gebhart/patrepeval huggingface dataset:
Evidence that facilitative glucose transporters may fold as beta-barrels. (1993)

A widely accepted model for the structure of the facilitative glucose transporters (GLUTs) predicts that they form 12 transmembrane alpha-helices and that the highly conserved sequence Ile-386-Ala-405 in GLUT1 is intracellular. We raised a polyclonal antibody against a synthetic peptide encompassing this conserved sequence and found that antibody treatment increased 2-deoxy-D-glucose (DOG) uptake in Xe-nopus oocytes expressing GLUT1, GLUT2, or GLUT4 only when applied to the extracellular side. This effect was dose dependent and was specifically blocked by competition with the peptide Ile-386-Ala-405; it was due to a decrease in the Km for the transport of DOG. To ascertain GLUT orientation, we raised anti-peptide antibodies against the last 21 and 25 C-terminal amino acids of GLUT1 and GLUT4, respectively, which were previously shown to be intracellular. These antibodies increased DOG uptake when injected into oocytes expressing GLUT1 and GLUT4, but not when added extracellularly. Prompted by the noted discrepancy, we found sequence similarity between GLUTs and porins, two of which are known from crystallography to form 16-stranded transmembrane antiparallel beta-barrels. Analysis of the hydrophobicity, amphiphilicity, and turn propensity of GLUT1 leads us to propose that GLUTs fold as porin-like transmembrane beta-barrels. This model is consistent with the results of the present antibody studies and also with previously published experimental evidence inconsistent with the 12-helix model.
Low-grade cerebral astrocytomas: Survival and quality of life after radiation therapy (1990)

Of 77 patients with supratentorial Grades I and II astrocytoma diagnosed from January 1975 to December 1984, 66 were treated with postoperative radiation therapy. The patients received a tumor dose of 5000 to 5500 cGy in 180 cGy fractions, five fractions per week, over 5.5 to 6 weeks. Overall actuarial survival at 2, 5, and 10 years was 71%, 55%, and 43%, respectively. Progression-free survival at 2, 5, and 10 years was 69%, 50%, and 39%, respectively. Survival for patients receiving postoperative radiation therapy in the range of 4500 to 5900 cGy was 78% and 66% at 2 and 5 years, respectively. Quality of life was determined at two points in time: 1 to 2 years postoperatively, and at last follow-up (2-12 years postoperatively). The occurrence of mental retardation was specifically addressed in long-term survivors, and was observed in 50% of children. Overall, however, 80% of short-term survivors and 67% of long-term survivors were intellectually and physically intact, without major neurologic deficit. Specific prognostic factors were assessed by multivariate analysis. Improved survival was observed with young patients, females, normal preoperative mental status, surgical resection (versus biopsy alone), involvement of only one lobe with tumor, and a history of preoperative seizures. A weighted prognostic factor score derived from these observations permits a clinically useful assessment of risk for individual patients.
0038 Sleeping with Low Levels of Artificial Light at Night Increases Systemic Inflammation in Humans (2019)

Artificial light at night (ALAN) has become a ubiquitous part of our society. Animal studies have shown that ALAN exposure promotes a depressive-like mood and increases peripheral inflammation likely due to circadian disruption. We hypothesized that sleeping with ALAN will increase systemic inflammation in humans. We enrolled 64 subjects [32 with obstructive sleep apnea (OSA) adherent to treatment and 32 without sleep disorders] in a randomized, crossover study to determine the effects of sleeping with ALAN (40 lux) or the usual dark condition (control) for 7 nights at home. Sleeping with ALAN was confirmed by an actigraph with an ambient light sensor. Outcome measurements were done at baseline and after sleeping in each condition. The primary outcome was changes in the high-sensitivity C-reactive protein (hsCRP) levels. Secondary outcomes include scores on the Pittsburgh Sleep Quality Index (PSQI), Center for Epidemiologic Studies Depression Scale (CES-D), Functional Outcomes of Sleep Questionnaire-10 (FOSQ-10), and Epworth Sleepiness Scale (ESS); Psychomotor Vigilance Testing (PVT); actigraphic sleep measures; and homeostatic model assessment of insulin resistance (HOMA-IR). A random effects linear regression model was used to assess differences adjusting for schedule, visit, and baseline levels. Post-hoc analyses combined results from OSA and non-OSA subjects. Fifty-eight (30 OSA and 28 non-OSA) subjects, aged 38.4±14.9 years, 33 of whom are male completed the protocol. A log transformation was used so the difference in hsCRP was expressed as a mean ratio. In the combined analysis, the mean hsCRP was 39% higher with ALAN than control (mean ratio=1.39; 95% CI: 1.08-1.80; p=0.012). The effects of ALAN for OSA and non-OSA subjects were not different. ALAN increased the CES-D score by 1.81 (p=0.017) and ESS score by 0.62 (p=0.071) points, and decreased the FOSQ-10 score by 0.36 (p=0.038) points while the PSQI score was unchanged (p=0.860). There were no significant differences in the PVT values, actigraphic sleep measures, or HOMA-IR. Sleeping with ALAN for seven days significantly increased hsCRP levels and modestly increased depression scores in humans. Rudi Schulte Research Institute
Molecular cloning and sequencing of the gene encoding an extracellular aspartic proteinase fromAspergillus fumigatus (1995)

