gebhart/patrepeval huggingface dataset:
Cycloadditions in mixed aqueous solvents: the role of the water concentration (2005)

Abstract We examined the kinetics of a series of cycloaddition reactions in mixtures of water with methanol, acetonitrile and poly(ethylene glycol) (MW 1000). The reactions include the Diels–Alder (DA) reaction between cyclopentadiene and N ‐ n ‐butylmaleimide or acridizinium bromide, the retro‐Diels‐Alder (RDA) reaction of 1,4,4a,9a‐tetrahydro‐4a‐methyl‐(1α,4α,4aα,9aα)‐1,4‐methaneanthracene‐9,10‐dione and the 1,3‐dipolar cycloaddition of benzonitrile oxide with N ‐ n ‐butylmaleimide. Plots of log k vs the molar concentration or volume fraction of water are approximately linear, but with a characteristic break around 40 M water. This break, absent for the RDA reaction, is ascribed to hydrophobic effects. Comparison with aqueous mixtures of the more hydrophobic 1‐propanol shows that these mixtures induce qualitatively similar effects on the rate, but that preferential solvation effects cause the mixtures of 1‐propanol to exhibit a more complex behavior of log k on composition. The results are analyzed using the Abraham–Kamlett–Taft model. The solvent effects in aqueous mixtures are not satisfactorily described by this model. For some cycloadditions, small maxima in rate are observed in highly aqueous mixtures of alcohols. The origin of these maxima and the aforementioned breaks is most likely the same. Copyright © 2005 John Wiley &amp; Sons, Ltd.
Bronchial Epithelial Cells Produce Lung Fibroblast Chemotactic Factor: Fibronectin (1989)

The interaction between the epithelial cells and the subjacent mesenchymal cells in the airway is thought to play a major role during tissue repair after airway injury and lung morphogenesis. To evaluate this interaction, we cultured human lung fibroblasts, and bovine and human bronchial epithelial cells, and determined that bronchial epithelial cell-conditioned medium has a chemotactic activity for lung fibroblasts. This activity had the characteristics of protein: it was nondialyzable, heat-labile, pepsin-labile, acid-stable, and lipid-inextractable. Molecular sieve chromatography on Sephadex G-150 and affinity chromatography on gelatin-Sepharose revealed that there was one peak of chemotactic activity in high molecular weight range, which bound to gelatin, thus suggesting that the chemotactic factor might be fibronectin. Production and secretion of fibronectin into the culture media were demonstrated by biosynthetic incorporation of radioactive amino acid into fibronectin followed by immunoprecipitation on SDS-PAGE and autoradiography. Release into the culture medium was confirmed by ELISA. The identity of fibronectin as the chemotactic activity was confirmed by the addition of antifibronectin antibody to the conditioned medium, which inhibited chemotaxis in dose-dependent manner. Thus, bronchial epithelial cells produce fibronectin which can function as a chemotactic factor for lung fibroblasts. This production of fibronectin by bronchial epithelial cells may play an important role in regulating interaction between the bronchial epithelial cells that line the lumenal surface of the bronchial epithelial wall and the mesenchymal fibroblasts that underlie the bronchial epithelial basement membrane.
Decomposition of Test Magnetic and Electropotential Images with Non-Dipole Structure According to Multipole Expansion (2007)

An approach to analysis of magnetic and electropotential maps, consisting in their expansion into orthogonal images using the two-dimensional Fourier transform, is suggested. The method has a unique solution, is performed correctly, possesses a possibility of space map filtration, error does not exceed 3 %. This approach can be useful in development of new methods of noninvasive diagnosis of electrophysiological abnormalities in human heart, characterized by the presence of complex (non-dipole) source of bioelectric activity.
THE DESIGN OF A COMPACT THz SOURCE BASED ON PHOTOCATHODE RF GUN (2013)

