gebhart/patrepeval huggingface dataset:
CD8<sup>+</sup> memory T-cell inflation renders compromised CD4<sup>+</sup> T-cell-dependent CD8<sup>+</sup> T-cell immunity via na&iuml;ve T-cell anergy (2017)

Whether inflation of CD8<sup>+</sup> memory T (mT) cells, which is often derived from repeated prime-boost vaccinations or chronic viral infections in the elderly, would affect late CD8<sup>+</sup> T-cell immunity is a long-standing paradox. We have previously established an animal model with mT-cell inflation by transferring ConA-stimulated monoclonal CD8<sup>+</sup> T cells derived from Ova-specific T-cell-receptor transgenic OTI mice into irradiation-induced lymphopenic B6 mice. In this study, we also established another two animal models with mT-cell inflation by transferring, 1) ConA-stimulated monoclonal CD8<sup>+</sup> T cells derived from lymphocytic choriomeningitis virus glycoprotein-specific T-cell-receptor transgenic P14 mice, and 2) ConA-stimulated polyclonal CD8<sup>+</sup> T cells derived from B6.1 mice into B6 mice with irradiation-induced lymphopenia. We vaccinated these mice with recombinant Ova-expressing <i>Listeria monocytogenes</i> and Ova-pulsed dendritic cells, which stimulated CD4<sup>+</sup> T cell-independent and CD4<sup>+</sup> T-cell-dependent CD8<sup>+</sup> T-cell responses, respectively, and assessed Ova-specific CD8<sup>+</sup> T-cell responses by flow cytometry. We found that Ova-specific CD8<sup>+</sup> T-cell responses derived from the latter but not the former vaccination were significantly reduced in mice with CD8<sup>+</sup> mT-cell inflation compared to wild-type B6 mice. We determined that naïve CD8<sup>+</sup> T cells purified from splenocytes of mice with mT-cell inflation had defects in cell proliferation upon stimulation in vitro and in vivo and upregulated T-cell anergy-associated Itch and GRAIL molecules. Taken together, our data reveal that CD8<sup>+</sup> mT-cell inflation renders compromised CD4<sup>+</sup> T-cell-dependent CD8<sup>+</sup> T-cell immunity via naïve T-cell anergy, and thus show promise for the design of efficient vaccines for elderly patients with CD8<sup>+</sup> mT-cell inflation.
A maximum-likelihood formalism for sub-resolution axial localization of fluorescent nanoparticles (2005)

One of the ongoing challenges in single particle fluorescence microscopy resides in estimating the axial position of particles with sub-resolution precision. Due to the complexity of the diffraction patterns generated by such particles, the standard fitting methods used to estimate a particle's lateral position are not applicable. A new approach for axial localization is proposed: it consists of a maximum-likelihood estimator based on a theoretical image formation model that incorporates noise. The fundamental theoretical limits on localization are studied, using Cramér-Rao bounds. These indicate that the proposed approach can be used to localize particles with nanometer-scale precision. Using phantom data generated according to the image formation model, it is then shown that the precision of the proposed estimator reaches the fundamental limits. Moreover, the approach is tested on experimental data, and sub-resolution localization at the 10 nm scale is demonstrated.
Variation Trained Drowsy Cache (VTD-Cache): A History Trained Variation Aware Drowsy Cache for Fine Grain Voltage Scaling (2011)

In this paper we present the “Variation Trained Drowsy Cache” (VTD-Cache) architecture. VTD-Cache allows for a significant reduction in power consumption while addressing reliability issues raised by memory cell process variability. By managing voltage scaling at a very fine granularity, each cache way can be sourced at a different voltage where the selection of voltage levels depends on both the vulnerability of the memory cells in that cache way to process variation and the likelihood of access to that cache location. After a short training period, the proposed architecture will micro-tune the cache, allowing significant power reduction with negligible increase in the number of misses. In addition, the proposed architecture actively monitors the access pattern and reconfigures the supply voltage setting to adapt to the execution pattern of the program. The novel and modular architecture of the VTD-Cache and its associated controller makes it easy to be implemented in memory compilers with a small area and power overhead. In a case study, the SimpleScalar simulation of the proposed 32 kB cache architecture reports over 57% reduction in power consumption over standard SPEC2000 integer benchmarks while incurring an area overhead of less than 4% and an execution time penalty smaller than 1%.
Coooolll: A Deep Learning System for Twitter Sentiment Classification (2014)

