gebhart/patrepeval huggingface dataset:
A Novel Single-Domain Na + -Selective Voltage-Gated Channel in Photosynthetic Eukaryotes (2020)

The evolution of Na<sup>+</sup>-selective four-domain voltage-gated channels (4D-Na<sub>v</sub>s) in animals allowed rapid Na<sup>+</sup>-dependent electrical excitability, and enabled the development of sophisticated systems for rapid and long-range signaling. While bacteria encode single-domain Na<sup>+</sup>-selective voltage-gated channels (BacNa<sub>v</sub>), they typically exhibit much slower kinetics than 4D-Na<sub>v</sub>s, and are not thought to have crossed the prokaryote-eukaryote boundary. As such, the capacity for rapid Na<sup>+</sup>-selective signaling is considered to be confined to certain animal taxa, and absent from photosynthetic eukaryotes. Certainly, in land plants, such as the Venus flytrap (<i>Dionaea muscipula</i>) where fast electrical excitability has been described, this is most likely based on fast anion channels. Here, we report a unique class of eukaryotic Na<sup>+</sup>-selective, single-domain channels (EukCatBs) that are present primarily in haptophyte algae, including the ecologically important calcifying coccolithophores, <i>Emiliania huxleyi</i> and <i>Scyphosphaera apsteinii</i> The EukCatB channels exhibit very rapid voltage-dependent activation and inactivation kinetics, and isoform-specific sensitivity to the highly selective 4D-Na<sub>v</sub> blocker tetrodotoxin. The results demonstrate that the capacity for rapid Na<sup>+</sup>-based signaling in eukaryotes is not restricted to animals or to the presence of 4D-Na<sub>v</sub>s. The EukCatB channels therefore represent an independent evolution of fast Na<sup>+</sup>-based electrical signaling in eukaryotes that likely contribute to sophisticated cellular control mechanisms operating on very short time scales in unicellular algae.
Halo-free Phase Contrast Microscopy (2017)

We present a new approach for retrieving halo-free phase contrast microscopy (hfPC) images by upgrading the conventional PC microscope with an external interferometric module, which generates sufficient data for reversing the halo artifact. Acquiring four independent intensity images, our approach first measures haloed phase maps of the sample. We solve for the halo-free sample transmission function by using a physical model of the image formation under partial spatial coherence. Using this halo-free sample transmission, we can numerically generate artifact-free PC images. Furthermore, this transmission can be further used to obtain quantitative information about the sample, e.g., the thickness with known refractive indices, dry mass of live cells during their cycles. We tested our hfPC method on various control samples, e.g., beads, pillars and validated its potential for biological investigation by imaging live HeLa cells, red blood cells, and neurons.
C-Substituted Macrocycles as Candidates for Radioimmunotherapy (2000)

The reaction between aryl aldehydes, the macrocyclic ligand 6-methyl-1,4,8,11-tetraazacyclotetradecane-6-amine (L1), and NaBH3CN produces the corresponding benzyl-substituted ligands in good yield. Copper(II) complexes of the ligands derived from salicylaldehyde (L2), p-hydroxybenzaldehyde (L4), and p-carboxybenzaldehyde (L5) were structurally characterized: [CuL2](ClO4)2.3H2O (monoclinic, P2(1)/c, a = 11.915(6) A, b = 13.861(2) A, c = 17.065(8) A, beta = 102.14(2) degrees, Z = 4); [CuL4](ClO4)2 (monoclinic, P2(1)/n, a = 9.550(3) A, b = 17.977(2) A, c = 14.612(4) A, beta 96.76(1) degrees, Z = 4), and [CuL4](ClO4)2 (monoclinic, P2(1)/n, a = 9.286(2) A, b = 11.294(1) A, c = 23.609(8) A, beta 93.68(1) degrees, Z = 4). Conjugation of several CuII complexes to a protein (bovine serum albumin) has been pursued with a view to the application of these macrocycles as bifunctional chelating agents in radioimmunotherapy.
Deep Multimodal Representation Learning from Temporal Data (2017)

