gebhart/patrepeval huggingface dataset:
Peptidylarginine deiminase from Porphyromonas gingivalis contributes to infection of gingival fibroblasts and induction of prostaglandin E2‐signaling pathway (2014)

Summary Porphyromonas gingivalis ( P. gingivalis ) expres‐ses the enzyme peptidylarginine deiminase ( PPAD ), which has a strong preference for C‐terminal arginines. Due to the combined activity of PPAD and Arg‐specific gingipains, P. gingivalis on the cell surface is highly citrullinated. To investigate the contribution of PPAD to the interaction of P. gingivalis with primary human gingival fibroblasts ( PHGF ) and P. gingivalis ‐induced synthesis of prostaglandin E 2 (PGE 2 ), PHGF were infected with wild‐type P. gingivalis ATCC 33277, an isogenic PPAD ‐knockout strain (∆ ppad ) or a mutated strain (C351A) expressing an inactive enzyme in which the catalytic cysteine has been mutated to alanine (PPAD C351A ). Cells were infected in medium containing the mutants alone or in medium supplemented with purified, active PPAD. PHGF infection was assessed by colony‐forming assay, microscopic analysis and flow cytometry. Expression of cyclo‐oxygenase 2 (COX‐2) and microsomal PGE synthase‐1 ( mPGES ‐1), key factors in the prostaglandin synthesis pathway, was examined by quantitative reverse transcription polymerase chain reaction (qRT‐PCR), while PGE 2 synthesis was evaluated by enzyme immunoassay. PHGF were infected more efficiently by wild‐type P. gingivalis than by the ∆ ppad strain, which correlated with strong induction of COX‐2 and mPGES ‐1 expression by wild‐type P. gingivalis , but not by the PPAD activity‐null mutant strains (Δ ppad and C351A). The impaired ability of the Δ ppad strain to adhere to and/or invade PHGF and both Δ ppad and C351A to stimulate the PGE 2 ‐synthesis pathway was fully restored by the addition of purified PPAD. The latter effect was strongly inhibited by aspirin. Collectively, our results implicate PPAD activity, but not PPAD itself, as an important factor for gingival fibroblast infection and activation of PGE 2 synthesis, the latter of which may strongly contribute to bone resorption and eventual tooth loss.
Heat Modulation of Intrinsic MR Contrasts for Tumor Characterization (2022)

(1) Background: The longitudinal relaxation time (T1), transverse relaxation time (T2), water proton chemical shift (CS), and apparent diffusion coefficient (ADC) are MR quantities that change with temperature. In this work, we investigate heat-induced intrinsic MR contrast types to add salient information to conventional MR imaging to improve tumor characterization. (2) Methods: Imaging tests were performed in vivo using different rat tumor models. The rats were cooled/heated to steady-state temperatures from 26–36 °C and quantitative measurements of T1, T2, and ADC were obtained. Temperature maps were measured using the proton resonance frequency shift (PRFS) method during the heating and cooling cycles. (3) Results: All tissue samples show repeatable relaxation parameter measurement over a range of 26–36 °C. Most notably, we observed a more than 3.3% change in T1/°C in breast adenocarcinoma tumors compared to a 1% change in benign breast fibroadenoma lesions. In addition, we note distinct values of T2/°C change for rat prostate carcinoma cells compared to benign tissue. (4) Conclusion: These findings suggest the possibility of improving MR imaging visualization and characterization of tissue with heat-induced contrast types. Specifically, these results suggest that the temporal thermal responses of heat-sensitive MR imaging contrast mechanisms in different tissue types contain information for improved (i) characterization of tumor/tissue boundaries for diagnostic and therapy purposes, and (ii) characterization of salient behavior of tissues, e.g., malignant versus benign tumors.
Stimulation of the pelvic nerve increases bladder capacity in the PGE 2 cat model of overactive bladder (2020)