Oligonucleotide primers based on conserved regions of the aspergillopepsins (EC 3.4.23.18) were used to PCR amplify a 650 bp segment of the gene encoding the extracellular aspartic proteinase (PEP) from Aspergillus fumigatus. The segment was used as a probe for isolating and sequencing the gene from a genomic library of the fungus. Likewise the cDNA was amplified by reverse PCR, cloned and sequenced. The pep gene was found to consist of four exons encoding for 395 aa. The pre-proenzyme deduced has an N-terminal leader sequence of 70 aa preceding the sequence of the mature enzyme consisting of 325 aa with a calculated molecular mass of 34.4 kDa and an isoelectric point of 3.95. The N-terminal sequence of the mature enzyme matched the N-terminal aa sequence of PEP exactly. The nucleotide and the aa sequences of the pre-proenzyme were 70% and 71% homologous to the corresponding sequences of the aspergillopepsin from A. niger var. awamori. Southern analysis of digested genomic A. fumigatus DNA with a specific PCR probe suggested the presence of a single copy of the pep gene.
Low Temperature Sintering of Alumina by CuO-TiO<sub>2</sub>-Nb<sub>2</sub>O<sub>5</sub> Additives (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Interface Properties and Physicochemical Characterization of the Low-Temperature Molten Salt Li/K/Cs Acetate (2013)

The surface of macroscopic films of the ternary molten salt mixture Li0.2K0.275Cs0.525[OAc] has been investigated by angle-resolved X-ray photoelectron spectroscopy (XPS) as a function of temperature. With increasing temperature a preferential depletion of K+ is observed by ∼40%. From temperature programmed desorption we find that the onset for the cation desorption follows the order Cs+, K+, and Li+, with activation energies of 125, 148, and 157 kJ mol–1, respectively; the corresponding value for the [OAc] anion is 147 kJ mol–1, which is, within the margin of error, identical to the average of the value found for the cations. Ultrathin films of the molten salt deposited on a Au(111) surface by physical vapor deposition show preferential enrichment of Cs+, in line with the lower activation energy and thus higher desorption rate of Cs[OAc] from the ternary mixture. Angle-resolved XPS of the molten salt/gold interface demonstrates that the first molten salt monolayer grows in a layer-by-layer growth, followed by three-dimensional island growth at higher coverages.
Laser assisted imprint of silicon nanostructure with good crystal quality (2005)

Excimer laser assisted imprint technology is implemented to create nanostructure on silicon substrate. Patterns with 25-nm feature sizes are successfully fabricated on quartz mold using electron beam lithography for nano-imprint. Transfer of nano-meter features to silicon is experimented. Parameters for optimal imprint are investigated. With a peak light intensity of 1/spl sim/2 J/cm/sup 2/, imprint pressure of 10/spl sim/100 g/cm/sup 2/, and high vacuum at 10/sup 6/ torr, nano-imprint has very good results. The carrier lifetimes before and after laser-assisted imprint are studied and discovered to vary from 1818 /spl mu/s to 640 /spl mu/s. This small damage of Si substrate is attributed to recrystallization of silicon.
Steering of high frequency low level photocurrents between summing busses beyond the g<inf>m</inf>/2&amp;#960;C limit (1980)