In recent years, Deep Learning has been successfully applied to multimodal learning problems, with the aim of learning useful joint representations in data fusion applications. When the available modalities consist of time series data such as video, audio and sensor signals, it becomes imperative to consider their temporal structure during the fusion process. In this paper, we propose the Correlational Recurrent Neural Network (CorrRNN), a novel temporal fusion model for fusing multiple input modalities that are inherently temporal in nature. Key features of our proposed model include: (i) simultaneous learning of the joint representation and temporal dependencies between modalities, (ii) use of multiple loss terms in the objective function, including a maximum correlation loss term to enhance learning of cross-modal information, and (iii) the use of an attention model to dynamically adjust the contribution of different input modalities to the joint representation. We validate our model via experimentation on two different tasks: video-and sensor-based activity classification, and audio-visual speech recognition. We empirically analyze the contributions of different components of the proposed CorrRNN model, and demonstrate its robustness, effectiveness and state-of-the-art performance on multiple datasets.
Plasmon-Induced Selective Enhancement of Green Emission in Lanthanide-Doped Nanoparticles (2017)

By introducing an 18 nm thick Au nanofilm, selective enhancement of green emission from lanthanide-doped (β-NaYF<sub>4</sub>:Yb<sup>3+</sup>/Er<sup>3+</sup>) upconversion nanoparticles (UCNPs) is demonstrated. The Au nanofilm is deposited on a microfiber surface by the sputtering method and then covered with the UCNPs. The plasma on the surface of the Au nanofilm can be excited by launching a 980 nm wavelength laser beam into the microfiber, resulting in an enhancement of the local electric field and a strong thermal effect. A 36-fold luminescence intensity enhancement of the UCNPs at 523 nm is observed, with no obvious reduction in the photostability of the UCNPs. Further, the intensity ratios of the emissions at 523-545 nm and at 523-655 nm are enhanced with increasing pump power, which is attributed to the increasing plasmon-induced thermal effect. Therefore, the fabricated device is further demonstrated to exhibit an excellent ability in temperature sensing. By controlling the pump power and the UCNP concentration, a wide temperature range (325-811 K) and a high temperature resolution (0.035-0.046 K) are achieved in the fabricated device.
A retrospective natural history study of patients (pts) with PDGFRα D842V mutant advanced gastrointestinal stromal tumor (GIST) previously treated with a tyrosine kinase inhibitor (TKI). (2018)

11533 Background: Activating mutations in KIT or PDGFRA kinases drive the vast majority of GIST in adult pts, making the disease highly amenable to targeted therapy. KIT-driven disease is more common (~80% of cases of advanced GIST), while PDGFRA-driven GIST is rare (~5-10% of cases of advanced GIST). TKIs have transformed therapy of advanced GIST; however, evidence suggests the benefit of currently approved TKIs has been predominantly in patients with KIT-driven GIST. We initiated this study to characterize response and survival of pts with PDGFRα D842 mutant GIST treated with currently approved TKIs. Methods: This was a multicenter, retrospective study of adult pts with locally advanced, metastatic, or recurrent PDGFRα D842 mutant GIST diagnosed between Jan 2000 and Jul 2016 who were treated with at least one TKI. Demographic and clinical data were collected through chart review and analyzed to determine overall survival (OS) and best overall response, duration of response, and progression-free survival (PFS) for each line of TKI therapy. Results: Twenty-two pts, all with PDGFRα D842V GIST, were identified at 3 US academic institutions: men, n = 15; median age, 57 y [range: 31-72]; median TKI lines of therapy, 4 [range: 1–8]. Ten pts had primary tumor size ≥ 15 cm, and 8 pts had mitotic index > 10/50 HPF at the time of diagnosis. Imatinib was the most common TKI used (n = 21); followed by sunitinib (n = 15), dasatinib (n = 8), sorafenib (n = 6), regorafenib (n = 4), nilotinib (n = 2) and pazopanib (n = 1). Imatinib was the first line TKI in 20 pts (91%). Only 1 (5%) pt responded to first-line TKI therapy (complete response to imatinib in a pt with residual disease following primary resection). Median PFS on first line TKI was 6.4 months. Median OS from initial diagnosis of GIST was 4.2 years. Conclusions: These results confirm and extend previous data suggesting that pts with advanced PDGFRα D842V GIST have a low response rate, and poor overall survival with currently available TKIs. To transform therapy for PDGFRa D842V GIST, novel TKIs that potently and selectively inhibit D842V mutant PDGFRα are needed.
Nickel, palladium and rhodium induced IFN-gamma and IL-10 production as assessed by in vitro ELISpot-analysis in contact dermatitis patients (2008)

