gebhart/patrepeval huggingface dataset:
Monocytes from Cystic Fibrosis Patients Are Locked in an LPS Tolerance State: Down-Regulation of TREM-1 as Putative Underlying Mechanism (2008)

Cystic Fibrosis (CF) is an inherited pleiotropic disease that results from abnormalities in the gene that codes for the chloride channel, Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). CF patients are frequently colonized by several pathogens, but the mechanisms that allow colonization in spite of apparently functional immune systems are incompletely understood. In this paper we show that blood peripheral monocytes isolated from CF patients are found in an endotoxin tolerance state, yet this is not due to a deficient TLR activation. On the other hand, levels of the amplifier of inflammatory responses, TREM-1 (Triggering Receptor Expressed on Myeloid cells), are notably down-regulated in monocytes from patients, in comparison to those extracted from healthy volunteers. Furthermore, the soluble form of TREM-1 (sTREM-1) was not detected in the sera of patients. Additionally, and in strict contrast to patients who suffer from Chronic Obstructive Pulmonary Disease (COPD), CF monocytes challenged ex vivo with LPS neither up-regulated membrane-anchored TREM-1 nor sTREM-1. Finally, similar levels of PGE(2) expression and p65 translocation into the nucleus were found in both patients and healthy volunteers, thus suggesting that TREM-1 regulation is neither controlled by PGE(2) levels nor by p65 activation in this case. However, PU.1 translocation into the nucleus was significantly higher in CF monocytes than in controls, suggesting a role for this transcription factor in the control of TREM-1 expression. We conclude that down-regulation of TREM-1 expression in cystic fibrosis patients is at least partly responsible for the endotoxin tolerance state in which their monocytes are locked.
Analysis of photoaffinity-labeled aryl hydrocarbon receptor heterogeneity by two-dimensional gel electrophoresis (1990)

The level of charge heterogeneity in the aryl hydrocarbon receptor (AhR) was examined by high-resolution denaturing two-dimensional (2D) gel electrophoresis. Hepa 1c1c7 cell cytosolic fraction was photoaffinity-labeled with 2-azido-3-[125I]iodo-7,8-dibromodibenzo-p-dioxin and applied to isoelectric focusing (IEF) tube gels. After optimization of focusing conditions a broad peak of radioactivity was detected in the apparent pI range of 5.2-5.7. IEF tube gels were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by visualization of the radiolabeled AhR by autoradiography; three distinct isoforms were detected. The same 2D electrophoretic isoform pattern was obtained when the AhR from Hepa 1c1c7 was photoaffinity-labeled in cell culture. BPrCl cells, a mutant line derived from Hepa 1c1c7 cells, contain an AhR that is unable to bind to DNA. Photoaffinity-labeled BPrCl cytosolic fractions were subjected to 2D gel electrophoretic analysis resulting in essentially the same molecular weight and isoform pattern as seen in Hepa 1c1c7 cytosol. This result would suggest that if a mutation is present in the BPrCl AhR it has not caused a significant change in its IEF pattern, although a small shift in the pI values was observed. Two-dimensional gel electrophoresis of photoaffinity-labeled cytosolic fractions from HeLa cells, the rat liver tumor cell line McA-RH7777, and buffalo rat thymus revealed three isoforms, essentially the same isoform pattern as in Hepa 1c1c7 cells. This would indicate that despite the considerable molecular weight polymorphism between species the level of charge heterogeneity is highly conserved.
High mobility group box protein 1 in complex with lipopolysaccharide or IL-1 promotes an increased inflammatory phenotype in synovial fibroblasts (2011)

HMGB1 in complex with LPS, IL-1α or IL-1β boosted proinflammatory cytokine- and MMP production in synovial fibroblasts from RA and OA patients. A mechanism for the pathogenic role of HMGB1 in arthritis could thus be through enhancement of inflammatory and destructive mechanisms induced by other proinflammatory mediators present in the arthritic joint.
Automated Quantification of Body Fat Distribution on Volumetric Computed Tomography (2006)

Preliminary results have shown that total compartmental fat, including visceral and subcutaneous fat, can be automatically and accurately segmented on volumetric CT.
WebFR3D--a server for finding, aligning and analyzing recurrent RNA 3D motifs (2011)