Narrow-band THz coherent Cherenkov radiation can be driven by a subpicosecond electron bunch traveling along the axis of a hollow cylindrical dielectric-lined waveguide. We present a scheme of compact THz radiation source based on the photocathode rf gun. On the basis of our analytic result, the subpicosecond electron bunch with high charge (800pC) can be generated directly in the photocathode rf gun. A narrow emission spectrum peaked at 0.24 THz with 2 megawatt (MW) peak power is expected to gain in the proposed scheme (the length of the facility is about 1.2 m), according to the analytical and simulated results. THEORY OFWAKEFIELDS IN A CYLINDRICAL DIELECTRIC-LINED WAVEGUIDE The structure of DLW is shown as Fig. 1. Fourier exFigure 1: The structure of DLW pansion of the longitudinal fields in a circular cylindrical waveguide takes the form: ( Ez(r, t) Hz(r, t) ) = 1 (2π) ∫∞ −∞ dωdk× ∞ ∑ l=−∞ exp [−i(ωt− kz − lθ)]× ( ez(r) −ihz(r) ) (1) For a given l in Eq. (1), the eigenmodes can be obtained with the boundary conditions[1][2]. The eigenfunctions will be designated by subscripts such as ez,n(r) , hz,n(r) and the eigenvalues byωn , kn , etc. For the transverse distribution of electron bunch is azimuthally symmetric, the electromagnetic field excited by the bunch is independent of θ , only TM0n modes are excited. In our case, the influence of the transverse distribution of electron bunch on the electromagnetic field is weak (the proof ∗Supported by National Natural Science Foundation of China (11205152) † hezhg@ustc.edu.cn will be presented in the next section ), so only the temporal distribution of electron bunch is considered. The orthonormality relation between any two eigenmodes and radiative power flow can be written as[2]
DYNAMIC STUDIES OF CERAMIDE ION CHANNELS ENABLED BY A RAPID-PERFUSION PLANAR LIPID MEMBRANE CHIP (2011)

A microfluidic system supporting rapid perfusion of reagents to an on-chip bilayer lipid membrane (BLM) has been developed to study dynamic response of membrane or membrane-bound proteins to different (bio)chemical boundary conditions. Comprising an open well supporting a simple diffusion painting method for bilayer formation and multilayer microchannel networks for perfusion of reagents to the membrane, this device supports dynamic injection of multiple reagents at different concentrations with perfusion switching times of several seconds. Here we report a series of studies on the formation and dissolution of ceramide ion channels through the perfusion of a ceramide channel inhibitor (La 3+ ) to induce channel disassembly, and a chelator for the inhibitor enabling the study channel reassembly dynamics. We discuss two models to explain the mechanism of La 3+ ceramide inhibition. This system can be applied to study membrane or ion channels with similar time constant, allowing important dynamic features to be probed.
Multimodal host–guest complexation for efficient and stable perovskite photovoltaics (2021)

Formamidinium lead iodide perovskites are promising light-harvesting materials, yet stabilizing them under operating conditions without compromising optimal optoelectronic properties remains challenging. We report a multimodal host-guest complexation strategy to overcome this challenge using a crown ether, dibenzo-21-crown-7, which acts as a vehicle that assembles at the interface and delivers Cs<sup>+</sup> ions into the interior while modulating the material. This provides a local gradient of doping at the nanoscale that assists in photoinduced charge separation while passivating surface and bulk defects, stabilizing the perovskite phase through a synergistic effect of the host, guest, and host-guest complex. The resulting solar cells show power conversion efficiencies exceeding 24% and enhanced operational stability, maintaining over 95% of their performance without encapsulation for 500 h under continuous operation. Moreover, the host contributes to binding lead ions, reducing their environmental impact. This supramolecular strategy illustrates the broad implications of host-guest chemistry in photovoltaics.
Comparison of Custom-made Versus Prefabricated Thumb Splinting for Carpometacarpal Arthrosis: A Systematic Review and Meta-analysis. (2018)

II.
NRG-HN003: Phase I and Expansion Cohort Study of Adjuvant Pembrolizumab, Cisplatin and Radiation Therapy in Pathologically High-Risk Head and Neck Cancer (2021)

The anti-PD1 monoclonal antibody pembrolizumab improves survival in recurrent/metastatic head and neck squamous cell carcinoma (HNSCC). Patients with locoregional, pathologically high-risk HNSCC recur frequently despite adjuvant cisplatin-radiation therapy (CRT). Targeting PD1 may reverse immunosuppression induced by HNSCC and CRT. We conducted a phase I trial with an expansion cohort (n = 20) to determine the recommended phase II schedule (RP2S) for adding fixed-dose pembrolizumab to standard adjuvant CRT. Eligible patients had resected HPV-negative, stage III-IV oral cavity, pharynx, or larynx HNSCC with extracapsular nodal extension or positive margin. RP2S was declared if three or fewer dose-limiting toxicities (DLT) occurred in a cohort of 12. DLT was defined as grade 3 or higher non-hematologic adverse event (AE) related to pembrolizumab, immune-related AE requiring over 2 weeks of systemic steroids, or unacceptable RT delay. A total of 34 patients enrolled at 23 NRG institutions. During the first cohort, only one DLT was observed (fever), thus RP2S was declared as pembrolizumab 200 mg every 3 weeks for eight doses, starting one week before CRT. During expansion, three additional DLTs were observed (wound infection, diverticulitis, nausea). Of the 34 patients, 28 (82%) received five or more doses of pembrolizumab. This regimen was safe and feasible in a cooperative group setting. Further development is warranted.
Expression of DCC Protein in Colorectal Tumors and Its Relationship to Tumor Progression and Metastasis (1999)

