gebhart/patrepeval huggingface dataset:
Distinct Methylation of IFNG in the Gut (2009)

Mucosal expression of proinflammatory cytokines plays a pivotal role in inflammatory bowel disease (IBD) pathogenesis. Epigenetic remodeling of chromatin via DNA methylation regulates gene expression. In this study, IFNG DNA methylation was analyzed within the mucosal compartment in both normal and IBD populations and compared to its peripheral counterparts. Overall IFNG methylation (across eight CpG sites) was significantly lower in lamina propria (LP) T cells compared to peripheral blood (PB) T cells. No methylation differences were detected when comparing PB T derived from normal to IBD patients. However, LP T-cell DNA derived from IBD patients displayed different levels of IFNG methylation of the upstream regulatory regions compared to DNA from normal controls. In fact, IFNG DNA promoter methylation levels functionally correlate with IFNG mRNA expression in unstimulated T cells, using quantitative real-time PCR. A 5% decrease in promoter methylation status is associated with nearly a 3-fold increase in IFNG expression. Likewise, methylation of the single -54 bp IFNG SnaB1 site strongly inhibited IFNG promoter expression. These results suggest that the epigenetic methylation status of IFNG may play a mechanistic role in the modulation of cytokine secretion in the mucosa.
Lightweight orthotic appliances (1976)

Graphite-filament reinforced polymer materials are used in applications requiring high tensile strength and modulus. Superior properties of graphite composite materials permit fabrication of supports that are considerably lighter, thinner, and stiffer than conventional components.
L-type Voltage-Gated Ca 2+ Channels Modulate Expression of Smooth Muscle Differentiation Marker Genes via a Rho Kinase/Myocardin/SRF–Dependent Mechanism (2004)

Vascular smooth muscle cell (SMC) contraction is mediated in part by calcium influx through L-type voltage-gated Ca2+ channels (VGCC) and activation of the RhoA/Rho kinase (ROK) signaling cascade. We tested the hypothesis that Ca2+ influx through VGCCs regulates SMC differentiation marker expression and that these effects are dependent on RhoA/ROK signaling. Depolarization-induced activation of VGCCs resulted in a nifedipine-sensitive increase in endogenous smooth muscle myosin heavy chain (SMMHC) and SM alpha-actin expression and CArG-dependent promoter activity, as well as c-fos promoter activity. The ROK inhibitor, Y-27632, prevented depolarization-induced increase in SMMHC/SM alpha-actin but had no effect on c-fos expression. Conversely, the Ca2+/calmodulin-dependent kinase inhibitor, KN93, prevented depolarization-induced increases in c-fos expression with no effect on SMMHC/SM alpha-actin. Depolarization increased expression of myocardin, a coactivator of SRF that mediates CArG-dependent transcription of SMC marker gene promoters containing paired CArG cis regulatory elements (SMMHC/SM alpha-actin). Both nifedipine and Y-27632 prevented the depolarization-induced increase in myocardin expression. Moreover, short interfering RNA (siRNA) specific for myocardin attenuated depolarization-induced SMMHC/SM alpha-actin transcription. Chromatin immunoprecipitation (ChIP) assays revealed that depolarization increased SRF enrichment of the CArG regions in the SMMHC, SM alpha-actin, and c-fos promoters in intact chromatin. Whereas Y-27632 decreased basal and depolarization-induced SRF enrichment in the SMMHC/SM alpha-actin promoter regions, it had no effect of SRF enrichment of c-fos. Taken together, these results provide evidence for a novel mechanism whereby Ca2+ influx via VGCCs stimulates expression of SMC differentiation marker genes through mechanisms that are dependent on ROK, myocardin, and increased binding of SRF to CArG cis regulatory elements.
Supplemental Figure S4 from Akt Inhibition Enhances Expansion of Potent Tumor-Specific Lymphocytes with Memory Cell Characteristics (2023)

&lt;p&gt;Supplemental Figure S4. Akti-treated tumor-specific Pmel CD8+ T cell have reduced phosphorylation of Akt and substrates in presence of pharmacologic inhibition of Akt.&lt;/p&gt;
Guidelines for the design, analysis and interpretation of ‘omics’ data: focus on human endometrium (2013)

