gebhart/patrepeval huggingface dataset:
Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites (1999)

The sterile alpha motif (SAM) is a protein interaction domain of around 70 amino acids present predominantly in the N- and C-termini of more than 60 diverse proteins that participate in signal transduction and transcriptional repression. SAM domains have been shown to homo- and hetero-oligomerize and to mediate specific protein-protein interactions. A highly conserved subclass of SAM domains is present at the intracellular C-terminus of more than 40 Eph receptor tyrosine kinases that are involved in the control of axonal pathfinding upon ephrin-induced oligomerization and activation in the event of cell-cell contacts. These SAM domains appear to participate in downstream signaling events via interactions with cytosolic proteins. We determined the solution structure of the EphB2 receptor SAM domain and studied its association behavior. The structure consists of five helices forming a compact structure without binding pockets or exposed conserved aromatic residues. Concentration-dependent chemical shift changes of NMR signals reveal two distinct well-separated areas on the domains' surface sensitive to the formation of homotypic oligomers in solution. These findings are supported by analytical ultracentrifugation studies. The conserved Tyr932, which was reported to be essential for the interaction with SH2 domains after phosphorylation, is buried in the hydrophobic core of the structure. The weak capability of the isolated EphB2 receptor SAM domain to form oligomers is supposed to be relevant in vivo when the driving force of ligand binding induces receptor oligomerization. A formation of SAM tetramers is thought to provide an appropriate contact area for the binding of a low-molecular-weight phosphotyrosine phosphatase and to initiate further downstream responses.
Inducible transcription of five globin genes in K562 human leukemia cells. (1983)

We studied the abundance and structure of globin mRNAs present in K562 cells both before and after induction of hemoglobin synthesis by hemin. In vitro translation of poly(A)+ RNA from K562 cells generated protein products corresponding to alpha, A gamma-, G gamma-, epsilon-, and zeta-globin mRNAs. Individual globin mRNAs increased 1.5- to 3-fold after induction. Similar results were obtained by measuring steady-state mRNA concentrations of induced and uninduced cells by using S1 nuclease mapping. Globin gene transcripts were correctly initiated and processed. In addition, S1 nuclease analysis revealed the presence of delta-globin mRNA in both control and induced cells. A small percentage of delta-globin transcripts appeared to be initiated upstream from the normal initiation site. beta-Globin mRNA was not detected in any studies. The results (i) suggest that hemin induction of K562 cells is mediated at a transcriptional level and (ii) reveal the dissociation of delta- and beta-globin gene expression in K562 cells compared with normal erythroid cells.
Preparation of epithelial cell aggregates incorporating matrigel microspheres to enhance proliferation and differentiation of epithelial cells (2017)

The objective of this study is to investigate the effect of matrigel microspheres (MM), gelatin hydrogel microspheres (GM), and matrigel-coated GM on the proliferated and biological functions of epithelial cells in cell aggregates incorporating the microspheres. The MM were prepared by a coacelvation method. When mammary epithelial EpH4 cells were cultured with the MM, GM, and matrigel-coated GM in round U-bottom wells of 96-multiwell culture plates which had been coated with poly (vinyl alcohol) (PVA) to suppress the cell adhesion, EpH4 cell aggregates with each microspheres homogeneously incorporated were formed. Higher EpH4 cells proliferation was observed for cell aggregates incorporating MM, GM, and matrigel-coated GM compared with the conventional 3-dimensional (3D) culture method. When examined to evaluate the epithelial differentiation of EpH4 cells, the β-casein expression was significantly higher for the cell aggregates incorporating MM than that of aggregates incorporating GM and matrigel-coated GM or the conventional 3D culture method. It is concluded that the proliferation and differentiation of mammary epithelial EpH4 cells were promoted by the incorporation of MM.
Modelling of a Vortex Water-Wall Argon Arc Lamp for Rapid Thermal Annealing Applications (2014)

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COMP 386-QMMM study of the thymine dimer radical anion splitting reaction: A comparison between the self-repair and the photolyase catalyzed process (2008)

