gebhart/patrepeval huggingface dataset:
Repeated H2O2 exposure drives cell cycle progression in an in vitro model of ulcerative colitis (2013)

The production of hydrogen peroxide (H2 O2 ) drives tumourigenesis in ulcerative colitis (UC). Recently, we showed that H2 O2 activates DNA damage checkpoints in human colonic epithelial cells (HCEC) through c-Jun N-terminal Kinases (JNK) that induces p21(WAF1) . Moreover, caspases circumvented the G1/S and intra-S checkpoints, and cells accumulated in G2/M. The latter observation raised the question of whether repeated H2 O2 exposures alter JNK activation, thereby promoting a direct passage of cells from G2/M arrest to driven cell cycle progression. Here, we report that increased proliferation of repeatedly H2 O2 -exposed HCEC cells (C-cell cultures) was associated with (i) increased phospho-p46 JNK, (ii) decreased total JNK and phospho-p54 JNK and (iii) p21(WAF1) down-regulation. Altered JNK activation and p21(WAF1) down-regulation were accompanied by defects in maintaining G2/M and mitotic spindle checkpoints through adaptation, as well as by apoptosis resistance following H2 O2 exposure. This may cause increased proliferation of C-cell cultures, a defining initiating feature in the inflammation-carcinoma pathway in UC. We further suggest that dysregulated JNK activation is attributed to a non-apoptotic function of caspases, causing checkpoint adaptation in C-cell cultures. Additionally, loss of cell-contact inhibition and the overcoming of senescence, hallmarks of cancer, contributed to increased proliferation. Furthermore, there was evidence that p54 JNK inactivation is responsible for loss of cell-contact inhibition. We present a cellular model of UC and suggest a sinusoidal pattern of proliferation, which is triggered by H2 O2 -induced reactive oxygen species generation, involving an interplay between JNK activation/inactivation, p21(WAF1) , c-Fos, c-Jun/phospho-c-Jun, ATF2/phospho-ATF2, β-catenin/TCF4-signalling, c-Myc, CDK6 and Cyclin D2, leading to driven cell cycle progression.
Unsupervised Domain Adaptation via Calibrating Uncertainties (2019)

Unsupervised domain adaptation (UDA) aims at inferring class labels for unlabeled target domain given a related labeled source dataset. Intuitively, a model trained on source domain normally produces higher uncertainties for unseen data. In this work, we build on this assumption and propose to adapt from source to target domain via calibrating their predictive uncertainties. The uncertainty is quantified as the Renyi entropy, from which we propose a general Renyi entropy regularization (RER) framework. We further employ variational Bayes learning for reliable uncertainty estimation. In addition, calibrating the sample variance of network parameters serves as a plug-in regularizer for training. We discuss the theoretical properties of the proposed method and demonstrate its effectiveness on three domain-adaptation tasks.
Keynote lecture 2: cardiovascular informatics: how to stop a heart attack before it happens (2009)

In this talk, first I will offer a short overview of the research activities of the Computational Biomedicine Laboratory, University of Houston. Then, I will present our research in the area of biomedical image computing for the mining of information from cardiovascular imaging data for the detection of persons with a high likelihood of developing a heart attack in the near future (vulnerable patients). Specifically, I'll present methods for detection and segmentation of anatomical structures, and shape and motion estimation of dynamic organs. The left ventricle in non-invasive cardiac MRI data is extracted using a novel multi-class, multi-feature fuzzy connectedness method and deformable models for shape and volume estimation. In non-invasive cardiac CT data, the thoracic fat is detected using a relaxed version of multi-class, multi-feature fuzzy connectedness method. Additionally, the calcified lesions in the coronary arteries are also identified and quantified using a novel hierarchical supervised learning framework from the CT data. In non-invasive contrast-enhanced CT, the coronary arteries are detected using our novel tubular shape detection method for motion estimation and possibly, for non-calcified lesion detection. In invasive IVUS imaging, our team has developed a unique IVUS acquisition protocol and novel signalimage analysis methods) for the detection (for the first time in vivo) of 'vasa vasorum' (VV). The VV are micro-vessels that are commonly present to feed the walls of larger vessels; however, recent clinical evidence has uncovered their tendency to proliferate around areas of inflammation, including the inflammation associated with vulnerable plaques. In summary, our work is focused on developing novel computational tools to mine quantitative parameters from the imaging data for early detection of asymptomatic cardiovascular patient. The expected impact of our work stems from the fact that sudden heart attack remains the number one cause of death in the US, and unpredicted heart attacks account for the majority of the $280 billion burden of cardiovascular diseases.
EFFECT OF FAN’S PARAMETERS ON ADHESION MECHANISM OF THRESHED RAPE MIXTURE TO CLEANING SIEVE (2020)