A highly rigorous approach to future studies, based on the guidelines provided here, is a prerequisite for obtaining data on biological systems which can be shared among researchers worldwide and will ultimately be of clinical benefit.
Protease-Stable Polycationic Photosensitizer Conjugates between Polyethyleneimine and Chlorin(e6) for Broad-Spectrum Antimicrobial Photoinactivation (2006)

We previously showed that covalent conjugates between poly-L-lysine and chlorin(e6) were efficient photosensitizers (PS) of both gram-positive and gram-negative bacteria. The polycationic molecular constructs increased binding and penetration of the PS into impermeable gram-negative cells. We have now prepared a novel set of second-generation polycationic conjugates between chlorin(e6) and three molecular forms of polyethyleneimine (PEI): a small linear, a small cross-linked, and a large cross-linked molecule. The conjugates were characterized by high-pressure liquid chromatography and tested for their ability to kill a panel of pathogenic microorganisms, the gram-positive Staphylococcus aureus and Streptococcus pyogenes, the gram-negative Escherichia coli and Pseudomonas aeruginosa, and the yeast Candida albicans, after exposure to low levels of red light. The large cross-linked molecule efficiently killed all organisms, while the linear conjugate killed gram-positive bacteria and C. albicans. The small cross-linked conjugate was the least efficient antimicrobial PS and its remarkably low activity could not be explained by reduced photochemical quantum yield or reduced cellular uptake. In contrast to polylysine conjugates, the PEI conjugates were resistant to degradation by proteases such as trypsin that hydrolyze lysine-lysine peptide bonds, The advantage of protease stability combined with the ready availability of PEI suggests these molecules may be superior to polylysine-PS conjugates for photodynamic therapy of localized infections.
The Benefits of Large-Scale Attenuation over the Antenna Array in Massive MIMO Systems (2016)

Massive multiple-input multiple-output (MIMO) is a potential candidate key technology for the fifth generation of wireless communication systems. In previous research, different power loss and shadowing effects on different individual antenna elements have been neglected. When characterizing the channel of a massive MIMO system and investigating the system performance, the large scale attenuation (LSA) over the antenna array has not been previously considered. In this paper, based on our proposed accurate geometrical propagation model, the spectral efficiency (in terms of bits/s/Hz sum-rate) result of maximal ratio combining (MRC) detection is investigated. From the simulation results, we find that the sum-rate performance for the MRC detection of our proposed more realistic channel model exceeds the results using the conventional model (where the LSA effect is not included). This proposed model LSA model is beneficial and informative for the research, design, and evaluation of the next generation of wireless communication systems employing massive MIMO configurations.
Spectroscopic studies of Yb3+-doped rare earth orthosilicate crystals (2004)

Infrared transmission and Raman scattering have been used to study Raman active phonons and crystal-field excitations in Yb3+-doped yttrium, lutetium and scandium orthosilicate crystals (Y2SiO5 (YSO), Lu2SiO5 (LSO) and Sc2SiO5 (SSO)), which belong to the same C2h6 crystallographic space group. Energy levels of the Yb3+ ion 2F5/2 manifold are presented. In the three hosts, Yb3+ ions experience high crystal field strength, particularly in Yb:SSO. Satellites in the infrared transmission spectra have been detected for the first time in the Yb3+-doped rare earth orthosilicates. They could be attributed to perturbed Yb3+ sites of the lattices or to magnetically coupled Yb3+ pairs.
A study on the effectiveness of non-verbal teaching materials in construction accidents prevention education: through an International comparative experiment (2023)

Safety is a top priority in the construction industry, therefore, safety training is essential to prevent construction casualties as the employment of foreign and young workers on construction sites worldwide increases. More studies are necessary to identify the effective training methods among novices and foreign workers. To address the gap, a rigorous comparative study of verbal and non-verbalized materials from two different countries was conducted. Statistically significant differences were found between nationalities in non-verbal materials due to different safety culture and background, and insignificant differences were found between both safety training materials with the same nationality. By comparing the outcomes of both training materials, the non-verbalized materials work effectively among the construction novices to provide visual aid to relate similar attitudes like technical trainees to the scenarios even without field experiences. The non-verbalized materials provide an alternative to passive learning methods to enhance the other safety training activities in the construction industry. The findings provide an initial stage for creating effective teaching materials that can be generally applied in other countries to capture the issues by a heterogeneous workforce personalized to suit the scenario of each country for better outcomes.
Utilization of median filters in power electronics: Traction drive applications (2013)

