gebhart/patrepeval huggingface dataset:
Pre‐Vulcanization of Large and Small Natural Rubber Latex Particles: Film‐Forming Behavior and Mechanical Properties (2019)

Abstract The pre‐vulcanized large rubber particle (LRP) and small rubber particle (SRP) latices are independently prepared to investigate their film‐forming process and mechanical properties after being cast into films. The surface morphologies and roughness of both LRP and SRP films are found to be dependent on crosslink densities. The networks inside each rubber particle (RP) restrict particle deformation resulting in residual contour of RP within the film surface. For highly crosslinked RP, the collapse of the top surface of the RPs in the LRP films appears to create many “crater‐like” structures within the film surfaces, while they present only protruding particles within the SRP and blend films. This seems to indicate that LRPs are easier to coalesce and form film than SRPs. Additionally, dynamic and mechanical properties and strain‐induced crystallization (SIC) behaviors of the latex films, are effectively enhanced after pre‐vulcanization. The pre‐vulcanized LRP films perform better tensile properties and SIC than the SRP can.
Identification and Characterization of the Lactating Mouse Mammary Gland Citrullinome (2020)

Citrullination is a post-translational modification (PTM) in which positively charged peptidyl-arginine is converted into neutral peptidyl-citrulline by peptidylarginine deiminase (PAD or PADI) enzymes. The full protein citrullinome in many tissues is unknown. Herein, we used mass spectrometry and identified 107 citrullinated proteins in the lactation day 9 (L9) mouse mammary gland including histone H2A, α-tubulin, and β-casein. Given the importance of prolactin to lactation, we next tested if it stimulates PAD-catalyzed citrullination using mouse mammary epithelial CID-9 cells. Stimulation of CID-9 cells with 5 µg/mL prolactin for 10 min induced a 2-fold increase in histone H2A citrullination and a 4.5-fold increase in α-tubulin citrullination. We next investigated if prolactin-induced citrullination regulates the expression of lactation genes β-casein (<i>Csn2</i>) and butyrophilin (<i>Btn1a1</i>). Prolactin treatment for 12 h increased β-casein and butyrophilin mRNA expression; however, this increase was significantly inhibited by the pan-PAD inhibitor, BB-Cl-amidine (BB-ClA). We also examined the effect of tubulin citrullination on the overall polymerization rate of microtubules. Our results show that citrullinated tubulin had a higher maximum overall polymerization rate. Our work suggests that protein citrullination is an important PTM that regulates gene expression and microtubule dynamics in mammary epithelial cells.
Monitoring the N-glycosylation of plant glycoproteins by fluorophore-assisted carbohydrate electrophoresis (2000)

We have evaluated the efficiency of a fast, simple and efficient method, fluorophore-assisted carbohydrate electrophoresis (FACE), for the characterization of plant N-linked glycans. After their enzymatic release from plant glycoproteins, N-glycans were reductively aminated to the charged fluorophore 8-aminonaphthalene-1, 3, 6-trisulfonic acid (ANTS) and separated using high resolution polyacrylamide gel electrophoresis. In addition, an affinity purification procedure using concanavalin A was developed for separation of ANTS-labeled high-mannose-type N-glycans from other plant oligosaccharides.
BILATERAL HUMERAL LENGTHENING IN PATIENTS WITH ACHONDROPLASIA (2010)