Selective electrical stimulation of the pudendal nerve exhibits promise as a potential therapy for treating overactive bladder (OAB) across species (rats, cats, and humans). More recently, pelvic nerve (PelN) stimulation was demonstrated to improve cystometric bladder capacity in a PGE<sub>2</sub> rat model of OAB. However, PelN stimulation in humans or in an animal model that is more closely related to humans has not been explored. Therefore, our objective was to quantify the effects of PGE<sub>2</sub> and PelN stimulation in the cat. Acute cystometry experiments were conducted in 14 α-chloralose-anesthetized adult, neurologically intact female cats. Intravesical PGE<sub>2</sub> decreased bladder capacity, residual volume, threshold contraction pressure, and mean contraction pressure. PelN stimulation reversed the PGE<sub>2</sub>-induced decrease in bladder capacity and increased evoked external urethral sphincter electromyographic activity without influencing voiding efficiency. The increases in bladder capacity generated by PelN stimulation were similar in the rat and cat, but the stimulation parameters to achieve this effect differed (threshold amplitude at 10 Hz in the rat vs. twice threshold amplitude at 1 Hz in the cat). These results highlight the potential of PGE<sub>2</sub> as a model of OAB and provide further evidence that PelN stimulation is a promising approach for the treatment of OAB symptoms.
Critical behavior of the random-bond Ashkin-Teller model: A Monte Carlo study (1995)

The critical behavior of a bond-disordered Ashkin-Teller model on a square lattice is investigated by intensive Monte Carlo simulations. A duality transformation is used to locate a critical plane of the disordered model. This critical plane corresponds to the line of critical points of the pure model, along which critical exponents vary continuously. Along this line the scaling exponent corresponding to randomness \ensuremath{\varphi}=(\ensuremath{\alpha}/\ensuremath{\nu}) varies continuously and is positive so that the randomness is relevant, and different critical behavior is expected for the disordered model. We use a cluster algorithm for the Monte Carlo simulations based on the Wolff embedding idea, and perform a finite size scaling study of several critical models, extrapolating between the critical bond-disordered Ising and bond-disordered four-state Potts models. The critical behavior of the disordered model is compared with the critical behavior of an anisotropic Ashkin-Teller model, which is used as a reference pure model. We find no essential change in the order parameters' critical exponents with respect to those of the pure model. The divergence of the specific heat C is changed dramatically. Our results favor a logarithmic type divergence at ${\mathit{T}}_{\mathit{c}}$, C\ensuremath{\sim}lnL for the random-bond Ashkin-Teller and four-state Potts models and C\ensuremath{\sim}ln lnL for the random-bond Ising model.
Double‐blind placebo‐controlled multicenter phase II trial to evaluate D‐methionine in preventing/reducing oral mucositis induced by radiation and chemotherapy for head and neck cancer (2018)

Although not meeting the primary end point, results of multiple assessments suggest that D-met decreased mucositis.
Review of technology for 157-nm lithography (2001)

This paper outlines the critical issues facing the implementation of 157-nm lithography as a sub-100-nm technology. The status of the present technology for mask materials, pellicles, optical materials, coatings, and resists is presented.
A Novel Dimerization Reaction of 1-Methyl-2-benzopyrylium Salts (1991)

Treatment of 1-methyl-2-benzopyrylium salts 1 with weak bases gives the anhydro bases 4, which rapidly react with the original cations as dienophile and diene respectively to form the spiro dimers 6.
Analyzing and Enhancing Closed-loop Stability in Reactive Simulation (2022)

Simulation has played an important role in efficiently evaluating self-driving vehicles in terms of scalability. Existing methods mostly rely on heuristic-based simulation, where traffic participants follow certain human-encoded rules that fail to generate complex human behaviors. Therefore, the reactive simulation concept is proposed to bridge the human behavior gap between simulation and real-world traffic scenarios by leveraging real-world data. However, these reactive models can easily generate unreasonable behaviors after a few steps of simulation, where we regard the model as losing its stability. To the best of our knowledge, no work has explicitly discussed and analyzed the stability of the reactive simulation framework. In this paper, we aim to provide a thorough stability analysis of the reactive simulation and propose a solution to enhance the stability. Specifically, we first propose a new reactive simulation framework, where we discover that the smoothness and consistency of the simulated state sequences are crucial factors to stability. We then incorporate the kinematic vehicle model into the framework to improve the closed-loop stability of the reactive simulation. Furthermore, along with commonly-used metrics, several novel metrics are proposed in this paper to better analyze the simulation performance.
Heterodimeric Fly Glycoprotein Hormone-α2 (GPA2) and Glycoprotein Hormone-β5 (GPB5) Activate Fly Leucine-Rich Repeat-Containing G Protein-Coupled Receptor-1 (DLGR1) and Stimulation of Human Thyrotropin Receptors by Chimeric Fly GPA2 and Human GPB5 (2005)