Reference EPFL-CONF-160196View record in Web of Science Record created on 2010-11-30, modified on 2017-05-12
Synthesis and vibrational analysis of a locked 14-s-cis conformer of retinal. (1992)

A 12-,N-ethano retinal Schiff base is synthesized to study the vibrational properties of a C<sub>14</sub>-C<sub>15</sub> s-cis conformer of retinal. The synthesis of the 12-,N-ethano retinal Schiff base and seven of its isotopomers is described. Raman and FTIR spectra of this compound and its isotopic derivatives are analyzed and the normal mode assignments compared to MNDO normal coordinate calculations. The frequency of the C<sub>14</sub>-C<sub>15</sub> stretch at 1096 cm<sup>-1</sup> is ~ 100 cm<sup>-1</sup> below typical values for s-trans conformers of retinal polyenes, supporting previous arguments that s-cis conformers will have characteristically low frequencies for the C-C stretch of the s-cis bond (Smith et al., Proc. Natl. Acad. Sci. U.S.A. 1986, 83,967-971). Deuteriation at the 15-position produces two modes at 950 and 1044 cm<sup>-1</sup> that contain C<sub>15</sub>D rock character. The elevated frequency (1044 cm<sup>-1</sup>) of the high-frequency component is a marker band for the C=N syn geometry and confirms an earlier analysis of the sensitivity of the C<sub>I5</sub>D rock frequency to Schiff base configuration (Ames et al., Biochemistry 1989, 28, 3681-3687). This work on retinals with chemically defined configuration and conformation provides a basis for further analysis of the geometry of these bonds in retinal-containing pigments.
Prevention of murine graft-versus-host disease and bone marrow alloengraftment across the major histocompatibility barrier after donor graft preincubation with anti-LFA1 immunotoxin (1991)

We have investigated the effects of the in vitro depletion of LFA1 positive cytolytic T lymphocytes, natural killer (NK) cells, and monocytes on the afferent phase of graft-versus-host disease (GVHD). Lethal GVHD was induced across the murine major histocompatibility complex by injecting C57BL/6 (H-2b) bone marrow (BM) cells (a source of stem cells) and splenocytes (S) (a source of T cells) into lethally irradiated B10.BR (H-2k) recipients. Because anti-LFA1 does not bind complement (C') effectively, we conjugated anti-LFA1 alpha chain monoclonal antibody (MoAb) to ricin toxin A chain (RTA) as a means of facilitating target cell elimination. A 2-hour preincubation of C57BL/6 bone marrow/spleen (BMS) with anti-LFA1-RTA in the presence of ammonium chloride (a potentiator of immunotoxin toxicity), but not a control immunotoxin (IT), reduced CTL activity by greater than 2 logs, significantly reduced NK cell activity, and prevented B10.BR mice from developing GVHD. Depletion of target cells by toxin-labeled-MoAb and not the blockade of the LFA1 molecule by the anti-LFA1 MoAb accounted for our results, because incubating cells with IT in the absence of a potentiator had no effect on GVHD prevention. In contrast, C57BL/6 recipients of C3H BMS grafts only partially benefited from anti-LFA1-RTA preincubation, demonstrating that in this system, different cells not expressing LFA1 were involved in GVHD generation. The same findings observed with anti-LFA1-RTA preincubation were observed with preincubation with L-leucyl-L-leucine methyl ester, a chemical compound eliminating cytolytic cells, providing further support that GVHD induction in the C3H/HeJ into C57BL/6 system is not entirely mediated by classical cytolytic T cells. We next tested anti-LFA1-RTA in a model devised to measure its effect on alloengraftment (B10.BR recipients given lower doses of irradiation). Anti-LFA1-RTA BM preincubation selectively reduced alloengraftment in the model. This observation, combined with experiments showing that LFA1-RTA preincubation, but not anti-Thy 1.2 + C' or control IT preincubation, reduced colony-forming unit-spleen formation, indicates that anti-LFA1 alpha chain IT may remove accessory cells or stem cells critical to engraftment. Still, anti-LFA1-RTA may be useful for clinical GVHD prevention when combined with positive selection techniques designed to enrich for stem cells.
Measurements of renal shear wave velocities in chronic kidney disease patients (2017)

