gebhart/patrepeval huggingface dataset:
Supplementary Figures and tables from A Functional Screen Identifies miRs That Induce Radioresistance in Glioblastomas (2023)

&lt;p&gt;S1A. List of miRNAs enriched independent of IR. S1B. Clonogenic survival assay was performed with 2 Gy IR in 12 different GBM lines. Bar graphs were generated with Mean {plus minus} S.D. of 3 independent experiments. S2A. IR sensitivity of LN229 with individual stable expression of miR-1, miR-125a, miR-150 and miR-425 was determined by clonogenic assay. Curves were generated with Mean {plus minus} S.D. of 3 independent experiments. For statistical analysis the areas under the curves were calculated by approximating them to trapezoids. Comparison was done with one-way ANOVA (p &lt; 0.05) and Tukey's post hoc (p &lt; 0.05) test. S2B. Expression of fused miR-1, miR-125a, miR-150 and miR-425 from pcDNA3.1 vector. S3. A) Illustration shows the construct of GFP-fused miRNA sponges. GFP is fused at the 3' end of 4 identical repeats of miRNA sponges in tandem. The sequence of each miRNA sponge is shown below. (B) Inhibition of GFP expression fused to miRNA sponges was tested by transfecting corresponding miRNA mimics. Comparison was done with one-way ANOVA (p &lt; 0.05) and Tukey's post hoc (p &lt; 0.05) test. S4A. Impact of individual miR-scr, miR-1, miR-125a, miR-150 and miR-425 and combined miR-4x' on apoptosis in LN229 cells. Cells were exposed to 10 Gy γ-IR and the activation of Caspase 3 and 7 was determined with Caspase-Glo 3/7 Assay System. Comparison was done with one-way ANOVA (p &lt; 0.05) and Tukey's post hoc (p &lt; 0.05) test. S4B. Phosphorylation of Chk1 S345 in LN229 cells transfected with indicated miRNA upon exposure to 10 Gy IR. The mean {plus minus} S.D. of 3 independent experiments is demonstrated. Comparison was done with one-way ANOVA (p &lt; 0.05) and Tukey's post hoc (p &lt;0.05) test. S5. Expression of PAI-1 was examined upon stimulation with TGF-β with or without TGF-β inhibitor in indicated GBM cell lines. Bar graphs were generated with Mean {plus minus} S.D. of 3 independent experiments. Comparison was done with one-way ANOVA (p &lt; 0.05) and Tukey's post hoc (p &lt; 0.05) test. Supplementary Table 1. Transcription factors that are predicted by prediction algorithms, MotifScanner and CisGenome, to regulate the expression of all 4 miRNAs within 5000 base pairs upstream of each miRNA. The commons factors predicted for all 4 miRNAs were listed in the table. Supplementary Table 2. Selected genes from our predictions that overlap with the list of factors whose silencing cause radioresistance have been shown in Table 2.&lt;/p&gt;
Erratum: Characterization of Mechanically Matched Hydrogel Coatings to Improve the Biocompatibility of Neural Implants (2017)

A correction to this article has been published and is linked from the HTML version of this paper. The error has not been fixed in the paper.
[Orthoreoviruses: are they pathogenic for man?] (2008)

The orthoreoviruses are segmented double strand RNA viruses and are the most abundant viruses in nature. Three main serotypes are known, named 1, 2 and 3. The designation "reovirus" is the acronym for "respiratory enteric orphan virus", expression underlining their respiratory and enteric origin and the fact that they are not associated with well defined clinical disease. Nevertheless, strains of orthoreoviruses have been isolated from several cases of symptomatic diseases in human, namely diseases of the central nervous system such as encephalitis and meningitis sometimes leading to patient death. These different cases show that orthoreoviruses could be pathogenic, causing fatal diseases. Orthoreoviruses infection in animals induces also several diseases. Indeed, according to the inoculation route and the serotype of inoculated strain, encephalitis or hepatitis can be observed. The RNA segments M2 and S1 seem to be involved in this neurovirulence property and are on the basis of cellular mechanisms, such as virus entry, virus replication and apoptosis. However, the mechanisms of virulence remain complex.
Buffer Overflow Probability of TCP Flows During Mobile Handovers (2008)