This paper presents three different applications of median filters in power electronic systems, specifically, in traction motor drives. While median filters are commonly used in signal processing, literature regarding their utilization in power electronics is very limited. The theory behind median filters is first introduced and then three example applications are discussed: speed estimation for an induction motor drive, current sensing in a three-phase inverter, and dc bus voltage sensing in a half-bridge inverter. Simulation and experimental results verify the simplicity and applicability of median filters for control and sensing in power electronics applications. Results show significant improvement in the filter output quality for all three applications compared to the filter input where numerical errors, data acquisition glitches, and noise are significantly reduced or eliminated in the output.
Modelling and Experimental Investigation of the Gas‐Induced Breakup of Liquid Threads Stretched by Gravity (2011)

Abstract Zur Herstellung eines Sprays mit enger Tropfengrößenverteilung haben sich Zerstäubungsverfahren basierend auf dem Prinzip des Zertropfens gedehnter Flüssigkeitsstrahlen bewährt. Die Vorhersage der zu erwartenden Tropfengröße in Abhängigkeit der Betriebsparameter ist zur Auslegung solcher Verfahren von besonderem Interesse. Vorgestellt wird ein Modell zur Beschreibung des Zerfalls laminar strömender, gedehnter Flüssigkeitsstrahlen unter Einwirkung des Erdschwerefelds und Berücksichtigung einer induzierten Gasströmung. Ziel der Arbeit ist die Vorhersage der Tropfengröße und die Validierung durch das Experiment.
At 90 Micrograms Per Kilogram, Recombinant Factor VIIa Partially Corrects Abnormal Hemostatic Function in Blood from Factor IX Deficient Patients. (2004)

Abstract Reports of the potential clinical utility of recombinant Factor VIIa (rFVIIa, NovoSeven®, NovoNordisk) in a variety of bleeding disorders have raised the possibility that this agent may have broad spectrum hemostatic properties. We have previously demonstrated that rFVIIa produces dose dependent correction of hemostatic status in patients with Factor VIII deficiency and/or Factor VIII inhibitor. In this study we measured the dose dependent effects of rFVIIa on Platelet Contractile Force (PCF), Clot Elastic Modulus (CEM) and Thrombin Generation Time (TGT) (Hemodyne® Analyzer, Hemodyne, Inc.) in patients with factor IX deficiency. Results were compared to those seen with recombinant factor IX (BeneFIX® [GI, Wyeth]) and factor nine concentrate (Mononine® [Aventis-Behring]). Blood from three patients with factor IX deficiency was collected via aseptic venipuncture into evacuated tubes containing 3.2% sodium citrate. The samples were spiked with increasing amounts of each hemostatic agent so as to yield levels ranging from 25 to 200% of the recommended dose. At baseline, each of the factor IX deficient patients had prolonged TGT, decreased PCF and decreased CEM. Despite the fact that each patient had less than 1% of normal factor IX activity, there was significant variability between the patients in their baseline values. TGT for the three patients varied from 587 to 1200 seconds. Baseline PCF ranged from 0.9 to 1.4 Kdynes, while CEM varied from 1.6 to 5.4 Kdynes/cm2. Normal TGT, PCF and CEM values for asymptomatic controls (mean ± SD, n=25) were 392±100 seconds, 7.8±1.3 Kdynes and 18.8±5.6 Kdynes/cm2 respectively. At the 100% of recommended dose, each of the factor IX agents produced shortening of the TGT, and increases in PCF and CEM. The degree of normalization of these parameters did not appear to depend on the baseline values. The patient with the worst baseline parameters completely normalized his values at 100% doses of BeneFIX® and Mononine®. The patient with the best baseline values also normalized his parameters with BeneFIX® but not with Mononine®. The patient with intermediate baseline abnormalities improved all parameters with both factor IX products but appeared to respond better to BeneFIX® at the 100% dose level. The response to NovoSeven®, at 100% of the dose recommended for treatment of factor VIII inhibitor patients, was detectable but clearly inferior to the response to the factor IX agents. These results indicate significant variability in hemostatic status between factor IX deficient patients both at baseline and in response to factor replacement. While rFVIIa has activity in these patients, the dose previously shown to correct TGT in factor VIII deficient patients may not be appropriate for factor IX deficient patients.
Multi-Stream Beam-Training for mmWave MIMO Networks (2018)

