gebhart/patrepeval huggingface dataset:
Role of SRP RNA in the GTPase Cycles of Ffh and FtsY (2001)

The bacterial homologues of the signal recognition particle (SRP) and its receptor, the Ffh*4.5S RNA ribonucleoprotein complex and the FtsY protein, respectively, form a unique complex in which both Ffh and FtsY act as GTPase activating proteins for one another, resulting in the mutual stimulation of GTP hydrolysis by both proteins. Previous work showed that 4.5S RNA enhances the GTPase activity in the presence of both Ffh and FtsY, but it was not clear how this was accomplished. In this work, kinetic and thermodynamic analyses of the GTPase reactions of Ffh and FtsY have provided insights into the role of 4.5S RNA in the GTPase cycles of Ffh and FtsY. We found that 4.5S RNA accelerates the association between Ffh and FtsY 400-fold in their GTP-bound form, analogous to its 200-fold catalytic effect on Ffh*FtsY association previously observed with the GppNHp-bound form [Peluso, P., et al. (2000) Science 288, 1640-1643]. Further, Ffh-FtsY association is rate-limiting for the observed GTPase reaction with subsaturating Ffh and FtsY, thereby accounting for the apparent stimulatory effect of 4.5S RNA on the GTPase activity observed previously. An additional step, GTP hydrolysis from the Ffh*FtsY complex, is also moderately facilitated by 4.5S RNA. These results suggest that 4.5S RNA modulates the conformation of the Ffh*FtsY complex and may, in turn, regulate its GTPase activity during the SRP functional cycle.
mediaDSP™: A platform for building programmable multicore video processors (2008)

This article consists of a collection of slides from the authors' conference presentation. Summary points include: a platform-based approach enables rapid development of video processing solutions; programmability is important for addressing problems that have no unique solution and demand customer-tailored solutions; programming of heterogeneous cores can be simplified by promoting a uniform infrastructure for the cores; the heterogeneous approach provides programmability where flexibility is required and fixed function to save cost and power.
An Integrated Modeling and Experimental Approach to Study the Influence of Environmental Nutrients on Biofilm Formation ofPseudomonas aeruginosa (2015)

The availability of nutrient components in the environment was identified as a critical regulator of virulence and biofilm formation in Pseudomonas aeruginosa. This work proposes the first systems-biology approach to quantify microbial biofilm formation upon the change of nutrient availability in the environment. Specifically, the change of fluxes of metabolic reactions that were positively associated with P. aeruginosa biofilm formation was used to monitor the trend for P. aeruginosa to form a biofilm. The uptake rates of nutrient components were changed according to the change of the nutrient availability. We found that adding each of the eleven amino acids (Arg, Tyr, Phe, His, Iso, Orn, Pro, Glu, Leu, Val, and Asp) to minimal medium promoted P. aeruginosa biofilm formation. Both modeling and experimental approaches were further developed to quantify P. aeruginosa biofilm formation for four different availability levels for each of the three ions that include ferrous ions, sulfate, and phosphate. The developed modeling approach correctly predicted the amount of biofilm formation. By comparing reaction flux change upon the change of nutrient concentrations, metabolic reactions used by P. aeruginosa to regulate its biofilm formation are mainly involved in arginine metabolism, glutamate production, magnesium transport, acetate metabolism, and the TCA cycle.
Genome-wide association study identifies ZFHX1B as a susceptibility locus for severe myopia (2013)

Severe myopia (defined as spherical equivalent < -6.0 D) is a predominant problem in Asian countries, resulting in substantial morbidity. We performed a meta-analysis of four genome-wide association studies (GWAS), all of East Asian descent totaling 1603 cases and 3427 controls. Two single nucleotide polymorphisms (SNPs) (rs13382811 from ZFHX1B [encoding for ZEB2] and rs6469937 from SNTB1) showed highly suggestive evidence of association with disease (P < 1 × 10(-7)) and were brought forward for replication analysis in a further 1241 severe myopia cases and 3559 controls from a further three independent sample collections. Significant evidence of replication was observed, and both SNP markers surpassed the formal threshold for genome-wide significance upon meta-analysis of both discovery and replication stages (P = 5.79 × 10(-10), per-allele odds ratio (OR) = 1.26 for rs13382811 and P = 2.01 × 10(-9), per-allele OR = 0.79 for rs6469937). The observation at SNTB1 is confirmatory of a very recent GWAS on severe myopia. Both genes were expressed in the human retina, sclera, as well as the retinal pigmented epithelium. In an experimental mouse model for myopia, we observed significant alterations to gene and protein expression in the retina and sclera of the unilateral induced myopic eyes for Zfhx1b and Sntb1. These new data advance our understanding of the molecular pathogenesis of severe myopia.
Low-frequency dynamics of counterion polarization in aqueous polyelectrolyte as studied by electric birefringence relaxation methods (1988)