In order to reduce the adhesion of moist threshed rape mixture and cleaning sieve, a method named “Hot-airflow Cleaning” has been proposed. Firstly, the key factors influencing anti-adhesion property were obtained based on the theoretical analysis. They were temperature, wind speed and fan inclination. Then, based on the single-factor experiments, the proper temperature of the fan was 30-50oC, the proper wind speed and inclination of the fan were 2-4 m/s and 15-45°, respectively. Finally, the fan’s parameters were optimized by Box-Behnken design. The results showed that the optimum technological parameters were temperature of 50 oC, a wind speed of 4 m/s and that fan inclination was 45°. This research could provide a reference for the improvement of cleaning system for rape combine harvesters.
Partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation (2020)

Transmembrane proteins (TMP) play a crucial role in several physiological processes. Despite their importance and diversity, only a few TMP structures have been determined by high-resolution protein structure characterization methods so far. Due to the low number of determined TMP structures, the parallel development of various bioinformatics and experimental methods was necessary for their topological characterization. The combination of these methods is a powerful approach in the determination of TMP topology as in the Constrained Consensus TOPology prediction. To support the prediction, we previously developed a high-throughput topology characterization method based on primary amino group-labelling that is still limited in identifying all TMPs and their extracellular segments on the surface of a particular cell type. In order to generate more topology information, a new step, a partial proteolysis of the cell surface has been introduced to our method. This step results in new primary amino groups in the proteins that can be biotinylated with a membrane-impermeable agent while the cells still remain intact. Pre-digestion also promotes the emergence of modified peptides that are more suitable for MS/MS analysis. The modified sites can be utilized as extracellular constraints in topology predictions and may contribute to the refined topology of these proteins.
Representing Small Commercial Building Faults in EnergyPlus, Part II: Model Validation (2019)

Automated fault detection and diagnosis (AFDD) tools based on machine-learning algorithms hold promise for lowering cost barriers for AFDD in small commercial buildings; however, access to high-quality training data for such algorithms is often difficult to obtain. To fill the gap in this research area, this study covers the development (Part I) and validation (Part II) of fault models that can be used with the building energy modeling software EnergyPlus® and OpenStudio® to generate a cost-effective training data set for developing AFDD algorithms. Part II (this paper) first presents a methodology of validating fault models with OpenStudio and then presents validation results, which are compared against measurements from a reference building. We discuss the results of our experiments with eight different faults in the reference building (a total of 39 different baseline and faulted scenarios), including our methodology for using fault models along with the reference building model to simulate the same faulted scenarios. Then, we present validation of the fault models by comparing results of simulations and experiments either quantitatively or qualitatively.
Peroxide modified polyolefin blends—Part II: Effects on LDPE/PP blends with polymer components of dissimilar initial viscosities (1992)