Forwarding of user data is suspended for a short time at mobile handovers, but arriving packets are still buffered in the network. The resulting sudden peak in utilization may overflow the buffer, and the subsequent bursty packet loss will cause TCP connections to significantly degrade their throughput. We derive an analytical model for buffer overflow probability calculation, given the congestion window increase function and network parameters. Numeric results for current TCP variants and realistic network parameters show that congestion loss occurs with significant probability, even for very large buffer settings.
Metabolic Coupling of Dehydration and Decarboxylation in the Curacin A Pathway:  Functional Identification of a Mechanistically Diverse Enzyme Pair (2006)

This study describes the functional identification of a pair of mechanistically diverse enzymes that catalyze the successive dehydration (CurE ECH1) and decarboxylation (CurF ECH2) of (S)-HMG-ACP to generate a 3-methylcrotonyl-ACP intermediate, the presumed precursor of the cyclopropyl ring in curacin A. The reactions catalyzed by ECH1 and ECH2 are found in a broad cross-section of microbial natural product gene clusters and participate in the introduction of carbon chain branch points and functional group diversity as key steps in the HMG-CoA synthase mediated addition of C-2 from acetate to the beta-carbonyl group of polyketide chains.
Liquid Crystalline Rod−Coil Block Copolymers by Stable Free Radical Polymerization:  Synthesis, Morphology, and Rheology (2003)

We have synthesized and characterized rod−coil diblock, triblock, and starblock copolymers of controlled molecular weight by stable free radical polymerization, where the rod part consists of “mesogen jacketed liquid crystalline segments” (MJLCP). The MJLCP segment examined in our studies is poly{2,5-(4-butylbenzoyl)oxystyrene} (PBBOS) while the coil part is poly(styrene). SAXS studies of the block copolymers at room temperature predominantly show only a first-order maximum in their SAXS spectra. Above the Tg of the two blocks (∼150 °C) no phase-separated morphology could be detected in temperature-dependent SAXS measurements of the block copolymers. Slow cooling regenerates the morphology, indicating very slow ordering kinetics. The effects of variation in molecular architecture and increasing topological constraint in going from homopolymer to star block copolymer on melt rheology (i.e., viscosity, relaxation times, and activation energies) are reported. In the master curves of all the block copolymers and homopolymers studied, nonterminal behavior was observed at low shear frequencies along with the absence of an entanglement plateau. In the PBBOS homopolymer an increase in molecular weight resulted in a decrease in the modulus of the nematic phase that was associated with a greater extent of shear orientation. On varying the molecular architecture from homopolymer to diblock to starblock copolymer, a decrease in the complex viscosity was observed that is attributable to the presence of polystyrene as the second block and the effect of topological constraints on molecular relaxation. The activation energies also follow the same trend as complex viscosity and relaxation times.
Video monitoring system framework for video on demand (1995)

This paper describes an experimental approach to a video monitoring system. Video monitoring is specifically intended for ensuring delivery of quality video to subscribers by video-on-demand systems, and is installed either at the local switching office or at the video servers. A framework for the monitoring system is provided. We discuss the constraints and present the results of some of our prototype development.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Aging Studies of Pt/Glassy Carbon Model Electrocatalysts (2008)

A model Pt catalyst nano-array on planar glassy carbon was synthesized and subjected to a potential cycle aging procedure. Preliminary experimental data suggest a similar degradation behavior as gas diffusion electrodes with an observed decrease in surface area (decrease in H2 and CO oxidation peak areas as determined by cyclic voltammetry). Atomic force microscopy topography images support this conclusion.
IgG response of rats and humans to the released products of schistosomula ofSchistosoma mansoni (1985)

The participation of products released from Schistosoma mansoni schistosomula (SRP-A) in the IgG antibody response of infected Brown-Norway rats and infected humans has been studied using immunoprecipitation with various antigenic preparations and in in vitro cytotoxicity assays. A large number of SRP-A molecules with a wide range of molecular weights was recognized by infected rat and human sera. Anti-SRP-A antibodies appeared in rat sera from day 28 after infection. In infected humans, a variable pattern of SRP-A recognition was observed between individuals. IgG antibodies obtained by immunization of rats with SRP-A without addition of adjuvants reacted with 3 major schistosomula surface proteins with molecular weights of 38, 32 and 21 kDa. These latter molecules were also revealed strongly by infected rat sera. Moreover, these antibodies were able to kill schistosomula in vitro in the presence of complement or eosinophils.
A Novel Method for Measurement of the Channel Length of Short Channel MOSFET's (1982)