These results strongly suggest that the different cytokine profiles elicited in vitro reflect different immune responses which may lead to the control of the allergic responses or to symptomatic allergic contact dermatitis. The development of sensitive and specific in vitro assays based on the determination of the cytokine profiles in response to contact allergens may have important diagnostic and prognostic implications and may prove extremely useful in complementing the diagnostic limits of traditional patch testing.
Strong Radical Character of the Catecholate Ligand of Catecholato(pyridine)iron Complexes Involved in the Catecholdioxygenase-model Reaction (1991)

Abstract Five-coordinated catecholato(pyridine)iron complexes were isolated from the THF solution of the iron complex used for the catecholdioxygenase model reaction. Formation and structure of species with a catecholate ligand having a strong radical character in the pyridine solution were shown spectroscopically, especially by the large down-field shift of the methyl resonance of 4-methylcatecholate complex in 2H NMR and by the large band at &amp;gt;1000 nm in electronic spectra. Effect of Et4NCl on the spectra indicated that the complexes are in equilibrium with the the chloride-pyridine ligand exchange.
Surface roughening of Ge(001) during 200 eV Xe ion bombardment and Ge molecular beam epitaxy (1990)

The kinetics of surface roughening of Ge(001) during 200 eV Xe ion bombardment and during Ge molecular beam epitaxy (MBE) are studied by real-time reflection high-energy electron diffraction. In both cases, initially smooth surfaces reach a steady state roughness which depends on temperature and incident ion or adatom flux. The data are analyzed in terms of a phenomenological model in which beam-induced roughening competes with beam-induced smoothening, and in which the defect creation rate and surface diffusivity are fitting parameters. For comparable fluxes, the temperature dependences for the net roughening induced by ions and adatoms are strikingly similar, implying a similarity in the surface diffusivities of vacancies and adatoms. For the case of ion-induced roughening, approximately one surface defect (in units of displaced surface atoms) is created per ion which is consistent with calculations assuming that a large fraction of atomic displacements recombine without producing surface defects at these ion energies.
Increased expression of Fas (APO‐1, CD95) on CD34+ haematopoietic progenitor cells after allogeneic bone marrow transplantation (2000)

Up-regulation of Fas/APO-1 (CD95) on haematopoietic progenitors and Fas-mediated apoptosis have been suggested to occur in a possible pathological mechanism in some bone marrow failure syndromes. We examined the expression of Fas antigen and susceptibility to Fas-mediated suppression of donor-derived haematopoietic cells of allogeneic bone marrow transplantation (BMT) recipients. Cytofluorometric analysis revealed low expression of Fas on CD34+ bone marrow cells from marrow donors or healthy controls. However, significantly higher expression of Fas antigen was observed on CD34+ bone marrow cells of BMT recipients, in whom engraftment of donor bone marrow (BM) cells was confirmed. The addition of an agonistic anti-Fas antibody (Ab) (CH-11) to haematopoietic stem cell culture of BM cells more strongly suppressed colony formation from granulocyte-macrophage colony-forming units (GM-CFU) and erythroid burst-forming units (BFU-E) after BMT. Pretreatment by blocking anti-Fas Ab (ZB4) abrogated the Fas-mediated GM-CFU and BFU-E suppression. Purified marrow CD34+ cells from BMT recipients were also susceptible to the Fas-mediated colony suppression. Thus, donor-derived CD34+ haematopoietic cells increased their expression of Fas antigen and were susceptible to Fas-mediated haematopoietic suppression. These findings provide new insight for understanding the haematological condition after BMT.
Current therapeutic trends in therapy for chronic viral hepatitis (1997)

