gebhart/patrepeval huggingface dataset:
Structural states of a RNA aptamer, molecular dynamics simulation study (2016)

Motivation RNA, which adopts a wide range of secondary structures is involved in several kind of chemical interactions and shows a notable structural plasticity. Due to remarkable chemical properties and an important physiological role of RNAs, there is a growing interest in development of RNA-based drugs and ligands of clinical relevance. However, RNAs structural and dynamic features as well as the main RNA-protein recognition effects remain largely unaddressed. We have studied the conformational behaviour and the dynamic of two different structural arrangements of an aptamer binding the bacillus anthracis ribosomal protein S8. This RNA aptamer has experimentally shown two different topologies in free state and in protein-bound state, although sequences differ for just few residues beyond the common internal loop. The role of the interacting protein on the RNA folding, stabilizing or inducing a particular conformation will be discussed. Methods Three molecular dynamic simulations of 300 ns each have been performed starting from three distinct aptamer structures: i) the aptamer free-state, using a representative model of a NMR ensemble of structures (pdb 2lun); ii) a similar aptamer bound to its target protein (4pdb) iii); an aptamer model built using the sequence of the RNA in the free state but with the structural arrangement of the bound-state to investigate a possible influence of the sequence on the RNA folding. All the systems under investigations were solvated in a truncated octahedral water box using explicit water models, with a least a 1.1 Å distance to the border, using Na+ counter-ions to neutralize. 6 steps of heating simulation from 50 K to 300K were carried out before to perform the final MD run of 300 ns in NPT conditions without restrains. The trajectories were analysed using the GROMACS utilities and X3DNA program. Results Our data show that both bound-state RNA arrangements are structurally stable, holding all the main interactions since the beginning of the simulations. The free-state RNA is the system with the largest flexibility, reaching an equilibrium after 40 ns of simulation. Although the NMR structure appears less rigid, during the total run it never matches the arrangement of the bound state. Definitely, within our time scale, a convergence of the free state with the bound-state trajectories has never been observed and the two different arrangements show differences in flexibility. Preliminary data suggest a significantly different behaviour of the free- and bound-state structures supporting a preminent role of the interacting partner protein on the RNA overall folding to induce a particular stable structural arrangement.
Dexamethasone implant improves anatomic response to anti-VEGF therapy in treatment-resistant Polypoidal Choroidal Vasculopathy (2021)

Abstract Background: A significant proportion of eyes with polypoidal choroidal vasculopathy (PCV) can be resistant to anti-vascular endothelial growth factor (VEGF) injections. We evaluated the efficacy of combination of Dexamethasone intravitreal implant (DXI) and anti-VEGF therapy in eyes resistant to anti-VEGF monotherapy. Materials and Methods: In this retrospective study, polypoidal choroidal vasculopathy (PCV) resistant to anti-VEGF injections were additionally injected with a Dexamethasone implant along with an anti-VEGF agent. Best-corrected visual acuity (BCVA), slit lamp examination, intraocular pressure, fundus evaluation and optical coherence tomography (OCT) data were analyzed. Anatomical response on OCT was the primary outcome measure. Gain in visual acuity, and injection-free interval after the Dexamethasone implant were evaluated as secondary outcome measures. Results: Twelve eyes of 11 patients were included in the study. The mean age of patients was 70.2 ± 11.8 years, and there were 8 females. The mean follow-up duration after DXI was 24.5 ±11 months. The mean number of anti-VEGF injections before DXI was 4.2 ± 1.9. The mean injection-free interval in these patients after DXI was 4.7± 0.6 months, which was significantly greater than the pre-injection mean of 1.6 ± 0.4 months (p&lt;0.001). The median log MAR BCVA immediately prior to DXI was 0.41 (Interquartile Range IQR 0.30-1.02) and after injection was 0.60 (IQR 0.27-1.03), which was not significant (p=0.59). The median OCT thickness after DXI in was 305 microns (IQR 206-417), which was significantly less than the pre-injection OCT thickness of 547 microns (IQR 432-685) (p=0.005). The mean IOP before DXI was 14.7 ± 2.3 mm Hg, and after the injection was 14.3 ± 2.7 mm Hg (p=0.36). Conclusions: Dexamethasone implant combined with anti-VEGF treatment can prolong the treatment-free interval in eyes with PCV resistant to anti-VEGF injection, while maintaining visual acuity.
Enhancing energy efficient network operation in multi-RAT cellular environments through sparse optimization (2013)