Background Chronic kidney disease (CKD) patients have advanced glomerulosclerosis and renal interstitial fibrosis. Shear wave elastography (SWE) is useful to diagnose liver fibrosis. However, there are few data available regarding evaluation of kidney function on the use of SWE. Purpose To assess the utility of SWE by evaluating the correlation between renal function and renal elasticity using SWE. Material and Methods A total of 187 participants who had available serum creatinine levels and also underwent SWE of the kidney using a transabdominal ultrasonography were recruited at Nagoya University Hospital. We measured the depth of the shear wave (SW) in the right and left kidneys and calculated the measurement success rates. The glomerular filtration rate (GFR) classification and shear wave value (SWV) were compared. Results The success rates of the right and left kidneys were 93.6% and 71.6%, respectively. Based on these results, the correlation between GFR classification and SWV were analyzed in only the right kidneys because the success rates and the number of enrolled patients were low for the left kidney. There were significant differences found between G1 and G3a, G2 and G3a, G3a and G3b, G3a and G4, and G3a and G5. SWV significantly negatively and positively correlated with the G2-G3a and G3a-G3b classifications. Conclusion There is no correlation between renal function and SW. However, we can diagnose the progression to the CKD stages G3a and G3b by observing the changes over time using the SWV.
Compressor Stability and Control: Review and Practical Implications (2001)

This paper discusses developments in axial compressor stability modeling over the last several years and related work in active control of rotating stall and surge. Several major themes have emerged during this work. One theme is the interplay between hydrodynamic perturbations in axial compressors and instability inception. The former obey linearized dynamical equations but their resonance and instability can trigger a variety of nonlinear events leading to violent oscillations in the compressor flow. An understanding of the key physical phenomena associated with stall inception as opposed to those governing fully developed stall or surge is critical to alleviating stall by design means or through active control. Another theme is the utility of actuators for understanding compressor stability. Active control work bas prompted the installation of high-response forcing devices in compressors; even without feedback these have yielded much new information about compressor unsteady behavior. Finally the paper reviews the methods and prospects for using active stabilization to extend the stable operating range of compressors, improving their surge margin and thus increasing overall reliability and performance. Experiments have progressed from laboratory scale demonstrations to full-scale rig and engine tests in about a decade. Competing theories about the physical mechanisms the difficulties associated with stabilization and the goals and control techniques for rotating stall have led to a rich research base on which compressor stability and control technology is being built.
The reality helmet (2003)

The Reality Helmet is an interactive experience, in which the user's vision and hearing is shielded off from the world. Video and sound is nevertheless recorded by the Reality Helmet, but through computer processing it presents sound to the user as vision, and likewise, vision is turned into a soundscape. The result is a form of artificial synesthesia. Other than as an appreciated art installation, which seems to make people calm and reflective, the Reality Helmet is used to explore relationships between the wearer's sense of presence and the kind of realism provided by the interactive environment.
Attenuation correction with extreme CT dose reduction for whole-body FDG PET/CT (2014)

502 Objectives Dose reduction for PET/CT can be achieved through proper selection of CT acquisition. If the sole purpose of the CT is for PET attenuation correction (CTAC) the CT technique can be greatly reduced compared to CT for diagnostic or localization purposes. Methods Patients receiving clinically indicated whole-body FDG PET/CT exams were recruited in an IRB-approved study to receive an additional CT acquisition using an extremely low dose technique (120 kVp, 5 mAs, 1.375 pitch, CTDIvol = 0.34 mGy). In addition, an anthropomorphic phantom study evaluated impact at a range of CT doses. CT and PET image volumes from the regular and low dose acquisitions were compared in the lung and abdomen regions. Results Low dose CT acquisitions were acquired at 1/10 to 1/60th the dose of a clinical CT exam. While biasing and noise artifacts were apparent in the CT images, there were no changes in the visual appearance of the PET images when attenuation correction used either the regular or very low dose CT acquisitions. In four patients, the SUVmax of the lung lesions did not change from regular to low dose CTAC (increased by on average 0.97% [-0.8% to 1.7]%). The background noise measured in uniform regions in the lung and abdomen were also largely unchanged in the PET images (-1.1% to 0.9% for lung and -0.4% to 1.7% for abdomen). The largest variation from regular to very low dose CTAC was in the bias of the background values of the PET image due to local artifacts in the CT which varied by as much as -12% to 7%. Conclusions While extremely low dose CT acquisitions cause severe degradations in the CT image, these do not propagate as substantial differences or artifacts in the PET image. For the lesion sizes examined in this data, measured patient and phantom images show essentially no change in lesion quantitation or noise levels when extremely low dose CT exams are performed for attenuation correction. Bias as much as 12% can occur in peripheral background regions, although these variations may not be clinically significant.
Vital signs from inside a helmet: A multichannel face-lead study (2015)