Introduction: Achondroplasia is a form of rhizomelic dwarfism. Even if patients can compensate for their short arms through the mobility in their spine during the childhood, the flexibility in their spine becomes less with aging. Because of that, as they get older they experience problems in maintaining personal hygiene especially in reaching the back. In addition putting on socks and tying their own shoes might become difficult. Methods: Inclusion criteria included any patient with a history of achondroplasia who had undergone humeral lengthening in the proximal part of the humerus (just distal to deltoid muscle insertion). Patients who had distal humeral (supracondylar) osteotomy and/or who received other than monolateral external fixator were excluded from the study. 50 humeri of 25 patients with achondroplasia were lengthened using Orthofix mono-lateral external fixator utilizing proximal humeral osteotomy. Sixteen patients were female and nine were male. Mean age was 15.4 months (range, 9.6 – 21.8). Lengthening was started at 7th day. Patients were lengthened at 1/4 turn four times a day reaching 1 mm/day. Physical therapy was performed 3 times a week. Goal of lengthening was around 10 cm or whatever length the patient could tolerate. Patients wore Sarmiento type fracture brace 4–6 weeks after the fixator was removed. Results: Mean follow-up time from surgery was 51.5 months (range, 6 – 143 months). Mean follow-up time from removal of external fixator was 44.7 months (range, 0 – 135 months). Average external fixation time was 7.3 months. In 20 humeri it was noted that the average duration of lengthening was 4.2 months (range, 3 – 5.8 months). A mean lengthening of 9.3 cm was obtained (range, 4.3 – 12.8 cm). At latest follow-up range of motion was not compromised due to lengthening. All patients had similar ROM before and after the surgery. Complications included radial nerve palsy in 8, pin tract infection in 7, fracture through regenerate in 3, premature consolidation in 1, nonunion in 1, delayed healing in 1. Radial nerve palsy recovered without intervention in one case. In others it recovered uneventfully after successful decompression. No complications at all occurred in 30 cases. Discussion: Fifty humeri of 25 patients with achondroplasia received successful humerus lengthening as part of extensive limb lengthening offered in our center. None of the patients had long term sequela, and all radial nerve palsies recovered. Patients were satisfied with the lengthening and found it easier to undergo through humerus lengthening compared to lower limb lengthening. After a mean follow-up time of almost 4 years, these patients returned back to their normal lives with optimum upper limb function with no hindrance in maintaining personal hygiene, putting on socks or tying their own shoes.
Association of the Hemoglobin to Serum Creatinine Ratio with In-Hospital Adverse Outcomes after Percutaneous Coronary Intervention among Non-Dialysis Patients: Insights from a Japanese Nationwide Registry (J-PCI Registry) (2020)

Although baseline hemoglobin and renal function are both important predictors of adverse outcomes after percutaneous coronary intervention (PCI), scarce data exist regarding the combined impact of these factors on outcomes. We sought to investigate the impact and threshold value of the hemoglobin to creatinine (Hgb/Cr) ratio, on in-hospital adverse outcomes among non-dialysis patients in a Japanese nationwide registry. We analyzed 157,978 non-dialysis patients who underwent PCI in 884 Japanese medical institutions in 2017. We studied differences in baseline characteristics and in-hospital clinical outcomes among four groups according to their quartiles of the Hgb/Cr ratios. Compared with patients with higher Hgb/Cr ratios, patients with lower ratios were older and had more comorbidities and complex coronary artery disease. Patients with lower hemoglobin and higher creatinine levels had a higher rate of in-hospital adverse outcomes including in-hospital mortality and procedural complications (defined as occurrence of cardiac tamponade, cardiogenic shock after PCI, emergency operation, or bleeding complications that required blood transfusion). On multivariate analyses, Hgb/Cr ratio was inversely associated with in-hospital mortality (odds ratio: 0.91, 95% confidence interval: 0.89-0.92; <i>p</i> < 0.001) and bleeding complications (odds ratio: 0.92, 95% confidence interval: 0.90-0.94; <i>p</i> < 0.001). Spline curve analysis demonstrated that these risks started to increase when the Hgb/Cr ratio was <15, and elevated exponentially when the ratio was <10. Hgb/Cr ratio is a simple index among non-dialysis patients and is inversely associated with in-hospital mortality and bleeding complications after PCI.
Loss compensation in long-range dielectric-loaded surface plasmon-polariton waveguides (2011)