In this paper, we develop a deep learn-ing system for message-level Twitter sen-timent classification. Among the 45 sub-mitted systems including the SemEval 2013 participants, our system (Coooolll) is ranked 2nd on the Twitter2014 test set of SemEval 2014 Task 9. Coooolll is built in a supervised learning framework by concatenating the sentiment-specific word embedding (SSWE) features with the state-of-the-art hand-crafted features. We develop a neural network with hybrid loss function 1 to learn SSWE, which en-codes the sentiment information of tweets in the continuous representation of words. To obtain large-scale training corpora, we train SSWE from 10M tweets collected by positive and negative emoticons, without any manual annotation. Our system can be easily re-implemented with the publicly available sentiment-specific word embed-ding. 1
Prevention of Chemotherapy-Induced Anemia and Thrombocytopenia by Constant Administration of Stem Cell Factor (2011)

SCF treatment can prevent the occurrence of chemotherapy-induced anemia and thrombocytopenia in mice, indicating a potential use of this cytokine in the supportive therapy of cancer patients.
In Silico Engineering of Synthetic Binding Proteins from Random Amino Acid Sequences (2018)

Synthetic proteins with high affinity and selectivity for a protein target can be used as research tools, biomarkers, and pharmacological agents, but few methods exist to design such proteins de novo. To this end, the In-Silico Protein Synthesizer (InSiPS) was developed to design synthetic binding proteins (SBPs) that bind pre-determined targets while minimizing off-target interactions. InSiPS is a genetic algorithm that refines a pool of random sequences over hundreds of generations of mutation and selection to produce SBPs with pre-specified binding characteristics. As a proof of concept, we design SBPs against three yeast proteins and demonstrate binding and functional inhibition of two of three targets in vivo. Peptide SPOT arrays confirm binding sites, and a permutation array demonstrates target specificity. Our foundational approach will support the field of de novo design of small binding polypeptide motifs and has robust applicability while offering potential advantages over the limited number of techniques currently available.
Synthesis and Angiotensin II Receptor Antagonist Activity of C-Linked Pyrazole Derivatives. (1994)

The synthesis and pharmacological activity of new nonpeptide angiotensin II (AII) receptor antagonists are presented. These 5-O-substituted and 5-C-substituted 3-alkylpyrazole derivatives represent a new series of antagonists and have led to the discovery of compounds with potent oral antihypertensive activity in a renal artery-ligated rat model. In vitro, they displayed a high affinity for rat adrenal AII receptors. In vivo structure-activity relationship study has shown the importance of the 4-[2'-(1H-tetrazol-5-yl)biphenyl-4-yl]methyl moiety for oral activity and the critical role of alkyl substituents at the 1- or 2-position. In the case of oral administration, 5-C derivatives were found to be, on the whole, more potent than 5-O derivatives. UP 221-78, 5-hydroxymethyl-3-n-propyl-1-(2,2,2-trifluoroethyl)-4- [[2'-(1H-tetrazol-5-yl)biphenyl-4-]methyl]-1H-pyrazole (79), displayed equivalent antihypertensive activity to the well known antagonist Losartan at 3 mg/kg p.o. in renal artery-ligated rats, with maximal decreases in mean arterial pressure of 60 and 63 mmHg for Losartan and UP 221-78, respectively.
Idiopathic Intracranial Hypertension in Female-to-Male Transgender Patients on Exogenous Testosterone Therapy (2023)

Testosterone therapy plays an essential role in FTM hormonal transitioning and may play a role in IIH. Patients undergoing testosterone therapy for gender transition should be informed of the possibility of developing IIH while on treatment, with obesity possibly increasing this risk. Comprehensive eye examinations should be considered in these patients before initiating hormone therapy.
Inhibition of epidural fibrosis with ADCONê-L: Effect on clinical outcome one year following re-operation for recurrent lumbar radiculopathy (1999)

