gebhart/patrepeval huggingface dataset:
Chemical Treatments for Reducing the Yellow Discoloration of Channel Catfish ( Ictalurus punctatus ) Fillets (2013)

The effect of chemical pretreatments on the color and carotenoid content of yellow discolored channel catfish fillets was studied. The color and carotenoid content of the fillets were analyzed by the L*a*b* color system and high-performance liquid chromatography, respectively. Untreated fillets turned more yellow and darker after 12-d storage. Sodium bicarbonate had a beneficial effect on reducing the degree of yellowness, but the fillets still turned darker after storage. Sodium bisulfite gave the best results with fillets becoming less yellow and brighter after storage. Ascorbic acid, butylated hydroxyanisole, citric acid, and sodium metabisulfite were not successful at reducing the discoloration. The sum of carotenoid contents of untreated fillets decreased significantly (P < 0.05) during storage as compared to the fresh fillets. However, the sum of the carotenoid contents of fillets treated by various chemicals was not significantly (P > 0.05) different from the fresh or untreated fillets. The appearance of catfish fillets may be improved during storage by pretreating with sodium bisulfite.
A conserved SUMO pathway repairs topoisomerase DNA-protein cross-links by engaging ubiquitin-mediated proteasomal degradation (2020)

Topoisomerases form transient covalent DNA cleavage complexes to perform their reactions. Topoisomerase I cleavage complexes (TOP1ccs) are trapped by camptothecin and TOP2ccs by etoposide. Proteolysis of the trapped topoisomerase DNA-protein cross-links (TOP-DPCs) is a key step for some pathways to repair these lesions. We describe a pathway that features a prominent role of the small ubiquitin-like modifier (SUMO) modification for both TOP1- and TOP2-DPC repair. Both undergo rapid and sequential SUMO-2/3 and SUMO-1 modifications in human cells. The SUMO ligase PIAS4 is required for these modifications. RNF4, a SUMO-targeted ubiquitin ligase (STUbL), then ubiquitylates the TOP-DPCs for their subsequent degradation by the proteasome. This pathway is conserved in yeast with Siz1 and Slx5-Slx8, the orthologs of human PIAS4 and RNF4.
Abstract C24: Methylation of AKAP12 promoter in lung cancer (2009)

Abstract AKAP12 play an important role in tumor growth suppression by inducing apoptosis with the regulation of multiple molecules in the cell cycle progression. This function of AKAP12 gene might be inhibited by epigenetic repression like other tumor suppressor genes. In the previous report, we showed that AKAP12 inactivation was associated with the promoter methylation in the lung cancer. In the present study, to investigate whether the promoter methylation of AKAP12 gene affects the expression of AKAP12 protein, we carried out in vitro methylation assay and protein analysis. We also performed methylation profiling of AKAP12 promoter using the bisulfite-sequencing in the additional matched normal and lung cancer tissue DNA, and serum DNA samples. The expression of the AKAP12 protein was down-regulated in lung cancer cells. The reduced expression of AKAP12 protein was restored by the treatment of the DNA methyltransferase inhibitor. AKAP12 fragments pGL3-837 M (methylated) and pGL3-443 M (methylated) showed low luciferase activities compared to the unmethylated constructs. CpG islands of the AKAP12 promoter were frequently methylated in tumor samples compared with normal tissue samples. Furthermore, CpG islands methylation of AKAP12 was more frequently found in non-relapse patients after surgery compared to early relapse patients within 2 years after surgery. In conclusion, our results demonstrated that AKAP12 expression was regulated by DNA methylation and AKAP12 promoter methylation was associated with lung cancer development and prognosis after surgery. This work was supported by a grant from the Korea Health 21 R&amp;D Project, Ministry of Health &amp; Welfare, Republic of Korea (A010250) and Seoul Research and Business Development Program (10574) Citation Information: Mol Cancer Ther 2009;8(12 Suppl):C24.
New Criteria for 0D/1D Knock Models to Predict the Knock Boundary for Different Gasoline Fuels (2021)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;As engine knock limits the efficiency of spark ignition engines and consequently further reduction of CO&lt;sub&gt;2&lt;/sub&gt; emissions, SI engines are typically designed to operate at the knock boundary. Therefore, a precise knock model is necessary to consider this phenomenon in an engine process simulation. The basis of the introduced 0D/1D knock model is to predict when the unburnt mixture auto-ignites, since auto-ignitions precede knocking events. The knock model further needs to evaluate the auto-ignition, because not every auto-ignition results in engine knock. As the introduced model’s prediction of the auto-ignition onset is already validated at extensive variations of operating conditions, this publication focusses on its evaluation. For this, two new, independent criteria are developed that take the pre-reactions of the unburnt mixture before the start of combustion into account to calculate a respective threshold for the auto-ignition onset at the knock boundary. In simulations, the operating point’s center of combustion is advanced until the 0D/1D knock model predicts an auto-ignition that occurs before its calculated threshold. For validation, the point where 50% of the mass is burned (MFB50) of this simulated operating point is compared to the MFB50 of the corresponding measured average working cycle at the knock boundary. To ensure a wide-ranging validation of the model, the measurement data cover extensively varied operating conditions like different engine configurations and gasoline fuels, varying compression ratio, turbulence, injection, EGR, wall temperature as well as engine load and speed. Although each introduced criterion is calibrated at only two operating points, the respective new 0D/1D knock model can predict the MFB50 at the knock boundary of the stated broad variations very precisely with a standard deviation below 2 °CA. Consequently, both new, independent criteria clearly improve the knock model and help to improve the development of SI engines in 0D/1D simulation.&lt;/div&gt;&lt;/div&gt;
Sustainable Electrochemical Decarboxylative Acetoxylation of Aminoacids in Batch and Continuous Flow (2021)