Hepatitis B virus (HBV), hepatitis C virus (HCV) and hepatitis delta virus (HDV) are associated with clinically significant chronic infection that may lead to the development of cirrhosis or even hepatocellular carcinoma (HCC). Intervention at the earliest possible stage is needed to prevent such untoward sequelae. Currently, interferon (IFN) is the only approved and widely used agent for the treatment of these infections, including in HBV patients with precore mutant hepatitis or decompensated cirrhosis, but its efficacy is far from satisfactory. Corticosteroid priming has been shown to increase the efficacy of IFN therapy in HBV patients with low abnormal serum transaminase levels, but only a few responders will clear serum hepatitis Bs antigen (HBsAg). Ongoing randomized controlled trials of thymosin alpha 1, lamivudine and famcyclovir have demonstrated encouraging preliminary results. Therapeutic vaccines, such as polypeptides with human leucocyte antigen (HLA)-specific hepatitis B core antigen (HBcAg) epitopes, are under phase II/III clinical trial. For HDV infection, the use of IFN in the early phase of acute superinfection tends to prevent chronic progression. For HCV infection, IFN used at higher doses for a longer period of time is associated with a higher sustained response, but overall it is still not satisfactory. The combined use of ribavirin or corticosteroid priming may improve the effect of IFN therapy by enhancing the durability of the response. Interferon in the acute phase of HCV infection may also prevent chronic progression. There is evidence to suggest that IFN therapy, when associated with response, tends to reduce the risk of cirrhosis or HCC and prolongs survival. There is no doubt that satisfactory treatment of chronic viral infection will require more effective agents and demand optimal treatment strategies, many of which are yet to be found.
Characterization of Al wire wedge bonding in power electronics package (2012)

Heavy Al wire wedge bonding is a dominant technique for power packages with high voltage. The parameters that impact the wedge bonding quality are mainly bonding process related and material related. Possible failure modes for wire bonding are non-stick of bond wire to the pad, die surface cratering or peeling of pad metallization, and wire break. In this paper, the dielectric damage under the top metal of the silicon die is investigated during the Al wire wedge bonding process for a power module package with 20 mil Al bond wires. FEA 3-D modeling is conducted to simulate the wedge bonding process. The high compressive stress in the dielectric layer is determined to cause the dielectric damage, by comparing the FEA simulation results and practical FA analysis results. To shorten the simulation time, DoEs with FEA 2-D models are performed to study the impact of bonding parameters, thickness of top metal and barrier metal of silicon die, and die tilt. With the guidance of the FEA simulation results, some practical tests are performed for the same parameters. The samples are further analyzed for cross sectional measurements by SEM, chemical etching/de-cap analysis. It is found that the FA results match well with the FEA modeling results.
Multi-phase adaptive on-time PFC for better light load efficiency and EMI performance (2011)

With the fast growing information technologies, high efficiency and high power density become the two major challenges for AC-DC front-end power supplies in all kinds of distributed power system applications. For the power factor correction (PFC) stage, the adaptive on-time control was proposed to achieve high efficiency over the whole load range. The EMI performance of single phase adaptive on time controlled PFC is tested in this paper, and multi-phase approach is used to improve the EMI performance. Since the switching frequency of the adaptive on time control is a variable, the novel adaptive phase angle control is proposed to achieve the best noise cancellation effect, leading to significant EMI filter size reduction. The experiment results show that both high efficiency and high power density can be achieved by the multi-phase adaptive on-time PFC approach.
Technical Basis for Revised Reference Crack Growth Rate Curves for Pressure Boundary Steels in LWR Environment (1980)

Reference fatigue crack growth rate curves have been contained in Appendix A of Section XI since its inception. The curves have been designed to be applicable to carbon and low alloy pressure vessel steels exposed to either air or light water reactor coolant environments. Data obtained over the past several years have shown a different behavior of these steels in the LWR environment than that predicted by the present reference curve. A revised set of reference curves have been formulated, incorporating a new curve shape as well as a dependency of growth rate on R ratio (minimum load/maximum load). This article provides the background and justification for such a revision, details the methodology used to develop the revised curves, and includes an evaluation of the adequacy and impact of the revised curves as compared with the single curve which they replace.
Photocatalytic activity of Au/TiO2 nanocomposite for azo-dyes degradation (2012)

The structural properties of Au/TiO2 catalyst were studied by X-ray diffraction, UV-visible diffuse reflectance, photoluminescene, scanning transmission and electron microscope, and temperature programmed reduction. The photocatalytic activity of the catalysts was evaluated for the degradation of various azo-dyes such as methylene blue, methyl orange, reactive blue-4, and eosin-B under solar irradiation. It was found that TiO2 catalyst modified with gold exhibits higher percentage of degradation compared to starting TiO2. For example, TiO2 showed 35% of methyl orange degradation whereas gold modified TiO2 possessed 82%. Effect of different parameters such as pH and dye concentration has been evaluated and the photocatalytic activity was correlated with physico-chemical properties. The dye degradation rate followed first order kinetics.
[Incompetence of the sphincter of Oddi in duodenal ulcer disease]. (1990)