A loss of heterozygosity (LOH) at the DCC gene locus was detected in colorectal tumors, and this LOH might be related to metastasis. The aim of this study was to determine DCC protein expression in colorectal cancer and to evaluate its prognostic value. Allelic loss of the DCC locus was observed in 16 of the 23 patients (66.7%). In all 16 patients with LOH, DCC expression was decreased in the cancer tissue compared with the adjacent normal mucosa. All 23 colorectal tumors had decreased expression of this protein relative to the adjacent normal colonic mucosa in Western blot analysis. The levels of DCC protein were significantly lower in cancer tissues than in adenoma tissues. Decreased DCC protein expression was also observed by immunohistochemistry in the colorectal cancer cases. There were significant correlations between DCC protein expression and histologic type, venous invasion, and hematogenous metastasis. Patients with DCC-protein-negative tumors had a greater relative risk of recurrence compared with those whose tumors were DCC protein-positive. The 5-year survival rate was 91.0% in patients with DCC-protein-positive tumors, and 58.8% in those with DCC-protein-negative tumors; these differences between the two groups of patients were significant (p < 0.01). In multivariate analysis using the Cox regression model, DCC protein expression emerged as an independent prognostic indicator. These findings suggested that a decrease in DCC expression may have an important role in the progression of colorectal cancers and may be a biologic marker of prognostic significance.
Experimental measurement of group velocity dispersionin photonic crystal fibre (1999)

The authors report measurements of group velocity dispersion in photonic crystal fibre using low coherence techniques. The results confirm theoretical predictions that photonic crystal fibre, unlike conventional step-index fibre, can exhibit anomalous waveguide dispersion while remaining singlemode. This allows the design of singlemode fibres with zero dispersion points at wavelengths much shorter than is possible in standard fibre.
On the Performance of Irregular Repetition Slotted ALOHA with an Age of Information Threshold (2022)

The present paper focuses on an IoT setting in which a large number of devices generate time-stamped updates addressed to a common gateway. Medium access is regulated following a grant-free approach, and the system aims at maintaining an up-to-date knowledge at the receiver, measured through the average network age of information (AoI). In this context, we propose a variation of the irregular repetition slotted ALOHA (IRSA) protocol. The scheme, referred to as age-threshold IRSA (AT-IRSA), leverages feedback provided by the receiver to admit to the channel only devices whose AoI exceeds a dynamically adapted target value. By means of detailed networks simulations, as well as of a simple yet tight analytical approximation, we demonstrate that the approach can more than halve the average network AoI compared to plain IRSA, and offers notable improvements over feedback-based state-of-the-art slotted ALOHA solutions recently proposed in the literature.
Problematic alcohol use associates with sodium channel and clathrin linker 1 (SCLT1) in trauma‐exposed populations (2017)

Excessive alcohol use is extremely prevalent in the United States, particularly among trauma-exposed individuals. While several studies have examined genetic influences on alcohol use and related problems, this has not been studied in the context of trauma-exposed populations. We report results from a genome-wide association study of alcohol consumption and associated problems as measured by the alcohol use disorders identification test (AUDIT) in a trauma-exposed cohort. Results indicate a genome-wide significant association between total AUDIT score and rs1433375 [N = 1036, P = 2.61 × 10<sup>-8</sup> (dominant model), P = 7.76 × 10<sup>-8</sup> (additive model)], an intergenic single-nucleotide polymorphism located 323 kb upstream of the sodium channel and clathrin linker 1 (SCLT1) at 4q28. rs1433375 was also significant in a meta-analysis of two similar, but independent, cohorts (N = 1394, P = 0.0004), the Marine Resiliency Study and Systems Biology PTSD Biomarkers Consortium. Functional analysis indicated that rs1433375 was associated with SCLT1 gene expression and cortical-cerebellar functional connectivity measured via resting state functional magnetic resonance imaging. Together, findings suggest a role for sodium channel regulation and cerebellar functioning in alcohol use behavior. Identifying mechanisms underlying risk for problematic alcohol use in trauma-exposed populations is critical for future treatment and prevention efforts.
Development of SPACE-II for rapid sample exchange at SPring-8 macromolecular crystallography beamlines (2020)