Loss compensation in long-range dielectric-loaded surface plasmon-polariton waveguides is theoretically analyzed when rare-earth-doped double tungstate crystalline material is used as the gain medium in three different waveguide configurations. We study the effect of waveguide geometry on loss compensation at the telecom wavelength of 1.55 μm, and demonstrate that a material gain as small as 12.5 dB/cm is sufficient for lossless propagation of plasmonic modes with sub-micron lateral confinement when using waveguide ridges with gain.
Task and resource coordination in human teams (2002)

Distributed decision making and coordination in multiperson teams are studied. The problems of resource allocation, in which a team shares a limited pool of resources to process a mix of tasks under various overlaps in team responsibility, are addressed. The modeling approach is to blend normative mathematical theories for team decision making with descriptive facets that capture known and observed human cognitive limitations and biases. Three modeling efforts in resource allocation and task sequencing are described: the first is for a dyad, the second for a three-person flat organization, and the third for a three-person team plus a leader. The resulting normative descriptive models show an excellent ability to replicate individual and team data across a wide range of independent variables and provide insight into the process of human decision making in distributed organizations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Generation of IL1‐like activity in response to biomedical polymer implants: A comparison of in vitro and in vivo models (1989)

Of the many factors determining host biocompatibility responses to implanted biomedical polymers, the cellular interactions at the tissue/material interface have been recognized to be some of the most important. The present study has combined results both from an in vitro cell culture system and from an in vivo animal model to examine this host response. In vitro results suggest that a variety of polymer materials can differentially activate human monocytes to produce a protein(s) having different biological activities. The polymers tested induce the production of the regulatory inflammatory protein interleukin 1 as well as a factor that enhances fibroblast proliferation and collagen synthesis. The observed activities of these factors appear to be related but not identical, and are dependent upon the specific polymer. Evaluation of exudate and tissue responses to these same polymer materials in an in vivo model are also presented. Both in vitro and in vivo results support the hypothesis that monocyte/macrophage activation with subsequent synthesis of regulatory factors such as interleukin 1 plays a significant role in determining the host response to biomedical polymer implants.
Platforms for Non-speakers Annotating Names in Any Language (2018)

We demonstrate two annotation platforms that allow an English speaker to annotate names for any language without knowing the language. These platforms provided high-quality "silver standard" annotations for low-resource language name taggers (Zhang et al., 2017) that achieved state-of-the-art performance on two surprise languages (Oromo and Tigrinya) at LoreHLT2017 1 and ten languages at TAC-KBP EDL2017 We discuss strengths and limitations and compare other methods of creating silver-and goldstandard annotations using native speakers. We will make our tools publicly available for research use.
"THIN" vs. "FAT" VISUALIZATION CLIENT (1998)

This paper explains the advantage of using low-cost, configurable, data visualization components, which can be embedded and distributed in electronic documents and reports. With the increasing use of electronic documents, distributed by Intranet and Internet, the opportunity to provide interactive visualization techniques within scientific and engineering reports has become practicable. This new technology of components allows authors of a report to distribute with a specific “data viewer”, for example, allowing the recipients to interactively examine the data in the same way as the original analyst. A “thin” client, by definition, have minimal software requirements necessary to function as a user interface front-end for a Web enabled application and raises the issue of client vs. server data visualization rendering. Real-time visual data manipulation doesn’t translate well into a “thin” client. While the VRML file format ’ allows distribution of 3D visualization scenes to the Web, the user has no direct access to the underlying data sources. The “mapping” of numerical data into geometry format (VRML) takes place at the server side. In the “thin” client model, nearly all functionality is delivered from the server side of the visualization engine while the client perform very simple display and querying functions. The visualization server controls data manipulation and information drill-down techniques. Web-based component technology can be used to overcome these limitations. Java allows the creation of “applets” and “Beans”, and we have Windows/COM components. These components can significantly increase the data interaction between the client application and the end user, and allow tasks to be executed on the client. Highly interactive user interface tasks are delivered that provide point-andclick navigation through multidimensional data structures. Visual data interfaces such as information drilling, moving a cutting plane through a volume data set etc are supported. This paper demonstrates the concept of using “Fat” visualization clients with several examples. The implications of using VRML is compared to sending data to the client and perform interactive client data visualization on a desktop with locally stored components embedded and distributed in electronic documents and reports.
Bias in Nucleotide Composition of Antisense Oligonucleotides (1996)

