gebhart/patrepeval huggingface dataset:
The biological process of lysine‐tRNA charging is therapeutically targetable in liver cancer (2020)

Abstract Background &amp; Aims Mature transfer RNAs (tRNA) charged with amino acids decode mRNA to synthesize proteins. Dysregulation of translational machineries has a fundamental impact on cancer biology. This study aims to map the tRNAome landscape in liver cancer patients and to explore potential therapeutic targets at the interface of charging amino acid with tRNA. Methods Resected tumour and paired tumour‐free (TFL) tissues from hepatocellular carcinoma (HCC) patients (n = 69), and healthy liver tissues from organ transplant donors (n = 21), HCC cell lines, and cholangiocarcinoma (CC) patient‐derived tumour organoids were used. Results The expression levels of different mature tRNAs were highly correlated and closely clustered within individual tissues, suggesting that different members of the tRNAome function cooperatively in protein translation. Interestingly, high expression of tRNA‐Lys‐CUU in HCC tumours was associated with more tumour recurrence (HR 1.1; P = .022) and worse patient survival (HR 1.1; P = .0037). The expression of Lysyl‐tRNA Synthetase (KARS), the enzyme catalysing the charge of lysine to tRNA‐Lys‐CUU, was significantly upregulated in HCC tumour tissues compared to tumour‐free liver tissues. In HCC cell lines, lysine deprivation, KARS knockdown or treatment with the KARS inhibitor cladosporin effectively inhibited overall cell growth, single cell‐based colony formation and cell migration. This was mechanistically mediated by cell cycling arrest and induction of apoptosis. Finally, these inhibitory effects were confirmed in 3D cultured patient‐derived CC organoids. Conclusions The biological process of charging tRNA‐Lys‐CUU with lysine sustains liver cancer cell growth and migration, and is clinically relevant in HCC patients. This process can be therapeutically targeted and represents an unexplored territory for developing novel treatment strategies against liver cancer.
Supplementary Figures from Adverse Metaphase Cytogenetics Can Be Overcome by Adding Bortezomib and Thalidomide to Fractionated Melphalan Transplants (2023)

&lt;p&gt;Supplementary Figure 1: Consort flow diagram of patient flow through TT4 arms Supplementary Figure 2: Cumulative Incidence of Death and Post-Relapse Survival (P-values for S-TT4 vs L-TT4; TRM, p = 0.61; MRM, p = 0.70; OIM, p = 0.25). Supplementary Figure 3: Clinical outcomes according to the presence of PETidentified focal lesions (FL; =&lt;3 v &gt;3) by TT4 arm Supplementary Figure 4: Ingenuity pathways identified a network of 8 interrelated genes.&lt;/p&gt;
Optimal frequency selection for energy efficient underwater acoustic networks (2012)

The underwater acoustic channel is characterized by a path loss that is dependent on both the distance and the frequency of communication. Given this dependence, it has been previously demonstrated that for a given communication distance, there is an optimal operating frequency, where conditions for signal propagation and noise are most favorable. In this work, we consider extending this optimal frequency concept to scenarios in which the frequencies that can be employed by the system are constrained. Such constraints are important considerations for practical system design. The first problem we study is to find a single frequency that minimizes the energy over a number of links of varying lengths. An approximate model for this frequency is proposed that is very close to the true optimal. We then generalize this problem to finding the best frequency band, within which the frequency can be tuned for different link lengths. We demonstrate how our model is applied to a 2-D network scenario. We simulate random node placement for such a network, and we observe that the optimal frequencies are very close to the proposed model.
Heterocyclic GABA analogues. Displacement of radiolabelled 3H-GABA from rat brain membrane preparations. (1987)

2,5-Dimethyl-1H-pyrrol-1-yl-butanoic acid (I) and 2,5-diethyl-1H-pyrrol-1-yl-butanoic acid (V) were synthesised as non basic analogues of 4-aminobutanoic acid (GABA) to investigate the influence of the pKa of the 4-nitrogen on the in vitro binding to GABA receptors. (I) displaced 3H-GABA from specific binding sites of synaptosomal membrane preparations from rat cerebellum with an IC50 of 0.5 microM and (V) with an IC50 of 0.4 microM. (I) was inactive in vivo in the bicuculline anticonvulsant test (mice i.p.). The authors conclude that a basic nitrogen is not necessary for the binding to the GABAergic receptors although the ensuing complex is likely to be pharmacologically ineffective.
Simulation and validation of a wobble plate pump with a focus on check valve dynamics (2018)

