gebhart/patrepeval huggingface dataset:
Localization precision partly mimics local concentration gradient. (2020)

&lt;p&gt;To test if the localization precision accounts for the gradient in localization density we observed in AF clusters (&lt;a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008656#ppat.1008656.g003" target="_blank"&gt;Fig 3&lt;/a&gt;), we simulated clusters of random localizations (&lt;b&gt;A&lt;/b&gt;) using cluster size data taken from our experimental STORM measurements (i.e. radius &lt;i&gt;r&lt;/i&gt;, number of localizations &lt;i&gt;n&lt;/i&gt;, localization precision &lt;i&gt;σ&lt;/i&gt;). The local density was then determined using a nearest neighbor search within a radius of 3&lt;i&gt;σ&lt;/i&gt;. We indeed observed that the simulated clusters exhibit an up to about 8-fold local enrichment (see one example in &lt;b&gt;A&lt;/b&gt;-&lt;b&gt;C&lt;/b&gt;). We then simulated clusters following the full distribution of experimental data (i.e. radius &lt;i&gt;r&lt;/i&gt;, number of localizations &lt;i&gt;n&lt;/i&gt;). Comparing with the density gradient observed in our experimental data (&lt;b&gt;D&lt;/b&gt; and&lt;a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008656#ppat.1008656.g003" target="_blank"&gt;Fig 3&lt;/a&gt;), we find that both distributions are well separated and that the described effect only accounts for density changes &lt; 8-fold.&lt;/p&gt; &lt;p&gt;(PDF)&lt;/p&gt;
Nanobiotechnology: quantum dots in bioimaging (2007)

Many biological systems, including protein complexes, are natural nanostructures. To better understand these structures and to monitor them in real time, it is becoming increasingly important to develop nanometer-scale signaling markers. Single-molecule methods will play a major role in elucidating the role of all proteins and their mutual interactions in a given organism. Fluorescent semiconductor nanocrystals, known as quantum dots, have several advantages of optical and chemical features over the traditional fluorescent labels. These features make them desirable for long-term stability and simultaneous detection of multiple signals. Here, we review current approaches to developing a biological application for quantum dots.
Unfolding cytochromes c-b₅₆₂ and Rd apo b₅₆₂ (2020)

We have analyzed the early stages of unfolding of cytochromes c-b₅₆₂ (PDB ID: 2BC5) and Rd apo b₅₆₂ (PDB ID: 1YYJ). Our geometrical approach proceeds from an analysis of the crystal structure reported for each protein. We quantify, residue-by-residue and region-by-region, the spatial and angular changes in the structure as the protein denatures, and quantify differences that result from the seven residues that differ in the two proteins. Using two independent analyses, one based on spatial metrics and the second on angular metrics, we establish the order of unfolding of the five helices in cyt c-b₅₆₂ and the four helices in the apo protein. For the two helices nearest the N-terminal end of both proteins, the ones in the apo protein unfold first. For the two helices nearest the C-terminal end, the interior helix of the apo protein unfolds first, whereas the terminal helix of the holo protein unfolds first. Excluded-volume effects (repulsive interactions) are minimized in turning regions; the overall range in Δ values is Δ = 36.3 A³ for cyt c-b₅₆₂ and Δ = 36.6 A³ for the apo protein, whereas the span for all 20 amino acids is Δ = 167.7 A³. As our work indicates that the interior helix of cytochrome c-b₅₆₂ is the first to fold, we suggest that this helix protects the heme from misligation, consistent with ultrafast folding over a minimally frustrated funneled landscape.
Ab initio study of the SN2 reactions of hydroxide and hydroperoxide with chloromethane (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAb initio study of the SN2 reactions of hydroxide and hydroperoxide with chloromethaneJeffrey D. Evanseck, James F. Blake, and William L. JorgensenCite this: J. Am. Chem. Soc. 1987, 109, 8, 2349–2353Publication Date (Print):April 1, 1987Publication History Published online1 May 2002Published inissue 1 April 1987https://pubs.acs.org/doi/10.1021/ja00242a018https://doi.org/10.1021/ja00242a018research-articleACS PublicationsRequest reuse permissionsArticle Views481Altmetric-Citations63LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
P-135: Electrooptics of Oblique Helicoidal Structures in Chiral Nematic Cells (2016)