Abstract Blends of high viscosity polypropylene (PP) and low viscosity low density polyethylene (LDPE) were prepared in the Brabender batch intensive mixer. The rheological mismatch of these immiscible blend components resulted in coarse blend morphologies and poor mechanical properties. By reacting these blends with 1800 ppm Lupersol 101 peroxide at 180°C, the morphology became much finer and, at 50/50 weight ratio, assumed co‐continuous phase structure. As a result, the mechanical properties improved significantly. The above observations are attributable to the fact that the peroxide reaction at this level of concentration removes the rheological disparity of the blend components, a condition that is more favorable for efficient dispersive mixing. It has been frequently stated that the scale and uniformity of dispersive mixing affects the uniformity and controllability of reactions occuring in molten blends. This work shows, for the first time, that reactions with peroxides alter the blend morphology in a beneficial manner. The two phenomena are, therefore, mutually dependent. © 1992 John Wiley &amp; Sons, Inc.
Compressed Sensing of Multichannel EEG Signals: The Simultaneous Cosparsity and Low-Rank Optimization (2015)

Goal: This paper deals with the problems that some EEG signals have no good sparse representation and single-channel processing is not computationally efficient in compressed sensing of multichannel EEG signals. Methods: An optimization model with L0 norm and Schatten-0 norm is proposed to enforce cosparsity and low-rank structures in the reconstructed multichannel EEG signals. Both convex relaxation and global consensus optimization with alternating direction method of multipliers are used to compute the optimization model. Results: The performance of multichannel EEG signal reconstruction is improved in term of both accuracy and computational complexity. Conclusion: The proposed method is a better candidate than previous sparse signal recovery methods for compressed sensing of EEG signals. Significance: The proposed method enables successful compressed sensing of EEG signals even when the signals have no good sparse representation. Using compressed sensing would much reduce the power consumption of wireless EEG system.
Room-temperature CW operation of 610 nm band AlGaInP strained multiquantum well laser diodes with multiquantum barrier (1992)

610 nm band AlGaInP compressively strained multiquantum-well laser diodes with a multiquantum barrier have been successfully fabricated by MOCVD using (100) GaAs substrates with a misorientation of 9° towards the (011) direction. The oscillating wavelength at 25°C is 615nm, which is the shortest ever reported for AlGaInP laser diodes operating at 25°C.
29.3 A 14b 1GS/s RF sampling pipelined ADC with background calibration (2014)

We describe a 14-bit 1GS/s pipelined ADC that relies on correlation-based background calibration to correct the inter-stage gain, settling (dynamic) and memory errors. An effective dithering technique is embedded in the calibration signal to break the dependence of the calibration on the input signal amplitude. In addition, to improve the sampling linearity, the ADC employs input distortion cancellation and another digital calibration to compensate for the non-linear charge injection (kickback) from the sampling capacitors on the input driver. The ADC is fabricated in a 65nm CMOS process and has an integrated input buffer. With a 140MHz and 2Vpp input signal, the SNR is 69dB, the SFDR is 86dB, and the power is 1.2W.
Numerical Simulation of Dispersed Multiphase Flow based on a Particle Tracking Method. 2nd Report. Verification of the Method for Bubble-lnduced Liquid Velocity Fields. (1996)

Single bubbles rising through stagnant liquids were calculated using a particle tracking method (PTM) and an interface tracking method (ITM) to examine whether or not the two-way particle tracking method proposed in the previous study can give good predictions for bubble-induced liquid velocity fields Comparisons of the two methods were conducted for two types of three-dimensional bubbles : one is a spherical bubble with a creeping flow and the other is a spherical-cap bubble with a wake. It was confirmed that liquid velocity fields predicted by PTM for both types of bubbles agreed qualitatively with those predicted by ITM, and PTM can accurately predict a liquid velocity distribution in a wake region, provided that the bubble diameter is greater than the computational cell size.
Reaction of 3-bromo-2,5-dimethylthiophene 1,1-dioxide with some Grignard reagents. The formation of a heterotricycloheptane derivative (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of 3-bromo-2,5-dimethylthiophene 1,1-dioxide with some Grignard reagents. The formation of a heterotricycloheptane derivativeGrigorios Nikitidis, Salo Gronowitz, Anders Hallberg, and Claes StaalhandskeCite this: J. Org. Chem. 1991, 56, 12, 4064–4066Publication Date (Print):June 1, 1991Publication History Published online1 May 2002Published inissue 1 June 1991https://pubs.acs.org/doi/10.1021/jo00012a052https://doi.org/10.1021/jo00012a052research-articleACS PublicationsRequest reuse permissionsArticle Views440Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Resource Allocation and HARQ Optimization for URLLC Traffic in 5G Wireless Networks (2018)