Abstract The low-frequency relaxation of aqueous polyelectrolytes was studied by both the time-domain electric birefringence (TEB) and the frequency-domain electric birefringence (FEB) methods. Both the methods allow us to determine the rotational relaxation time τr of the polyion as well as the dielectric relaxation time τ given as a harmonic mean of τr and the intrinsic relaxation time τr of counterion polarization. The values of the relaxation times obtained by these two methods agree very well with each other, where τr is found to be smaller than τr by an order of magnitude. The observed value of τr suggests that the translational diffusion constant of counterions along the polyion should be much smaller than that in the free medium.
Heat sinks with fluted and wavy plate fins in natural and low-velocity forced convection (2002)

The effect on heat transfer of geometrically rearranging the surface area of a finned heat sink is investigated. Novel heat sinks with fluted and wavy plate fin configurations are designed and fabricated together with conventional longitudinal-plate and pin fin heat sinks. The experimental apparatus, consisting of the guard heater assembly, isolation chamber, wind tunnel, and data acquisition instrumentation, is described. The thermal performance of the novel and conventional heat sinks is measured and compared for the horizontal and vertical base plate orientations under natural and low-velocity forced convection conditions. Results, presented as the Nusselt number against the Rayleigh or Reynolds numbers, reveal that the pin fin heat sink generally outperforms the other heat sinks, when the heat sink surface area is held constant. A significant effect on heat transfer of the orientation of the forced flow with respect to the buoyancy flow is observed. Overall, the novel heat sink designs do not yield significantly better thermal performance than an optimized conventional longitudinal-plate heat sink.
Data from Targeting the Spleen Tyrosine Kinase with Fostamatinib as a Strategy against Waldenström Macroglobulinemia (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Waldenström macroglobulinemia (WMG) is a lymphoproliferative disorder characterized by good initial responses to standard therapeutics, but only a minority of patients achieve complete remissions, and most inevitably relapse, indicating a need for novel agents. B-cell receptor signaling has been linked to clonal evolution in WMG, and Spleen tyrosine kinase (Syk) is overexpressed in primary cells, suggesting that it could be a novel and rational target.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We studied the impact of the Syk inhibitor fostamatinib on BCWM.1 and MWCL-1 WMG-derived cell lines both &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt;, as well as on primary patient cells.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; In WMG-derived cell lines, fostamatinib induced a time- and dose-dependent reduction in viability, associated with activation of apoptosis. At the molecular level, fostamatinib reduced activation of Syk and Bruton's tyrosine kinase, and also downstream signaling through MAPK kinase (MEK), p44/42 MAPK, and protein kinase B/Akt. As a single agent, fostamatinib induced tumor growth delay in an &lt;i&gt;in vivo&lt;/i&gt; model of WMG, and reduced viability of primary WMG cells, along with inhibition of p44/42 MAPK signaling. Finally, fostamatinib in combination with other agents, including dexamethasone, bortezomib, and rituximab, showed enhanced activity.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Taken together, these data support the translation of approaches targeting Syk with fostamatinib to the clinic for patients with relapsed and possibly even newly diagnosed WMG. &lt;i&gt;Clin Cancer Res; 21(11); 2538–45. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Miniature peristaltic pump Technology and applications (2000)