We investigate theoretically and experimentally electrooptic effects in chiral nematic liquid crystals with small bend elastic constant. In the electric field, the director forms a conical helicoid with a controllable pitch and cone angle. The resulting optical Bragg reflector is electrically tunable from ultraviolet to infrared being applicable for displays, filters, and lasers.
Effects of Antidepressant Treatment on Symptom Measures of Attention in Adolescents with Depression: A Preliminary Open-Label Study (2021)

<b><i>Objective:</i></b> The effects of selective serotonin reuptake inhibitor (SSRI) on deficits in attention and executive function in adolescents with major depressive disorder (MDD) are relatively unknown. We aimed to investigate changes in symptom measures of attention in adolescents with MDD treated with escitalopram. <b><i>Methods:</i></b> The study included 82 MDD adolescents and 54 healthy controls aged from 12 to 17 years. Symptom measures of attention were assessed using the Attention-Deficit/Hyperactivity Disorder Rating Scale (ADHD-RS) and Child Behavior Checklist attention problems scale at baseline and during week 8. Adolescents who showed at least 40% improvement in the Children's Depression Rating Scale-Revised (CDRS-R) scores from baseline to week 8 were referred to as "responders." <b><i>Results:</i></b> No baseline differences were found between the responders (<i>n</i> = 47) and nonresponders (<i>n</i> = 35) in their age, sex, intelligence quotient, CDRS-R score, and attention measures. Linear mixed models showed significant group-by-time interaction effect in the ADHD-RS inattention subscale score, but not in the other attention measures. <b><i>Conclusion:</i></b> Our results suggest that treating depressive symptoms with SSRI may lead to improvements in attention in MDD adolescents. Monitoring changes in symptom measures of attention can be useful when treating adolescents with MDD. ClinicalTrials.gov identifier: NCT03547219.
P‐126: Outcoupling of Waveguide Modes and Surface Plasmon Polaritons in OLEDs (2012)

Abstract We investigated the improvement in luminous efficiency of a fluorescent blue OLED with a perforated WO 3 layer. The perforated WO 3 layer was fabricated by using a colloidal lithograph, and was inserted between a transparent anode and organic layers in the OLED device. The current efficiency was increased by around 70% at a current density of 100 mA/cm 2 , due to an enhanced outcoupling of waveguide modes and surface plasmon polaritons.
Reparation des cassures double-brin de l'adn par recombinaison homologue, homeologue et illegitime au cours de la transformation de la levure saccharomyces cerevisiae (1994)