In this study we investigated if specific sequence motifs occur with a higher frequency in antisense oligonucleotides than can be expected on the basis of the mRNA composition to get an impression of the importance of these motifs for antisense effects. Computer analysis of 206 antisense oligonucleotides extracted from the literature and from sequence databases, all targeted against human mRNA, was performed. We compared the sequence composition of these oligonucleotides with the average of 100 equally large and randomly selected sequences from sequence databases and of their target mRNA. We found that the frequency of sequence motifs containing GG, CCC, CC, GAC, and CG is significantly higher and TT and that TCC is significantly lower in antisense oligonucleotide sequences than in the randomly selected mRNA sequences. We conclude that there is a bias in the nucleotide composition of antisense oligonucleotides. Some of these biased sequence motifs have been reported to induce nonantisense effects mediated by protein binding. Further analysis of the biologic function of these motifs is necessary to investigate if they should be avoided or incorporated into future designs of therapeutic effective oligonucleotides.
Development of a Toxicogenomics in Vitro Assay for the Efficient Characterization of Compounds (2006)

In vitro toxicogenomics represents a useful approach for evaluating the toxic properties of new drug candidates early in the drug discovery process using minimal amounts of compounds. The aim of this study was to develop in vitro-based gene expression assays for two prototypical toxicological classes: aryl hydrocarbon receptor (AhR) agonists and peroxisome proliferator activated receptor alpha (PPAR alpha) agonists. Primary rat hepatocytes were exposed to a number of class-specific compounds, including 3-methylcholanthrene, aroclor, and beta-napthoflavone as AhR agonists, bezafibrate, clofibrate, and Wy-14643 as peroxisome proliferators, and chlorpheniramine, penicillin and spectinomycin as negative controls. Global gene expression profiles were generated with microarrays for each class of compounds. Using linear discriminant analysis coupled with permutation-based t-test, gene signatures were established to classify compounds according to a discriminant score. The final gene signatures consist of eight genes for AhR agonism and 11 genes for PPAR alpha agonism, and were further validated using additional compounds. The assay was initially developed using a microarray platform. The authors then evaluated whether it could be transferred to a more cost-effective platform with higher throughput. The results indicate that a small set of genes can be used to quantitatively assess the degree to which a compound falls into a certain mechanistic toxicological class. While this study only focused on two classes, it could be expanded to encompass other toxicological mechanistic classes as well. Furthermore, by adapting this type of assay to a higher throughput platform, in vitro toxicogenomics can represent an effective approach to generate robust toxicological data early in the drug discovery process.
One pass quality control and low complexity RDO in a quadtree based scalable image coder (2013)

This paper presents a joint quality control (QC) and rate distortion optimization (RDO) algorithm applied to a still image codec called Locally Adaptive Resolution (LAR). LAR supports scalability in resolution for both lossy and lossless coding and has low complexity. This algorithm is based on the study of the relationship between compression efficiency and relative parameters. The RDO model is proposed firstly to find suitable parameters. Relying on this optimization, relationships between the distortion of reconstructed image and quantization parameter can be described with a new linear model. This model is used for parametric configuration to control compression distortion. Experimental results show that this algorithm provides an effective solution for an efficient one pass codec with automatic parameters selection and accurate QC. This algorithm could be extended to codecs with similar functions, such as High Efficiency Video Coding (HEVC).
Multimode Tree Coding of Speech with Perceptual Pre-Weighting and Post-Weighting (2010)