Multi-stream 60 GHz communication has the potential to achieve data rates up to $100$ Gbps via multiplexing multiple data streams. Unfortunately, establishing multi-stream directional links can be a high overhead procedure as the search space increases with the number of spatial streams and the product of AP-client beam resolution. In this paper, we present MUlti-stream beam-Training for mm-wavE networks (MUTE) a novel system that leverages channel sparsity, GHz-scale sampling rate, and the knowledge of mm-Wave RF codebook beam patterns to construct a set of candidate beams for multi-stream beam steering. In 60 GHz WLANs, the AP establishes and maintains a directional link with every client through periodic beam training. MUTE repurposes these beam acquisition sweeps to estimate the Power Delay Profile (PDP) of each beam with zero additional overhead. Coupling PDP estimates with beam pattern knowledge, MUTE selects a set of candidate beams that capture diverse or ideally orthogonal paths to obtain maximum stream separability. Our experiments demonstrate that MUTE achieves 90% of the maximum achievable aggregate rate while incurring only 0.04% of exhaustive search's training overhead.
Long-term clinical and radiographic outcomes of the Prestige LP artificial cervical disc replacement at 2 levels: results from a prospective randomized controlled clinical trial (2017)

OBJECTIVE The aim of this study was to assess long-term clinical safety and effectiveness in patients undergoing anterior cervical surgery using the Prestige LP artificial disc replacement (ADR) prosthesis to treat degenerative cervical spine disease at 2 adjacent levels compared with anterior cervical discectomy and fusion (ACDF). METHODS A prospective, randomized, controlled, multicenter FDA-approved clinical trial was conducted at 30 US centers, comparing the low-profile titanium ceramic composite-based Prestige LP ADR (n = 209) at 2 levels with ACDF (n = 188). Clinical and radiographic evaluations were completed preoperatively, intraoperatively, and at regular postoperative intervals to 84 months. The primary end point was overall success, a composite variable that included key safety and efficacy considerations. RESULTS At 84 months, the Prestige LP ADR demonstrated statistical superiority over fusion for overall success (observed rate 78.6% vs 62.7%; posterior probability of superiority [PPS] = 99.8%), Neck Disability Index success (87.0% vs 75.6%; PPS = 99.3%), and neurological success (91.6% vs 82.1%; PPS = 99.0%). All other study effectiveness measures were at least noninferior for ADR compared with ACDF. There was no statistically significant difference in the overall rate of implant-related or implant/surgical procedure-related adverse events up to 84 months (26.6% and 27.7%, respectively). However, the Prestige LP group had fewer serious (Grade 3 or 4) implant- or implant/surgical procedure-related adverse events (3.2% vs 7.2%, log hazard ratio [LHR] and 95% Bayesian credible interval [95% BCI] -1.19 [-2.29 to -0.15]). Patients in the Prestige LP group also underwent statistically significantly fewer second surgical procedures at the index levels (4.2%) than the fusion group (14.7%) (LHR -1.29 [95% BCI -2.12 to -0.46]). Angular range of motion at superior- and inferior-treated levels on average was maintained in the Prestige LP ADR group to 84 months. CONCLUSIONS The low-profile artificial cervical disc in this study, Prestige LP, implanted at 2 adjacent levels, maintains improved clinical outcomes and segmental motion 84 months after surgery and is a safe and effective alternative to fusion. Clinical trial registration no.: NCT00637156 (clinicaltrials.gov).
Contact Angles and Hysteresis on Surfaces with Chemically Heterogeneous Islands (2003)

