole grains as a selection criterion is limiting because the majority of existing studies often use a broader meaning to define whole grains. When considering only whole grain studies that met the FDA definition we found insufficient scientific evidence to support a claim that whole grain intake reduces the risk of CVD. However, a whole grain and CVD health claim is supported when using a broader concept of whole grain to include studies that included intake of bran and germ as well as whole grain. The scientific evidence on the relationship of whole grain consumption and diabetes is suggestive but inconclusive whether or not the definition of whole grains was in accordance with that of the FDA. This type of analysis is complicated by variation among different types of whole grains due to their diversity in nutrients and bioactive components. This project was sponsored by Kellogg Company, USA.
A Monolithic Forward-View Optical Scanner by a Pair of Upright MEMS Mirrors on a SiOB for LiDAR Applications (2021)

A forward-view optical scanner made of a MEMS mirror typically needs a second mirror to fold the optical beam forward, and thus an assembly structure is required, which drastically increases the overall size and weight of the scanner. This paper reports an ultra-small forward-view optical scanner with two vertically oriented micromirrors integrated on a silicon optical bench (SiOB). A new latch structure is proposed to secure the mirror frame at its vertical position and an array of meander thin-film stripes is designed to assist the latching process. The new design has been successfully fabricated and shows much-improved verticality with a maximum deviation of less than ±2° from 90°. With an optical aperture of 0.7 mm, the form factor of the MEMS chip is 4.9 mm (length) by 4.7 mm (width) by 1.8 mm (height). The measured forward field of view (FoV) of the vertical micromirrors reaches 21° in both axes at non-resonance with the voltage amplitude less than 4 V. The first resonant frequency (corresponding to the mirror frame rotation mode) of the micromirror is about 630 Hz. A fiber-pigtail bonded forward scanner is assembled with a footprint of 2 cm by 1.2 cm and a weight of 0.6 g. A forward scanning LiDAR has been built with this new MEMS scanner. The non-resonant scanning capability enables forward-view adaptive resolution and zoom-in scanning capability. [2021-0132]
Protective Role of Interleukin-6 duringYersinia enterocoliticaInfection Is Mediated through the Modulation of Inflammatory Cytokines (2004)

ABSTRACT Yersinia enterocolitica is a gram-negative enteric pathogen responsible for a number of gastrointestinal disorders. A striking feature of the pathology of a Y. enterocolitica infection is inflammation. Recently, we demonstrated a role for interleukin-1α (IL-1α) in the establishment of intestinal inflammation in response to a Y. enterocolitica infection. A cytokine directly affected by IL-1 levels is IL-6. A previous report suggested that IL-6 plays an anti-inflammatory role during Y. enterocolitica infection, and in other systems IL-6 has been shown to be proinflammatory. Therefore, a closer examination of the roles of IL-6 and inflammatory cytokines in the control of Y. enterocolitica infection in IL-6 −/− mice was undertaken. Y. enterocolitica organisms were more virulent in the IL-6 −/− mice (60-fold decreased 50% lethal dose) and colonized systemic tissues more rapidly and to a higher level than in the wild-type mice. One role of IL-6 during a Y. enterocolitica infection may be the downmodulation of the inflammatory response. The IL-6 −/− mice have a more robust T H 1 T-cell response, as well as hyperinflammatory pathologies. These phenotypes appear to be due to the misregulation of tumor necrosis factor alpha, monocyte chemotactic protein 1, IL-10, transforming growth factor β1, and gamma interferon in the IL-6 −/− mouse. These data provide further insight into the intricate cytokine signaling pathways involved in the regulation of inflammatory responses and the control of bacterial infections.
The future of human cerebral cartography: a novel approach (2015)

Cerebral cartography can be understood in a limited, static, neuroanatomical sense. Temporal information from electrical recordings contributes information on regional interactions adding a functional dimension. Selective tagging and imaging of molecules adds biochemical contributions. Cartographic detail can also be correlated with normal or abnormal psychological or behavioural data. Modern cerebral cartography is assimilating all these elements. Cartographers continue to collect ever more precise data in the hope that general principles of organization will emerge. However, even detailed cartographic data cannot generate knowledge without a multi-scale framework making it possible to relate individual observations and discoveries. We propose that, in the next quarter century, advances in cartography will result in progressively more accurate drafts of a data-led, multi-scale model of human brain structure and function. These blueprints will result from analysis of large volumes of neuroscientific and clinical data, by a process of reconstruction, modelling and simulation. This strategy will capitalize on remarkable recent developments in informatics and computer science and on the existence of much existing, addressable data and prior, though fragmented, knowledge. The models will instantiate principles that govern how the brain is organized at different levels and how different spatio-temporal scales relate to each other in an organ-centred context.
Electro-Optical and Acousto-Optical Devices (2018)