Digital hydraulic piston pumps that use electrically controlled on/off valves to individually control the flow from each piston is a promising technique as these pumps are highly efficient at part displacement and respond quickly. However, digital pumps can still use check valves on the inlet, a fact that makes analysing wobble plate pumps (WPP) and their check valves interesting. Here, we measured the cylinder pressures of a WPP and compared these results with results from a simulation model we developed. In addition, we used linear analysis to investigate how different design parameters affect the valve’’s behaviour. From the measurements we found that the cylinder pressure is clearly affected the flow from other pistons and also that the system is not as stiff as expected. From the linear analysis, a criterion of how to design the valve to avoid instability was derived.
Is Pre-eclampsia Preventable? (1991)

Pre-eclampsia is characterised by reduced utero-placental blood flow which in turn results from vascular damage occurring early in pregnancy. Endothelial damage and reduced prostacyclin and nitric oxide synthesis will initiate excessive platelet aggregation, fibrin deposition and vascular occlusion. Prevention of pre-eclampsia is dependent on affecting this process. Antiplatelet therapy is being assessed as a prophylaxis. Screening tests using increased platelet turnover as their basis are also being assessed.
Depth boundary reconstruction method using the relations with neighboring pixels (2013)

In this paper, we propose a depth boundary reconstruction method for effective view synthesis. To prevent the introduction of undesired depth value, the depth boundaries are reconstructed by selected pixel value through the relations with neighboring pixels. Experimental results show how the proposed method works well for view synthesis.
ChemInform Abstract: Theoretical Study of B2H+ 5, B2H+ 6, and B2H6. (1989)

Abstract The B 2 H 5 + ion is predicted to have the triply hydrogen‐bridged structure (I) with D3h symmetry.
Statin Use and COVID-19 Infectivity and Severity in South Korea: Two Population-Based Nationwide Cohort Studies (2021)

Our findings indicate that prior statin use is related to a decreased risk of worsening clinical outcomes of COVID-19 and length of hospital stay but not to that of SARS-CoV-2 infection.
Integration of pulp and paper technology with bioethanol production (2013)

Three guiding principles result in attractive economics: (1) re-use existing assets to the maximum extent; (2) keep the process as simple as possible; (3) match the recalcitrance of the biomass with the severity of the pretreatment.
Novel Staphylococcal Cassette Chromosome mec Type, Tentatively Designated Type VIII, Harboring Class A mec and Type 4 ccr Gene Complexes in a Canadian Epidemic Strain of Methicillin-Resistant Staphylococcus aureus (2008)

Staphylococcal cassette chromosome mec (SCCmec) is a mobile genetic element characterized by flanking terminal direct and, in most cases, inverted repeat sequences, the mec and ccr gene complexes, and their surrounding DNA regions. Unique combinations of the mec and ccr gene complexes generate various SCCmec types. Six SCCmec types have been reported to date. We describe here a novel SCCmec type identified in a Canadian methicillin-resistant Staphylococcus aureus (MRSA) epidemic strain. MRSA clinical isolates were screened for known SCCmec types by multiplex and conventional PCR methods. Three phenotypically and genotypically identical MRSA clinical isolates with a pulsotype identical to CMRSA9 were identified locally and found to be nontypeable by available SCCmec typing schemes. Complete sequencing of the SCCmec element revealed a nucleotide fragment of 32,168 bp integrated at an identical chromosomal integration site (attBscc) at the 3' end of the orfX gene. The nucleotide sequences at the chromosome-SCCmec junction regions were typical of other SCCmec types, but the element harbored a unique combination of class A mec and type 4 ccr gene complexes. Sequence recombination analysis suggested that this unique SCCmec type may be derived from homologous recombination between the previously described SCC(RP62A) of S. epidermidis strain RP62A and SCC composite island of S. epidermidis ATCC 12228, respectively, or via recombination of other staphylococcal strains that carry the same or similar mobile cassettes. We identified a previously undescribed type of SCCmec from isolate C10682, tentatively designated type VIII, and we provide compelling evidence supporting the ability of SCC elements to transfer horizontally or undergo recombination to generate new SCCmec types.
DIAGNOSTIC AND SURGICAL IMAGING ANATOMY (2006)