Between February 1994 and January 1997, 102 of the 146 patients treated by coronary artery bypass grafting (CABG) had undergone magnetic resonance angiography (MRA) of the brain and neck before the operation, and arterial stenosis or occlusion had been detected in 38 (36.9%) of them. Two of these patients had complicating severe calcification of the ascending aorta, and CABG was performed without cardiopulmonary bypass (CPB). Seven patients without stenotic lesions on MRA were also treated by CABG without CPB for other complications. In addition to the 102 patients one patient had been found to have occlusion of the left common carotid artery and poor enhancement of the distal portion, and as a result we switched from CABG to percutaneous transluminal angioplasty (PTCA). We enrolled 93 patients in this study excluding these 10 patients. The patients were distributed into the three groups according to the MRA findings. Group C = no stenotic lesions (58 patients). Group S = stenosis of < 70% (26 patients), Group SS = stenosis of > or = 70% (9 patients). Enhancement distal to the stenotic or occlusive lesions was good in all patients in group S and SS. We then examined them for the incidence of postoperative neurological complications. There were no significant differences among the three groups in regard to age, male/female ratio, or incidence of hypertension and hyperlipidemia. In Group S, the incidence of diabetes was significantly higher than in the other Groups. The incidence of prior stroke was significantly higher and the number of coronary arteries affected was significantly larger in group SS than the other groups. There were no significant differences among the three groups with regard to intraoperative variables. The lowest mean arterial pressure on CPB was 44.3 +/- 7.4 mmHg, 48.0 +/- 8.8 mmHg, 46.3 +/- 7.8 mmHg in Group C, S, and SS, respectively, In all groups the lowest mean arterial pressure on CPB was below 50 mmHg. There were no significant differences among the three groups with regard to time to awaken and time to extubation. Two patients experienced transient conciousness disturbance after CABG, one in Group C, the other in Group SS, but no new lesions were detected by brain CT. Only one patient, in Group C. suffered a stroke and had a new lesion on brain CT a month after the operation. No strokes occurred in the perioperative period. In nine patients with good enhancement distal to the severe stenotic or occlusive lesion on MRA of the brain and neck the lowest mean arterial pressure on CPB was below 50 mmHg, but there was no postoperative neurological complications due to the low perfusion pressure on CPB. The results of this study suggested that CABG with CPB can be performed safely in patients with good enhancement distal to the stenotic or occlusive lesions on MRA of the brain and neck.
Translational Regulation of the Human Achaete-scute Homologue-1 by Fragile X Mental Retardation Protein (2008)

Fragile X syndrome is a common inherited cause of mental retardation that results from loss or mutation of the fragile X mental retardation protein (FMRP). In this study, we identified the mRNA of the basic helix-loop-helix transcription factor human achaete-scute homologue-1 (hASH1 or ASCL1), which is required for normal development of the nervous system and has been implicated in the formation of neuroendocrine tumors, as a new FMRP target. Using a double-immunofluorescent staining technique we detected an overlapping pattern of both proteins in the hippocampus, temporal cortex, subventricular zone, and cerebellum of newborn rats. Forced expression of FMRP and gene silencing by small interference RNA transfection revealed a positive correlation between the cellular protein levels of FMRP and hASH1. A luciferase reporter construct containing the 5'-untranslated region of hASH1 mRNA was activated by the full-length FMRP, but not by naturally occurring truncated FMR proteins, in transient co-transfections. The responsible cis-element was mapped by UV-cross-linking experiments and reporter mutagenesis assays to a (U)(10) sequence located in the 5'-untranslated region of the hASH1 mRNA. Sucrose density gradient centrifugation revealed that hASH1 transcripts were translocated into a translationally active polysomal fraction upon transient transfection of HEK293 cells with FMRP, thus indicating translational activation of hASH1 mRNA. In conclusion, we identified hASH1 as a novel downstream target of FMRP. Improved translation efficiency of hASH1 mRNA by FMRP may represent an important regulatory switch in neuronal differentiation.
Reflection control for immersion lithography at 45/32-nm nodes (2008)

A new dual bottom antireflectant consisting of an organic antireflectant and a SixOyNz:H (SiON) layer has been designed for metal layers to cover both 45nm and 32nm node logic devices. Simulations have been used to optimize the optical constants of the organic antireflectant. The new antireflectant system has been evaluated on a 1.2NA tool for metal layers. The same organic antireflectant has been successfully applied to via layers at a different thickness. The overall patterning performance including profiles, line width roughness (LWR), overlap depth of focus margin (ODOF) and critical dimension (CD) uniformity before and after etch has been evaluated. The new antireflectant system meets all the patterning requirements for a manufacturable process. An immersion tool at 1.2NA was used to perform lithography tests. Simulation was performed by using ProlithTM software.
Point-of-care Detection and Real-time Monitoring of Intravenously Delivered Drugs via Tubing with an Integrated SERS Sensor (2013)

We demonstrate a commercially viable approach for detection and identification of drugs flowing within tubing, through the use of a plasmonic nanodome array SERS surface that is incorporated into a plastic flow cell connected with tubing.
Plans for Microbial Biology Experiments on the Gateway (2019)