In a prospective multicenter study, 20 patients underwent re-operation for recurrent radiculopathy after lumbo-sacral discectomy, and were treated with ADCON-L (Adhesion Control in a Barrier Gel) to inhibit epidural fibrosis following secondary surgery. Outcomes after re-operation were assessed at six and 12 months using: Visual Analog Scales to measure radicular and back pain, straight leg raising exams, and self-assessment of activity-related radicular pain. Each parameter was compared to baseline values, obtained immediately prior to the re-operation. The long term clinical results at 12 months after re-operation (summarized below) demonstrate a significant improvement of all clinical parameters, and correlated with the results seen at six months. Radicular pain, measured when most severe, was reduced from an average pre-operative score of 8.1-3.7 (p < 0.005). The straight leg raising angle increased from an average pre-operative value of 41 degrees-67 degrees (p < 0.005). Activity-related pain mean score was 4.6, vs. 17.0 pre-operatively (p < 0.005). Low back pain, measured when most severe, was reduced from an average pre-operative score of 6.1 to 3.1 (p < 0.012). These clinical findings compare very favorably with data reported in the literature. There were no adverse events or complications related to the use of ADCON-L.
Fsw Implementation on the Space Shuttle's External Tank (2013)

This paper presents, in viewgraph form, friction stir welding on the external tank of the Space Shuttle. The topics include: 1) Friction Stir Welding Process; 2) Implementation Status; and 3) Summary.
DNA from formalin-fixed tissue: extraction or repair? That is the question (2007)

Abstract Establishing effective DNA-based protocols for use on archival material fixed in formaldehyde (formalin) is a particularly challenging task. Formalin fixation induces cross-linking with nucleic acids and proteins, thereby reducing the amount and quality of the extracted DNA. Previous attempts have primarily focused on optimizing DNA extraction protocols. Here we focus on the use of enzymes capable of in vitro repair of DNA extracts prior to amplification of the nucleic acids by the polymerase chain reaction (PCR). The amplification success of mitochondrial DNA was greater using the repair enzyme assay (56%) than with the regular PCR assay (20%), and even more convincing results were obtained with the amplified nuclear ribosomal region (91% versus 21%). These results indicate that in vitro repair of DNA damage (depurinated sites, strand nicks and base modifications) increases the number of samples that amplify, amplify to a greater extent and amplify fewer ancillary bands and that DNA repair has been overlooked as a way of improving the efficiency of molecular methods used on formalin-fixed samples. Fidelity has not been specifically investigated, but preliminary results indicate that misincorporation is not a major problem.
Moonshine: An Online Randomness Distiller for Zero-Involvement\n Authentication (2021)

Context-based authentication is a method for transparently validating another\ndevice's legitimacy to join a network based on location. Devices can pair with\none another by continuously harvesting environmental noise to generate a random\nkey with no user involvement. However, there are gaps in our understanding of\nthe theoretical limitations of environmental noise harvesting, making it\ndifficult for researchers to build efficient algorithms for sampling\nenvironmental noise and distilling keys from that noise. This work explores the\ninformation-theoretic capacity of context-based authentication mechanisms to\ngenerate random bit strings from environmental noise sources with known\nproperties. Using only mild assumptions about the source process's\ncharacteristics, we demonstrate that commonly-used bit extraction algorithms\nextract only about 10% of the available randomness from a source noise process.\nWe present an efficient algorithm to improve the quality of keys generated by\ncontext-based methods and evaluate it on real key extraction hardware.\nMoonshine is a randomness distiller which is more efficient at extracting bits\nfrom an environmental entropy source than existing methods. Our techniques\nnearly double the quality of keys as measured by the NIST test suite, producing\nkeys that can be used in real-world authentication scenarios.\n
Catalytic Asymmetric Synthesis of Cyclic Ethers Containing an α‐Tetrasubstituted Stereocenter (2013)

'Ether' furan or pyran: The exo-selective cyclization of enantioenriched allenols is accomplished with high chirality transfer using as little as 0.02 mol % of a gold catalyst. The new method is effective in the synthesis of a wide range of enantioenriched cyclic ethers, which are prepared in excellent yields in three steps from readily available propargylic phosphates.
RF-mobility gain: concept, measurement campaign, and exploitation (2009)

Self-directed movement of radio devices can enable large amounts of power gain since the sources of fluctuations in received signal power due to multipath-induced small-scale fading have highly localized effects. We call the gain achieved by finding a better location the mobility gain. Experimental data for indoor as well as outdoor measurement studies are used to illustrate the potential of this RF-Mobility Gain concept over a wide range of frequencies. An analysis of the RF data reveals that a small amount of energy spent on searching for a better location can pay large dividends in long-term power expenditures for RF transmission. Challenges in building such a system for peer-to-peer links and network applications are discussed along with potential coordination algorithms.
The Apoplastic Oxidative Burst Peroxidase in Arabidopsis Is a Major Component of Pattern-Triggered Immunity (2012)