WebFR3D is the on-line version of 'Find RNA 3D' (FR3D), a program for annotating atomic-resolution RNA 3D structure files and searching them efficiently to locate and compare RNA 3D structural motifs. WebFR3D provides on-line access to the central features of FR3D, including geometric and symbolic search modes, without need for installing programs or downloading and maintaining 3D structure data locally. In geometric search mode, WebFR3D finds all motifs similar to a user-specified query structure. In symbolic search mode, WebFR3D finds all sets of nucleotides making user-specified interactions. In both modes, users can specify sequence, sequence-continuity, base pairing, base-stacking and other constraints on nucleotides and their interactions. WebFR3D can be used to locate hairpin, internal or junction loops, list all base pairs or other interactions, or find instances of recurrent RNA 3D motifs (such as sarcin-ricin and kink-turn internal loops or T- and GNRA hairpin loops) in any PDB file or across a whole set of 3D structure files. The output page provides facilities for comparing the instances returned by the search by superposition of the 3D structures and the alignment of their sequences annotated with pairwise interactions. WebFR3D is available at http://rna.bgsu.edu/webfr3d.
Optimal Wide Area Controller and State Predictor for a Power System (2007)

An optimal wide area controller is designed in this paper for a 12-bus power system together with a Static Compensator (STATCOM). The controller provides auxiliary reference signals for the automatic voltage regulators (AVR) of the generators as well as the line voltage controller of the STATCOM in such a way that it improves the damping of the rotor speed deviations of the synchronous machines. Adaptive critic designs theory is used to implement the controller and enable it to provide nonlinear optimal control over the infinite horizon time of the problem and at different operating conditions of the power system. Simulation results are provided to indicate that the proposed wide area controller improves the damping of the rotor speed deviations of the generators during large scale disturbances. Moreover, a robust radial basis function network based identifier is presented in this paper to predict the states of a multimachine power system in real-time. This wide area state predictor (WASP) compensates for transport lags associated with the present communication technology for wide area monitoring of the electric power grid. The WASP is also robust to partial loss of information caused by larger than expected transport lags or even failed sensors throughout the network
Multi-script handwriting recognition with FOHDEL (2002)

Until now handwritten character recognition systems used script specific methodologies. We present a unified syntactic approach for multi-script recognition. The fuzzy pattern description language FOHDEL is used to store fuzzy features in the form of fuzzy rules. First we briefly describe the proposed recognition methodology for Latin, Devanagari and Kanji scripts by analyzing their characteristic properties. Further we present the main features of FOHDEL by a comparative rule generation of three scripts under experiment. Finally the system integration of the proposed multi-script recognition scheme in the existing Latin recognition system is presented.
High contrast asymmetric Fabry–Perot electro-absorption modulator with zero phase change (1993)

By analyzing the exciton line shapes of quantum wells, we can determine the wavelengths and biases at which they exhibit large absorption changes and zero refractive index changes relative to zero bias. To use this effect, we placed GaAs/AlGaAs quantum wells in the intrinsic region of a reverse-biased p-i-n diode asymmetric Fabry–Perot modulator. We then developed a sample that could be post-growth processed to optimize all relevant parameters. We used computer simulation to determine the exact post-growth correction required and produced reflection modulators with 90% reflection change and zero relative phase change.
Effect of Glucose Degradation Products on the Peritoneal Membrane in a Chronic Inflammatory Infusion Model of Peritoneal Dialysis in the Rat (2004)

Using a chronic inflammatory infusion model of PD in the rat, we show that dialysis with GDP-containing PD fluid is associated with increased VEGF production and peritoneal vascularization. Use of low GDP solutions may therefore be beneficial in maintaining the function and structure of the peritoneal membrane during long-term PD.
Prostate cancer serum biomarker discovery through proteomic analysis of alpha‐2 macroglobulin protein complexes (2008)