Introduction of acetoxy groups to organic molecules is important for the preparation of many active ingredients and synthetic intermediates. A commonly used and attractive strategy is the oxidative decarboxylation of aliphatic carboxylic acids, which entails the generation of a new C(sp3)-O bond. This reaction has been traditionally carried out using excess amounts of harmful lead(IV) acetate. A sustainable alternative to stoichiometric oxidants is the Hofer-Moest reaction, which relies in the 2-electron anodic oxidation of the carboxylic acid. However, examples showing electrochemical acetoxylation of amino acids are scarce. Herein we present a general and scalable procedure for the anodic decarboxylative acetoxylation of amino acids in batch and continuous flow mode. The procedure has been applied to the derivatization of several natural and synthetic amino acids, including key intermediates for the synthesis of active pharmaceutical ingredients. Good to excellent yields were obtained in all cases. Transfer of the process from batch to a continuous flow cell signficantly increased reaction throughput and space-time yield, with excellent product yields obtained even in a single-pass. The sustainability of the electrochemical protocol has been examined by evaluating its green metrics. Comparison with the conventional method demonstrates that an electrochemical approach has a significant positive effect on the greenness of the process
Acide ursodésoxycholique et cholestases (1995)

L'acide ursodesoxycholique (AUDC) represente un apport important dans le traitement des maladies cholestatiques. Son absence d'effets secondaires permet de l'utiliser de facon prolongee. Son effet benefique est clair dans la cirrhose biliaire primitive. Dans la cholangite sclerosante primitive, l'AUDC a egalement un effet benefique sur l'evolution de la maladie lorsqu'il est administre precocement et en attente de transplantation hepatique. Dans la mucoviscidose, la maladie de Byler, l'atresie des voies biliaires, les ductopenies et les anomalies du metabolisme des acides biliaires, l'AUDC exerce un effet favorable, a la fois sur la fonction hepatocytaire et sur l'etat nutritionnel des enfants, et peut permettre de retarder la transplantation hepatique, rendant celle-ci realisable dans de meilleures conditions. Dans les autres maladies (hepatites medicamenteuses, prevention du rejet d'allogreffes, maladie du greffon contre l'hote, cholestase associee a la nutrition parenterale, cholestase liee a des stenoses des voies biliaires, cholestase recurrente gravidique, cholestase recidivante idiopathique), la place de l'AUDC est encore incertaine. Au cours des hepatites chroniques actives et des maladies alcooliques du foie, la place de l'AUDC reste egalement a preciser. Le mecanisme d'action de l'AUDC au cours des maladies cholestatiques repose sur le remplacement des acides biliaires endogenes, qui s'accumulent dans le parenchyme hepatique au cours des cholestases, par l'AUDC, qui est denue d'effets cytotoxiques. De plus, l'AUDC pourrait avoir un effet benefique en reduisant l'expression hepatique des molecules du complexe majeur d'histocompatibilite et par un effet cytoprotecteur direct.
A P-Tree based Outlier Detection Method. (2004)

