gebhart/patrepeval huggingface dataset:
Human Primary T Cells: A Practical Guide v5 (2018)

Human primary T cells are invaluable and feasible model systems to study the characteristics of the human immune cells in various contexts, including but not limited to cancer immunotherapy. Following isolation of T cells from fresh human blood samples, it is possible to culture, expand, and manipulate these cells, which allows extensive investigation for research purposes. Techniques for isolation and handling of T cells are well-established but parts of the protocols can highly vary across different labs. These differences in the protocols are, often, there due to historical reasons and are only supported by anecdotal evidence. We systematically modified basic components of the T cell culturing protocols and collected data on how they altered the final yield. Here, based on these data, we provide practical hints and tips on basic cellular and molecular techniques for handling primary human T cells. We hope that this guide will serve as a reference point to allow evaluate, discuss, and improve current practices in T cell culturing and manipulation.
Crystal structure of the human receptor activity‐modifying protein 1 extracellular domain (2008)

Receptor activity-modifying protein (RAMP) 1 forms a heterodimer with calcitonin receptor-like receptor (CRLR) and regulates its transport to the cell surface. The CRLR.RAMP1 heterodimer functions as a specific receptor for calcitonin gene-related peptide (CGRP). Here, we report the crystal structure of the human RAMP1 extracellular domain. The RAMP1 structure is a three-helix bundle that is stabilized by three disulfide bonds. The RAMP1 residues important for cell-surface expression of the CRLR.RAMP1 heterodimer are clustered to form a hydrophobic patch on the molecular surface. The hydrophobic patch is located near the tryptophan residue essential for binding of the CGRP antagonist, BIBN4096BS. These results suggest that the hydrophobic patch participates in the interaction with CRLR and the formation of the ligand-binding pocket when it forms the CRLR.RAMP1 heterodimer.
Abstract 506: The Effect of Human Recombinant DNase-1 Treatment on Skeletal Muscle Ischemia Reperfusion Injury (2013)

Objective Nucleosomes are known to exacerbate tissue injury, thus exogenous DNase-1 has been suggested as a novel therapeutic strategy to limit tissue injury in a stroke model. Our aim was to assess the effect of recombinant DNase-1 treatment on skeletal muscle fiber injury, tissue inflammation and levels of circulating nucleosomes in a mouse model of hind limb ischemia-reperfusion-injury (IR). Methods C57BL6 mice were subjected to IR (1.5hr Ischemia/24hr Reperfusion) or sham conditions. Mice were treated with either 50μg DNase-1 IP every 6 hours (DNase-1) or buffer (Control) at the same time intervals. Sham mice were anesthetized for 1.5 hours and allowed to recover for 24 hours. Muscles were harvested to quantify muscle fiber injury, DNAse-1 protein and calcium dependent endonuclease activity. Muscle markers of inflammation Myeloperoxidase (MPO), Keratinocyte chemoattractant (KC) and Plasma nucleosomes were quantified. Results Skeletal muscle fiber injury (numbers p&lt;0.05) and endonuclease activity (numbers p&lt;0.001) were greater in the DNase-1 group compared to control and sham. DNase-I localized predominantly to the extracellular matrix and severely injured muscle fibers. There was no significant difference in the plasma levels of nucleosomes or markers of inflammation (MPO or KC). Conclusions These novel findings suggest that in contrast to brain IR, hind limb IR increases DNAse-1 activity, and that exogenous treatment with DNase-1 exacerbates muscle injury independent of markers of inflammation. DNase-1 may be a therapeutic target that warrants further investigation. Table to Be Inserted
Classical chaos in one-dimensional hydrogen in strong dc electric fields (1989)

We analyze the effect of a dc electric field on classical chaos in one-dimensional hydrogen in a microwave field in the n nonmixing regime and also in the inter-n-mixing regime where significant dc field-induced ionization occurs. We study the ac field-induced nonlinear classical resonances, the threshold of chaos, and the number of states trapped in the resonances. In the strong-n-mixing and ionizing regime (unclamping dc field), we find the chaotic dynamics depend sharply on the dc field and the number of states trapped in the resonances, allowing the system to undergo a transition from a regime of classical behavior to a regime of uniquely quantum behavior as the dc field is changed. We show that ionization by classical chaos competes favorably with ionization by tunneling in the transition region, and that tunneling allows very sensitive spectroscopy of this region.
Bioproduction of 4-vinylphenol from corn cob alkaline hydrolyzate in two-phase extractive fermentation using free or immobilized recombinant E. coli expressing pad gene (2014)