The Jet Propulsion Laboratory (JPL) is a NASA Federally Funded Research and Development Center (FFRDC). It is endowed with NASA equipment that is managed and staffed by California Institute of Technology with a highly educated and world-class community of six thousand engineers and scientists. JPL's principal NASA responsibility is to design, build, test and operate robotic spacecraft for the exploration of the solar system and to observe our universe across the whole EMR spectrum. Essentially, to go where no one has gone before and, in doing so, determine the origins of our solar system and the universe. The days of large, multi-instrumented, billion-dollar robotic spacecraft are over. The emphasis is now on miniaturizing instruments and spacecraft and reducing the costs of fabrication, test, launch and operation. The ramifications of miniaturization are global, encompassing every element of a spacecraft, instrument, lander or penetrator Micro pumps, valves and flow meters were conceived to address the variety of fluid flow control elements. This paper discusses the evolution of this technology from other MEMS programs and presents a variety of space' applications.
RAT-based malicious activities detection on enterprise internal networks (2015)

The detection of APT has recently become an urgent problem needing to be resolved. Attackers use Remote Access Trojan/Remote Administration Tools (RATs), which often bypass general security measures, and the traditional detection techniques don't consider reconnaissance activities after RAT infections. We analyzed the behavior of the reconnaissance for this paper so that RAT-based malicious activities on internal networks can be divided from the operations of normal users. Based on the features of their behaviors, we propose a detection technique that monitors the communications on internal networks and extracts the communication sequences of the reconnaissance. The result from our evaluation showed that the proposed technique can detect 99.26 % of the experimental reconnaissance communications by using the real 34 RATs (29 families) and 4 SMB-based remote management methods, and also work without false-positive on an actual organization's internal network.
Numerical reconstruction of images from endoscopic holograms (1992)

The formation of an on-axis hologram at the tip of a miniaturized endoscope has been simulated. The reconstruction of the real image from the hologram, collected on a CCD-camera, can be achieved numerically through electronic data processing. Calculations have been performed in order to evaluate the influence on the image quality of the limitations of microendoscopy: limited aperture, sampling through multimode fiber bundle (MMB). The Modulation Transfer Function (MTF) of the system can be derived.
CMOS-compatible zero-index metamaterial (Conference Presentation) (2017)

Zero-index metamaterials (ZIMs) offer exotic optical properties such as uniform spatial phase and infinite wavelength, as well as photonic applications including super-coupling and omnidirectional phase matching in nonlinear optics.

Here we present an on-chip ZIM consisting of a square array of air-holes in a 220-nm-thick silicon-on-insulator (SOI) wafer. This design enables mass production of ZIM-based photonic devices at low cost and high fidelity using standard CMOS fabrication technology.

To transition from the high-aspect ratio inverse case of silicon pillars under transverse magnetic (TM) polarization, our design is instead intended for a transverse electric (TE) polarization because of TE modes are, in general, better confined than TM modes for a given thin film. Furthermore, the larger volume fraction of silicon provided by the air-holes structure improves the confinement as compared with the silicon-pillars structure. We optimized the design to obtain a zero index corresponding to a finite impedance of 0.8 at 1550 nm. The bandstructure of the metamaterial shows a Dirac-cone dispersion at the center of the Brillouin zone at 1550 nm. These results indicate that this metamaterial possesses an impedance-matched, isotropic zero index at 1550 nm.

To experimentally verify that the metamaterial has a zero index, we fabricated a right-triangular prism measuring twenty unit cells across. The measured effective index of this prism crosses zero linearly at 1630 nm and shows positive and negative indices at short and longer wavelengths, respectively, indicating a Dirac-cone induced zero index. This measurement is in excellent agreement with the result of full-wave simulation.
EXTENDED EX-VIVO MYOCARDIAL PRESERVATION IN THE BEATING STATE USING A NOVEL PEG-HEMOGLOBIN BASED SOLUTION (2002)