Outlier detection can discover unexpected and interesting knowledge, which is often important to the information society. In this paper, we developed an efficient density-based outlier detection method for large datasets. In our method, outliers are efficiently detected from the candidate data subsets which contain potential outliers. Furthermore, the algorithm is implemented using a vertical data organization model, P-Tree, which speed up the algorithm significantly. We tested our method with NHL data. Experiment shows that our method has an order of magnitude speed improvement over the contemporary approaches.
A new method of determining the optical properties of cotton fibers using polarizing interference microscopy (1983)

Abstract The refractive indices, birefringence, and cross‐sectional area of cotton fibers was measured using interference polarizing microscope constructed by M. Pluta. A new technique was suggested by realizing the measurements at the perpendicular position of the duplicated image of fiber to the interference fringe. The proposed procedure is a combination of modification of Hamza method and Pluta dual wavelength method, and it was possible to measure at once the three mentioned features of single fiber at one time.
Paper # 161: The Effect of Tibial Tunnel Coronal Location of Anatomic Double‐Bundle Anterior Cruciate Ligament Reconstruction on Knee Kinematics in a Porcine Model (2011)

IntroductionAnatomic placement is a consideration in anterior cruciate ligament (ACL) reconstruction when using either single-bundle or double-bundle (DB) technique. Although most previous studies have focused on the femoral footprint, the native ACL footprint on the tibial side are also widely varied in both sagittal and coronal planes.[1Tallay A. et al.Anatomical study of the human anterior cruciate ligament stump's tibial insertion footprint.Knee Surg Sports Traumatol Arthrosc. 2008; 16: 741-746Crossref PubMed Scopus (52) Google Scholar] Specifically, the anteromedial (AM) footprint position is sometimes observed on the lateral side relative to posterolateral (PL) position. In such cases, if the AM bundle is placed in the “anteromedial” position, the AM graft would be placed non-anatomically on the medial side. However, little is known about the effect of the medio-lateral (ML) position for the AM bundle on knee kinematics. Thus, the purpose of this study was to evaluate knee kinematics and the in situ force of the ACL graft after two different AM placements of double-bundle ACL reconstructions, whose tibial AM placements were either non-anatomically lateral and anatomically medial, and to compare those two ACL reconstructed knees. The hypothesis was that the tibial ML position would have a significant effect on knee kinematics and the in situ force of the ACL graft and that of the anatomic AM placement better restores normal knee kinematics and in situ force of the ACL.
Supplemental Data File 1 from Machine-Learning Prediction of Tumor Antigen Immunogenicity in the Selection of Therapeutic Epitopes (2023)

&lt;p&gt;Supplemental Data File&lt;/p&gt;
Fall-sown small grain cover crops for weed suppression and soil moisture management in an irrigated organic agroecosystem (2022)