Glycoprotein hormones play important roles in thyroid and gonadal function in vertebrates. The glycoprotein hormone alpha-subunit forms heterodimers with different beta-subunits to activate TSH or gonadotropin (LH and FSH) receptors. Recent genomic analyses allowed the identification of another alpha-subunit, GPA2, and another beta-subunit, GPB5, in human, capable of forming heterodimers to activate TSH receptors. Based on comparative genomic searches, we isolated the fly orthologs for human GPA2 and GPB5, each consisting of 10 cysteine residues likely involved in cystine-knot formation. RT-PCR analyses in Drosophila melanogaster demonstrated the expression of GPA2 and GPB5 at different developmental stages. Immunoblot analyses further showed that fly GPA2 and GPB5 subunit proteins are of approximately 16 kDa, and coexpression of these subunits yielded heterodimers. Purified recombinant fly GPA2/GPB5 heterodimers were found to be glycoproteins with N-linked glycosylated alpha-subunits and nonglycosylated beta-subunits, capable of stimulating cAMP production mediated by fly orphan receptor DLGR1 but not DLGR2. Although the fly GPA2/GPB5 heterodimers did not activate human TSH or gonadotropin receptors, chimeric fly GPA2/human GPB5 heterodimers stimulated human TSH receptors. These findings indicated that fly GPA2/GPB5 is a ligand for DLGR1, thus showing the ancient origin of this glycoprotein hormone-seven transmembrane receptor-G protein signaling system. The fly GPA2 also could form heterodimers with human GPB5 to activate human TSH receptors, indicating the evolutionary conservation of these genes and suggesting that the GPA2 subunit may serve as a scaffold for the beta-subunit to activate downstream G protein-mediated signaling.
Supplementary Table 1 from Differential Cellular Internalization of Anti-CD19 and -CD22 Immunotoxins Results in Different Cytotoxic Activity (2023)

Supplementary Table 1 from Differential Cellular Internalization of Anti-CD19 and -CD22 Immunotoxins Results in Different Cytotoxic Activity
The Blame Game: Understanding Blame Assignment in Social Media (2023)

Psychological studies on morality have proposed underlying linguistic and semantic factors. However, current empirical studies often lack the nuances and complexity of real life. This article examines how well the findings of prior studies generalize to a corpus of over 30000 narratives of tense social situations submitted to a popular social media forum. A poster describes interpersonal moral situations or misgivings; other users judge from the post whether the poster (protagonist) or an opposing side (antagonist) is morally culpable. We extend and apply natural language processing (NLP) techniques to understand the effects of descriptions of the people involved in these posts. We conduct extensive experiments to investigate the effect sizes of features to understand how they affect the assignment of blame on social media. Our findings show that aggregating psychological theories enables understanding real-life moral situations. We also find evidence of bias blame assignment on social media, such as that males are likelier to receive blame no matter whether they are protagonists or antagonists.
Multi-antenna Techniques in Ultra Mobile Broadband Communication Systems (2008)

Theoretically, multi-antenna techniques offers significant capacity benefits, but realizing these gains in deployed wireless systems remains a very challenging problem. MIMO has been used in wireless LAN systems with great success. However, due to the hugely varying spatial profiles and velocity patterns of the access terminals, integrating MIMO techniques in a wireless WAN system has been a difficult design problem. This paper introduces the design paradigms of Ultra-Mobile Broadband, which is poised to become the successor of EVDO as the next generation of high speed wireless system. UMB allows the use of MIMO in various forms to suit the deployment scenario, and elicit as much gain as possible.
Phase I safety trial of intravenous ascorbic acid in patients with severe sepsis (2014)

ClinicalTrials.gov identifier NCT01434121.
Forward-looking objective functions: concept and applications in high level synthesis (2002)

The effectiveness of traditional CAD optimization algorithms is proportional to the accuracy of the targeted objective functions. However, behavioral synthesis tools are not used in isolation; they form a strongly connected design flow where each tool optimizes its own objective function without considering the consequences on the optimization goals of the subsequently applied tools. Therefore, efforts to optimize one aspect of a design often have unforeseen negative impacts on other phases of the design process. Our objective is to establish a systematic way of developing and validating new types of objective functions that consider the effects on subsequently applied synthesis steps. We demonstrate the generic forward-looking objective function (FLOF) strategy on three main steps in behavioral synthesis: (i) transformation, (ii) scheduling, and (iii) register assignment. We show how the FLOF can be used in the first two phases to reduce the total number of registers required in the third phase.
LOSS OF LUTEINIZING HORMONE BIOACTIVITY IN PATIENTS WITH PROSTATIC CANCER TREATED WITH AN LHRH AGONIST AND A PURE ANTIANDROGEN (1986)