Purpose: Cardiac preservation for transplantation is generally limited by ischemic hypothermic storage of 4 to 6 hours. Prior studies in our laboratory have demonstrated that hypothermic perfusion preservation using a novel oxygen carrying hemoglobin solution may extend preservation times to 8 hrs and decrease ischemic injury. The purpose of this study was to compare cardiac function after 12 and 24 hrs of continuous hypothermic perfusion with a PEG-Hemoglobin (Hb) solution to the clinical standard (if hypothermic ischemic preservation. Methods: The hearts of 33 anesthetized and intubated NZW rabbits were harvested after cold cardioplegic arrest. Group l(n = 8) hearts were perfused with a PEG-Hb solution at 20°C and 30 mmHg for 24 hours. Group II(n = 5) hearts were preserved similarly with PEG-Hb for 12 hours, Group III(n=12) hearts for 8 hours with PEG-Hb, and Croup IV(n = 8) by cold ischemic storage fur 4 hours at 4°C. Left Ventricular (LV) function was measured in the nun-working state at 15 min, 1 hour, and 2 hour intervals after transfer to a standard crystalloid Langendorff circuit. Results: Developed LV pressure at 0.5cc LV volume was similar in all Groups at all lime points Maximum + dP/dT at 0.5 cc LV volume was greater initially in Croups I and I1 compared to Group IV ((p < 0.05), and was similar at other time points except Group II was inferior to Group IV at 2 hours p < 0.05) Maximum −dp/dT at 0.5cc LV volume was also greater in Groups I, II, and III compared to Group IV initially, hut all were similar, it I hour and inferior performance to Croup IV at 2 hours (p < 0.05). Conclusion: Continuous perfusion preservation of rabbit hearts for time increments up to 24 hrs with this novel PEG-Hb solution at 30 mmHg and 20 C yields LV function that is similar to 4 hrs of ischemic hypothermic storage. Extended cardiac perfusion preservation with this PEC-Hb solution deserves further investigation in large animal transplant models.
Protective Role of LGP2 in Influenza Virus Pathogenesis (2014)

Influenza A virus triggers a contagious respiratory disease that can cause considerable morbidity and mortality. Using an in vitro approach, we previously demonstrated that the pattern recognition receptor retinoic acid-inducible gene I (RIG-I) plays a key role in influenza A virus-mediated immune response. However, the importance of RIG-I signaling in vivo has not been thoroughly examined, because of the lack of an appropriate mouse models. To circumvent this issue, we generated a new transgenic mouse overexpressing LGP2 (hereafter, "LGP2 TG mice"), a major regulator of the RIG-I signaling pathway. The time course of several parameters was compared in infected wild-type and LGP2 TG mice. We found that LGP2 TG mice displayed significantly reduced inflammatory mediators and a lower leukocyte infiltration into the bronchoalveolar airspace. More importantly, LGP2 TG mice had a significant survival advantage. Hence, our in vivo study reveals that LGP2 is a major downregulator of the influenza A virus-triggered detrimental inflammatory response.
Ultrastructure and Morphogenesis of the Apyrene and Eupyrene Spermatozoa in the Gypsy Moth (Lepidoptera: Lymantriidae) (2000)

Abstract The ultrastructure and morphogenesis of apyrene and eupyrene spermatozoa of Lymantria dispar (L.) is examined. Apyrene prophase I spermatocytes are characterized by sparse perinuclear membrane, smaller nuclei, bivalents lacking synaptonemal complexes, and few mitochondria. Eupyrene prophase I spermatocytes are characterized by dense perinuclear sheathing, large nuclei, diffuse chromatin, synaptonemal complexes, and numerous mitochondria. Apyrene metaphase I is atypical involving chromatin clumping and mis-segregation. Eupyrene metaphase I spermatocytes show localized meiotic centromeres and sheathed nuclear division. However, kinetochores are amorphous and difficult to discern. Apyrene spermiogenesis involves the morphogenesis of the axoneme and mitochondrial derivatives in the absence of differentiating nuclei and acrosomes. Eupyrene spermiogenesis involves the differentiation of nuclei, axonemes, acrosome tubes, mitochondrial derivatives, lacinate appendages, and reticular appendages. Both eupyrene spermatozoa and apyrene spermatozoa undergo additional morphogenesis upon leaving the testis. The most apparent of these are the loss of lacinate appendages in eupyrene sperm and the gain of an extracellular sheathing in both eupyrene sperm and apyrene sperm.
THz photonic band-gap prisms fabricated by fiber drawing (2012)

We suggest a novel form of polymeric based 3D photonic crystal prisms for THz frequencies which could be fabricated using a standard fiber drawing technique. The structures are modeled and designed using a finite element analyzing technique. Using this simulation software we theoretically study their performance.
Nitroxide Radicals as Highly Reactive Redox Mediators in Dye‐Sensitized Solar Cells (2012)