A 100 element photosensor signal processor has been developed that allows the detection and steering of A-O deflected high frequency (up to 1GHz) photogenerated signals between two output summing busses. Such a detector architecture provides the vehicle for summing a single or several preselected frequency bands from amongst 100 contiguous frequency band intervals on a preselected summing bus. All the frequency intervals not selected are automatically summed on the second summing bus. A Bragg cell is used to deflect monotonically, with frequency, a laser beam across the 100 detector elements according to the R-F frequency applied to the transducer attached to the Bragg cell. This A-0 arrangement provides the means for distributing the deflected laser beam across the 100 element photosensor in a monotonic frequency ensemble consisting of 100 contiguous frequency band intervals. The combination of the 100 element photosensor chip with a Bragg cell can be used to produce a spectrum analyzer and/or an electronically programmable filter bank for excising certain R-F frequencies. The photodetector's output signals are steered to a preselected suming bus by electric field switches which have a wide band frequency response.The wide band frequency response is possible even though the signal currents are very small (< 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-6</sup> amps) and would be limited to the g <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</inf> /2ΠC frequency corner normally inherent with conventional transistor switches.
Fast Numerical Computation of Current Distribution and AC Losses in Helically Wound Thin Tape Conductors: Single-Layer Coaxial Arrangement (2010)

In this paper, we introduce a very fast method to compute the current distribution in helically wound thin conductors when one or many of them are arranged in a symmetrical manner to form a single-layer power cable. The method relies on two different approaches to find the magnetic vector potential due to helically wound current sheets. By invoking relevant symmetry arguments associated with the geometry of the problem and neglecting the thickness of the tape conductors, we show that this 3-D problem can be reduced to a computationally small 1-D problem whose domain lies along the half-width of any of the constituting conductor. As a consequence, the proposed method is very efficient in terms of computational time, and it is more accurate than many previous 2-D methods that cannot take into account the twist pitch. Since the nonlinear resistivity of the superconducting material can easily be treated with this method, it can be used to find current and field distributions, as well as ac losses in high-temperature superconductor coils and cables made of coated tapes. To verify the validity of the proposed method, we performed experimental measurements of ac losses in two configurations of solenoid-type cables made of a sample of YBCO-coated conductor tape. Excellent agreement was observed between the experimental data and the simulation results.
Convergence in parameters and predictions using computational experimental design (2013)

Typically, biological models fitted to experimental data suffer from significant parameter uncertainty, which can lead to inaccurate or uncertain predictions. One school of thought holds that accurate estimation of the true parameters of a biological system is inherently problematic. Recent work, however, suggests that optimal experimental design techniques can select sets of experiments whose members probe complementary aspects of a biochemical network that together can account for its full behaviour. Here, we implemented an experimental design approach for selecting sets of experiments that constrain parameter uncertainty. We demonstrated with a model of the epidermal growth factor-nerve growth factor pathway that, after synthetically performing a handful of optimal experiments, the uncertainty in all 48 parameters converged below 10 per cent. Furthermore, the fitted parameters converged to their true values with a small error consistent with the residual uncertainty. When untested experimental conditions were simulated with the fitted models, the predicted species concentrations converged to their true values with errors that were consistent with the residual uncertainty. This paper suggests that accurate parameter estimation is achievable with complementary experiments specifically designed for the task, and that the resulting parametrized models are capable of accurate predictions.
Charge dynamics electron microscopy: nanoscale imaging of femtosecond plasma dynamics (2022)