Electro-optical and acoustic-optical devices are extremely important components of modern technological instruments and users devices. They are also frequently used in scientific research. They are based on the phenomena of photoconduction, photo-detection, and electro-optic and acousto-optic modulation. These concepts, the theory behind them, and their main applications are described in great detail in this chapter.
Faculty Opinions recommendation of Induction of dendritic spines by an extracellular domain of AMPA receptor subunit GluR2. (2003)

Synaptic transmission from excitatory nerve cells in the mammalian brain is largely mediated by AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid)-type glutamate receptors located at the surface of dendritic spines. The abundance of postsynaptic AMPA receptors correlates with the size of the synapse and the dimensions of the dendritic spine head. Moreover, long-term potentiation is associated with the formation of dendritic spines as well as synaptic delivery of AMPA receptors. The molecular mechanisms that coordinate AMPA receptor delivery and spine morphogenesis are unknown. Here we show that overexpression of the glutamate receptor 2 (GluR2) subunit of AMPA receptors increases spine size and density in hippocampal neurons, and more remarkably, induces spine formation in GABA-releasing interneurons that normally lack spines. The extracellular N-terminal domain (NTD) of GluR2 is responsible for this effect, and heterologous fusion proteins of the NTD of GluR2 inhibit spine morphogenesis. We propose that the NTD of GluR2 functions at the cell surface as part of a receptor-ligand interaction that is important for spine growth and/or stability. PMID: 12904794 Funding information This work was supported by: Telethon, Italy Grant ID: TCP01014
Interferon epsilon mRNA expression could represent a potential molecular marker in cervical cancer. (2018)

The effects of the immune system response in the malignant transformation process have been described. Molecules such as interferons are involved in such process. Interferons are small single-chained glycoproteins, involved in the first line of defense against pathogens such as viruses, bacteria, and parasites. Interferon epsilon (IFNε) is located in the 9p21.3 cytogenetic region, transcribes into a single exon mRNA. Contrary to other family members, IFNε exerts low antiviral activity. In the present work molecular alterations such as copy number variation (CNV) and expression were analyzed by available microarrays and fifty-nine cervical tissues ranging from normal to cancer and three cell lines were assessed for IFNε expression by RT-PCR, immunohistochemistry, and immunocytofluorescence. No significant CNV alterations were observed. Positive immunosignal was primarily present in the proliferative basal strata cells in the normal tissue, whereas in cervical cancer, all epithelial transformed cells were positive. The cell lines analyzed were HPV16, -18, and negative, all three cell-lines were positive for cytoplasmic protein presence. Interestingly, at the mRNA level, increased band intensity was observed, as the lesions were higher, and IFNε up-regulation in CC (<i>P=0.0001</i>) is reported here. Our results suggest that up-regulation is present as an independent event from single or multiple HPV infection (<i>P=0.90</i>). In conclusion, we suggest that IFNε mRNA up-regulation could represent a potential molecular marker in CC. Expression of IFNε might not be related to HPV infection or CNV, which could have an important role in cellular homeostasis and could influence immune related events in cervical carcinogenesis.
Playback-Buffer Equalization for Streaming Media using Stateless Transport Prioritization (2003)

Streaming media applications are plagued with playback disruptions due to client buffer underflow resulting from fluctuations in network throughput. When some clients are experiencing buffer underflow and disruptions, other clients may have excess buffered data. This suggests that disruptions can be reduced by the redistribution of resources to provide higher throughput to streaming sessions with less buffered data, that is, to sessions with greater need. This paper proposes a scheme that achieves an effective or endto-end result of the above dynamic resource allocation without the use of either explicit per-session resource reservation or across-session coordination. Instead, each packet is stamped at the source with the buffer occupancy of the session, and prioritized scheduling is performed at the resource bottleneck to favor packets with smaller buffer occupancy. Due to the actions of end-to-end congestion control, higher throughput can then be maintained for streaming sessions with less buffer. Experimental and simulation results show that the proposed scheme can increase the mean time between playback disruptions by a factor of 4 for fixed initial buffer time, or reduce the required initial buffer by a factor of 2.5 for fixed probability of hitting a playback disruption.
Enhanced tunable Raman amplification/attenuation and parametric Raman wavelength conversion in submicrometer silicon waveguides via temperature variation (2011)

