gebhart/patrepeval huggingface dataset:
Innate immune pathways in afferent lymph following vaccination with poly(I:C)-containing liposomes (2013)

Many modern vaccines use defined adjuvants to stimulate the innate immune system and shape the adaptive immune response. The exact nature of these innate signals and whether immune differentiation can originate within the periphery is not known. Here we used an ovine lymphatic cannulation model to characterise the cellular and transcriptomic profile of the afferent lymph following injection of a liposomal vaccine formulation incorporating diphtheria toxoid and the innate stimulator poly(I:C) over a 78-h period. The response to this vaccine featured an early activation of broad pro-inflammatory pathways (e.g. TLR signalling and inflammasome pathways) and the transient recruitment of granulocytes into the lymph. At 24 h a more monocytic cellular profile arose coinciding with a transition to a specific antiviral response characterised by the up-regulation of genes associated with the receptors typical for the viral mimic, poly(I:C) (e.g. TLR3, RIG-I and MDA5). At the latest time points the up-regulation of IL-17A and IL-17F suggested that Th17 cells may participate in the earliest adaptive response to this vaccine. These data provide the most comprehensive picture of the cellular and molecular mechanisms that link the periphery to the draining lymph node following vaccination, and indicate that the immune response is capable of specialising within the periphery.
3-Dimensional FEM simulations of resonances in the impedance characteristic of ceramic multilayer capacitors (1999)

Abstract Resonances in the impedance spectra of Ceramic Multilayer Capacitors (MLCs) with X7R dielectric are calculated and compared with measured resonance spectra. The simulations have been performed with the Finite Element Method applied to a 3-dimensional model of a capacitor. The model is verified with spectra of faultless size 1210 and 1812 capacitors. Investigations on the influence of an introduced crack in the longitudinal direction of a type 1210 MLC work out a good agreement between simulations and measurements. These results can be used as input data for a non-destructive failure test based on impedance spectroscopy.
Characterization of Ligands for Fish Taste Receptors (2007)

Recent progress in the molecular biology of taste reception has revealed that in mammals, the heteromeric receptors T1R1/3 and T1R2/3 respond to amino acids and sweeteners, respectively, whereas T2Rs are receptors for bitter tastants. Similar taste receptors have also been characterized in fish, but their ligands have not been identified yet. In the present study, we conducted a series of experiments to identify the fish taste receptor ligands. Facial nerve recordings in zebrafish (Danio rerio) demonstrated that the fish perceived amino acids and even denatonium, which is a representative of aversive bitter compounds for mammals and Drosophila. Calcium imaging analysis of T1Rs in zebrafish and medaka fish (Oryzias latipes) using an HEK293T heterologous expression system revealed that both T1R1/3 and a series of T1R2/3 responded to amino acids but not to sugars. A triple-labeling, in situ hybridization analysis demonstrated that cells expressing T1R1/3 and T1R2/3s exist in PLCbeta2-expressing taste bud cells of medaka fish. Functional analysis using T2Rs showed that zfT2R5 and mfT2R1 responded to denatonium. Behavior observations confirmed that zebrafish prefer amino acids and avoid denatonium. These results suggest that, although there may be some fish-specific way of discriminating ligands, vertebrates could have a conserved gustatory mechanism by which T1Rs and T2Rs respond to attractive and aversive tastants, respectively.
Characterization of In20Ge15Sb10Te55Phase Change Material for Phase Change Memory with Low Power Operation and Good Data Retention (2012)

An indium-incorporated germanium–antimony–telluride material, In20Ge15Sb10Te55 (IGST), was investigated as a recording material for phase change memory. The crystallization temperature of IGST was 226 °C, which is 75 °C higher than that of conventional GST. The reset current of the device using IGST was about 10 mA for a plug 180 nm in diameter, which enabled a low-power operation, compared with the GST-based device. A cycle endurance of up to 1.5×104 was achieved. The data retention was estimated to be 10 years at 145 °C. These data clearly show that IGST exhibits promising characteristics as a recording material for phase change memory.
Autonomous Sensor Motes Employing Liquid-Bearing Rotary Stages (2014)