In plants, reactive oxygen species (ROS) associated with the response to pathogen attack are generated by NADPH oxidases or apoplastic peroxidases. Antisense expression of a heterologous French bean (Phaseolus vulgaris) peroxidase (FBP1) cDNA in Arabidopsis thaliana was previously shown to diminish the expression of two Arabidopsis peroxidases (peroxidase 33 [PRX33] and PRX34), block the oxidative burst in response to a fungal elicitor, and cause enhanced susceptibility to a broad range of fungal and bacterial pathogens. Here we show that mature leaves of T-DNA insertion lines with diminished expression of PRX33 and PRX34 exhibit reduced ROS and callose deposition in response to microbe-associated molecular patterns (MAMPs), including the synthetic peptides Flg22 and Elf26 corresponding to bacterial flagellin and elongation factor Tu, respectively. PRX33 and PRX34 knockdown lines also exhibited diminished activation of Flg22-activated genes after Flg22 treatment. These MAMP-activated genes were also downregulated in unchallenged leaves of the peroxidase knockdown lines, suggesting that a low level of apoplastic ROS production may be required to preprime basal resistance. Finally, the PRX33 knockdown line is more susceptible to Pseudomonas syringae than wild-type plants. In aggregate, these data demonstrate that the peroxidase-dependent oxidative burst plays an important role in Arabidopsis basal resistance mediated by the recognition of MAMPs.
SU‐C‐137‐04: Effective Control Limits for Predictive Maintenance (PdM) of Accelerator Beam Uniformity (2013)

Purpose: Predictive maintenance programs employ non‐invasive methods to monitor the performance of systems to determine when preemptive intervention is required to maintain high quality performance. The focus of this study is to evaluate the effectiveness of a modified calculation method for the control limits of process control charts (PCC) that will reduce false positive alarms but detect clinically relevant changes in beam uniformity (flatness and symmetry). Methods: Steering coil currents (SCC) for the transverse and radial planes are adjusted such that a reproducibly useful photon or electron beam is available. Performing controlled experiments varying a single SCC, we were able to determine the magnitude of change required to produce a 1% change in beam uniformity. The average and range (Xbar/R) control chart limit calculation was reformulated incorporating a scaling factor (Cm). After monitoring the SCC of 3 accelerators for several months, without detecting any PCC alarms, we intentionally changed the transverse angle and position SCC independently until the beam symmetry differed by ∼1.1% from baseline as confirmed by computerized beam profile scan in water using an ion chamber. These experimental SCC values were plotted in the PCC to determine if they would exceed the modified control limits. Results: The experimental SCC value exceeded the PCC limit for each of the steering coils. Additionally, the capability of the new control limit calculation method was confirmed when an anomaly was detected in the operation of an accelerator in clinical use. Instability in the operation of the 18 MV photon beam was predicted by SPC analysis prior to it being confirmed by service and daily check devices. If the analysis had been performed using the original methodology, a number of false positives would have been reported. Conclusion: Reformulated X‐bar/R chart control limits of SCC can provide an effective predictive maintenance tool for accelerator beam uniformity. This project is supported by a grant from Varian Medical Systems.
An Efficient Chemoenzymatic Approach to (S)-γ-Fluoroleucine Ethyl Ester (2005)

[reaction: see text] An asymmetric synthesis of (S)-gamma-fluoroleucine ethyl ester 1 is described. The key transformation involves a lipase-catalyzed dynamic ring-opening of 2-(3-butenyl)azlactone 7b with EtOH to give amide ester (S)-6b in 84% enantiomeric excess. Removal of the N-pentenoyl group with N,N'-dibromodimethylhydantoin in the presence of trifluoroacetic acid afforded the titled compound, which was isolated as its hydrogen sulfate salt in 75% yield and >97% ee.
Biomedical applications of functionalised carbon nanotubes (2004)

The organic functionalisation of carbon nanotubes can improve substantially their solubility and biocompatibility profile; as a consequence, their manipulation and integration into biological systems has become possible so that functionalised carbon nanotubes hold currently strong promise as novel systems for the delivery of drugs, antigens and genes.
An Evaluation of the Laryngeal Tube?? During General Anesthesia Using Mechanical Ventilation (2003)