Understanding and actively controlling the spatio-temporal dynamics of non-equilibrium electron clouds is fundamental for the design of light and electron sources, novel high-power electronic devices, and plasma-based applications. However, electron clouds evolve in a complex collective fashion on nanometer and femtosecond scales, producing electromagnetic screening that renders them inaccessible to existing optical probes. Here, we solve the long-standing challenge of characterizing the evolution of electron clouds generated upon irradiation of metallic structures using an ultrafast transmission electron microscope to record the charged plasma dynamics. Our approach to charge dynamics electron microscopy (CDEM) is based on the simultaneous detection of electron-beam acceleration and broadening with nanometer/femtosecond resolution. By combining experimental results with comprehensive microscopic theory, we provide deep understanding of this highly out-of-equilibrium regime, including previously inaccessible intricate microscopic mechanisms of electron emission, screening by the metal, and collective cloud dynamics. Beyond the present specific demonstration, the here introduced CDEM technique grants us access to a wide range of non-equilibrium electrodynamic phenomena involving the ultrafast evolution of bound and free charges on the nanoscale.
Novel HDAC inhibitors exhibit pre-clinical efficacy in lymphoma models and point to the importance ofCDKN1Aexpression levels in mediating their anti-tumor response (2014)

We investigated the pre-clinical activities of two novel histone deacetylase inhibitors (HDACi), ITF-A and ITF-B, in a large panel of pre-clinical lymphoma models. The two compounds showed a dose-dependent anti-proliferative activity in the majority of cell lines. Gene expression profiling (GEP) of diffuse large B-cell lymphoma (DLBCL) cells treated with the compounds showed a modulation of genes involved in chromatin structure, cell cycle progression, apoptosis, B-cell signaling, and genes encoding metallothioneins. Cell lines showed differences between the concentrations of ITF-A and ITF-B needed to cause anti-proliferative or cytotoxic activity, and cell cycle and apoptosis genes appeared implicated in determining the type of response. In particular, CDKN1A expression was higher in DLBCL cells that, to undergo apoptosis, required a much higher amount of drug than that necessary to induce only an anti-proliferative effect.In conclusion, the two novel HDACi ITF-A and ITF-B demonstrated anti-proliferative activity across different mature B-cell lymphoma cell lines. Basal CDKN1A levels appeared to be important in determining the gap between HDACi concentrations causing cell cycle arrest and those that lead to cell death.
Supplementary Figure 3B from Biological properties of potent inhibitors of class I phosphatidylinositide 3-kinases: from PI-103 through PI-540, PI-620 to the oral agent GDC-0941 (2023)

Supplementary Figure 3B from Biological properties of potent inhibitors of class I phosphatidylinositide 3-kinases: from PI-103 through PI-540, PI-620 to the oral agent GDC-0941
Ste20‐like kinase SLK displays myofiber type specificity and is involved in C2C12 myoblast differentiation (2004)

Cell growth and terminal differentiation are controlled by complex signaling cascades that regulate the expression of specific subsets of genes implicated in cell fate and morphogenic processes. We have recently cloned and characterized a novel Ste20-like kinase termed SLK that is associated with adhesion structures during cell adhesion and spreading. However, the specific function of SLK is poorly understood. To gain further insight into the role of SLK, we have characterized its activity, expression, and distribution in skeletal muscle and during the in vitro differentiation of C2C12 myoblasts. Although SLK is expressed ubiquitously in adult tissues, our results show that it is predominantly expressed in muscle masses during development. Furthermore, SLK activity is upregulated during the differentiation of C2C12 myoblasts. In addition, we have found that SLK localizes presynaptically at neuromuscular junctions and that it is preferentially expressed in types I and IIA myofibers at major myofibrillar striations. Supporting a role in myoblast function and differentiation, SLK expression is induced in Myf5- and Pax7-positive activated satellite cells during regeneration and expression of dominant negative SLK in C2C12 cultures impairs myoblast fusion, suggesting a role for SLK in muscle cell differentiation.
Enhancement of Catalytic Activity in Epoxide Hydration by Increasing the Concentration of Cobalt(III)/Salen in Porous Polymer Catalysts (2016)

Abstract The rational design of catalytic materials from the reaction characteristics is expected to be a useful strategy to create highly efficient catalysts. Herein, according to a well‐established reaction pathway of epoxide hydration catalyzed a dual‐molecular system of Co 3+ /salen in which a high concentration of active sites is favorable to enhance the activity, we provide an alternative way to prepare a highly efficient heterogeneous catalyst with a high concentration of Co 3+ /salen from the polymerization of vinyl‐functionalized salen monomers followed by the loading of Co 3+ species (Co 3+ /POL‐salen). Co 3+ /POL‐salen has a hierarchical porosity and an extraordinary hydrothermal stability. Importantly, catalytic tests in epoxide hydration demonstrate that Co 3+ /POL‐salen affords excellent high activities, which are even better than those of the homogeneous version. This phenomenon is related to the very high concentration of Co 3+ /salen in the catalyst. In addition, this catalyst can be recycled readily because of its excellent hydrothermal stability.
In-plane plasmonic antenna arrays resolve nanoscopic phase separation in model lipid membranes (Conference Presentation) (2017)