Chronic treatment of adult men with LHRH agonists causes a decrease in serum testosterone and 5 alpha-dihydrotestosterone to castrate levels. In the presence of such low levels of circulating testicular androgens, the concentration of serum LH measured by radioimmunoassay (RIA) sometimes remains normal or is only partially inhibited. In order to assess the biological activity of circulating LH, we have used the mouse interstitial cell assay. Blood samples were obtained from patients with prostatic carcinoma treated with the LHRH agonist [D-Trp6] LHRH ethylamide in combination with the pure antiandrogen Flutamide (Euflex). While serum LH levels measured by RIA were only partially reduced from 2.2 +/- 0.3 (SEM) to 1.1 +/- 0.1 ng/ml after 3 months of therapy, bioactive LH was markedly inhibited from 0.43 +/- 0.04 to 0.030 +/- 0.007 ng/ml, thus causing the ratio of biologically active to radioimmunoassayable LH to drop from 0.26 +/- 0.03 to 0.03 +/- 0.01. In the same patients, serum testosterone levels were decreased from 3.91 +/- 0.51 to 0.14 +/- 0.05 ng/ml after 3 months of treatment. In patients treated for 6 months, the bio/immuno ratio was still reduced at 0.032 +/- 0.005. These data show a marked loss of LH biological activity during treatment of adult men with an LHRH agonist and an antiandrogen. The close parallelism observed between serum testosterone and bioactive LH levels suggests that the loss of biological activity of the gonadotrophin is mainly, if not exclusively, responsible for the inhibition of testicular androgen secretion observed during chronic treatment with LHRH agonists.
Laser frequency combs for astronomical observations (2008)

A direct measurement of the universe's expansion history could be made by observing in real time the evolution of the cosmological redshift of distant objects. However, this would require measurements of Doppler velocity drifts of about 1 centimeter per second per year, and astronomical spectrographs have not yet been calibrated to this tolerance. We demonstrate the first use of a laser frequency comb for wavelength calibration of an astronomical telescope. Even with a simple analysis, absolute calibration is achieved with an equivalent Doppler precision of approximately 9 meters per second at about 1.5 micrometers - beyond state-of-the-art accuracy. We show that tracking complex, time-varying systematic effects in the spectrograph and detector system is a particular advantage of laser frequency comb calibration. This technique promises an effective means for modeling and removal of such systematic effects to the accuracy required by future experiments to see direct evidence of the universe's putative acceleration.
Anisotropic thermal behavior of extrusion‐based large scale additively manufactured carbon‐fiber reinforced thermoplastic structures (2022)

Abstract Large format additive manufacturing (AM) enables rapid manufacturing of large parts and structures with minimum waste in material and energy. Extrusion‐based AM deposition processes provide parts with highly anisotropic thermal properties, which are not typically reflected in textbook values for these materials. In order to develop accurate models that describe the directionally dependent thermal behavior of these materials in processing and service, accurate measurements of specific heat capacity and thermal conductivity are required. This work characterizes, documents, and analyzes the effect of the anisotropic nature of the extrusion‐based deposition process on the specific heat capacity and thermal conductivity of the resulting AM products. All measurements were made over a temperature range of 20–180°C using the transient plane source technique, also referred to as the hot disk technique. Three of the most commonly used large format AM feedstock materials that utilize carbon fiber reinforcement were examined in this work: acrylonitrile butadiene styrene, polyphenylene sulfide and polyphenylsulfone. These findings can serve as a thermal design/process guideline for future large format AM applications.
Influence of Branching on Network Formation and the Thermomechanical Properties of UV-Curable Polyester Powder Coating Resins (2022)