In situ extractive fermentation was used to produce 4-vinyl derivatives from hydroxycinnamic acids extracted from corn cobs by recombinant Escherichia coli cells expressing Lactobacillus plantarum phenolic acid descarboxylase (PAD) gene. This microorganism mainly produced 4-vinylphenol (4VP) from p-coumaric acid (p-CA). In the first study , we observed that the concentrations of 4VP are higher than 1g/L which had a negative impact on decarboxylation of p-CA to 4VP by recombinant E. coli cells. Because of this, and in order to improve the downstream process, a two-phase aqueous-organic solvent system was developed. The results of the extractive fermentation indicated that it was possible to use hydrolyzates as aqueous phase to bioproduce 4VP, and recover simultaneously the product in the organic phase containing hexane. The detoxification of pre-treated corn cob alkaline hydrolyzate improved 4VP production up to 1003.5mg/L after 24h fermentation (QP=41.813mg/Lh). Additionally, preliminary experiments using cells immobilized in calcium alginate showed to be a good system for the biotransform of p-CA to 4VP in extractive fermentation, although the process hindered partially the recovery of 4VP in the organic phase.
Effect of in-plane shear strain on phase states and dielectric properties of epitaxial ferroelectric thin films (2008)

A modified thermodynamic potential based on the eight-order Landau–Devonshire polynomial is derived for ferroelectric thin films grown on dissimilar substrates that induce anisotropic tensile/compressive strains and the shear strain in the film plane. The effect of the shear strain on the ferroelectric phase transition occurring in considered films is analyzed theoretically. It is shown that the application of the shear strain suppresses the formation of ferroelectric c phase and raises the temperature of aa∗ phase formation. The directional dependence of in-plane dielectric permittivity of a ferroelectric film is also calculated and compared with the dependence observed in (Ba0.60Sr0.40)TiO3 films deposited on NdGaO3.
In Silico Design and In-Vivo Analysis of the Pediaflow™ Pediatric Ventricular Assist Device (2011)

Mechanical circulatory support for the smallest newborn pediatric patients has historically been limited to extracorporeal membrane oxygenation, which can only provide several days to weeks of full cardiac support; far short of the median waiting time for pediatric heart transplantation of nearly three months [1]. Recently, new technologies have been developed, including the PediaFlow pediatric ventricular assist device, to address this need. The PediaFlow device is a magnetically levitated (mag lev), mixed flow turbodynamic blood pump which has been developed in large part in silico using CFD-based inverse design optimization and closed form rotor dynamics models [2, 3]. Each prototype undergoes a series of in vitro and in vivo tests to verify the accuracy of the simulations in predicting performance and biocompatibility. The overall goal is continued refinement and progress towards an implantable pump that produces 0.3 −1.5 L/min for up to 6 months in pediatric heart failure patients from 5 to 15 kg. We describe here the design principles and test procedures for the first three prototypes as well as the predicted performance for a fourth prototype currently being prepared for testing (Figure 1).
22‐3: 5 µm Thickness of Low‐Retardation Plastic Foil with Gas Barrier and Transparent Conductive Layer for Bendable Devices (2020)

A 5 µm thickness foil with low retardation less than 1 nm and excellent thermal stability at 150˚C was presented. Over 10,000 cycles bending tests at 0.5 mm radius were achieved as a substrate of gas barrier and transparent conductive films.
Papillomavirus E7 Oncoproteins Share Functions with Polyomavirus Small T Antigens (2014)