Over the last few years, there has been a significant shift in the design and operation of radio access networks from coverage and capacity optimization to energy efficiency. This paper presents a novel algorithm that exploits the redundancy in a multi radio access technology (multi-RAT) network based on UMTS and LTE technologies to reduce the overall energy consumption. The energy-efficiency gains are achieved by reconfiguring the network so as to find a set of active network components that consumes the least amount of energy and that is necessary to provide the quality of service required by the users. The problem is formulated as an integer programming problem, the solution of which shows the components that should be active in order to minimize the energy consumption. Since the problem is intractable for large networks, we relax the initial problem and apply techniques successfully used in, for example, sparse signal reconstruction or statistical estimation. The resulting relaxed problem is solved by means of majorization-minimization methods to obtain algorithmic solutions leading to a low total energy consumption. The potential of the proposed approach for huge energy savings in multi-RAT environments is demonstrated in a dynamic simulation setup.
Converter topological and solid state protective device trade-offs for future shipboard MVDC systems (2015)

The search for the optimum architecture for Medium Voltage DC (MVDC) Integrated Power Systems must take into account the short circuit protection in addition to overarching goals of efficiency, survivability and cost effectiveness. A comparison study is performed for architectures with a suitable combination of protective devices and power conversion. This leads also to an optimum MVDC bus voltage somewhere between 15kVdc and 20kVdc. Hardware implementation using packaged SiC devices, currently under development, is explored. The inherent speed of operation of Solid state protective devices will also play a role in fault isolation, hence reducing stress level on all system components.
Maintenance of Efficacy and Continuing Safety of Golimumab for Active Ulcerative Colitis: PURSUIT-SC Maintenance Study Extension Through 1 Year (2016)

Subcutaneous golimumab q4w through 2 years maintained clinical benefit and reduced corticosteroid use among patients who did well in the maintenance study. No new safety signals were observed.
The robot localization problem (1995)

We consider the following problem: given a simple polygon P and a star-shaped polygon V , find a point (or the set of points) in P from which the portion of P that is visible is translation-congruent to V . The problem arises in the localization of robots equipped with a range-finder and a compass --- P is a map of a known environment, V is the portion visible from the robot&amp;apos;s position, and the robot must use this information to determine its position in the map. We give a scheme that preprocesses P so that any subsequent query V is answered in optimal time O(m + log n + A), where m and n are the number of vertices in V and P , and A is the number of points in P that are valid answers (the output size). Our technique uses O(n 5 ) space and preprocessing in the worst case; within certain limits, we can trade off smoothly between the query time and the preprocessing time and space. In the process of solving this problem, we also devise a data structure for output-sensitive determinati...
Visualization of Dispersed Phase Flow in Centrifugal Extractor Using Taylor-Couette Vortex Flow (2011)

For studying the designs and running operations of an extractor which uses Taylor-Couette vortex flow, we focused on a metal extraction system as one of the extraction models of heat generating nuclides and observed the flow patterns of dispersed phase by dyeing the phase in the extractor, and we investigated the effects of hydrophobic coating applied to the inner cylinder surface on the flow characteristics. Moreover, for the quantitative measurement and analysis of the flow field, we evaluated the applicability of Ultrasonic Velocity Profiler (UVP) to flow field measurement. Thorough these visualization methods of dispersed phase in a centrifugal extractor using Taylor-Couette vortex flow, we examined the relation between flow field and extraction characteristics of the extractor.
Synthesis of a Functionalized Oxabicyclo[2.2.1]-Heptene-Based Chemical Library (2011)