We analytically characterize the temperature dependence of Raman amplification, Raman attenuation, and parametric Raman wavelength conversion (PRWC) in submicrometer silicon waveguides (WGs) over the temperature range of 100 to 500 K, near the O-band and C-band wavelengths of 1.33 and 1.55 μm. The efficiencies of Raman amplification/attenuation and PRWC are studied in the context of how the interplay among the Raman gain, two-photon absorption, free-carrier absorption, sidewall roughness, pump-signal-input intensity ratio, and phase matching condition influences the wave propagation in the submicrometer WG at different temperatures. Our results show that the effects of temperature variation can be harnessed to enhance and tune the Raman amplification/attenuation and PRWC. This offers a more dynamic control of the Raman performances of submicrometer silicon WG devices as compared to conventional silicon Raman WG devices operating at a fixed (room) temperature.
A disclosure form for work submitted to medical journals: a proposal from the International Committee of Medical Journal Editors. (2020)

Many factors, including professional and personal relationships and activities, can influence the design, conduct, and reporting of the clinical science that informs health-care decisions. The potential for conflict of interest exists when these relationships and activities may bias judgment. 1 International Committee of Medical Journal Editors. Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals. www.icmje.org/icmje-recommendations.pdf (accessed Dec 17, 2019). Google Scholar Many stakeholders—editors, peer reviewers, clinicians, educators, policy makers, patients, and the public—rely on the disclosure of authors' relationships and activities to inform their assessments. Trust in the transparency, consistency, and completeness of these disclosures is essential.
Adenylate cyclase toxin from Bordetella pertussis (1989)

Bordetella pertussis adenylate cyclase (AC) toxin is a calmodulin-activated adenylate cyclase enzyme which has the capacity to enter eukaryotic target cells and catalyze the conversion of endogenous ATP into cyclic AMP. In this work, the AC holotoxin molecule is identified and isolated. It is a single polypeptide of apparent 216 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Monoclonal antibodies which immunoprecipitate AC activity from extracts of wild type B. pertussis (BP338) react with this 216-kDa band on Western blots, and it is absent from a transposon Tn5 mutant (BP348) specifically lacking AC toxin. Isolation of the 216-kDa protein to greater than 85% purity by hydrophobic chromatography, preparative sucrose gradient centrifugation, and affinity chromatography using either calmodulin-Sepharose or monoclonal antibody coupled to Sepharose 4B yields stepwise increases in AC toxin potency, to a maximum of 88.3 mumol of cAMP/mg of target cell protein/mg of toxin. Electroelution of the 216-kDa band following sodium dodecyl sulfate-polyacrylamide gel electrophoresis yields a preparation with both AC enzyme and toxin activities. These data indicate that this protein represents the AC holotoxin molecule.
Traditional soil particle sphericity, roundness and surface roughness by computational geometry (2015)

Definitions of soil particle sphericity, roundness and roughness have existed since at least the 1930s. In the 1950s, charts of typical sphericity and roundness values were developed to alleviate tedious manual determination. They allowed users to classify particles by visual comparison to typical particles possessing ranges of sphericity and roundness. The original definitions and somewhat subjective chart methods are still widely used today. This paper describes robust numerical methods based on computational geometry to determine precisely the traditional values from two-dimensional images of particles. Statistical methods including locally weighted regression and K-fold cross-validation were used to discretise a mean particle surface and thereby quantify and remove roughness. The paper details the algorithms for identifying particle corners and fitting circles to them for computation of roundness. Conclusions are also drawn regarding the most appropriate definition for particle sphericity from among five that are commonly cited. Finally, recommendations are made for the minimum image resolutions and particle perimeter discretisation necessary to obtain accurate results.
Iterative Structure-Based Peptide-Like Inhibitor Design against the Botulinum Neurotoxin Serotype A (2010)

The botulinum neurotoxin serotype A light chain (BoNT/A LC) protease is the catalytic component responsible for the neuroparalysis that is characteristic of the disease state botulism. Three related peptide-like molecules (PLMs) were designed using previous information from co-crystal structures, synthesized, and assayed for in vitro inhibition against BoNT/A LC. Our results indicate these PLMS are competitive inhibitors of the BoNT/A LC protease and their K(i) values are in the nM-range. A co-crystal structure for one of these inhibitors was determined and reveals that the PLM, in accord with the goals of our design strategy, simultaneously involves both ionic interactions via its P1 residue and hydrophobic contacts by means of an aromatic group in the P2' position. The PLM adopts a helical conformation similar to previously determined co-crystal structures of PLMs, although there are also major differences to these other structures such as contacts with specific BoNT/A LC residues. Our structure further demonstrates the remarkable plasticity of the substrate binding cleft of the BoNT/A LC protease and provides a paradigm for iterative structure-based design and development of BoNT/A LC inhibitors.
ChemInform Abstract: LOW ACTIVATION ENERGY CONDUCTION IN POLYCRYSTALLINE α‐ALUMINA DOPED WITH SILICON AND SODIUM (1985)