Alpha-2 macroglobulin (A2M) functions as a universal protease inhibitor in serum and is capable of binding various cytokines and growth factors. In this study, we investigated if immunoaffinity enrichment and proteomic analysis of A2M protein complexes from human serum could improve detection of biologically relevant and novel candidate protein biomarkers in prostate cancer. Serum samples from six patients with androgen-independent, metastatic prostate cancer and six control patients without malignancy were analyzed by immunoaffinity enrichment of A2M protein complexes and MS identification of associated proteins. Known A2M substrates were reproducibly identified from patient serum in both cohorts, as well as proteins previously undetected in human serum. One example is heat shock protein 90 alpha (HSP90α), which was identified only in the serum of cancer patients in this study. Using an ELISA, the presence of HSP90α in human serum was validated on expanded test cohorts and found to exist in higher median serum concentrations in prostate cancer (n = 18) relative to control (n = 13) patients (median concentrations 50.7 versus 27.6 ng/mL, respectively, p = 0.001). Our results demonstrate the technical feasibility of this approach and support the analysis of A2M protein complexes for proteomic-based serum biomarker discovery.
Athermalization of optical instruments from the optomechanical viewpoint (1992)

The refractive properties and physical dimensions of optical components change with temperature, and hence also do the characteristics of optical systems. Athermalization is the principle of stabilizing the optical performance with respect to temperature, either by designing the optical elements and mounts to be mutually compensating, or by including movable corrective mechanisms. For refractive materials, two coefficients can be defined which characterize the thermooptical sensitivity, one applicable to uniform temperature changes, and the other to spatial temperature gradients. For normal optical glasses, the effects are small, but for plastics, infrared materials, and liquids, the thermal effects can be so great as to limit their usefulness. Passive athermalization is analogous to achromatism and optical systems can be designed simultaneously achromatic and athermal. The use of composite, and high expansion mounts employing plastics or fluids, gives greater control of thermo-optical effects. Active athermalization uses auxiliary power to drive compensating elements to maintain optical performance. Commercial optical design programs can be used to model and analyze thermally perturbed systems accurately.
Quality Control and Evaluation of Digital Dot Proof (2013)

Digital proofing reproduce color through FM dot proof,which can't measure the printing effect or reflect practical problem during printing by observing dot shape. Screen proofing experiments were carried out with data control printing to imitate AM dot. ΔE was regarded as the major quality control parameter to measure the improvement of printing quality of proof. The proof was analyzed and evaluated from the aspects of dot shape reproduction,dot transfer characteristics,and color reproduction. The result showed that the dot proof can reproduce printing effect from color aspect and has the salient superiority in imitating dot shape which digital proof can't replace,which can offer the true and predictable printing effective.
New single-ended resonant inverter circuit and system for induction-heating cooking apparatus (1989)

A novel type of single-ended resonant inverter using a new bipolar Darlington transistor that operates efficiently in the frequency range from 20 kHz to about 50 kHz is considered. The inverter implementation for an induction-heating cooker includes a unique power control strategy. The analysis and performance evaluations for the circuit design are also carried out.
Isoleucyl-tRNA Synthetase Mutations in <i>Staphylococcus aureus</i> Clinical Isolates and In Vitro Selection of Low-Level Mupirocin-Resistant Strains (2003)

Additionally, a low-level resistance to mupirocin (LLR-Mup) in S. aureus emerged as the result of independent, spontaneous mutational events within the usual chromosomal isoleucyl-tRNA synthetase (ileS) gene, with the mutations occurring only with unsuitable usage of mupirocin (5).Hence, we compared the ileS gene sequences obtained from mupirocin-susceptible MRSA (SA-7S) and those obtained from mupirocin-resistant MRSA (SA-7R) (4) where the resistance was acquired by in vitro selection from the original strain (SA-7S).In recent studies using isolates from Europe and North America, ileS gene mutation points correlating with LLR-Mup were reported (1).In this study, we report on ileS gene fulllength sequences from LLR-Mup MRSA strains, which were isolated in Japan and compared with those of the reported ileS gene mutation for molecular heterogeneity in isolates (1).A total of 258 MRSA isolates from different patients in 15 hospitals at the Tohoku area, Japan, were investigated.The MIC of mupirocin was determined by E-test (AB Biodisk, Solna, Sweden) (9).By the results of this susceptibility test, six strains (SA-1 to -6) were LLR-Mup (Table 1).The SA-7R strain was initially a mupirocin-susceptible strain (SA-7S; MIC, 0.025 g/ml) but developed LLR-Mup (MIC, 16 g/ml) following seven cycles of serial passage while being exposed to one-half the MIC of mupirocin by the agar dilution method (4).Genomic DNAs of these eight strains (SA-1 to SA-6, 7S, and 7R) were extracted by a method described elsewhere (6).The entire ileS gene was amplified by PCR as previously described (1).IleS-1 (5Ј-TACCGCGAGCAATCGTCCCT-3Ј) and IleS-2 (5Ј-TGTTGGCATCGTGGGCATAG-3Ј) were de-
Postoperative Complications After Glaucoma Surgery for Primary Angle-Closure Glaucoma vs Primary Open-Angle Glaucoma (2011)