DNA tumor viruses have provided major insights into how cancers develop. Some viruses, like the human papillomaviruses, can cause cancer directly. Both the papillomaviruses and the polyomaviruses have served as tools for understanding pathways that are often perturbed in cancer. Here, we have compared the functions of transforming proteins from several DNA tumor viruses, including two papillomaviruses and two polyomaviruses. We tested the papillomavirus E6 and E7 oncoproteins in three functional assays and found that E7 can provide some or all of the functions of the SV40 small T antigen, another well-characterized oncoprotein, in two of these assays. In a third assay, papillomavirus E7 has the same effect as the murine polyomavirus small T protein. In summary, we report several new functions for the papillomavirus E7 proteins, which will contribute new insights into the roles of viruses in cancer and the cellular pathways they perturb in carcinogenesis.
Assays for the Identification and Prioritization of Drug Candidates for Spinal Muscular Atrophy (2014)

Spinal muscular atrophy (SMA) is an autosomal recessive genetic disorder resulting in degeneration of α-motor neurons of the anterior horn and proximal muscle weakness. It is the leading cause of genetic mortality in children younger than 2 years. It affects ∼1 in 11,000 live births. In 95% of cases, SMA is caused by homozygous deletion of the SMN1 gene. In addition, all patients possess at least one copy of an almost identical gene called SMN2. A single point mutation in exon 7 of the SMN2 gene results in the production of low levels of full-length survival of motor neuron (SMN) protein at amounts insufficient to compensate for the loss of the SMN1 gene. Although no drug treatments are available for SMA, a number of drug discovery and development programs are ongoing, with several currently in clinical trials. This review describes the assays used to identify candidate drugs for SMA that modulate SMN2 gene expression by various means. Specifically, it discusses the use of high-throughput screening to identify candidate molecules from primary screens, as well as the technical aspects of a number of widely used secondary assays to assess SMN messenger ribonucleic acid (mRNA) and protein expression, localization, and function. Finally, it describes the process of iterative drug optimization utilized during preclinical SMA drug development to identify clinical candidates for testing in human clinical trials.
Effect of the spin-twist structure on the spin-wave dynamics in Fe55Pt45/Ni80Fe20 exchange coupled bi-layers with varying Ni80Fe20 thickness (2014)

We have investigated optically induced ultrafast magnetization dynamics of a series of Fe55Pt45/Ni80Fe20 exchange spring bi-layers with varying Ni80Fe20 thickness. Rich spin-wave spectra are observed; whose frequency shows a strong dependence on the Ni80Fe20 layer thickness. Micromagnetic simulations based on a simplified magnetic microstructure were able to reproduce the experimental data qualitatively. The spin twist structure introduced in the Ni80Fe20 layer gives rise to new modes in the composite system as opposed to the bare Ni80Fe20 films.
HDAC inhibition improves cardiopulmonary function in a feline model of diastolic dysfunction (2020)

Heart failure with preserved ejection fraction (HFpEF) is a major health problem without effective therapies. This study assessed the effects of histone deacetylase (HDAC) inhibition on cardiopulmonary structure, function, and metabolism in a large mammalian model of pressure overload recapitulating features of diastolic dysfunction common to human HFpEF. Male domestic short-hair felines (<i>n</i> = 31, aged 2 months) underwent a sham procedure (<i>n</i> = 10) or loose aortic banding (<i>n</i> = 21), resulting in slow-progressive pressure overload. Two months after banding, animals were treated daily with suberoylanilide hydroxamic acid (b + SAHA, 10 mg/kg, <i>n</i> = 8), a Food and Drug Administration-approved pan-HDAC inhibitor, or vehicle (b + veh, <i>n</i> = 8) for 2 months. Echocardiography at 4 months after banding revealed that b + SAHA animals had significantly reduced left ventricular hypertrophy (LVH) (<i>P</i> < 0.0001) and left atrium size (<i>P</i> < 0.0001) versus b + veh animals. Left ventricular (LV) end-diastolic pressure and mean pulmonary arterial pressure were significantly reduced in b + SAHA (<i>P</i> < 0.01) versus b + veh. SAHA increased myofibril relaxation ex vivo, which correlated with in vivo improvements of LV relaxation. Furthermore, SAHA treatment preserved lung structure, compliance, blood oxygenation, and reduced perivascular fluid cuffs around extra-alveolar vessels, suggesting attenuated alveolar capillary stress failure. Acetylation proteomics revealed that SAHA altered lysine acetylation of mitochondrial metabolic enzymes. These results suggest that acetylation defects in hypertrophic stress can be reversed by HDAC inhibitors, with implications for improving cardiac structure and function in patients.
Demonstration of Antiviral Activity of far-UVC Microplasma Lamp Irradiation Against SARS-CoV-2 (2021)