In 96.6% of patients intubated with the Laryngeal Tube, it was possible to maintain oxygenation, ventilation, and respiratory mechanics during mechanical ventilation.
Selected-ion flow tube studies of reactions of the radical cation (HC3N)+• in the interstellar chemical synthesis of cyanoacetylene (1986)

The radical cation (HC 3 N) +• was produced in a Selected-Ion Flow Tube (SIFT) apparatus from cyanoacetylene by electron impact and reacted at room temperature in helium buffer gas with a selection of molecules including H 2 , CO, HCN, CH 4 , H 2 O, O 2 , HC 3 N, C 2 H 2 , OCS, C 2 H 4 , and C 4 H 2 . The observed reactions exhibited a wide range of reactivity and a variety of pathways including charge transfer, hydrogen atom transfer, proton transfer, and association. Association reactions were observed with CO, O 2 , HCN, and HC 3 N. With the latter two molecules association was observed to proceed close to the collision limit, which is suggestive of covalent bond formation perhaps involving azine-like N—N bonds. For HC 3 N an equally rapid association has been observed by Buckley etal. with ICR (Ion Cyclotron Resonance) measurements at low pressures and this is suggestive of radiative association. The hydrogen atom transfer reaction of ionized cyanoacetylene with H 2 is slow while similar reactions with CH 4 and H 2 O are fast. The reaction with CO fails to transfer a proton. These results have implications for synthetic schemes for cyanoacetylene as proposed in recent models of the chemistry of interstellar gas clouds. Proton transfer was also observed to be curiously unfavourable with all other molecules having a proton affinity higher than (C 3 N) • . Also, hydrogen-atom transfer was inefficient with the polar molecules HCN and HC 3 N. These results suggest that interactions at close separations may lead to preferential alignment of the reacting ion and molecule which is not suited for proton transfer or hydrogen atom transfer.
Longitudinal investigation of a xenograft tumor zebrafish model using polarization-sensitive optical coherence tomography (2022)

Breast cancer is a leading cause of death in female patients worldwide. Further research is needed to get a deeper insight into the mechanisms involved in the development of this devastating disease and to find new therapy strategies. The zebrafish is an established animal model, especially in the field of oncology, which has shown to be a promising candidate for pre-clinical research and precision-based medicine. To investigate cancer growth in vivo in zebrafish, one approach is to explore xenograft tumor models. In this article, we present the investigation of a juvenile xenograft zebrafish model using a Jones matrix optical coherence tomography (JM-OCT) prototype. Immunosuppressed wild-type fish at 1-month post-fertilization were injected with human breast cancer cells and control animals with phosphate buffered saline in the tail musculature. In a longitudinal study, the scatter, polarization, and vasculature changes over time were investigated and quantified in control versus tumor injected animals. A significant decrease in birefringence and an increase in scattering signal was detected in tumor injected zebrafish in comparison to the control once. This work shows the potential of JM-OCT as a non-invasive, label-free, three-dimensional, high-resolution, and tissue-specific imaging tool in pre-clinical cancer research based on juvenile zebrafish models.
Production of 2-hydroxyparaconic and itatartaric acids by Ustilago cynodontis and simple recovery process of the acids. (1990)

Ustilago cynodontis K320 was selected as the best strain for the production of /-itatartaric acid and its lactone, /-2-hydroxyparaconic acid, in shake culture under acidic conditions. Factors affecting the acid production were examined to optimize the culture conditions for maximal production of itatartaric and 2-hydroxyparaconic acids and efforts were made to simplify the recovery of the acids. Fermentation in a jar was continued until the accumulated itaconic acid and erythritol were completely consumed. 2-Hydroxyparaconic acid (49 g) was easily recovered as a crystalline mass (about 96% in purity) from 1 1 of the culture filtrate by a process consisting of concentration, lactonization of itatartaric acid to 2-hydroxyparaconic acid, and ethyl acetate extraction. Sodium itatartarate was prepared from the recovered 2-hydroxyparaconic acid by saponification.
ChemInform Abstract: TETRACYANOETHYLENE INSERTION INTO THE TIN‐SULFUR BOND (1978)

Abstract Zinn‐tetraphenylmercaptid (I) bildet mit Tetracyanethylen (II) in Benzol die orange gefärbte, beständige Lösung einer Komplexverbindung, aus der man selbst nach 72‐stündigem Kochen die Ausgangskomponenten quantitativ wiedergewinnen kann.