DIAGNOSTIC AND SURGICAL IMAGING ANATOMY: BRAIN, HEAD, NECK, AND SPINE Author: H. Ric Harnsberger, MD Anne G. Osborn, MD, FACR Andre J. Macdonald, MBChB, Jeffrey S. Ross, MD, Kevin R. Moore, MD Karen L. Salzman, MD Bibliographic Data: Lippincott Williams & Wilkins, 2006. ISBN: 1-931884-29-3, 800 pages, hard cover, $249.00. Reviewer's Expert Opinion Description: This is an all encompassing neuroimaging atlas. With great detail and precision, it explores the complex anatomy of the brain, spine, head, and neck. Purpose: According to the author, the purpose is to provide physicians with a neuroanatomy atlas that will improve both the accuracy and efficiency of image interpretation. Given the complexity of this subject, the objectives are worthy, and the book is much needed. The authors meet their goals and in many ways exceed them. This book makes all of my other neuroanatomy atlases useless. Audience: The book is written for both radiologists and surgeons looking to improve their knowledge of neuroimaging anatomy. This book is perfect not only for people at the attending level, but also for residents or anyone trying to navigate through the complexities of neuroanatomy. The authors are some of the top neuroradiologists in the country and their publication demonstrates their expertise. Features: Via both beautifully colored illustrations and detailed neuroimaging slides, the book covers all neuroanatomy including the spine, head, and neck. The book is amazing in its detail, and the quality of the images is unsurpassed. All structures are depicted using multiple modalities (primarily computed tomography and magnetic resonance imaging) in all three planes. The beautifully colored art enhances the appearance and usefulness of the book. If you are not familiar with the Diagnostic Imaging series, you might have difficulty navigating the book at first because its setup is unique. There are no real shortcomings to the book, although there are one or two typographical errors. Assessment: This is, by far, the best neuroimaging atlas. I have many atlases, including Imaging Atlas of Human Anatomy, 3rd edition, by Weir and Abrahams (Elsevier, 2003), Cross-sectional Human Anatomy, by Dean and Herbener (Lippincott Williams & Wilkins, 2000), Atlas of Human Anatomy, 4th edition, by Netter (Elsevier, 2006), and Atlas of the Visible Human Male, by Spitzer and Whitlock (Jones and Bartlett, 1997). For neuroanatomy, I can honestly say that my use of these other sources will decrease dramatically, if not entirely. Reviewer: Seth Jay Kligerman, MD, MS (University of Colorado School of Medicine)
Phases formation in cerium-doped hydroxyapatite (2021)

Abstract Cerium-substituted hydroxyapatites (Ce-HAs) with an estimated content of Ce 3 + of 0; 0.1; 0.25; 0.5 mol. % were prepared by two different synthesis methods: precipitation from aqueous solutions of salts and mechanochemical synthesis. The powders after synthesis were heat-treated at 1250 °C to achieve well-crystallized phases. The X-ray diffraction analysis (XRD), scanning electron microscopy (SEM), energy dispersive analysis (EDA), and dilatometry methods revealed that cerium ions didn’t not fully incorporate into the HA structure, but rather were transform to the CeO2 phase. It was attributed to the transition of Ce valency (III)→(IV) through the oxidation reaction under air conditions during materials heating. Two different synthesis methods provided similar phase composition of the obtained compounds, though different microstructure of the resulted ceramics. It was shown that cerium introduction prevents HA sintering during thermal activation, possibly due to contribution of large atomic mass of cerium ions and formation of cerium (IV) oxide at the crystal boundaries.
Timed pattern generation for noise-on-delay calculation (2002)

Computing the noise on delay effects is required for all circuits from simple ASIC designs to microprocessors. Transistor-level simulation engines make accurate delay calculation affordable only if the number of simulation per stage is very small. We propose a solution that predicts the alignment of aggressor signals with respect to the victim signal to induce the worst-case noise effect on delay. The aggressor alignment can be used to setup a detailed simulation. The worst-case delay in the presence of noise is predicted within 5% error for more than 99% of the cases tested using an average of 1.27 simulations per stage transition.
Using Urban Farmer Perceptions of Urban Agricultural Resources to Inform Extension Programming: A Q Methodology Study (2023)