Immediate inactivation of up to 99.99% of the coronavirus was achieved with a dose of less than 8 mJ/cm2 and complete inactivation was observed by real-time RT-PCR; therefore, far-UVC (222 nm) is a promising candidate for the effective inactivation of SARS-CoV-2.
Frequency noise power spectral density of a molecular THz-laser using a fs- fibre laser comb with 1 GHz repetition rate (2018)

We report the measurement of the frequency noise power spectral density (FNPSD) of a CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> pumped molecular-laser emitting at 2.5THz. The measurement relies on the generation of a beatnote between the THz frequency and the harmonic of the IGHz repetition rate of a fs-fiber comb. We obtain a frequency noise of ~0.1 Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Hz at 50kHz, limited by the phase noise of the frequency comb. This shows the potential of (i) molecular lasers as ultra-low phase noise sources of THz radiation, and of (ii) fs-fiber combs, in combination with electro-optic detection, as frequency-agile and low phase-noise THz local oscillators.
EFFICACY OF SYNTHETIC OXYGEN CARRYING SUBSTANCES (1995)

Kobavashi, Koichi; Izumi, Yotarou; Yamahata, Ken; Sakai, Hiromi1; Takeoka, Shinji1; Nishide, Hiroyuki1; Tsuchida, Eishun1 Author Information
FARP‐1 deletion is associated with lack of response to autism treatment by early start denver model in a multiplex family (2020)

These results represent a paradigmatic example of the heuristic potential of genetic markers in predicting treatment response and possibly in supporting the targeted prescription of specific early intervention approaches.
Solutions of polynomial systems derived from the steady cavity flow problem (2009)

We propose a general algorithm to approximately enumerate all solutions of a zero-dimensional polynomial system with respect to a given cost function. The algorithm is developed and is used to study a polynomial system obtained by discretizing the steady cavity flow problem in two dimensions. The key technique on which our algorithm is based is to solve polynomial optimization problems via sparse semidefinite program relaxations (SDPR), which has been adopted successfully to solve reaction-diffusion boundary value problems recently. The cost function to be minimized is derived from discretizing the kinetic energy of the fluid. The solutions of the enumeration algorithm are shown to converge to the minimal kinetic energy solutions for SDPR of increasing order. We take advantage of Groebner basis method to tune the performance of the algorithm, demonstrate the algorithm with SDPR of first and second order on polynomial systems for different scenarios of the cavity flow problem and succeed in approximately deriving the k smallest kinetic energy solutions. The question of whether these solutions converge to solutions of the steady cavity flow problem is discussed, and we pose a conjecture for the minimal energy solution for increasing Reynolds number.
Trafficking of Grafted Pancreatic Islets Into the Brain Lateral Ventricles: Implications for Cognition (2019)

There is a tremendous interest in insulin delivery to the brain for the treatment of Alzheimer’s disease (AD). Recently, we showed increased insulin content in the brain and improved cognitive functions in a rat model of sporadic AD following transplantation of pancreatic islets in the cranial subarachnoid space (cSAS).1 However, it remains unclear whether the islets grafted in the cSAS can migrate to other brain regions. Here, we report islet trafficking from cSAS to the brain ventricular system in a rat AD-like model induced by injection of streptozotocin into lateral ventricles (LVs), followed by islet transplantation in cSAS, as described previously.1 The cognitive improvement of the AD-like rats persisted for 6 months after transplantation (unpublished data), and viable syngeneic islets were identified in the cortex, olfactory bulb, and in the LVs (Figure 1A–C). The islets detected in the LVs expressed insulin, glucagon, proinsulin, and glucose transporter 2 (Figure 1D–F). It is likely that the grafted islets migrated across the cSAS from the transplantation site to the LVs. The islet migration could be triggered by cerebrospinal fluid flow and facilitated by expansion of brain ventricles after intraventricular administration of streptozotocin.2 Another possibility is a targeted migration of grafted islets toward the streptozotocin-induced injury to the LVs endothelial lining, where they secreted insulin and other reparative factors. Such tropism toward remote injured tissue is typical for neural stem cells.3 Our results provide new insights and strategies for cell delivery to the brain for therapy of neurodegenerative cognitive dysfunctions.FIGURE 1.: A, Hematoxylin and eosin staining of grafted islets located on cerebral cortex, olfactory bulb (B), and in the LV (C). D–F, Immunohistochemical staining of grafted islets located in the LV. Nuclei (blue) were labeled with Dapi. The arrows show the islets. Bars: 100 µm (A, B, and E), 200 µm (C and D), and 20 µm (F). CC, cortical cortex; Glut2, glucose transporter 2; HC, hippocampus; LV, lateral ventricle; OB, olfactory bulb.
The roles of sub‐micron and microscale roughness on shear‐driven thrombosis on titanium alloy surfaces (2022)