Abstract Polykristallines Al 2 O 3 mit einer zweiten Phase von glasartigem Aluminosilicat zeigt in Gegenwart von Na Leitfähigkeit mit niedriger Aktivierungsenergie (es 66.5 kJ/mol).
Mitochondria1 Asparaginyl‐tRNA Synthetase Encoded by the Yeast Nuclear Gene YCR24c (1997)

One of the open reading frames located on yeast Saccharomyces cerevisiae chromosome III, YCR24c, appeared to code for a protein of unknown function, but the predicted sequence showed similarity with asparaginyl-tRNA synthetase from Escherichia coli, with 38% amino acid identity. There is a putative mitochondrial targeting signal at the N-terminus of the YCR24c product. Northern blot analysis of total RNA from a wild-type strain sigma1278b confirmed that YCR24c was transcribed. Disruption of the chromosomal copy of YCR24c in a respiratory-competent haploid cell induced a petite phenotype, but did not affect cell viability. This respiratory-defective phenotype is typical for a mutation in a nuclear gene that induces a non-functional mitochondrial protein synthesis system. The protein encoded by YCR24c was expressed in Escherichia coli in a histidine-tagged form and isolated. The enzyme aminoacylated unfractionated Escherichia coli tRNA with asparagine. These results identified YCR24c as the structural gene for yeast mitochondrial asparaginyl-tRNA synthetase.
<title>Dexterous robotic sampling for Mars in-situ science</title> (1997)

Robotic exploration of the Martian surface will provide important scientific data on planetary climate, life history, and geologic resources. In particular, robotic arms will assist in the detailed visual inspection, instrumented analysis, extraction, and earth return of soil and rock samples. To this end, we are developing new robotic manipulation concepts for use on landers and rovers, wherein mass, volume, power and the ambient Mars environment are significant design constraints. Our earlier work led to MarsArmI, a 2.2 meter, 3-dof hybrid metal/composite, dc-motor actuated arm operating under coordinated joint-space control; NASA's Mars Surveyor '98 mission utilizes this design concept. More recently, we have conceived and implmented new, all- composite, very light robot arms: MarsArmII, a 4.0 kilogram, 2.3 meter arm for lander operations, and MicroArm-1 and MicroArm-2, two smaller 1.0+ kilogram, .7 meter rover arms for mobile sample acquisition and Mars sample return processing. Features of these arms include our creation of new 3D machined composites for critical load-bearing parts; actuation by high-torque density ultrasonic motors; and, visually-designated inverse kinematics positioning with contact force adaptation under a novel task-level, dexterous controls paradigm. Our demonstrated results include robotic trenching, sample grasp-manipulation-and-transfer, and fresh rock surface exposure-probing via the science operator's 'point-and-shoot' visual task designation in a stereo workspace. Sensor-referenced control capabilities include real-time adaptation to positioning error and environmental uncertainties (e.g., variable soil resistance and impediments), and the synthesis of power optimal trajectories for free space manipulation.
Automated Data Processing (ADP) Research and Development (1995)

Monitoring a comprehensive test ban treaty (CTBT) will require screening tens of thousands of seismic events each year. Reliable automated data analysis will be essential in keeping up with the continuous stream of events that a global monitoring network will detect. We are developing automated event location and identification algorithms by looking at the gaps and weaknesses in conventional ADP systems and by taking advantage of modem computational paradigms. Our research focus is on three areas: developing robust algorithms for signal feature extraction, integrating the analysis of critical measurements, and exploiting joint estimation techniques such as using data from acoustic, hydroacoustic, and seismic sensors. We identify several important problems for research and development; e.g., event location with approximate velocity models and event identification in the presence of outliers. We are employing both linear and nonlinear methods and advanced signal transform techniques to solve these event monitoring problems. Our goal is to increase event-interpretation throughput by employing the power and efficiency of modem computational techniques, and to improve the reliability of automated analysis by reducing the rates of false alarms and missed detections.