The association of post-bulbar duodenal scarring and incompetence of the sphincter of Oddi is rare. Radiographic and endoscopic procedures should exclude concomitant neoplastic disease invading the duodenum, and duodenal Crohn's disease. The pancreatico-biliary system should be visualized before attributing ampullar reflux to duodenal ulcer disease. The treatment is that of the primary disease.
Requirements for superoxide-dependent tyrosine hydroperoxide formation in peptides (2004)

Superoxide reacts rapidly with other radicals, but these reactions have received little attention in the context of oxidative stress. For tyrosyl radicals, reaction with superoxide is 3-fold faster than dimerization, and forms the addition product tyrosine hydroperoxide. We have explored structural requirements for hydroperoxide formation using tyrosine analogues and di- and tri-peptides. Superoxide and phenoxyl radicals were generated using xanthine oxidase, peroxidase and the respective tyrosine derivative, or by gamma-radiation. Peroxides were measured using FeSO4/Xylenol Orange. Tyrosine and tyramine formed stable hydroperoxides, but N-acetyltyrosine and p-hydroxyphenylacetic acid did not, demonstrating a requirement for a free amino group. Using [14C]tyrosine, the hydroperoxide and dityrosine were formed at a molar ratio of 1.8:1. Studies with pre-formed hydroperoxides, and measurements of substrate losses, indicated that, in the absence of a free amino group, reaction with superoxide resulted primarily in restitution of the parent compound. With dipeptides, hydroperoxides were formed only on N-terminal tyrosines. However, adjacent lysines promoted hydroperoxide formation, as did addition of free lysine or ethanolamine. Results are compatible with a mechanism [d'Alessandro, Bianchi, Fang, Jin, Schuchmann and von Sonntag (2000) J. Chem. Soc. Perkin Trans. II, 1862-1867] in which the phenoxyl radicals react initially with superoxide by addition, and the intermediate formed either releases oxygen to regenerate the parent compound or is converted into a hydroperoxide. Amino groups favour hydroperoxide formation through Michael addition to the tyrosyl ring. These studies indicate that tyrosyl hydroperoxides should be formed in proteins where there is a basic molecular environment. The contribution of these radical reactions to oxidative stress warrants further investigation.
Cerebrospinal fluid immunoglobulin G promotes oligodendrocyte progenitor cell migration (2004)

Multiple sclerosis (MS) is characterized by demyelination of the CNS with associated neurological deficits. Remyelination can occur but is often incomplete. The process of myelin repair requires the proliferation and migration of oligodendrocyte progenitor cells (OPC) into the lesion from the neighboring areas. OPC migration is altered by several factors, including antibodies that bind to OPC surface proteins. We have previously reported elevated anti-OSP/claudin-11 antibodies in the cerebrospinal fluid (CSF) of MS patients and that anti-OSP/claudin-11 antibodies generated in rabbits can inhibit OPC migration. In the study presented here, we investigated the effect of CSF IgG from MS patients and controls on OPC migration in culture. Rat OPC cultured with CSF from MS patients tended to migrate more than those cultured with control CSF, but this did not reach statistical significance. To determine whether the IgG fraction in the CSF influenced migration, we removed it using protein-A sepharose. A dramatic decrease in OPC migration was found in both MS (45 +/- 24 vs.16 +/- 9) and control (40 +/- 19 vs. 22 +/- 13) samples after IgG was removed (P <.05). Anti-OSP/claudin-11 antibody concentration did not significantly correlate with OPC migration. These data demonstrate that CSF IgG promotes OPC migration. Identification of the specific IgG fraction responsible for this effect could lead to novel therapies to promote recovery in MS.
Establishing continuous assessment using measurements (1999)

Software process assessments have become commonplace in the software industry. Assessments are sometimes regarded, however, as too infrequent, expensive and disruptive. Hence, there is a clear need for alternative ways to assess the current status of software processes and monitor the implementation of improvement activities. An assessment of software processes is based on finding indicators for establishing whether certain processes exist and how well they are performed. Based on the assessment outcome, improvement actions will be identified and guided with appropriate measurements. The software process (re-) assessment can be supported and made more frequent by using data from these measurements, and thus reducing the cost of the assessment. In the European project PROFES (PROduct-Focused Improvement of Embedded Software processes) an integrated, product-focused process improvement methodology has been developed and tested in the industrial partner sites. Among other things, PROFES ...