Urban farmers face challenges as they work among traditionally underserved populations, are new to farming, and may not recognize the resources available to them. The United States Department of Agriculture (USDA) prioritizes urban food production research and has recognized the unique challenges faced by urban farmers. The purpose of this study was to better understand the perspectives of urban farmers toward urban agricultural resources. Using the USDA Urban Agricultural Toolkit (2016) as a conceptual framework, this study found three perspectives of Oklahoma agricultural producers regarding urban agricultural resource challenges: The Visionary Farmer, The Business-minded Farmer, and The Learning Farmer. Visionary Farmers emphasize the application of urban agriculture toward urban social and community-building needs. Business-minded Farmers recognize the need for economic and financial education and resources for urban farmers. Learning Farmers highlight the need for continued agricultural education in urban agricultural operations. The findings suggest an opportunity for Extension and farmer-serving agencies to provide innovative communication, programming and support designed to address the unique struggles of urban farmers.
In vitrosusceptibility ofMycobacterium abscessuscomplex and feasibility of standardizing treatment regimens (2020)

In vitro activity was demonstrated for clofazimine, bedaquiline and eravacycline, indicating potential for inclusion as standardized therapy for M. abscessus complex infections.
Distributed Runtime Verification of Metric Temporal Properties for Cross-Chain Protocols (2022)

Transactions involving multiple blockchains are implemented by cross-chain protocols. These protocols are based on smart contracts, programs that run on blockchains, executed by a network of computers. Because smart contracts can automatically transfer ownership of cryptocurrencies, electronic securities, and other valuable assets among untrusting parties, verifying the runtime correctness of smart contracts is a problem of compelling practical interest. Such verification is challenging since smart contract execution is time-sensitive, and the clocks on different blockchains may not be perfectly synchronized. This paper describes a method for runtime monitoring of blockchain executions. First, we propose a generalized runtime verification technique for verifying partially synchronous distributed computations for the metric temporal logic (MTL) by exploiting bounded-skew clock synchronization. Second, we introduce a progression-based formula rewriting scheme for monitoring \MTL specifications which employ SMT solving techniques and report experimental results.
PHOTOPHYSICAL PROBES FOR MONITORING THE ELECTRIC FIELD/MICROPOLARITY WITHIN THE FAUJASITE SUPERCAGE* (1992)

Abstract— The micropolariry of the supercages of zeolites is a reflection of the electric field provided by the cations present within them. The notion of polarity within the cages of X and Y zeolite does not have precisely the same meaning as in solution. In this study, pyrene, pyrenealdehyde, and para‐ dimethylaminobenzonitrile have been used as photophysical probes to monitor the polarity of the zeolite interior. With pyrenealdehyde and para ‐dimethylaminobenzonitrile the supercage wherein the probe is expected to reside is more polar or possesses a higher electric field when the cation is Li or Na. The polarity/electric field of the supercage decreases with cation size (Li &gt; Na &gt; K &gt; Rb &gt; Cs) and the supercage is more polar in the case of X zeolites than in Y zeolites. The results with pyrene are generally consistent with those with the other two probes. However, pyrene is unable to sense the difference between Li. Na and other cations.
Einleitung (2002)

Eine lange Zeit schlagen bei vielen Selbständigen zwei Herzen in der Brust.
On wind forcing and observed oceanic wave number spectra (1988)

When oceanic internal waves are forced by rapidly translating winds and wind stress is applied as a body force which is uniform within and vanishes outside a surface layer, their spectrum has a vertical wave number shape indistinguishable from the Garrett and Munk observational synthesis. Bandwidth and high‐wave number dependence are functions of the stress gradient layer thickness and vertical structure. The close correspondence between the predicted spectrum of forced waves and observed spectra suggests that the wave number shape of the near‐inertial part of the oceanic internal wave spectrum is a consequence of wind forcing. The same mechanism is consistent with observed equatorial wave number spectra. Conversely, if mid‐latitude near‐inertial internal waves and equatorial waves are directly wind forced, then their observed wave number spectra imply that the vertical gradient of stress due to wind is nearly a step function which cuts off sharply at a depth comparable to observed seasonal pycnocline depths.
Development of an Inspection System for Defect Detection in Pressed Parts Using Laser Scanned Data (2014)