STI is for a presentation being given by Tony Ricco to the European Space Agency's Topical Team on Astrobiology.
MIRAS Calibration and Performance: Results From the SMOS In-Orbit Commissioning Phase (2011)

After the successful launching of the Soil Moisture and Ocean Salinity satellite in November 2009, continuous streams of data started to be regularly downloaded and made available to be processed. The first six months of operation were fully dedicated to the In-Orbit Commissioning Phase, with an intense activity aimed at bringing the satellite and instrument into a fully operational condition. Concerning the payload Microwave Imaging Radiometer with Aperture Synthesis, it was fully characterized using specific orbits dedicated to check all instrument modes. The procedures, already defined during the on-ground characterization, were repeated so as to obtain realistic temperature characterization and updated internal calibration parameters. External calibration maneuvers were tested for the first time and provided absolute instrument calibration, as well as corrections to internal calibration data. Overall, performance parameters, such as stability, radiometric sensitivity and radiometric accuracy were evaluated. The main results of this activity are presented in this paper, showing that the instrument delivers stable and well-calibrated data thanks to the combination of external and internal calibration and to an accurate thermal characterization. Finally, the quality of the visibility calibration is demonstrated by producing brightness temperature images in the alias-free field of view using standard inversion techniques. Images of ocean, ice, and land are given as examples.
Gas permeability analysis of photo‐cured cyclohexyl‐substituted polysiloxane films (2006)

Abstract A photo‐cured cyclohexyl‐substituted polysiloxane (PDCHS) film was prepared and compared with polydimethylsiloxane (PDMS) for the determination of permeability coefficients using various penetrants (H 2 , N 2 , O 2 , CO 2 , CH 4 , C 3 H 6 , and C 3 H 8 ). Penetrant sorption isotherms and local effective diffusion coefficients as a function of local penetrant concentration were also determined. The crosslink density of the films was measured via dynamic mechanical thermal analysis and was found to be 6.46 × 10 4 mol/m 3 for PDMS and 1.82 × 10 3 mol/m 3 for PDCHS. Photo‐differential scanning calorimetry was used to calculate percent conversion under the conditions used for curing and was found to be (99.6 ± 0.3)% for PDMS and (98.4 ± 0.3)% for PDCHS. When cured, the PDCHS films had a lower crosslink density and lower permeance. It was postulated that the cycloaliphatic substitution along the polysiloxane backbone may not have full rotational ability affording closer intermolecular interactions, thus reducing the available free volume. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 102:2343–2351, 2006
Exploring the limits of cycle time for VLSI processing (2002)

Theoretical cycle time of 17.5 hours has been demonstrated on 13-mask 0.35-/spl mu/m CMOS using 100% single-wafer processing and real-time process control. The process time during which "the wafer state was being altered" was only 9.4 hours. In this experiment, total cycle time of less than 72 hours (3 days) was demonstrated. Under ideal conditions (e.g., no queues) it should be possible to manufacture advanced ICs with cycle times as short as approximately 2 hours per mask level.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Image-guided Tumor Ablation: Proposal for Standardization of Terms and Reporting Criteria (2003)

The field of image-guided tumor ablation requires standardization of terms and reporting criteria to facilitate effective communication of ideas and appropriate comparison between treatments with different technologies, such as chemical ablation (ethanol or acetic acid) and thermal therapies, such as radiofrequency, laser, microwave, ultrasound, and cryoablation. On the basis of this premise, a working committee was established with the goal of producing a proposal on such standardization. The intent of the Working Group is to provide a framework that will facilitate the clearest communication between investigators and will provide the greatest flexibility in comparisons between the many new, exciting, and emerging technologies. The members of the Working Group now propose a vehicle for reporting the various aspects of image-guided ablation therapy, including classifications of therapies and procedures, appropriate descriptors of image guidance, and terms to define imaging and pathologic findings. Methods for standardizing the reporting of follow-up findings and complications and other important aspects that require attention when reporting clinical results are addressed. It is the group's hope and intention that adherence to the recommendations of this proposal will facilitate achievement of the group's main objective: improved precision and communication in this field that lead to more accurate comparison of technologies and results and ultimately to improved patient outcomes.
A Statistical Method for Constructing Transcriptional Regulatory Networks Using Gene Expression and Sequence Data (2004)