Abstract : The liquid bearing technology provides a self-centering, friction and wear resistant bearing capable of supporting static and dynamic loads. The liquid bearing design uses satellite droplets arranged around a central droplet. The satellite droplets are pinned to the rotor by patterning of the hydrophobic surface coating, but slide across the stator's hydrophobic coating. The center droplet maintains alignment between the rotor and stator. Experimental data and models demonstrate the performance and stability of the design. Superhydrophobic coatings are required to successfully retain the satellite droplets on the rotor and to permit sliding of the droplets across the stator surface. The satellite droplet liquid bearing was characterized to have minimum startup torque at 0.3 microN-m, rotational drag coefficient at 0.94 10-3 microN-m/rpm, and maximum rotation rate at 14400 deg/sec for an input torque of 2.3 microN-m. The tilt stiffness of the satellite bearing design was measured at 5.4 microN-m/deg. Tilt stiffness measurement and analytical models provide the design tools needed for predicting pull-in instability threshold gaps and voltages.
Isolation of Acyl-CoA:Cholesterol Acyltransferase Inhibitor fromPersicaria vulgaris (2002)

In the course of our search for Acyl-CoA:cholesterol acyltransferase (ACAT) inhibitors from natural sources, a new type of ACAT inhibitor was isolated from the methanol extract of Persicaria vulgaris. On the basis of spectral evidence, the structure of the active compound was identified as pheophorbide A. Pheophorbide A inhibited ACAT activity with an IC 50 value of 1.1 microg/ml in an enzyme assay using rat liver microsomes with a dose dependent fashion.
Intratumoral activity of ONC201 in adult recurrent glioblastoma patients. (2018)

e14034 Background: ONC201 is an antagonist of the G protein-coupled receptor DRD2 that crosses the blood-brain barrier and induces tumor cell apoptosis in preclinical models. The anti-tumor activity of ONC201 is pronounced in cells with low DRD5 expression and is associated with induction of the ATF4/CHOP/DR5-mediated integrated stress response pathway to trigger apoptosis. We previously reported the single agent activity of ONC201 in 17 adult patients with recurrent glioblastoma that demonstrated the safety, systemic pharmacodynamics, and a durable objective response when administered orally once every 3 weeks. Here, we evaluated the intratumoral drug concentrations and pharmacodynamic activity of ONC201 in adult recurrent glioblastoma patients who were treated on a weekly schedule. Methods: Six patients ≥18 years old with first recurrence of glioblastoma who were eligible for salvage surgical resection were enrolled. ONC201 was administered orally as 625 mg once a week. Salvage surgery was performed approximately 24 hours after the second dose of ONC201 and patients continued on ONC201 until radiographic and/or clinical progression. Tumor tissue was flash-frozen and formalin-fixed for assessments of intratumoral drug concentrations and pharmacodynamics, respectively. Results: Of the 6 enrolled patients, 5 had sufficient tissue for evaluation. Intratumoral drug concentrations exceeded therapeutic thresholds: median 1.5 µM (range 600 nM – 9.3 µM). Investigation of biomarkers related to downstream signaling induced by ONC201 revealed heterogeneous intratumoral induction of ATF4, CHOP, and DR5 expression along with tumor cell apoptosis (TUNEL). Stronger induction of the pharmacodynamic signaling biomarkers was associated with stronger induction of apoptosis and inversely associated with DRD5 expression, but not with drug concentration. No drug-related adverse events were reported in this cohort. Conclusions: ONC201 achieves intratumoral concentrations in recurrent glioblastoma patients that are well tolerated and result in pharmacodynamic signaling and tumor cell apoptosis.
Treatments and Outcomes for Lower Lumbar (L3–L5) Burst Fractures (2011)

Bhandutia, Amit K. BS; Gruskay, Jordan A. BA; Helgeson, Melvin D. MD; Yadlapalli, Navin K. BS; Gowda, Ashok L. MD; Su, Brian W. MD; Ratliff, John K. MD; Anderson, D. Greg MD; Vaccaro, Alexander R. MD, PhD Author Information
'All In One' SARS-CoV-2 variant recognition platform: Machine learning-enabled point of care diagnostics (2022)