In past few decades several researches have been conducted in the field of 3D parts inspection system. The accuracy level of manufactured parts has been improved remarkably within this period. The use of laser sensors in 3D part measurement process has introduced a significant improvement in data acquisition process regarding time and cost. However for quality control process, due to lack of appropriate technique to process and inspect the scanned point cloud data, high accuracy level could not have been achieved so far. Therefore the industries are still compelled to use same traditional coordinate measuring machines (CMMs) despite of being very slow. In this paper, a robust inspecting technique to detect defects in 3D pressed parts has been proposed. Point cloud data are segmented for the extraction of features. These segmented features are used for shape matching during feature based registration process to localize them with the respective CAD model and bring into same coordinate frame. A modified Iterative closest point (ICP) algorithm is proposed for the registration process. After the registration has been completed these scanned model and CAD model are compared to find defects in the manufactured parts.
Combination of the SNH/aza-Diels–Alder Reactions as Effective Synthetic Approach to 8-Hydroxy(methoxy)-Substituted 2-[6-(1-Methylindol-3-yl)pyridin-2-yl]quinoline Ligands/Fluorophores (2021)

8-Hydroxy(methoxy)-substituted 2-[6-(1-methylindol-3-yl)pyridin-2-yl]quinoline ligands were synthesized by means of combination of SNH reaction between 8-methoxy-substituted 2-(6-aryl-1,2,4-triazin-3-yl)quinolones and indole and aza-Diels–Alder reaction of the obtained 1,2,4-triazines with 2,5-norbornadiene. The demethylation of quinoline moiety of 1,2,4-triazine precursor during aza-Diels–Alder reaction in autoclave was demonstrated.
Testing of Perpetual Pavement with Warm Asphalt Concrete Surface Mixes in the Ohio APLF (2008)

In September 2006, 4 lanes of asphalt concrete pavement were constructed in the Ohio Accelerated Pavement Loading Facility. One entire lane and one-half of each of the 3 remaining lanes were constructed as a 16-inch (40.6 cm) thick perpetual pavement over 6 inches (15.2 cm) of 304 dense graded aggregate base (DGAB). The other half of the 3 lanes had reduced thicknesses of 13 (33.0), 14 (35.6), and 15 (38.1) inches (cm) of perpetual pavement over 9 (22.9), 8 (20.3), and 7 (17.8) inches (cm), respectively, of 304 DGAB to determine how dynamic responses and rutting on these sections compared to that measured on the 16-inch (40.6 cm) thick sections. The surface courses on these 4 lanes included conventional hot mixed asphalt concrete, and warm mix asphalt concrete containing Evotherm, Sasobit, and Aspha-Min. LVDTs, strain gauges, and pressure cells were installed in sections with the 4 pavement thicknesses to measure dynamic responses under rolling dual tires, and under an FWD load plate as surface deflections were measured at 3 nominal loads and 3 temperatures. Thermocouples were added to monitor temperature gradients in the pavement structures. Lateral profiles of the 4 lanes were recorded periodically to compare rutting of the 4 surface mixes and 4 pavement thicknesses under repeated applications of 9,000 lb. (40 kN) rolling dual tires at 3 temperatures. The 3 warm asphalt concrete mixes had more early rutting under rolling wheel loads than the conventional mix, with Evotherm having the most rutting. Certain pavement responses were higher under 9,000 lb. (40 kN) dual tires rolling at 5 mph than under the FWD load plate at the same load.
Mast cell activation contributes to sickle cell pathobiology and pain in mice (2013)

Sickle cell anemia (SCA) is an inherited disorder associated with severe lifelong pain and significant morbidity. The mechanisms of pain in SCA remain poorly understood. We show that mast cell activation/degranulation contributes to sickle pain pathophysiology by promoting neurogenic inflammation and nociceptor activation via the release of substance P in the skin and dorsal root ganglion. Mast cell inhibition with imatinib ameliorated cytokine release from skin biopsies and led to a correlative decrease in granulocyte-macrophage colony-stimulating factor and white blood cells in transgenic sickle mice. Targeting mast cells by genetic mutation or pharmacologic inhibition with imatinib ameliorates tonic hyperalgesia and prevents hypoxia/reoxygenation-induced hyperalgesia in sickle mice. Pretreatment with the mast cell stabilizer cromolyn sodium improved analgesia following low doses of morphine that were otherwise ineffective. Mast cell activation therefore underlies sickle pathophysiology leading to inflammation, vascular dysfunction, pain, and requirement for high doses of morphine. Pharmacological targeting of mast cells with imatinib may be a suitable approach to address pain and perhaps treat SCA.