5G wireless networks are expected to support ultra-reliable low latency communications (URLLC) traffic which requires very low packet delays (<; 1 ms) and extremely high reliability (~99.999%). In this paper, we focus on the design of a wireless system supporting downlink URLLC traffic. Using a queuing network-based model for the wireless system, we characterize the effect of various design choices on the maximum URLLC load it can support, including: 1) system parameters such as the bandwidth, link SINR, and QoS requirements; 2) resource allocation schemes in orthogonal frequency-division multiple access (OFDMA)-based systems; and 3) hybrid automatic repeat request schemes. Key contributions of this paper which are of practical interest are: 1) study of how the minimum required system bandwidth to support a given URLLC load scales with associated QoS constraints; 2) characterization of optimal OFDMA resource allocation schemes which maximize the admissible URLLC load; and 3) optimization of a repetition code-based packet re-transmission scheme.
Influence of Myopia on the Progression of Normal Tension Glaucoma (2007)

Purpose: To evaluate the influence of myopia on the progression of normal tension glaucoma. Methods: A retrospective study of 72 patients with normal tension glaucoma who were treated from 1984. Subjects were divided into 4 groups which are myopic group (D-1). The change of MD (Mean deviation) and CPSD (corrected pattern standard deviation) of non-myopic group were compared to other myopic groups. In addition, we corrected each analysis in commensurate with age, basal IOP, post treated IOP, existence of hypertension and diabetes mellitus in order to preclude the possibility which these factors would influence to the progression. Results: There was no statistically significant difference between non-myopic group and each myopic groups in MD and CPSD changes against refraction. Moreover, with the correction of other factors, there was no statistically significant difference (Mixed method, P>0.1). Conclusions: Myopia did not affect the progression of normal tension glaucoma once treated.
Supplementary Data from Activity and Resistance of a Brain-Permeable Paradox Breaker BRAF Inhibitor in Melanoma Brain Metastasis (2023)

Supplementary Data from Activity and Resistance of a Brain-Permeable Paradox Breaker BRAF Inhibitor in Melanoma Brain Metastasis
Detection of Giardia antigen in stool samples before and after treatment. (1995)

A double antibody sandwich ELISA technique, using a chromatography purified Giardia antiserum, was applied to detect faecal antigen in patients infected with Giardia lamblia before and after treatment. The assay could detect antigens in 98% of infected cases with false positive reactions in 3 cases infected with E. histolytica. There was a significant direct relation between the antigen level in stool samples and the number of Giardia cysts. The mean level of copro-antigen was slightly lower in children, below 10 years, than in older patients, without significant difference. On the other hand, the lowest cyst count was noticed in elder patients, over 20 years. The level of faecal antigens decreased significantly after successful treatment in patients with giardiasis. It was concluded that detection of Giardia antigens by ELISA technique in the stool samples was a highly sensitive (98%) and specific (91%) diagnostic method. It is also considered as a good monitor for treatment success.
Fibroblast Growth Factor 21 as an emerging metabolic regulator: clinical perspectives (2012)