The incidences of postoperative complications and reoperations in the first year after glaucoma surgery were similar for PACG and POAG.
Charge Trapping and Exciton Dynamics in Large-Area CVD Grown MoS<sub>2</sub> (2016)

There is keen interest in monolayer transition metal dichalcogenide films for a variety of optoelectronic applications due to their direct band gap and fast carrier dynamics. However, the mechanisms dominating their carrier dynamics are poorly understood. By combining time-resolved terahertz (THz) spectroscopy and transient absorption, we are able to shed light on the optoelectronic properties of large area CVD grown mono- and multilayer MoS2 films and determine the origins of the characteristic two-component excited state dynamics. The photoinduced conductivity shows that charge carriers, and not excitons, are responsible for the subpicosecond dynamics. Identical dynamics resulting from sub-optical gap excitation suggest that charge carriers are rapidly trapped by midgap states within 600 fs. This process complicates the excited state spectrum with rapid changes in line-width broadening in addition to a red-shift due to band gap renormalization and simple state-filling effects. These dynamics are insensitive to film thickness, temperature, or choice of substrate, which suggests that carrier trapping occurs at surface defects or grain boundaries. The slow dynamics are associated with exciton recombination and lengthen from 50 ps for monolayer films to 150 ps for multilayer films indicating that surface recombination dominates their lifetime. We see no signatures of trions in these MoS2 films. Our results imply that CVD grown films of MoS2 hold potential for high-speed optoelectronics and provide an explanation for the absence of trions in some CVD grown MoS2 films.
Effects of supplemental nitrogen application on physiological characteristics, dry matter and nitrogen accumulation of winter rapeseed (Brassica napus L.) under waterlogging stress (2020)

Waterlogging stress is a common limiting factor for winter rapeseed, which greatly affects the growth and potential production. The present study was conducted to investigate the effects of waterlogging with different durations (0day (D0), 6days (D6) and 9days (D9)) and supplemental nitrogen fertilization (N1, 0 kg ha<sup>-1</sup>; N2, 30 kg ha<sup>-1</sup>; N3, 60 kg ha<sup>-1</sup> and N4, 90 kg ha<sup>-1</sup>) on the physiological characteristics, dry matter and nitrogen accumulation in winter rapeseed (Chuanyou36). The results showed that the supplementary application of nitrogen fertilizer could effectively improve the physiological indexes of winter rapeseed in both pot and field experiments. The supplemental nitrogen increased the chlorophyll content in leaves, enhanced the activities of SOD, CAT, and POD, and decreased the MDA content in leaves and roots of rapeseed. The chlorophyll contents, the antioxidant enzyme activity of leaves and roots significantly increased under D6N3 and D9N4 conditions in both (pot and field) experiments. However, MDA contents significantly decreased compared with waterlogging without nitrogen application. Moreover, the application of nitrogen fertilizer after waterlogging increased the accumulation of dry matter and nitrogen in rapeseed at different growth stages. Therefore, waterlogging stress significantly inhibited the growth and development of rapeseed, but the application of nitrogen fertilizer could effectively reduce the damage of waterlogging. The N-induced increase in waterlogging tolerance of rapeseed might be attributed to the strong antioxidant defense system, maintenance of photosynthetic pigments and the nutrient balance.
Lectin microarray (2009)