The 7-oxabicyclo[2.2.1]heptene ring system is a common structural motif in many pharmacologically interesting molecules. We recognized the potential to employ this highly oxygenated and conformationally-restricted scaffold in diversity-oriented synthesis to generate a library of non-chiral but topologically complex compounds. Herein, we report the synthesis and biological evaluation of two 96-member tricyclic libraries containing the oxabicyclo[2.2.1]heptene framework using acetal formation as the key step.
Fourth Annual Conference of the American Society for Nanomedicine (2014)

The 4th Conference of the American Society for Nanomedicine is being held March 28-30, 2014 at the Universities at Shady Grove, Rockville, Maryland. The meeting's theme is on defining the role of nanomedicines for nervous system diagnostics and disease but balanced by broad and timely topics for nanotechnology. Nanoneuromedicine, as defined by the development of small drug formulations for the diagnosis and treatment of degenerative, inflammatory, infectious, vascular, addictive, behavioral and metabolic disorders of the nervous system, will provide a focus for each of the scientific sessions. This research is interdisciplinary and it's in its infancy. The hurdles that preclude translation from bench to bedside would include its delivery across the blood brain barrier, limiting nervous system toxicities, and improving drug targeting to diseased brain subregions. These all pose challenges. Multidisciplinary works in neuroscience (neurobiology, neurochemistry, neurophysiology, and neuroinflammation), bioimaging, and polymer chemistry to facilitate outcomes for formulation manufacture will be vigorously discussed. How drugs reach sites of action need include neural cell specific subcellular compartments. The ASNM meeting will showcase nanoneuromedicine research from leading investigators of divergent scientific backgrounds who define this new field. It will also serve as an incubator for developing investigators and broad new field discoveries. Welcome to the conference and enjoy!
Liquid/liquid extraction of biomass-derived lignin from lignocellulosic pretreatments (2016)

The extraction of lignin from lignocellulosic pretreatments regards the transfer of lignin from the fractionation solvent to a different medium for valorization.
The Flavin Reductase Activity of the Flavoprotein Component of Sulfite Reductase from Escherichia coli (1995)

Sulfite reductase (SiR) from Escherichia coli has a alpha 8 beta 4 subunit structure, where alpha 8 is a flavoprotein (SiR-FP) containing both FAD and FMN as prosthetic groups. It also exhibits a NADPH:flavin oxidoreductase activity with exogenous riboflavin, FMN, and FAD serving as substrates. The flavin reductase activity may function during activation of ribonucleotide reductase or during ferrisiderophore reduction. A plasmid containing cysJ gene, coding for the alpha subunit, overexpresses flavin reductase activity by 100-fold, showing that alpha is the site of free flavin reduction. The overproducer allows a fast and simple preparation of large amounts of the flavoprotein. Kinetic studies of its flavin reductase activity demonstrates a ping-pong bisubstrate-biproduct reaction mechanism. NADP+ inhibition studies show that both substrates, NADPH and free flavins, bind to the same site. While the FAD cofactor mediates the electron transfer between NADPH and free flavins, the FMN cofactor is not essential since a FMN-depleted SiR-FP retains a large proportion of activity. In contradiction with previous reports, SiR-FP is found to contain 1.6-1.7 flavin per alpha subunit. This result, together with the sequence homology between SiR-FP and NADPH-cytochrome P-450 reductase, suggests a new model for the structure of the protein with one FMN and one FAD prosthetic group per alpha subunit.
Wideband Compact PI Equivalent Circuit for Modeling On-Chip Spiral Inductors (2011)