These results demonstrated that at high shear rates, thrombi form regardless of surface topography at the scales applied. At lower shear rates, micron-scale surface features cause thrombus formation, whereas submicron features result in innocuous platelet adhesion. These findings have implications for manufacturing costs and other considerations.
Quantum cryptography (1995)

Abstract Quantum cryptography is a new method for secret communications offering the ultimate security assurance of the inviolability of a law of nature. In this paper we shall describe the theory of quantum cryptography, its potential relevance and the development of a prototype system at Los Alamos, which utilizes the phenomenon of single-photon interference to perform quantum cryptography over an optical fibre communications link.
ENHANCEMENT OF IMMUNOSUPPRESSION BY SUBSTITUTION OF FISH OIL FOR OLIVE OIL AS A VEHICLE FOR CYCLOSPORINE (1989)

As previously reported, acute cyclosporine-induced nephrotoxicity is characterized by a decline in glomerular filtration rate and a selective intrarenal production of the vasoconstrictor thromboxane (TxA2), but not vasodilator prostaglandin E2 (PGE2), or prostacyclin (PGI2), cyclooxygenase metabolites. Fish oils (FO), that are rich in n-3 polyunsaturated fatty acids have a high affinity for cyclooxygenase but serve as poor substrate inhibit TxA2 synthesis. We have shown that when FO replaces olive oil (OO) as the vehicle for CsA, CsA-induced nephrotoxicity and increased TxA2 synthesis are obviated in rodent models. In this study, we demonstrate that the FO vehicle for CsA does not compromise CsA's immunosuppressive properties as deduced from studies of a delayed-type hypersensitivity (DTH) model in BALB/c mice and in a rat heart transplant model. In fact, concurrent FO administration with CsA actually enhances immunosuppression. A dose of CsA incapable of blunting DTH when injected in OO was suppressive when given in FO. Administration of as little as 0.05 ml of FO vehicle potentiated the suppressive action of CsA. In addition, nonconcurrent dietary supplementation of FO in animals receiving CsA caused an increase in the immunosuppressive action of CsA in DTH. FO alone reduced DTH as compared with OO, but was far less effective than CsA plus FO. Furthermore, doses of CsA (5 mg/kg/day or 1.5 mg/kg/day), which are subtherapeutic when administered with OO, prolonged engraftment of Lewis recipients of Lewis x Brown-Norway F1 hearts when CsA was solubilized with FO. These studies indicate that concurrent administration of CsA and FO potentiates the activity of CsA and thus increases its therapeutic index. Thus, CsA plus FO is potentially a safe, potent antirejection therapy worthy of clinical testing, especially insofar as FO prevents CsA-induced acute nephrotoxicity in the rodent.
Propagation Over Clutter: Physical Stochastic Model (2008)

Propagation of radio signals from a base above clutter, such as buildings and trees, to a mobile immersed in clutter is treated theoretically by accounting for random diffuse scattering at the mobile. Small-scale fading and distance-dependent loss are treated in a unified way, as opposed to the heuristic methodologies, which formulate them as separate factors. Closed form expressions are derived for path gain and for angular spectrum at the base in both urban and heavily foliated environments. The resulting predictions are in close agreement with widely accepted models and empirical results. The angular spectrum at the base in urban environments is found to be Lorentzian of width close to that reported for measurements in Aarhus. In foliated environments, vegetation is represented as statistically homogeneous diffuse scattering medium, resulting in a Gaussian-shaped angular spectrum at the base.