It is essential to measure physiological parameters such as heart rate variability and respiratory rate of drivers to evaluate their performance. The results from this measurement can be used to assess the state of body and mind, for instance concentration and stress. However, current systems only work in controlled environments, or sensors obstruct and interfere with operations of the driver. In this study, a face-lead ECG is placed inside a helmet to enhance comfort and convenience in racing scenarios. Multiple electrodes were attached to facial locations, which exhibit good contact with a helmet, and bipolar configurations were examined between the left and right side of the subject's face. Standard and data-driven filtering algorithms were employed to improve the extraction of R peaks from the ECG data. The so-extracted R peaks were subsequently used to estimate heart activity and respiration effort, and the results were compared with standard recording protocols. It is shown that ECG recordings obtained from locations on the lower jaw match closely with conventional recording paradigms (limb-lead ECG), highlighting the potential of vital sign monitoring from within a racing helmet.
Insights and Example Use Cases on Industrial Transfer Learning (2022)

Despite the high solution potential of machine learning for common problems in automation technology, there are only few examples of its application in real-world manufacturing practice. In order to find the reason for this phenomenon, the authors identify the hurdles for conventional machine learning using four exemplary use cases namely self-learning robots, wear prediction, visual object detection, and predictive quality in manufacturing. While these use-cases differ in principle, the problems engineers face when using conventional machine learning approaches to solve them are related, such as the lack of manifold training data or high dynamics of industrial processes. The authors showcase that utilizing deep transfer learning and continual learning approaches in the industrial context – subsumed under the term industrial transfer learning – can overcome these hurdles. Even for industrial transfer learning, there is a deficiency regarding preconditions for the large-scale deployment of such approaches, but unlike in conventional machine learning, it is principally possible to establish those. The article concludes with a discussion of these prerequisites and makes suggestions as to how they could be fulfilled.
Hardware Prediction for Data Coherency of Scientific Codes on DSM (2000)

This paper proposes a hardware mechanism for reducing coherency overhead occurring in scientific computations within DSM systems. A first phase aims at detecting, in the address space regular patterns (called streams) of coherency events (such as requests for exclusive, shared or invalidation). Once a stream is detected at a loop level, regularity of data access can be exploited at the loop level (spatial locality) but also between loops (temporal locality). We present a hardware mechanism capable of detecting and exploiting efficiently these regular patterns. Expectable benefits as well as hardware complexity are discussed and the limited drawbacks and potential over-heads are exposed. For a benchmarks suite of typical scientific applications results are very promising both in terms of coherency streams and the effectiveness of our optimizations.
The Association Between Sex and Mortality Among Burn Patients as Modified by Age (2005)