Resolving the various interactions of lipids and proteins in the plasma membrane of living cells with high spatiotemporal resolution is of upmost interest [1]. Here we introduce an innovative design of plasmonic nanogap antennas to monitor single-molecule events on model biological membranes at physiological relevant concentrations by means of fluorescence correlation spectroscopy. Our design involves the fabrication of in-plane plasmonic nanogap antennas arrays embedded in nanometric-size boxes to provide full surface accessibility of the hotspot-confined region. Using these antennas we recently reported fluorescence enhancement factors of 104-105 times on individual molecules diffusing in solution, together with nanoscale detection volumes in the zeptoliter range [2]. In principle, the planarity of these antennas should enable similar studies on biological membranes without unwanted membrane curvature effects. To show their applicability, we recorded the diffusion of individual molecules inserted in multi-component lipid bilayers as a simple mimetic system that recapitulates some of the most important features of cell membranes. We prepared membranes of different compositions: saturated phospholipids, sphingolipids and cholesterol and used antennas of different gap sizes (10-45 nm). The diffusion of individual molecules on membranes consisting of phospholipids and/or in a mixture with sphingolipids resulted Brownian, confirming homogenous lipid distribution. Interestingly, the strong confinement of antennas revealed the formation of transient (<1ms lifetime) nanoscopic domains of ~11 nm in size upon cholesterol addition. These results indicate that in-plane antennas represent a highly promising non-invasive tool to investigate the nanoscale dynamic organization of biological membranes and its impact in biological function. References: [1] D. Lingwood, K. Simons, Science 327, 46 (2010). [2] V. Flauraud et al, submitted.
Combining Tensor Decompositions and Graph Analytics to Provide Cyber Situational Awareness at HPC Scale (2019)

This paper describes MADHAT (Multidimensional Anomaly Detection fusing HPC, Analytics, and Tensors), an integrated workflow that demonstrates the applicability of HPC resources to the problem of maintaining cyber situational awareness. MADHAT combines two high-performance packages: ENSIGN for large-scale sparse tensor decompositions and HAGGLE for graph analytics. Tensor decompositions isolate coherent patterns of network behavior in ways that common clustering methods based on distance metrics cannot. Parallelized graph analysis then uses directed queries on a representation that combines the elements of identified patterns with other available information (such as additional log fields, domain knowledge, network topology, whitelists and blacklists, prior feedback, and published alerts) to confirm or reject a threat hypothesis, collect context, and raise alerts. MADHAT was developed using the collaborative HPC Architecture for Cyber Situational Awareness (HACSAW) research environment and evaluated on structured network sensor logs collected from Defense Research and Engineering Network (DREN) sites using HPC resources at the U.S. Army Engineer Research and Development Center DoD Supercomputing Resource Center (ERDC DSRC). To date, MADHAT has analyzed logs with over 650 million entries.
Neurologische Assessments bei Morbus Wilson (2016)

Einleitung: Morbus Wilson ist eine autosomal-rezessiv vererbbare Erkrankung des Kupferstoffwechsel und führt unbehandelt zu hepatischen Komplikationen, sowie zu neuropsychiatrischen Störungen, welche Aktivitäten des täglichen Lebens in vielen Fällen unmöglich machen. Zur neurologischen Evaluation dieser Patienten wurden zwei spezifische neurologische Assessments etabliert. Die „Unified Wilson's Disease Rating Scale“ (UWDRS) und die „Global Assessment Scale for Wilson's Disease“ (GAS for WD). Ein direkter Vergleich beider Scoring-Systeme ist bisher noch nicht erfolgt. Ebenso wurde noch keine Korrelation dieser Scores mit der Schwere der Leberbeteiligung durchgeführt.