Exchanged: The organic radical 2-azaadamantan-N-oxyl (AZA; see picture) is found to be a stable and highly reactive redox mediator in dye-sensitized solar cell (DSSC) electrolytes. This radical has an appropriate redox potential and significantly high values for the diffusivity, heterogeneous electron-transfer rate, and electron self-exchange reaction rate. In a DSSC the AZA-based electrolyte achieves an excellent photovoltaic performance. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
MPST: A Corpus of Movie Plot Synopses with Tags (2018)

Social tagging of movies reveals a wide range of heterogeneous information about movies, like the genre, plot structure, soundtracks, metadata, visual and emotional experiences. Such information can be valuable in building automatic systems to create tags for movies. Automatic tagging systems can help recommendation engines to improve the retrieval of similar movies as well as help viewers to know what to expect from a movie in advance. In this paper, we set out to the task of collecting a corpus of movie plot synopses and tags. We describe a methodology that enabled us to build a fine-grained set of around 70 tags exposing heterogeneous characteristics of movie plots and the multi-label associations of these tags with some 14K movie plot synopses. We investigate how these tags correlate with movies and the flow of emotions throughout different types of movies. Finally, we use this corpus to explore the feasibility of inferring tags from plot synopses. We expect the corpus will be useful in other tasks where analysis of narratives is relevant.
Comparison of Soil Sampling Devices for Soil Bulk Density Determination for Carbon Sequestration Monitoring (2014)

Soil bulk density is often used to adjust soil carbon (C) values for changes in soil density because of management differences in C-sequestration studies. Often hand-sampling devices used for soil fertility monitoring may be used for sampling soil to a depth of up to 30 cm. Four sampling devices of differing characteristics that can be used with hand-sampling equipment across full tillage, reduced tillage, and no-tillage to determine soil bulk density were evaluated. There were no significant differences in soil bulk density values between three cylindrical devices, which measured from 19 to 31 mm in diameter. However, a 21 mm × 76 mm rectangular device gave significantly lower bulk density values than the cylindrical devices. Calculation of soil organic carbon (SOC) mass per unit area showed similar results for the cylindrical devices with the rectangular device giving a significantly lower value than the cylindrical devices. Using a cylindrical device on a hand probe in a consistent manner will give satisfactory results when sampling surface soils.
Reduced Graphene Oxide-Poly(3,4-ethylenedioxythiophene) Polystyrenesulfonate Based Dual-Selective Sensor for Iron in Different Oxidation States (2015)

A dual-selective sensor platform for detection of iron in ferrous (Fe2+) and ferric (Fe3+) oxidation states was developed. Upon dispersing reduced graphene oxide (rGO) sheets into poly(3,4-ethylenedioxythiophene) polystyrenesulfonate (PEDOT:PSS) polymer, we deposited a hybrid film of rGO-PEDOT:PSS onto a glassy carbon electrode (GCE) surface. Effective intercalation of rGO sheets in PEDOT:PSS film was observed by Raman spectroscopy, UV–vis-NIR spectroscopy, and scanning electron microscopy. The rGO-PEDOT:PSS/GCE sensor showed high electrocatalytic activity for Fe2+/Fe3+ redox reaction. Using amperometry with controlled applied potential, we demonstrated selective detection of both Fe2+ and Fe3+ with rGO-PEDOT:PSS/GCE. The sensor responded linearly to Fe2+ from 20–833 μM (at 0.6 V) and Fe3+ from 1–833 μM (at 0.4 V) in 0.5 M KCl + 0.05 M HCl. The presence of several common metal and organic interferents such as Cu2+, Co2+, Ag+, Pb2+, Cd2+, Zn2+, Mn2+, Ni2+, Hg2+, l-glycine, l-cysteine, l-tyrosine, glucose, KCN, guanine, uric acid, xanthan, salicylate, tartrazine, and naphthol yellow did not affect the selective detection of Fe2+ and Fe3+. In addition, detection of Fe2+ and Fe3+ ions in a red wine sample and iron supplement tablets were performed with satisfactory results. The sensor was also useful in determining oxidation kinetics of Fe2+ using hydrogen peroxide and measuring Fe3+ by differential pulse voltammetry. Thus, rGO/PEDOT:PSS hybrid film based electrode we developed can serve as a practical sensor for detecting iron in its different oxidation states in real samples for different applications.