Abstract Adoption of cover crops in arid agroecosystems has been slow due to concerns regarding limited water resources and possible soil moisture depletion. In irrigated organic systems, potential ecosystem services from cover crops also must be considered in light of the concerns for water conservation. A constructive balance could be achieved with fall-sown small grain cover crops; however, their impacts on irrigated organic systems are poorly understood. Our first objective was to determine the ability of fall-sown small grains [cereal rye ( Secale cereale L), winter wheat ( Triticum aestivum L.), barley ( Hordeum vulgare L.) and oat ( Avena sativa L.)] to suppress winter weeds in an irrigated, organic transition field in the southwestern USA. Small grains were planted following the legume sesbania ( Sesbania exaltata (Raf.) Rydb. ex A.W. Hill) during Fall 2012 and Fall 2013. In Spring 2013 and 2014, weed densities and biomass were determined within each cover crop treatment and compared against unplanted controls. Results indicated that both barley and oat were effective in suppressing winter weeds. Our second objective was to compare weed suppression and soil moisture levels among seven barley varieties developed in the western United States. Barley varieties (‘Arivat’, ‘Hayes Beardless’, ‘P919’, ‘Robust’, ‘UC603’, ‘UC937’, ‘Washford Beardless’) were fall-sown in replicated strip plots in Fall 2016. Weed densities were measured in Spring 2017 and volumetric soil moisture near the soil surface (5.1 cm depth) was measured at time intervals beginning in December 2016 and ending in March 2017. With the exception of ‘UC937’, barley varieties caused marked reductions in weed density in comparison with the unplanted control. Soil moisture content for the unplanted control was consistently lower than soil moisture contents for barley plots. Barley variety did not influence volumetric soil moisture. During the 2017–2018 growing season, we re-examined three barley varieties considered most amenable to the cropping system requirements (‘Robust’, ‘UC603’, ‘P919’), and these varieties were again found to support few weeds (≤ 5.0 weeds m −2 ). We conclude that several organically certified barley varieties could fill the need for a ‘non-thirsty’ cover crop that suppresses winter weeds in irrigated organic systems in the southwestern United States.
Automatic 3D Object Segmentation in Multiple Views using Volumetric Graph-Cuts (2007)

We propose an algorithm for automatically obtaining a segmentation of a rigid object in a sequence of images that are calibrated for camera pose and intrinsic parameters. Until recently, the best segmentation results have been obtained by interactive methods that require manual labelling of image regions. Our method requires no user input but instead relies on the camera fixating on the object of interest during the sequence. We begin by learning a model of the object is colour, from the image pixels around the fixation points. We then extract image edges and combine these with the object colour information in a volumetric binary MRF model. The globally optimal segmentation of 3D space is obtained by a graph-cut optimisation. From this segmentation an improved colour model is extracted and the whole process is iterated until convergence. Our first finding is that the fixation constraint, which requires that the object of interest is more or less central in the image, is enough to determine what to segment and initialise an automatic segmentation process. Second, we find that by performing a single segmentation in 3D, we implicitly exploit a 3D rigidity constraint, expressed as silhouette coherency, which significantly improves silhouette quality over independent 2D segmentations. We demonstrate the validity of our approach by providing segmentation results on real sequences.
Tissue-Specific Differences in Human Transfer RNA Expression (2006)

Over 450 transfer RNA (tRNA) genes have been annotated in the human genome. Reliable quantitation of tRNA levels in human samples using microarray methods presents a technical challenge. We have developed a microarray method to quantify tRNAs based on a fluorescent dye-labeling technique. The first-generation tRNA microarray consists of 42 probes for nuclear encoded tRNAs and 21 probes for mitochondrial encoded tRNAs. These probes cover tRNAs for all 20 amino acids and 11 isoacceptor families. Using this array, we report that the amounts of tRNA within the total cellular RNA vary widely among eight different human tissues. The brain expresses higher overall levels of nuclear encoded tRNAs than every tissue examined but one and higher levels of mitochondrial encoded tRNAs than every tissue examined. We found tissue-specific differences in the expression of individual tRNA species, and tRNAs decoding amino acids with similar chemical properties exhibited coordinated expression in distinct tissue types. Relative tRNA abundance exhibits a statistically significant correlation to the codon usage of a collection of highly expressed, tissue-specific genes in a subset of tissues or tRNA isoacceptors. Our findings demonstrate the existence of tissue-specific expression of tRNA species that strongly implicates a role for tRNA heterogeneity in regulating translation and possibly additional processes in vertebrate organisms.
The design of a semi-automated football table (2010)

This paper presents the design of a semiautomated football table. One side of the table is equipped with automated rods, whereas the other side has regular rods. With this setup one or two human players can play against a computer controlled adversary. The paper describes the design and integration of a suitable hardware setup with vision based control algorithms that control the automated rods to intercept and return the ball.
Bisphosphonated Benzoxazinorifamycin Prodrugs for the Prevention and Treatment of Osteomyelitis (2008)

Benzoxazinorifamycins are potent antibacterial agents currently in development. Tethering these antibiotics to a bisphosphonate functional group by a cleavable linker allows the delivery of these agents to osseous tissues, where they can be released over time to treat bone infections. Various linker strategies are presented herein to develop osteotropic prodrugs, the activities of which are examined in vitro and in vivo.
Ca 2+ and cAMP open differentially dilating synaptic fusion pores (2022)