A low delay and low complexity speech coder based on Multimode Tree Coding is proposed. In our Multimode Tree Coder, a simple mode classification method along with frame energy are used to classify the input speech frames into five different modes. Each mode is coded at a suitable bit-rate using a Tree coder with computationally efficient perceptual error pre-weighting and post-weighting filters, and a G.727 Code Generator. At an average bit-rate about 12 kbps for 50% Voice Activity sequences, the variable rate Multimode Tree Coder produces speech quality equivalent to the G.727 ADPCM coder at 32 kbps, resulting in nearly 63% bit-rate saving. Apart from bit-rate savings, a low delay of 6.125 ms, and low complexity are achieved by our Multimode Tree Coder, making it an interesting alternative to the AMR-NB Codec.
A genome-wide linkage study of autism spectrum disorder and the broad autism phenotype in extended pedigrees (2018)

Inclusion of subclinical phenotypes such as BAP should be more widely employed in genetic studies of ASD as a way of identifying inherited genetic variants for the disorder. Moreover, the results underscore the need for approaches to identifying genetic risk factors in extended pedigrees that are robust to high levels of inter/intrafamilial locus and allelic heterogeneity.
Functional Piglet Model for the Clinical Syndrome and Postmortem Findings Induced by Staphylococcal Enterotoxin B (2004)

Staphylococcal enterotoxin (SE) B causes serious gastrointestinal illness, and intoxication with this exotoxin can lead to lethal toxic shock syndrome. In order to overcome significant shortcomings of current rodent and nonhuman primate models, we developed a piglet model of lethal SEB intoxication. Fourteen-day-old Yorkshire piglets were given intravenous SEB, observed clinically, and sacrificed at 4, 6, 24, 48, 72, or 96 hrs posttreatment. Clinical signs were biphasic with pyrexia, vomiting, and diarrhea within 4 hrs, followed by terminal hypotension and shock by 96 hrs. Mild lymphoid lesions were identified as early as 24 hrs, with severe lymphadenopathy, splenomegaly, and prominent Peyer's patches found by 72 hrs. Widespread edema-most prominent in the mesentery, between loops of spiral colon, and in retroperitoneal connective tissue-was found in animals at 72 hrs. Additional histologic changes included perivascular aggregates of large lymphocytes variably present in the lung and brain, circulating lymphoblasts, and lymphocytic portal hepatitis. Preliminary molecular investigation using gene array has uncovered several gene profile changes that may have implications in the pathophysiology leading to irreversible shock. Five genes were selected for further study, and all showed increased mRNA levels subsequent to SEB exposure. The use of this piglet model will continue to elucidate the pathogenesis of SEB intoxication and facilitate the testing of new therapeutic regimens that may better correlate with human lesions.
Evaluation of Short-Term Changes in Serum Creatinine Level as a Meaningful End Point in Randomized Clinical Trials (2015)

Observational studies have shown that acute change in kidney function (specifically, AKI) is a strong risk factor for poor outcomes. Thus, the outcome of acute change in serum creatinine level, regardless of underlying biology or etiology, is frequently used in clinical trials as both efficacy and safety end points. We performed a meta-analysis of clinical trials to quantify the relationship between positive or negative short-term effects of interventions on change in serum creatinine level and more meaningful clinical outcomes. After a thorough literature search, we included 14 randomized trials of interventions that altered risk for an acute increase in serum creatinine level and had reported between-group differences in CKD and/or mortality rate ≥3 months after randomization. Seven trials assessed interventions that, compared with placebo, increased risk of acute elevation in serum creatinine level (pooled relative risk, 1.52; 95% confidence interval, 1.22 to 1.89), and seven trials assessed interventions that, compared with placebo, reduced risk of acute elevation in serum creatinine level (pooled relative risk, 0.57; 95% confidence interval, 0.44 to 0.74). However, pooled risks for CKD and mortality associated with interventions did not differ from those with placebo in either group. In conclusion, several interventions that affect risk of acute, mild to moderate, often temporary elevation in serum creatinine level in placebo-controlled randomized trials showed no appreciable effect on CKD or mortality months later, raising questions about the value of using small to moderate changes in serum creatinine level as end points in clinical trials.