A novel wideband nine-element PI equivalent circuit is proposed for modeling on-chip deep-submicron spiral inductors. Mathematical formulations derived by analyzing three quality factors enable fast and accurate extraction of all model elements as frequency-independent values. The model was confirmed using three spiral inductors that were realized in a 90 nm CMOS process and compared with other models to demonstrate its superior accuracy.
Photobiomodulation of the brain: a new paradigm (Conference Presentation) (2017)

Photobiomodulation (PBM) describes the use of red or near-infrared light to stimulate, heal, regenerate, and protect tissue that has either been injured, is degenerating, or else is at risk of dying. One of the organ systems of the human body that is most necessary to life, and whose optimum functioning is most worried about by humankind in general, is the brain. The brain suffers from many different disorders that can be classified into three broad groupings: traumatic events (stroke, traumatic brain injury, and global ischemia), degenerative diseases (dementia, Alzheimer’s and Parkinson’s), and psychiatric disorders (depression, anxiety, post traumatic stress disorder). There is some evidence that all these seemingly diverse conditions can be beneficially affected by applying light to the head. There is even the possibility that PBM could be used for cognitive enhancement in normal healthy people. In this transcranial PBM (tPBM) application, near-infrared (NIR) light is often applied to the forehead because of the better penetration (no hair, longer wavelength). Some workers have used lasers, but recently the introduction of inexpensive light emitting diode (LED) arrays has allowed the development of light emitting helmets or “brain caps”. This presentation will cover the mechanisms of action of photobiomodulation to the brain, and summarize some of the key pre-clinical studies and clinical trials that have been undertaken in this area.
Characteristics of Arc Discharge Generated by Opening NbTi Mechanical PCS and Effects of Arc on Superconducting Contact Connection (1998)

A persistent current switch (PCS) in the GWh class SMES system for load leveling needs to have high OFF resistance as well as zero ON resistance for high efficient SMES operations. So far, the authors have successfully developed NbTi mechanical PCS which has zero ON resistance, i. e. zero contact resistance, and can flow the current up to 200A without quench. The PCS should break current of a few tens amperes even with the counter pulsed technique to reduce the breaking current. The current breaking generates arc discharge which alters the contact condition. Since the superconducting connection strongly depends on conditions of contact surfaces, it is necessary to clarify the influence of the arc discharge on the PCS performance. In this study, arc discharge characteristics of NbTi mechanical PCS and influence of arc on superconducting connection at contact are experimentally investigated using a circuit including a superconducting coil of 1 H and a damping resistance in liquid helium. Arc discharge characteristics are almost similar although arc maintain voltage of 12 V is smaller than that observed with copper contact. Arc discharge does not degrade but rather improves the PCS performance as long as the breaking current is smaller than 50 A. The improvement is attributed to enhanced bridge formation on the contact surfaces and removal effect of the surface oxide film by arc discharge.
A case for unlimited watchpoints (2012)

Numerous tools have been proposed to help developers fix software errors and inefficiencies. Widely-used techniques such as memory checking suffer from overheads that limit their use to pre-deployment testing, while more advanced systems have such severe performance impacts that they may require special-purpose hardware. Previous works have described hardware that can accelerate individual analyses, but such specialization stymies adoption; generalized mechanisms are more likely to be added to commercial processors. This paper demonstrates that the ability to set an unlimited number of fine-grain data watchpoints can reduce the runtime overheads of numerous dynamic software analysis techniques. We detail the watchpoint capabilities required to accelerate these analyses while remaining general enough to be useful in the future. We describe a hardware design that stores watchpoints in main memory and utilizes two different on-chip caches to accelerate performance. The first is a bitmap lookaside buffer that stores fine-grained watchpoints, while the second is a range cache that can efficiently hold large contiguous regions of watchpoints. As an example of the power of such a system, it is possible to use watchpoints to accelerate read/write set checks in a software data race detector by nearly 9x.
Artificial Intelligence–Enabled Evaluation of Pain Sketches to Predict Outcomes in Headache Surgery (2022)