Reducing the sample-exchange time is a crucial issue in maximizing the throughput of macromolecular crystallography (MX) beamlines because the diffraction data collection itself is completed within a minute in the era of pixel-array detectors. To this end, an upgraded sample changer, SPACE-II, has been developed on the basis of the previous model, SPACE (SPring-8 Precise Automatic Cryo-sample Exchanger), at the BL41XU beamline at SPring-8. SPACE-II achieves one sample-exchange step within 16 s, of which its action accounts for only 11 s, because of three features: (i) the implementation of twin arms that enable samples to be exchanged in one cycle of mount-arm action, (ii) the implementation of long-stroke mount arms that allow samples to be exchanged without withdrawal of the detector and (iii) the use of a fast-moving translation and rotation stage for the mount arms. By pre-holding the next sample prior to the sample-exchange sequence, the time was further decreased to 11 s in the case of automatic data collection, of which the action of SPACE-II accounted for 8 s. Moreover, the sample capacity was expanded from four to eight Uni-Pucks. The performance of SPACE-II has been demonstrated in over two years of operation at BL41XU; the average number of samples mounted on the diffractometer in one day was increased from 132 to 185, with an error rate of 0.089%, which counted incidents in which users could not continue with an experiment without recovery work by entering the experimental hutch. On the basis of these results, SPACE-II has been installed at three other MX beamlines at SPring-8 as of July 2019. The fast and highly reliable SPACE-II is now one of the most important pieces of infrastructure for the MX beamlines at SPring-8, providing users with the opportunity to fully make use of limited beamtime with brilliant X-rays.
Measuring Fitness and Precision of Automatically Discovered Process Models: A Principled and Scalable Approach (2020)

Automated process discovery techniques allow us to generate a process model from an event log consisting of a collection of business process execution traces. The quality of process models generated by these techniques can be assessed with respect to several criteria, including <i>fitness</i> , which captures the degree to which the generated process model is able to recognize the traces in the event log, and <i>precision</i> , which captures the extent to which the behavior allowed by the process model is observed in the event log. A range of fitness and precision measures have been proposed in the literature. However, existing measures in this field do not fulfil basic monotonicity properties and/or they suffer from scalability issues when applied to models discovered from real-life event logs. This article presents a family of fitness and precision measures based on the idea of comparing the <inline-formula><tex-math notation="LaTeX">$k$</tex-math></inline-formula> th order Markovian abstraction of a process model against that of an event log. The article shows that this family of measures fulfils the aforementioned properties for suitably chosen values of <inline-formula><tex-math notation="LaTeX">$k$</tex-math></inline-formula> . An empirical evaluation shows that representative exemplars of this family of measures yield intuitive results on a synthetic dataset of model-log pairs, while outperforming existing measures of fitness and precision in terms of execution times on real-life event logs.
Mode of Occurrence of Kasugamycin Resistant Rice Blast Fungus (1976)

Kasugamycin sensitivity was evaluated of 207 isolates of Pyricularia oryzae, derived from 3 fields where the antibiotic had given poor blast control and also from 3 fields where the antibiotic still remained effective. From each of the former 3 fields, resistant isolates were found together with sensitive ones, but all isolates from the latter 3 fields were sensitive to the antibiotic. Isolates from each lesion on rice plants were either all resistant or all sensitive, and in no case resistant and sensitive isolates were found together in the same lesion. The frequency distribution of kasugamycin sensitivity among the 207 isolates, as evaluated by agar diffusion method, indicated the clear distinction between resistant and sensitive strains, and no intermediate resistant strains were detected. With regard to mycelial growth on agar plates, sporulation in vitro, number and length of lesions on inoculated leaves, no significant difference was found between sensitive group and resistant group. Frequency of the resistant clones among conidia from stock cultures did not vary within the range of selection pressure from 100 to 500μg/ml kasugamycin, but varied with strains, and with culture condition. A single spore culture just before the selection test led to a low frequency of resistant conidia, suggesting that the resistant clones might have occurred at least partly, by spontaneous mutation during stock culture.
Expression and activation of protein kinase C-ζ in eosinophils after allergen challenge (1999)