Transcriptional regulation is one of the most important means of gene regulation. Uncovering transcriptional regulatory network helps us to understand the complex cellular process. In this paper, we describe a comprehensive statistical approach for constructing the transcriptional regulatory network using data of gene expression, promoter sequence, and transcription factor binding sites. Our simulation studies show that the overall and false positive error rates in the estimated transcriptional regulatory network are expected to be small if the systematic noise in the constructed feature matrix is small. Our analysis based on 658 microarray experiments on yeast gene expression programs and 46 transcription factors suggests that the method is capable of identifying important transcriptional regulatory interactions and uncovering the corresponding regulatory network structures.
Development of Automotive Rubber Parts with New Recycling Technology (2000)

&lt;div class="htmlview paragraph"&gt;Rubber is a thermosetting material and as such is generally considered difficult to recycle; therefore there is a demand for the development of rubber recycling technology to protect the environment and conserve resources. Some technologies exist to recycle vulcanized rubber, but none of these has high enough productivity to produce reclaimed rubber, and re-vulcanized rubber does not have the same properties as virgin rubber materials.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Now a new recycling technology, called Shear Flow Stage Reactor, has been developed for rubber reclamation. This new technology has high productivity and can achieve the same properties as virgin materials. Automotive parts have been developed and are being produced with recycled Ethylene-Propylene-diene Rubber (EPDM) based on this new technology. The performance of the developed parts is the same as the parts made from virgin materials. This new technology can be applied to other rubber materials, such as Natural Rubber (NR), NR/Styrene-butadiene rubber (SBR), and Butyl rubber (IIR) with appropriate reclaim conditions and will be an important new technology for rubber recycling.&lt;/div&gt;
β‐Microglobulin is Bound to Streptococcal M Protein (1981)

The presence of receptors for three human proteins (fibrinogen, IgG, and beta 2-microglobulin (beta 2m)) was studied in group A streptococcal strains. M type 1, 12 and 14, and in M protein-negative variants of these strains. Fibrinogen binding was detected in all six strains. IgG did not bind to the two type-12 strains and uptake was low in both type-14 strains. The type-1, M protein-positive strain was negative in binding experiments with radiolabelled IgG, whereas the M protein-negative variant was strongly positive. Aggregated beta 2m showed a high degree of reactivity with the M protein-positive strains but not with the corresponding M protein-negative variants. The results indicate that the receptor for aggregated beta 2m is located on M protein in group A streptococci.
Millimeter Wave MIMO Prototype: Measurements and Experimental Results (2017)

Millimeter-wave multi-input multi-output (mm-Wave MIMO) systems are one of the candidate schemes for 5G wireless standardization efforts. In this context, the main contributions of this article are three-fold. 1) We describe parallel sets of measurements at identical transmit-receive location pairs with 2.9, 29 and 61 GHz carrier frequencies in indoor office, shopping mall, and outdoor settings. These measurements provide insights on propagation, blockage and material penetration losses, and the key elements necessary in system design to make mm-Wave systems viable in practice. 2) One of these elements is hybrid beamforming necessary for better link margins by reaping the array gain with large antenna dimensions. From the class of fully-flexible hybrid beamformers, we describe a robust class of directional beamformers towards meeting the high data-rate requirements of mm-Wave systems. 3) Leveraging these design insights, we then describe an experimental prototype system at 28 GHz that realizes high data-rates on both the downlink and uplink and robustly maintains these rates in outdoor and indoor mobility scenarios. In addition to maintaining large signal constellation sizes in spite of radio frequency challenges, this prototype leverages the directional nature of the mm-Wave channel to perform seamless beam switching and handover across mm-Wave base-stations thereby overcoming the path losses in non-line-of-sight links and blockages encountered at mm-Wave frequencies.