Point of care (PoC) devices are highly demanding to control current pandemic, originated from severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). Though nucleic acid-based methods such as RT-PCR are widely available, they require sample preparation and long processing time. PoC diagnostic devices provide relatively faster and stable results. However they require further investigation to provide high accuracy and be adaptable for the new variants. In this study, laser-scribed graphene (LSG) sensors are coupled with gold nanoparticles (AuNPs) as stable promising biosensing platforms. Angiotensin Converting Enzyme 2 (ACE2), an enzymatic receptor, is chosen to be the biorecognition unit due to its high binding affinity towards spike proteins as a key-lock model. The sensor was integrated to a homemade and portable potentistat device, wirelessly connected to a smartphone having a customized application for easy operation. LODs of 5.14 and 2.09 ng/mL was achieved for S1 and S2 protein in the linear range of 1.0-200 ng/mL, respectively. Clinical study has been conducted with nasopharyngeal swabs from 63 patients having alpha (B.1.1.7), beta (B.1.351), delta (B.1.617.2) variants, patients without mutation and negative patients. A machine learning model was developed with accuracy of 99.37% for the identification of the SARS-Cov-2 variants under 1 min. With the increasing need for rapid and improved disease diagnosis and monitoring, the PoC platform proved its potential for real time monitoring by providing accurate and fast variant identification without any expertise and pre sample preparation, which is exactly what societies need in this time of pandemic.
Temporal Variability of Water Quality Parameters at the Elkhorn Slough Estuary using Wavelets (2021)

In recent decades, significant temporal variability has been observed in water quality parameters, especially in coastal settings. To ensure sustainable water resources management, it is important to document the dominant scales of variation of these parameters and identify the underlying factors causing these variations. These variations are typically governed by a complex interplay of factors including, but not limited to, anthropogenic controls (e.g., a culvert), climatic conditions and hydro-biogeochemical processes. To decipher these underlying controls, there is a significant need for advanced statistical approaches. Here, we use wavelet analysis on an extensive water quality parameter dataset available from the Elkhorn Slough estuary, located in Monterey Bay, California, for over 15 years. Results from the wavelet analysis indicate that ammonia, nitrite, nitrate, and salinity have a dominant 12-month frequency at the head of the estuary. An exception to the rule was orthophosphate at this location, which showed multi-scale frequencies, varying from 4-32 months in addition to the commonly observed annual-scale variation. While the parameters showed consistent 12-month frequency at the head of the estuary, salinity, ammonia, and nitrite exhibited multi-year frequencies at the mouth. In conclusion, mixing of different source waters in a tidally-controlled estuarine environment can result in significant spatial and temporal variability in water quality parameters.
Fusion Cast Refractories NAZS: Influence of the Nay<sub>2</sub>O Content on Both the Phasal Composition and the Microstructure (1997)

Fusion cast refractories involving Al 2 O 3 , ZrO 2 , SiO 2 and Na 2 O (NAZS) are widely used in the glass melting furnace due to their good resistance to chemical corrosion. We have studied compositions of the quaternary system with ZrO 2 = 34 wt%, SiO 2 = 15 wt%, 48 wt% < Al 2 O 3 < 50 wt%, and 0 wt% < Na 2 O < 2 wt%. Results of both the XRD and optical microscopic analysis show that the compositions studied display primary crystals of ZrO 2 , binary eutectic Al 2 O 3 - ZrO 2 , and an interstitial «glassy» phase. This interstitial material is actually a mixture formed with an aluminosilicate glassy phase and possibly small crystals of Al 2 O 3 and ZrO 2 and mullite. The glassy phase contains all the SiO 2 and Na 2 O of the system and a small part of ZrO 2 . The high resolution 29 Si NMR spectra show the presence of the silicon environments typical of mullite ; the fraction of these sites decresases as the composition in Na 2 O increases.
Molecular Mechanisms of Antisense Oligonucleotides (2017)

In 1987, when I became interested in the notion of antisense technology, I returned to my roots in RNA biochemistry and began work to understand how oligonucleotides behave in biological systems. Since 1989, my research has focused primarily on this topic, although I have been involved in most areas of research in antisense technology. I believe that the art of excellent science is to frame large important questions that are perhaps not immediately answerable with existing knowledge and methods, and then conceive a long-term (multiyear) research strategy that begins by answering the most pressing answerable questions on the path to the long-term goals. Then, a step-by-step research pathway that will address the strategic questions posed must be implemented, adjusting the plan as new things are learned. This is the approach we have taken at Ionis. Obviously, to create antisense technology, we have had to address a wide array of strategic questions, for example, the medicinal chemistry of oligonucleotides, manufacturing and analytical methods, pharmacokinetics and toxicology, as well as questions about the molecular pharmacology of antisense oligonucleotides (ASOs). Each of these endeavors has consumed nearly three decades of scientific effort, is still very much a work-in-progress, and has resulted in hundreds of publications. As a recipient of the Lifetime Achievement Award 2016 granted by the Oligonucleotide Therapeutic Society, in this note, my goal is to summarize the contributions of my group to the efforts to understand the molecular mechanisms of ASOs.
Entwicklung von neuen Werkstoffen durch chemische Nanotechnologien (1999)