Lectin microarray is a new technology that utilizes a panel of lectins immobilized on well-defined substrate for high-throughout analysis of glycans and glycoproteins. In this article, we have reviewed the fabrication and detection schemes in lectin microarray and discussed its novel applications in glycomics. We have also demonstrated a lectin array on PDMS with MALDI-TOF-MS for glycoprotein analysis. This method has been demonstrated for differential analysis of serum glycoproteins in oral cancer and healthy control subjects.
Investigation of Doubly Salient Structure for Permanent Magnet Vernier Machines Using Flux Modulation Effects (2019)

Recently, the permanent magnet vernier machine (PMVM) is studied extensively because of its merits such as the high torque density. Similar to the magnetic gears, the PMVM operates on the principle of flux modulation. However, there is a distinct difference in between the two as unlike the magnetic gear, in case of PMVM, the winding MMF harmonics rotates with different speed as that of the fundamental. As a result, these harmonics are capable of making a working magnetic field by interacting with different permeance harmonics. Therefore, this paper aims to provide an analytical explanation of this whole process, which is helpful to understand the effect of the flux modulation on the output torque. Furthermore, using the analytical formulation, this work finds the optimal geometric parameters which maximize the working magnetic field and hence the torque. A detailed analysis of the PMVM with the doubly salient structure is studied and the performance is analyzed using the finite element method (FEM) and the experimental setup. The FEM and experimental results verify the maximum torque production by using the optimal geometric parameters in the PMVM modeling, obtained using the analytical formulation.
Selective Modulation of the Therapeutic Efficacy of Anticancer Drugs by Selenium Containing Compounds against Human Tumor Xenografts (2004)

We demonstrated that selenium is a highly effective modulator of the therapeutic efficacy and selectivity of anticancer drugs in nude mice bearing human tumor xenografts of colon carcinoma and squamous cell carcinoma of the head and neck. The observed in vivo synergic interaction is highly dependent on the schedule of selenium.
Learning to Globally Edit Images with Textual Description (2018)

We show how we can globally edit images using textual instructions: given a source image and a textual instruction for the edit, generate a new image transformed under this instruction. To tackle this novel problem, we develop three different trainable models based on RNN and Generative Adversarial Network (GAN). The models (bucket, filter bank, and end-to-end) differ in how much expert knowledge is encoded, with the most general version being purely end-to-end. To train these systems, we use Amazon Mechanical Turk to collect textual descriptions for around 2000 image pairs sampled from several datasets. Experimental results evaluated on our dataset validate our approaches. In addition, given that the filter bank model is a good compromise between generality and performance, we investigate it further by replacing RNN with Graph RNN, and show that Graph RNN improves performance. To the best of our knowledge, this is the first computational photography work on global image editing that is purely based on free-form textual instructions.
Clinical evidence for the adenoma—carcinoma sequence (1999)

A review is given on evidence supporting or rejecting the hypothesis of a colorectal adenoma-carcinoma sequence. The majority of studies discuss adenomas from a clinical point of view, but pathology has also been considered in detail, and molecular biology has been touched on. It is concluded the adenoma stage is, most probably, a phase on the way to carcinoma. But it remains to be shown what effect the removal of adenomas will have in the long run on the incidence of colorectal carcinoma.
Location3: How Users Share and Respond to Location-Based Data on Social (2021)

In August 2010 Facebook launched Places, a location-based service that allows users to check into points of interest and share their physical whereabouts with friends. The friends who see these events in their News Feed can then respond to these check-ins by liking or commenting on them. These data consisting of the places people go and how their friends react to them are a rich, novel dataset. In this paper we first analyze this dataset to understand the factors that influence where users check in, including previous check-ins, similarity to other places, where their friends check in, time of day, and demographics. We show how these factors can be used to build a predictive model of where users will check in next. Then we analyze how users respond to their friends’ check-ins and which factors contribute to users liking or commenting on them. We show how this can be used to improve the ranking of check-in stories, ensuring that users see only the most relevant updates from their friends and ensuring that businesses derive maximum value from check-ins at their establishments. Finally, we construct a model to predict friendship based on check-in count and show that cocheck-ins has a statistically significant effect on friendship.