Wetting behavior was studied on surfaces with a single, circular heterogeneous island. Lyophobic islands were created on lyophilic Si wafers using polystyrene. Alternately, lyophobic perfluoroalkoxy fluoropolymer film was etched to make lyophilic domains. Contact angles and hysteresis were measured with water and hexadecane. Small sessile drops were deposited on the center of an island and liquid was sequentially added, eventually forcing the contact line to advance beyond the island perimeter onto the surrounding area. Even though the underlying contact area contained a mixture of lyophilic and lyophobic domains, the contact angles, both advancing and receding, were equal to the angles exhibited by the homogeneous periphery. Or in other words, if the heterogeneity was completely contained with the contact area and did not intersect the contact line, then no area averaging of the contact angles occurred. These findings suggest that interactions at the contact line, not the contact area, control wetting of heterogeneous surfaces.
Spring-Shaped Inductor Tuned With a Microelectromechanical Electrothermal Actuator (2020)

We present a spring-shaped tunable inductor, fabricated using a silicon-on-insulator (SOI) multiuser micro-electromechanical system process. The inductor has a simple planar design and is monolithically integrated in the SOI wafer. The inductor is tuned using a thermal actuator on the same silicon structure layer. Thus, the complexity and cost of fabrication are greatly minimized. The device is compact, with dimensions of 0.90 mm × 0.55 mm. In addition to cost-effective design and small surface area, the device has good tuning range and Q-factor. The experimental results show that the inductor can be tuned to 20%, 17%, and 15% at 2, 3, and 5 GHz, respectively. In air at 0 and 11.5 V, Q-factors of 7.27 and 4.64 obtained at 2 GHz, and 7.21 and 5.92 at 5 GHz. The series resonance frequency is >20 GHz.
Anti-Ly-1 antibody induces interleukin 2 release from T cells. (1986)

In this report we show that a signal provided by binding of anti-Ly-1 antibody to the Ly-1 cell surface protein, along with a second signal provided by mitogen, can trigger a T cell into activation and increase [Ca2+]i and the release of IL2. At optimal concentrations, the effects of anti-Ly-1 and IL 1 are additive, suggesting a different activation pathway for each.
Palladium-Catalyzed Amination of Aryl Nonaflates (2003)

The first detailed study of the palladium-catalyzed amination of aryl nonaflates is reported. Use of ligands 2-4 and 6 allows for the catalytic amination of electron-rich and -neutral aryl nonaflates with both primary and secondary amines. With use of Xantphos 5, the catalytic amination of a variety of functionalized aryl nonaflates resulted in excellent yields of anilines; even 2-carboxymethyl aryl nonaflate is effectively coupled with a primary alkylamine. Moderate yields were obtained when coupling halo-aryl nonaflates with a variety of amines, where in most cases the aryl nonaflate reacted in preference to the aryl halide. Overall, aryl nonaflates are an effective alternative to triflates in palladium-catalyzed C-N bond-forming processes due to their increased stability under the reaction conditions.
Application of the Quanta image sensor concept to linear polarization imaging—a theoretical study (2016)

Research efforts in linear polarization imaging have largely targeted the development of novel polarizing filters with improved performance and the monolithic integration of image sensors and polarization filter arrays. However, as pixel sizes in CMOS image sensors continue to decrease, the same limitations that have an impact on color and monochrome CMOS image sensors will undoubtedly affect polarization imagers. Issues of low signal capacity and dynamic range in small pixels will severely limit the useful polarization information that can be obtained. In this paper, we propose to leverage the benefits of the relatively new Quanta image sensor (QIS) concept to mitigate the anticipated limitations of linear polarization imaging as pixel sizes decrease. We address, by theoretical calculation and simulation, implementation issues such as alignment of polarization filters over extremely small pixels used in the QIS concept and polarization image formation from single-bit output of such pixels. We also present design innovations aimed at exploiting the benefits of this new imaging concept for simultaneous color and linear polarization imaging.
Response to Comment on “Remeasuring the Double Helix” (2009)

We measured the mean and variance of end-to-end length in short DNA fragments in solution and reported evidence of DNA stretching that is cooperative over more than two turns of the double helix. Becker and Everaers suggest that the structural fluctuations we observed arise from bending motions of the DNA, rather than stretching. We present three experimental tests of this bending-based explanation.
Factors influencing cross-presentation of non-self antigens expressed from recombinant adeno-associated virus vectors (2001)

The present results indicate that immune responses to non-self antigens expressed from rAAV vectors depend on the accessibility of such antigens to different local antigen-presenting cells.