Werkstoffe spielen eine immer größere Rolle bei der Entwicklung innovativer Produkte und Prozesse. In diesem Zusammenhang werden die Spezialisierung und die Anforderungen an solche Werkstoffe immer größer und damit die Mengen pro Anwendungsfall immer kleiner. Dies führt zu dem Fall, daß viele Werkstoffe für mögliche Produktinnovationen nicht entwickelt werden, da der "return of invest" bei den typischen Werkstoffherstellern nicht mehr gewährleistet ist. Damit entsteht eine wichtige Aufgabe für die Forschung, Werkstoffe in Bereichen mit Anwendungspotential zu entwickeln. Vor dem Hintergrund dieser Aufgabe hat das INM eine breite Palette an Grundlagenforschungen mit hohem Anwendungspotential begonnen und in seinem Fachgebiet, nämlich nichtmetallisch-anorganischer Werkstoffe und Komposite entwickelt, so daß die Anwendungspotentiale sichtbar werden. Die Zielsetzung der Grundlagenarbeiten basiert im wesentlichen auf neu entwickelten Methoden zur Herstellung von Nanopartikeln und nanostrukturierten Werkstoffen über chemisch synthetische Verfahren. Der Stand der Technik zur Herstellung von Nanopartikeln umfaßt Inertgasverdampfung, hochenergetisches Mahlen, Gasphasenreaktionen und chemische Synthesen. Während in den Gasphasenverfahren schon sehr viele Ergebnisse vorliegen, werden chemische Synthesen zunehmend interessant, besonders deswegen, weil die chemische Verfahrenstechnik die Möglichkeit zur preisgünstigen Herstellung bietet. Die Arbeiten finden im Bereich der keramischen Werkstoffe, der Glaswerkstoffe, der Beschichtungswerkstoffe von Glaskeramik und Kunststoffen mit nanostrukturierten Werkstoffen und im Bereich der anorganisch-organischen Nanokomposite (NANOMERe) statt.
Variable Reference Alignment: An Improved Peak Alignment Protocol for NMR Spectral Data with Large Intersample Variation (2012)

In an effort to address the variable correspondence problem across large sample cohorts common in metabolomic/metabonomic studies, we have developed a prealignment protocol that aims to generate spectral segments sharing a common target spectrum. Under the assumption that a single reference spectrum will not correctly represent all spectra of a data set, the goal of this approach is to perform local alignment corrections on spectral regions which share a common "most similar" spectrum. A natural beneficial outcome of this procedure is the automatic definition of spectral segments, a feature that is not common to all alignment methods. This protocol is shown to specifically improve the quality of alignment in (1)H NMR data sets exhibiting large intersample compositional variation (e.g., pH, ionic strength). As a proof-of-principle demonstration, we have utilized two recently developed alignment algorithms specific to NMR data, recursive segment-wise peak alignment and interval correlated shifting, and applied them to two data sets composed of 15 aqueous cell line extract and 20 human urine (1)H NMR profiles. Application of this protocol represents a fundamental shift from current alignment methodologies that seek to correct misalignments utilizing a single representative spectrum, with the added benefit that it can be appended to any alignment algorithm.
Spatial relationship of photosystem I, photosystem II, and the light-harvesting complex in chloroplast membranes. (1977)