Although an increased risk of death among female patients suffering thermal injury has been noted, the differential influence of age has received little attention. Because experimental evidence suggests that sex hormones influence the immune response to thermal injury, an age-related sex influence on patient mortality is biologically plausible as the hormone milieu changes with the onset of menopause. The goal of this study was to estimate the association between sex and mortality after thermal injury in a large, population-based sample. The National Trauma Data Bank yielded data for more than 6200 burn patients 20 years of age or older. Logistic regression was used to calculate mortality odds ratios (OR) with 95% confidence intervals (CIs) for men relative to women, both overall and by age. Adjustments for age, race, burn etiology, percent body surface area burned, comorbid conditions, and inhalation injury were performed. For the overall study population, the adjusted risk of death was approximately 30% lower for males (OR 0.67, 95% CI 0.52-0.87). Within age strata, the adjusted association was statistically significant only in those aged 20 to 34 years (OR 0.45; 95% CI 0.24-0.87); 35 to 49 years (OR 0.71; 95% CI 0.39-1.30); 50 to 64 years (OR 0.55; 95% CI 0.31-1.00); and 65 years or older (OR 0.85; 95% CI 0.57-1.27). The results of the present study not only indicate that women have an increased odds of mortality after thermal injury but also demonstrate a differential effect of age on the association between sex and mortality. On the basis of the findings of the present study as well as the results of experimental studies, further clinical research is needed to investigate the impact of sex hormones on mortality among burn patients.
Hole‐extraction layer dependence of defect formation and operation of planar CH<sub>3</sub>NH<sub>3</sub>PbI<sub>3</sub> perovskite solar cells (2016)

Three planar CH 3 NH 3 PbI 3 (MAPbI 3 ) solar cells having the same structure except a hole‐extraction layer (HEL) showed distinctive difference in operation characteristics. Analysis of frequency‐dependent capacitance and dielectric‐loss spectra of the three MAPbI 3 devices showed two types of recombination‐loss channels with different time constants that we attributed respectively to interface and bulk defects. Discrepancy in defect formation among the three devices with a HEL of PEDOT:PSS, NiO x , or Cu‐doped NiO x was not surprising because grain‐size distribution and crystalline quality of MAPbI 3 can be affected by surface energy and morphology of underlying HELs. We were able to quantify interface and bulk defects in these MAPbI 3 solar cells based on systematic and simultaneous simulations of capacitance and dielectric‐loss spectra, and current–voltage characteristics by using the device simulator SCAPS. magnified image Defect density reduction is essential for efficient planar solar cells. Defect density in MAPbI 3 layers, with respect to which an open‐cell voltage and a fill factor vary, can be investigated by using capacitance–frequency spectra.
Purdue Solar Cell Model (PSM) - CIGS/CdTe (2017)

&lt;p&gt;Purdue Solar Cell Model (PSM), previously known as the TAG (technology agnostic) model, is a suite of compact models developed for solar cells of c-Si, a-Si, perovskites, CIGS, CdTe, and HIT. This package is for CIGS/CdTe.&lt;/p&gt;
Fabrication and mechanical characterization of glass fiber reinforced UV-cured composites from epoxidized vegetable oils (1997)

Novel fiberglass-reinforced composites were fabricated by the ultraviolet and visible (solar) irradiation of epoxidized vegetable oils in the presence of onium salt cationic photoinitiators. A variety of layup techniques and experimental conditions were explored to optimize composite fabrication. It was demonstrated that composites prepared by wet layup techniques containing up to five plies of glass cloth could be cured by a direct, 25-min exposure to solar irradiation. A series of composite samples were prepared using mixtures of epoxidized vegetable oils and synthetic epoxy resins, and their mechanical properties were evaluated. Based on these measurements, it may be concluded that photochemical routes to the fabrication of composites derived from epoxidized vegetable oils provide a simple, direct, and inexpensive route to the fabrication of composites with many potential low-performance applications. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 64: 2073–2087, 1997
High-index optical materials for 193nm immersion lithography (2006)

We report on our comprehensive survey of high-index UV optical materials that may enable extension of immersion lithography beyond a numerical aperture of 1.45. Band edge, refractive index, and intrinsic birefringence (IBR) at 193 nm determine basic viability. Our measurements of these properties have reduced the list of potential candidates to: ceramic spinel, lutetium aluminum garnet, and a class of germanium garnets. We discuss our measurements of the intrinsic properties of these materials and assess the present status of their material quality relative to requirements. Ceramic spinel has no significant IBR, but transmission and scatter for the best samples remain at least two orders of magnitude from specifications. Improving these would require a major development effort. Presently available lutetium aluminum garnet has material quality much closer to the specifications. However, the IBR is about three times the required value. The germanium garnets offer the possibility of a lower IBR, but a suitable candidate material has yet to be established.