A submicron effective channel length of MOSFET is measured accurately by means of an EBIC technique. For accuracy, it is necessary to vary the primary electron beam energy specifically to achieve lowest practical values. When the beam penetration depth in silicon is deeper than the junction depth, the peak of the EBIC does not accurately indicate the location of p‐n junction. The fluctuation involved in this measurement technique is very small, less than ±0.025 μm. By varying the incident beam voltage, a precise depth profile of the p‐n junctions, especially drawback of the junction which is caused by channel implantation, could be also measured.
Design and Fabrication of an Active Gravity Balanced Planar Mechanism Using Auxiliary Parallelograms (1999)

This paper describes the design of an active gravity balanced planar mechanism, where auxiliary parallelograms are used to physically locate the center of mass of the mechanism. A sliding carriage positions a counterweight directly above the center of mass of the mechanism in order to make the system gravity balanced. The sliding carriage uses joint encoder data from the mechanism to compute the location of the center of mass. Experiment results demonstrate the effectiveness of the approach.
Low-Sideband Resonant Subwavelength Grating Array Design (2002)

A systematic method for the design of arrayed resonant subwavelength gratings is described. Design goals are peak reflectance of unity, narrow spectral bandwidth, and low sideband reflectivity for use in an arrayed grating structure.
Study on Demonstration Project with the Immobilized-Microorganisms-Aquatic Plants Strengthened Purification System in Pre-dem (2006)

The immobilized-microorganisms-aquatic strengthened purification system is designed to dispose wastewater in pre-dem so as to decrease the pollution burden of Taihu Lake.Through adding high effective microorganisms of 30(mg/kg) in the pre-dem during the period of domestication and then 20(mg/kg) per month,the activity of microbe is intensified.During the monitoring,the mass concentrations of the influent are 0.54～1.59(mg/L) of TN,0.079～0.172(mg/L) of TP and 5.41～13.40(mg/L) of COD_(Mn);HRT of pre-dem is about 9 d;the removal rates of TN,TP and COD_(Mn) are up to 45.0%,42.2% and 50.8%, respectively.The number of microorganisms in immobilized-microorganisms area is 1～2 degrees higher than that in hydrophyte root area.Denitration microorganisms can add up to 10~9,and the amount in hydrophyte root area is 2～3 degrees higher than that in demonstration natural waters.The results indicate that immobilized-microorganisms-aquatic strengthened purification system is adapted to the environment and it is efficient,but the long-time function to pre-dem would be further tested.
Contour-based kernel modeling and verification for E-Beam lithography (2015)

In E-beam lithography, the double or multiple Gaussian kernels used to describe the electron scattering behavior have been discussed extensively for critical dimensions (CDs) larger than the e-beam blur size. However in e-beam direct write on wafer, CD dimensions are close to the beam blur size because of requirements in both resolution and throughput. This situation gives rise to a severe iso-dense CD bias. Hence the accuracy of the modeling kernel is required to achieve a larger common process window. In this paper we present contour-based kernel modeling and verification for e-beam lithography. The edge contours of CD-SEM images of the contact hole array pattern with duty ratio splits are used in this Gaussian kernel modeling study. A 2-step optimization sequence is proposed to improve the fitting efficiency and robustness. In the first step, roundness is the primary and the most effective index at the corner region which is sensitive to determine the beam blur size. The next step is to minimize the deviation of the through-pitch proximity effect by adjusting the ratio of the electron backscattering to the electron forward scattering. The more accurate cost index, edge placement error, is applied in the subsequent optimization step with constrained beam blur sizes extracted from the previous step. The optimum modeling kernel parameters can be obtained by the lowest cost deviation of the simulation contours and the CD-SEM extracted edge contours after optimization iterations. For early study of the proximity impact on future EBDW systems, the exposure experiment is performed on an EBM-8000 mask writer to build the modeling kernel. The prediction accuracy of the optimum modeling kernel on 60-nm features with different pattern densities is also verified experimentally to be within 1.5 nm.
A plate reader-based method for cell water permeability measurement (2009)