Protein kinase (PK) C is an increasingly diverse family of enzymes that has been implicated in a range of cellular functions within the eosinophil. Using isoform-specific polyclonal antibodies, we have explored the expression of PKC isoforms in circulating eosinophils. Initial studies demonstrated the presence of the alpha, betaI, betaII, and zeta and the low-level expression of the delta, epsilon, iota, and micro isoforms but no detectable expression of the gamma, eta, and theta isoforms in both normal and asthmatic subjects. There was no difference in the total protein expression between these two groups. Subsequent studies examined the expression and activation of PKC isoforms in circulating eosinophils from asthmatic patients before and 24 h after a late asthmatic response to an inhaled allergen. Cellular fractionation showed PKC-alpha and PKC-betaII to be mainly located in the cytosol, whereas PKC-betaI was constitutively more expressed in the membrane. No changes in expression or subcellular localization of these isoforms were seen after allergen challenge. In contrast, PKC-zeta expression was increased after allergen challenge, and we demonstrated a significant PKC-zeta translocation to the membrane, in keeping with activation of the enzyme. Our results suggest that 24 h after allergen exposure of asthmatic patients, there is increased expression and activation of eosinophil PKC-zeta that correlates with late asthmatic responses recorded between 4 and 10 h postallergen challenge.
IL-36 signaling amplifies Th1 responses by enhancing proliferation and Th1 polarization of naive CD4+ T cells (2012)

The interleukin-1 (IL-1) superfamily of cytokines comprises a set of pivotal mediators of inflammation. Among them, the action of IL-36 cytokines in immune responses has remained elusive. In a recent study, we demonstrated a direct effect of IL-36 on immune cells. Here we show that, among T cells, the IL-36 receptor is predominantly expressed on naive CD4(+) T cells and that IL-36 cytokines act directly on naive T cells by enhancing both cell proliferation and IL-2 secretion. IL-36β acts in synergy with IL-12 to promote Th1 polarization and IL-36 signaling is also involved in mediating Th1 immune responses to Bacillus Calmette-Guerin infection in vivo. Our findings point toward a critical function of IL-36 in the priming of Th1 cell responses in vitro, and in adaptive immunity in a model of mycobacterial infection in vivo.
ChemInform Abstract: Structural and Crystal Chemical Properties of Alkali Rare‐Earth Double Phosphates. (2016)

Abstract Crystals of K 3 Ln(PO 4 ) 2 (Ln: Lu, Yb, Er, Ho, Dy, Gd, Nd, Ce, Y, Sc) and M 3 Lu(PO 4 ) 2 (M: Rb, Cs) are prepared from a M 4 P 2 O 7 /Ln 2 O 3 flux (Pt crucible, 1235 °C, 4 h) and their crystal structures are determined by single crystal XRD and powder neutron diffraction.
Enzymatic synthesis of double-stranded DNA containing radio-actively labeled O6-ethylguanine as the only modified base (1981)

This paper describes the enzyme-catalyzed in vitro synthesis of double-stranded DNA (ds-DNA) containing [3H]-labeled O(6)-ethylguanine (O(6)-EtGua), an alkylation product strongly implicated in mutagenesis and carcinogenesis by ethylating N-nitroso carcinogens. Single-stranded DNA (ss-DNA) containing O(6)ethyl-[8-3H]-2'-deoxyguanosine was synthesized using terminal deoxynucleotidyl transferase. The parameters determining yield of reaction, base ratios, and DNA chain length, were investigated. The O(6)-EtGua-containing ss-DNA could be replicated by DNA polymerase I, as indicated by the incorporation of [8,5'-3H]-2'-deoxyguanosine-5'-monophosphate and by the resistance of the replication product to nuclease S1 digestion. ds-DNA's with chain lengths between approximately 200 and 1000 base-pairs and O(6)-EtGua/guanine molar ratios of approximately 10(-2)--10(-3) were synthesized. Their use in the analysis of enzymatic mechanisms involved in the elimination of O(6)-alkylguanine from the DNA of mammalian cells is discussed. The procedure of synthesis described for (O(6)-EtGua)-containing ds-DNA may also be applicable for the production of ds-DNA containing structurally modified bases other than O(6)-EtGua.