Fibroblast growth factor 21 (FGF21), a metabolic hormone predominantly produced by the liver, is also expressed in adipocytes and the pancreas. It regulates glucose and lipid metabolism through pleiotropic actions in these tissues and the brain. In mice, fasting leads to increased PPAR-α mediated expression of FGF21 in the liver where it stimulates gluconeogenesis, fatty acid oxidation, and ketogenesis, as an adaptive response to fasting and starvation. In the fed state, FGF21 acts as an autocrine factor in adipocytes, regulating the activity of PPAR-γ through a feed-forward loop mechanism. Administration of recombinant FGF21 has been shown to confer multiple metabolic benefits on insulin sensitivity, blood glucose, lipid profile and body weight in obese mice and diabetic monkeys, without mitogenic or other side effects. Such findings highlight the potential role of FGF21 as a therapeutic agent for obesity-related medical conditions. However, in human studies, high circulating FGF21 levels are found in obesity and its related cardiometabolic disorders including the metabolic syndrome, type 2 diabetes, non-alcoholic fatty liver disease and coronary artery disease. These findings may indicate the presence of FGF21 resistance or compensatory responses to the underlying metabolic stress, and imply the need for supraphysiological doses of FGF21 to achieve therapeutic efficacy. On the other hand, serum FGF21 has been implicated as a potential biomarker for the early detection of these cardiometabolic disorders. This review summarizes recent developments in the understanding of FGF21, from physiological and clinical perspectives.
Kinetic Spectrophotometric Method for the Determination of Ranitidine and Nizatidine in Pharmaceuticals (2002)

An accurate and simple kinetic method is described for the determination of ranitidine and nizatidine in pure form and in pharmaceuticals. The method is based on the reaction of the compounds with 7-chloro-4-nitrobenz-2-oxa-1,3-diazole in pH 7.4 borate buffer at 60 degrees C for a fixed time of 25 min for both compounds. The absorbance of the reaction product is measured at 495 nm for ranitidine and nizatidine. Calibration graphs were linear over the concentration range of 2-20 microg/mL, with limits of detection of 0.13 (3.7 x 10(-7) M) and 0.25 microg/mL (7.5 x 10(-7) M) for ranitidine and nizatidine, respectively. The proposed method was applied successfully to the determination of ranitidine in tablets and ampoules with average recoveries of 100.26+/-0.69 and 100.29+/-0.59%, respectively, and to the determination of nizatidine in capsules with an average recovery of 104.26+/-0.44%. The results obtained are in good agreement with those obtained by the other methods used for comparison. A proposal of the reaction pathway is also presented.
Adrenal Near-Infrared Autofluorescence (2022)

Normal and abnormal adrenal tissues possess natural NIR autofluorescence. Highest autofluorescence levels were associated with cortisol-producing tumors. Confocal imaging demonstrated the highest intensity in the zona reticularis. NIR cameras may have the potential to improve identification of adrenal tissue during surgery.
Transferrin Receptor 2-α Supports Cell Growth Both in Iron-chelated Cultured Cells and in Vivo (2000)

In most cells, transferrin receptor (TfR1)-mediated endocytosis is a major pathway for cellular iron uptake. We recently cloned the human transferrin receptor 2 (TfR2) gene, which encodes a second receptor for transferrin (Kawabata, H., Yang, R., Hirama, T., Vuong, P. T., Kawano, S., Gombart, A. F., and Koeffler, H. P. (1999) J. Biol. Chem. 274, 20826-20832). In the present study, the regulation of TfR2 expression and function was investigated. A select Chinese hamster ovary (CHO)-TRVb cell line that does not express either TfR1 or TfR2 was stably transfected with either TfR1 or TfR2-alpha cDNA. TfR2-alpha-expressing cells had considerably lower affinity for holotransferrin when compared with TfR1-expressing CHO cells. Interestingly, in contrast to TfR1, expression of TfR2 mRNA in K562 cells was not up-regulated by desferrioxamine (DFO), a cell membrane-permeable iron chelator. In MG63 cells, expression of TfR2 mRNA was regulated in the cell cycle with the highest expression in late G(1) phase and no expression in G(0)/G(1). DFO reduced cell proliferation and DNA synthesis of CHO-TRVb control cells, whereas it had little effect on TfR2-alpha-expressing CHO cells when measured by clonogenic and cell cycle analysis. In addition, CHO cells that express TfR2-alpha developed into tumors in nude mice whereas CHO control cells did not. In conclusion, TfR2 expression may be regulated by the cell cycle rather than cellular iron status and may support cell growth both in vitro and in vivo.
Objective measurement of contrast sensitivity function using contrast sweep visual evoked responses (1998)

One can objectively measure CSF with CSVER and this may be useful in patients in whom the psychophysical method is limited.