A series of branched, UV-curable polyester oligomers were synthesized from neopentyl glycol, terephthalic acid, and variable amounts of trimellitic anhydride (TMA). 1H NMR spectroscopy and MALDI-ToF-MS confirmed that TMA was successfully incorporated into the oligomeric backbone. Differential scanning calorimetry experiments and zero-shear viscosity measurements were conducted to probe the thermal and rheological properties of the branched polyester resins. The Tg and the zero-shear melt viscosity were affected by the extent of branching as well as the functionality of the end group. UV-cured thin films were subsequently prepared and characterized via differential scanning calorimetry, thermal gravimetric analysis, dynamic mechanical analysis, tensile tests, and Soxhlet extractions. In general, the crosslink density of the films increased with the extent of branching. Linear and lightly branched samples (i.e., 2.5 and 5.0 mol % TMA) had higher % elongations at break, while the more highly branched samples (i.e., 7.5 mol % TMA) had higher Young’s moduli and tensile strengths. However, further increases in the extent of branching (i.e., 10.0 mol % TMA) negatively affected the mechanical properties of the film due to poor crosslinked network development. The insights from this study highlight the importance of optimizing the extent of branching for UV-curable polyester coating resins.
Chemokine stromal cell-derived factor-1 induction by C/EBPβ activation is associated with all-trans-retinoic acid-induced leukemic cell differentiation (2007)

Stromal cell-derived factor-1 (SDF-1/CXCL12) is one of the essential chemokines, which mediates hematopoietic differentiations. However, the mechanism by which SDF-1 expression is regulated in granulocyte differentiation is poorly understood. Here, we suggest a novel mechanism by which all-trans-retinoic acid (ATRA) induces the expression of SDF-1 during the differentiation of promyelomonocytic leukemic U937 cells. Moreover, we also demonstrate that activation of transcription factor C/EBPbeta by ATRA regulates SDF-1 expression in U937 cells. In addition, we show that the cyclin-dependent kinase inhibitors p21(WAF1/CIP1) and Pyk2 are up-regulated by SDF-1 and increased markedly by the costimulation of ATRA and SDF-1. Furthermore, ATRA and SDF-1alpha additively induce U937 cell differentiation. Indeed, silencing the expression of SDF-1 inhibits ATRA-induced granulocyte differentiation significantly. Taken together, these results indicate that SDF-1alpha is involved in granulocyte differentiation in response to ATRA, mediated by the activation of the transcription factor C/EBPbeta.
Synthesis and Cyclization of 3-Aryl-2-(arylacetoxy)acrylates: A Three-Step Access to Pulvinones (2007)

(4-Methoxybenzyl)magnesium chloride was acylated with dialkyl oxalates 14a,b,d or S,S-di-tert-butyl dithiooxalate (14c) to give 2-hydroxy-3-(4-methoxyphenyl)acrylates and -thioacrylates 17a-d. Esterification with phenylacetic anhydride or (4-methoxyphenyl)acetic acid/N,N′-dicyclohexylcarbodiimide stereoselectively furnished 2-(arylacetoxy)-3-(4-methoxyphenyl)acrylates and thioacrylates (Z)-18a-d. Treating the latter with potassium tert-butoxide induced Dieckmann condensations, which led to isomerically pure pulvinones 1g,h in up to 88% yield.
Routine cytodiagnosis of pulmonary malignancies. (1981)

Anesthesiologists normally discard the material routinely suctioned from the tracheal tube of patients under general endotracheal anesthesia. We preserved, and later examined microscopically, specimens from 10,621 patients. We found 11 cytologically abnormal smears from subjects with unsuspected pulmonary involvement, an incidence slightly more than 1:1,000. The accuracy of our method was assessed by calculation of the percent of abnormal smears obtained from patients with prediagnosed bronchogenic carcinomas: 40% when suctioned material was immediately spread on slides, and 67% when cellular concentration was achieved by mucolysis followed by filtration or centrifugation. Secretions normally discarded can reveal much information that would otherwise be missed. Our method may be useful if applied to patients at risk (heavy smokers, workers with asbestos, nitrosamine, or benzopyrine, miners of radioactive material, etc) who undergo general anesthesia for incidental surgery.
Dispersion management for a sub-10-fs, 10 TW optical parametric chirped-pulse amplifier (2007)

We report the amplification of three-cycle, 8.5 fs optical pulses in a near-infrared noncollinear optical parametric chirped-pulse amplifier (OPCPA) up to energies of 80 mJ. Improved dispersion management in the amplifier by means of a combination of reflection grisms and a chirped-mirror stretcher allowed us to recompress the amplified pulses to within 6% of their Fourier limit. The novel ultrabroad, ultraprecise dispersion control technology presented in this work opens the way to scaling multiterawatt technology to even shorter pulses by optimizing the OPCPA bandwidth.