This study indicates that structured algorithmic analysis is able to correlate pain patterns drawn by patients to Migraine Headache Index percentage improvement with good accuracy (94%). Further studies on larger data sets and inclusion of other significant clinical screening variables are required to improve outcome predictions in headache surgery and apply this tool to clinical practice.
Fault Detection of Photovoltaic (PV) Modules through Analysis of Reverse I/V Curves (2016)

This paper presents a new way of fault detection for photovoltaic (PV) modules by means of reverse I/V curves analysis. The method of work starts by selecting solar cell samples with and without faults. The first step is to measure the direct and reverse I/V curves of each solar cell under investigation. Simulations with one diode model [1] and two diodes model [2] are also performed, comparing the models to the I/V measurements. The second step is to implement three PV modules, each one consisting of four solar cells, with at least one fault in each PV module. At this step, the objective is to trace the reverse I/V curves per PV module, with the breakdown voltage. Given the results of all measurements, we can analyze, compare and discuss on the correlation between the signatures of each fault type and the resultant reverse I/V curves and the infrared (IR) thermal signature for each PV module.
Stilbene Derivatives from Two Species of Gnetaceae. (2002)

Five new stilbene oligomers (gnemonols A, B and C, gnemonoside E and gnetal) were isolated together with 2b-hydroxyampelopsin F and gnetin E from Gnetum gnemon and G. gnemonoides. The structures of the compounds were elucidated on the basis of spectral evidence.
Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome (2018)

Adaptive laboratory evolution (ALE) has emerged as a new approach with which to pursue fundamental biological inquiries and, in particular, new insights into the systemic function of a gene product. Two <i>E. coli</i> knockout strains were constructed: one that blocked the Pentose Phosphate Pathway (<i>gnd</i> KO) and one that decoupled the TCA cycle from electron transport (<i>sdhCDAB</i> KO). Despite major perturbations in central metabolism, minimal growth rate changes were found in the two knockout strains. More surprisingly, many similarities were found in their initial transcriptomic states that could be traced to similarly perturbed metabolites despite the differences in the network location of the gene perturbations and concomitant re-routing of pathway fluxes around these perturbations. However, following ALE, distinct metabolomic and transcriptomic states were realized. These included divergent flux and gene expression profiles in the <i>gnd</i> and <i>sdhCDAB</i> KOs to overcome imbalances in NADPH production and nitrogen/sulfur assimilation, respectively, that were not obvious limitations of growth in the unevolved knockouts. Therefore, this work demonstrates that ALE provides a productive approach to reveal novel insights of gene function at a systems level that cannot be found by observing the fresh knockout alone.
Isotropic dielectric functions of highly disordered AlxGa1−xInP (0⩽x⩽1) lattice matched to GaAs (1999)

Determination of the complex dielectric function and the critical-point energies of (AlxGa1−x)0.51In0.49P, over the full range of composition x and for photon energies E from 0.75 to 5 eV is reported from variable angle of incidence spectroscopic ellipsometry. Native-oxide effects on the (AlxGa1−x)0.51In0.49P optical functions are removed numerically. The highly disordered state of the metalorganic vapor-phase epitaxy grown samples is analyzed by transmission electron microscopy. Optical anisotropy investigations revealed that the order-induced optical birefringence is negligible throughout. The augmentation of A. D. Rakić and M. L. Majewski [J. Appl. Phys. 80, 5909 (1996)] to Adachi’s critical-point model, i.e., consideration of Gaussian-like broadening function instead of Lorentzian broadening, is used for calculation of the isotropic (AlxGa1−x)0.51In0.49P dielectric function ∈. The optical functions spectra consistently match the experimental data, whereas previously reported model dielectric functions fail to reproduce the correct absorption behavior of the quaternary, especially near the fundamental band-to-band transition. The results are compared to those presented previously, and influence of spontaneous chemical ordering is discussed.