Cell volume and water permeability measurements in cultured mammalian cells are typically conducted under a light microscope. Many of the employed approaches are time consuming and not applicable to a study of confluent epithelial cell monolayers. We present here an adaptation of a calcein-quenching-based approach for a plate reader. A standard curve of fluorescence intensities at equilibrium has been recorded, following a shift from 285 mosmol/kgH(2)O to a series of altered extracellular osmolyte concentrations, ranging from final concentrations of 185 to 585 mosmol/kgH(2)O, by changing buffer d-mannitol concentrations. Similarly, according average cell volumes have been measured in suspension in a Coulter counter (particle-sizing device). Based on these measurements, we have derived an equation that facilitates the modeling of cell volume changes based on fluorescence intensity changes. We have utilized the method to study the role of a carboxyl-terminus aquaporin (AQP)-2 phosphorylation site, which is known to affect AQP2 membrane trafficking, in heterologous type I Madin-Darby canine kidney cells. We find that water permeability in cells expressing phosphorylation site mutants was in the following order: AQP2-S256D > AQP2 wild-type > AQP2-S256A. We propose that the method can be applied to study AQP function and more generally to study cell volume changes in adherent cell lines. Furthermore, it should be adaptable for AQP inhibitor screening in chemical compound libraries.
First Demonstration of SDN-based Segment Routing in Multi-layer Networks (2015)

Segment Routing enabling dynamic optical bypass in a multi-layer network is experimentally demonstrated. Edge nodes are efficiently configured by an enhanced SDN controller, showing effective scalability performance under different label stacking conditions.
Fullerene C70 as a p-type donor in organic photovoltaic cells (2014)

Fullerenes and their derivatives have been widely used as n-type materials in organic transistor and photovoltaic devices. Though it is believed that they shall be ambipolar in nature, there have been few direct experimental proofs for that. In this work, fullerene C70, known as an efficient acceptor, has been employed as a p-type electron donor in conjunction with 1,4,5,8,9,11-hexaazatriphenylene hexacarbonitrile as an electron acceptor in planar-heterojunction (PHJ) organic photovoltaic (OPV) cells. High fill factors (FFs) of more than 0.70 were reliably achieved with the C70 layer even up to 100 nm thick in PHJ cells, suggesting the superior potential of fullerene C70 as the p-type donor in comparison to other conventional donor materials. The optimal efficiency of these unconventional PHJ cells was 2.83% with a short-circuit current of 5.33 mA/cm2, an open circuit voltage of 0.72 V, and a FF of 0.74. The results in this work unveil the potential of fullerene materials as donors in OPV devices, and provide alternative approaches towards future OPV applications.
Finding Genetic Risk Factors of Gestational Diabetes (2012)

Gestational diabetes mellitus (GDM) is a complex metabolic disorder of pregnancy that is suspected to have a strong genetic predisposition. It is associated with poor perinatal outcome, and both GDM women and their offspring are at increased risk of future development of type 2 diabetes mellitus (T2DM). During the past several years, there has been progress in finding the genetic risk factors of GDM in relation to T2DM. Some of the genetic variants that were proven to be significantly associated with T2DM are also genetic risk factors of GDM. Recently, a genome-wide association study of GDM was performed and reported that genetic variants in CDKAL1 and MTNR1B were associated with GDM at a genome-wide significance level. Current investigations using next-generation sequencing will improve our insight into the pathophysiology of GDM. It would be important to know whether genetic information revealed from these studies could improve our prediction of GDM and the future development of T2DM. We hope further research on the genetics of GDM would ultimately lead us to personalized genomic medicine and improved patient care.
Reduction-responsive core-crosslinked hyaluronic acid-b-poly(trimethylene carbonate-co-dithiolane trimethylene carbonate) micelles: synthesis and CD44-mediated potent delivery of docetaxel to triple negative breast tumor in vivo (2018)