ABSTRACT Neuronal dense-core vesicles (DCVs) contain neuropeptides and much larger proteins that affect synaptic growth and plasticity. Rather than using full collapse exocytosis that is common in endocrine cells, DCVs at a native intact synapse, the Drosophila neuromuscular junction, release their contents via fusion pores formed by kiss and run exocytosis. Here fluorogen activating protein (FAP) imaging reveals the permeability range of synaptic DCV fusion pores and then shows that this constraint is circumvented by cAMP-induced extra fusions with dilating pores that result in DCV emptying. These Ca 2+ -independent full fusions require PKA-R2, a PKA phosphorylation site on the fusion clamp protein complexin and the acute presynaptic function of Rugose/Neurobeachin, a PKA-R2 anchor implicated in learning and autism. Therefore, localized Ca 2+ -independent cAMP signaling opens dilating fusion pores to release large cargo proteins that cannot pass through the narrower fusion pores that normally dominate spontaneous and Ca 2+ -evoked synaptic protein release. Hence, two independent exocytosis triggers (Ca 2+ and cAMP) vary the composition of released proteins at the synapse by differentially adjusting DCV fusion pores.
Tubulin acetyltransferase discovered: Ciliary role in the ancestral eukaryote expanded to neurons in metazoans (2010)

The emergence of α- and β-tubulins from an FtsZ-like prokaryotic homolog represented a defining event in eukaryogenesis. It permitted, together with actin and molecular motors, the establishment of a cytoskeleton able to support dynamic events such as cell division and trafficking of vesicles and proteins. It also served as the foundation for the microtubule-based cilium, an organelle with motility and sensory functions that replaced the less versatile prokaryotic flagellum (1). As it turns out, a mechanism to stabilize the ciliary axoneme, involving acetylation of α-tubulin, evolved in the ancestral eukaryote (2–4). This reversible modification situated inside the microtubule lumen still operates in extant ciliated protists and is exploited by metazoans to support ancillary microtubule functions, particularly in neurons (5). The concurrent discovery of an α-tubulin acetyltransferase by two separate groups, published in PNAS (3) and in Nature (4), now paves the way for a detailed understanding of the cellular and physiological roles conferred by tubulin acetylation.
Smartphone‐coupled Electrochemical Analysis of Cellular Superoxide Anions Based on Mnx(PO4)y Monolayer Modified Porous Carbon (2019)

Abstract Here we established a palm‐sized electrochemical sensor for the determination of cell‐released superoxide anions (O 2 .− ) based on a self‐developed portable potentiostat (xenSTAT) which can perform fast analysis with visual real‐time data and customizable parameters. The xenSTAT was equipped with Bluetooth and USB interfaces, thus being able to be connected with both smartphones and computers for electrochemical analysis. A novel Nanozyme based on Mn x (PO 4 ) y monolayer modified porous carbon cubic was synthesized and used as functional material on the surface of working electrode. By using cyclic voltammetry (CV) and chronoamperometry, xenSTAT was demonstrated to exhibit satisfying sensitivity and excellent stability for real‐time monitoring of O 2 .− released from cancer cells. With decreased cost, customizable development, small size and convenient usage, the xenSTAT described in this work could promote the commercialization and widespread of in‐house built electrochemical sensors for the monitoring of O 2 .− in the future.
TiO2 Nanowire Bundle Microelectrode Based Impedance Immunosensor for Rapid and Sensitive Detection of Listeria monocytogenes (2008)

A novel TiO 2 nanowire bundle microelectrode based immunosensor was demonstrated as a more sensitive, specific, and rapid technology for detection of Listeria monocytogenes. TiO 2 nanowire bundle was prepared through a hydrothermal reaction of alkali with TiO 2 powder and connected to gold microelectrodes with mask welding. Monoclonal antibodies were immobilized on the surface of a TiO 2 nanowire bundle to specifically capture L. monocytogenes. Impedance change caused by the nanowire-antibody-bacteria complex was measured and correlated to bacterial number. This nanowire bundle based immunosensor could detect as low as 10 (2) cfu/ml of L. monocytogenes in 1 h without significant interference from other foodborne pathogens.