We have previously demonstrated (Armond, P. A., C. J. Arntzen, J.-M. Briantais, and C. Vernotte. 1976. Arch. Biochem. Biophys. 175:54-63; and Davis, D. J., P. A. Armond, E. L. Gross, and C. J. Arntzen. 1976. Arch. Biochem. Biophys. 175:64-70) that pea seedlings which were exposed to intermittent illumination contained incompletely developed chloroplasts. These plastids were photosynthetically competent, but did not contain grana. We now demonstrate that the incompletely developed plastids have a smaller photosynthetic unit size; this is primarily due to the absence of a major light-harvesting pigment-protein complex which is present in the mature membranes. Upon exposure of intermittent-light seedlings to continuous white light for periods up to 48 h, a ligh-harvesting chlorophyll-protein complex was inserted into the chloroplast membrane with a concomitant appearance of grana stacks and an increase in photosynthetic unit size. Plastid membranes from plants grown under intermediate light were examined by freeze-fracture electron microscopy. The membrane particles on both the outer (PF) and inner (EF) leaflets of the thylakoid membrane were found to be randomly distributed. The particle density of the PF fracture face was approx. four times that of the EF fracture face. While only small changes in particle density were observed during the greening process under continuous light, major changes in particle size were noted, particularly in the EF particles of stacked regions (EFs) of the chloroplast membrane. Both the changes in particle size and an observed aggregation of the EF particles into the newly stacked regions of the membrane were correlated with the insertion of light-harvesting pigment-protein into the membrane. Evidence is presented for identification of the EF particles as the morphological equivalent of a "complete" photosystem II complex, consisting of a phosochemically active "core" complex surrounded by discrete aggregates of the light-harvesting pigment protein. A model demonstrating the spatial relationships of photosystem I, photosystem II, and the light-harvesting complex in the chloroplast membrane is presented.
Telomerization of Butadiene with Starch under Mild Conditions (2009)

The design of industrial products based on bioresources is a challenging issue. Modification of starch, by hydrophobic chemical substituents, results in an innovative hydrophobic material. Herein, the hydrophobic part of the derivative, comprised of octadienyl chains, is introduced through catalytic butadiene telomerization. The process is efficiently conducted on starch in its granular form in an aqueous medium using hydrosoluble palladium complexes. After optimization, a turnover number (TON) of up to 550 was achieved in the presence of [(pi-allyl)PdCl](2) catalyst and, unusually, by using dimethylisosorbide as a cosolvent.
Search for supersymmetry with Higgs boson to diphoton decays using the razor variables at s=13TeV (2018)

An inclusive search for anomalous Higgs boson production in the diphoton decay channel and in association with at least one jet is presented, using LHC proton-proton collision data collected by the CMS experiment at a center-of-mass energy of 13 TeV and corresponding to an integrated luminosity of 35.9 fb -1 . The razor variables M R and R 2 , as well as the momentum and mass resolution of the diphoton system, are used to categorize events into different search regions. The search result is interpreted in the context of strong and electroweak production of supersymmetric particles. We exclude bottom squark pair-production with masses below 450 GeV for bottom squarks decaying to a bottom quark, a Higgs boson, and the lightest supersymmetric particle (LSP) for LSP masses below 250 GeV. For wino-like chargino-neutralino production, we exclude charginos with mass below 170 GeV for LSP masses below 25 GeV. In the GMSB scenario, we exclude charginos with mass below 205 GeV for neutralinos decaying to a Higgs boson and a goldstino LSP with 100% branching fraction.
Minimally Invasive Techniques for the Treatment of Osteoporotic Vertebral Fractures (2006)

Osteoporotic vertebral compression fractures are a leading cause of disability and morbidity in the elderly. The consequences of these fractures include pain, progressive vertebral collapse with resultant spinal kyphosis, and systemic manifestations. Nonsurgical measures have proved unsuccessful in a portion of this population and for this group, minimally invasive vertebral augmentation can be beneficial. Vertebroplasty is designed to address vertebral fracture pain. It involves percutaneous injection of polymethylmethacrylate (PMMA) directly into a fractured vertebral body with the goals of pain relief and prevention of further collapse of the fractured vertebra. Kyphoplasty is designed to address the kyphotic deformity as well as the fracture pain. It involves the percutaneous insertion of an inflatable bone tamp into a fractured vertebral body. Bone tamp inflation works to elevate the end plates and create a cavity to be filled with PMMA with the goals of pain relief, restoration of vertebral body height, and reduced kyphotic deformity. Optimizing surgical technique can improve outcomes and decrease complication rates, and decrease radiation exposure to the patient and surgical team. Obtaining a biopsy prior to cement injection has proved efficacious and may result in the diagnosis of occult pathology underlying a seemingly routine vertebral fracture. As competence and surgical success are acquired, the indications will continue to expand to encompass more challenging pathologies. Recently, vertebral augmentation during spinal decompression and instrumented fusion for burst fracture with neurologic insult has been reported to be successful.