Future cancer therapy relies on the development of simple, selective and bioresponsive nanomedicines. Herein, we report that reduction-responsive core-crosslinked hyaluronic acid-b-poly(trimethylene carbonate-co-dithiolane trimethylene carbonate) micelles (HA-CCMs) can be easily synthesized and achieve efficient CD44-mediated delivery and triggered cytoplasmic release of docetaxel (DTX) to MDA-MB-231 human triple negative breast tumor in vivo. DTX-loaded HA-CCMs exhibited a favorable size of 85 nm, low drug leakage and glutathione-responsive DTX release. HA-CCMs were efficiently taken up by CD44-overexpressing MDA-MB-231 cells as indicated by flow cytometry. DTX-loaded HA-CCMs induced selective apoptotic activity toward MDA-MB-231 cells in vitro. Notably, over 7-fold longer blood circulation time and 4-fold stronger tumor accumulation were observed for DTX-loaded HA-CCMs compared to free DTX. Cy5-labeled HA-CCMs revealed deep tumor penetration at 6 h post injection. DTX-loaded HA-CCMs were shown to effectively suppress the progression of MDA-MB-231 tumor and significantly extend mice survival time. These hyaluronic acid-shelled and disulfide-crosslinked micelles with great simplicity and selectivity are highly promising for treating various CD44-overexpressing cancers.
Quantitative analysis of resistance to natural killer attacks reveals stepwise killing kinetics (2014)

Molecular mechanisms can protect cancer cells from immune attacks. At the level of bulk tissue, these survival mechanisms are often indistinguishable and simply appear as reduced cell death. However, by tracking individual cell survival and death times, we found broad variation in the kinetics of immune evasion. In response to attacks by natural killer cells, we observed that some cancer lines exhibited exponential survival time distributions. Slowly killed cancer lines had reduced exponential rate constants. In contrast, a line engineered to express the serpin protein PI-9, which is known to promote resistance to immune killing, exhibited a markedly nonexponential survival time distribution. By following the histories of individual cancer cells with multiplexed reporters, we obtained evidence that two or more immune attacks are likely required to kill serpin-expressing cells. Thus, resistance is a finite and measurable quantity, with a distinct kinetic signature. A quantitative model based on independently measured parameters is consistent with our conclusions.
Clinical Short-wire TENS (Transcutaneous Electric Nerve Stimulator) Study For Mitigation of Pain in the Dayton VA Medical Center (1997)

A prototype TENS device was developed consisting of a significantly reduced wire structure for the purpose of generating electrical field signals to actively mitigate pain. This new microprocessor system was tested with patients from the Dayton VA Medical Center in Dayton, Ohio, and compared to the treatment obtained via a traditional stimulator. The device developed in this study has additional operational advantages besides the obvious patient compliance of a system with little or no entangling wires.
Probability of conductive bond formation in a percolating network of nanowires with fusible tips (2018)

Meeting the heat dissipation demands of microelectronic devices requires development of polymeric composites with high thermal conductivity. This property is drastically improved by percolation networks of metallic filler particles that have their particle-to-particle contact resistances reduced through thermal or electromagnetic fusing. However, composites with fused metallic fillers are electrically conductive, which prevents their application within the chip-board and the inter-chip gaps. Here, we propose that electrically insulating composites for these purposes can be achieved by the application of fusible metallic coatings to the tips of nanowires with thermally conductive but electrically insulating cores. We derive analytical models that relate the ratio of the coated and total nanowire lengths to the fraction of fused, and thus conductive, bonds within percolating networks of these structures. We consider two types of materials for these fusible coatings. First, we consider silver-like coatings, which form only conductive bonds when contacting the silver-like coating of another nanowire. Second, we consider liquid metal-like coatings, which form conductive bonds regardless of whether they contact a coated or an uncoated segment of another nanowire. These models were validated using Monte Carlo simulations, which also revealed that electrical short-circuiting is highly unlikely until most of the wire is coated. Furthermore, we demonstrate that switching the tip coating from silver- to liquid metal-like materials can double the fraction of conductive bonds. Consequently, this work provides motivation to develop scalable methods for fabrication of the hybrid liquid-coated nanowires, whose dispersion in a polymer matrix is predicted to yield highly thermally conductive but electrically insulating composites.