gebhart/patrepeval huggingface dataset:
A stationary phase protein in <i>Escherichia coli</i> with binding activity to the major σ subunit of RNA polymerase (1998)

Switching of the transcription pattern in Escherichia coli during the growth transition from exponential to stationary phase is accompanied by the replacement of the RNA polymerase-associated sigma70 subunit (sigmaD) with sigma38 (sigmaS). A fraction of the sigma70 subunit in stationary phase cell extracts was found to exist as a complex with a novel protein, designated Rsd (Regulator of sigma D). The intracellular level of Rsd starts to increase during the transition from growing to stationary phase. The rsd gene was identified at 90 min on the E. coli chromosome. Overexpressed and purified Rsd protein formed complexes in vitro with sigma70 but not with other sigma subunits, sigmaN, sigmaS, sigmaH, sigmaF, and sigmaE. Analysis of proteolytic fragments of sigma70 indicated that Rsd binds at or downstream of region 4, the promoter -35 recognition domain. The isolated Rsd inhibited transcription in vitro to various extents depending on the promoters used. We propose that Rsd is a stationary phase E. coli protein with regulatory activity of the sigma70 function.
A Framework for the Design of Effective Graphics for Scientific Visualization (1992)

This proposal presents a visualization framework, based on a data model, that supports the production of effective graphics for scientific visualization. Visual representations are effective only if they augment comprehension of the increasing amounts of data being generated by modern computer simulations. These representations are created by taking into account the goals and capabilities of the scientist, the type of data to be displayed, and software and hardware considerations. This framework is embodied in an assistant-based visualization system to guide the scientist in the visualization process. This will improve the quality of the visualizations and decrease the time the scientist is required to spend in generating the visualizations. I intend to prove that such a framework will create a more productive environment for tile analysis and interpretation of large, complex data sets.
Study of B72.3 combining sites by molecular modeling and site-directed mutagenesis (2000)

A B72.3 Fab/sTn(2) complex was modeled from the known structure of B72.3 Fab and the dimeric Tn-serine cluster (sTn(2)). In the complex model, the side chains of 15 heavy- and light-chain complementarity-determining region (CDR) residues and the main chains of two light-chain CDR residues contact the sTn(2) epitope. Among 15 CDR residues which contact sTn(2) in the model, two heavy-chain residues (Ser95 and Tyr97) and light-chain CDR residue (Tyr96) have been confirmed in a previous study. To test the accuracy of the computational model, further site-directed mutagenesis was performed by alanine scanning on the remaining 12 residues that are predicted in the model to have side-chain interactions with sTn(2). Of these 12 mutants, eight that are all from the heavy-chain (His32Ala, Ala33Leu, Tyr50Ala, Ser52Ala, Asn52Ala, Asp56Ala, Lys58Ala and Tyr96Ala) had significantly reduced sTn(2) affinities, and four consisting of three light-chain mutations (Asn32Ala, Trp92Ala and Thr94Ala) and one heavy-chain mutation (His35Ala) retained wild-type sTn(2) affinity. On the whole, this evidence suggests that the complex model, although not perfect, is correct in many of its features. In a more general vein, these results lend credibility to the computational modeling approach for the study of the molecular basis of antigen-antibody complexes.
ShieldGen: Automatic Data Patch Generation for Unknown Vulnerabilities with Informed Probing (2007)

In this paper, we present ShieldGen, a system for automatically generating a data patch or a vulnerability signature for an unknown vulnerability, given a zero-day attack instance. The key novelty in our work is that we leverage knowledge of the data format to generate new potential attack instances, which we call probes, and use a zero-day detector as an oracle to determine if an instance can still exploit the vulnerability; the feedback of the oracle guides our search for the vulnerability signature. We have implemented a ShieldGen prototype and experimented with three known vulnerabilities. The generated signatures have no false positives and a low rate of false negatives due to imperfect data format specifications and the sampling technique used in our probe generation. Overall, they are significantly more precise than the signatures generated by existing schemes. We have also conducted a detailed study of 25 vulnerabilities for which Microsoft has issued security bulletins between 2003 and 2006. We estimate that ShieldGen can produce high quality signatures for a large portion of those vulnerabilities and that the signatures are superior to the signatures generated by existing schemes.
A Ratiometric Sensor Using Single Chirality Near‐Infrared Fluorescent Carbon Nanotubes: Application to In Vivo Monitoring (2015)

Advances in the separation and functionalization of single walled carbon nanotubes (SWCNT) by their electronic type have enabled the development of ratiometric fluorescent SWCNT sensors for the first time. Herein, single chirality SWCNT are independently functionalized to recognize either nitric oxide (NO), hydrogen peroxide (H(2)O(2)), or no analyte (remaining invariant) to create optical sensor responses from the ratio of distinct emission peaks. This ratiometric approach provides a measure of analyte concentration, invariant to the absolute intensity emitted from the sensors and hence, more stable to external noise and detection geometry. Two distinct ratiometric sensors are demonstrated: one version for H(2)O(2), the other for NO, each using 7,6 emission, and each containing an invariant 6,5 emission wavelength. To functionalize these sensors from SWCNT isolated from the gel separation technique, a method for rapid and efficient coating exchange of single chirality sodium dodecyl sulfate-SWCNT is introduced. As a proof of concept, spatial and temporal patterns of the ratio sensor response to H(2)O(2) and, separately, NO, are monitored in leaves of living plants in real time. This ratiometric optical sensing platform can enable the detection of trace analytes in complex environments such as strongly scattering media and biological tissues.
Exchange spring media for perpendicular recording (2005)

A novel type of exchange spring media is proposed for magnetic recording systems consisting of a hard/soft bilayer. Finite element micromagnetic simulations show that the reversal modes induced by the external write field are significantly different from the thermally activated switching processes. Thus, the bilayers can be optimized in order to achieve a high thermal stability without increase of coercive field. In grains with identical size and coercivity an optimized bilayer reaches an energy barrier exceeding those of optimized single phase media by more than a factor of two. Additionally the lower angular dependence of coercivity of exchange spring media will improve the signal to noise ratio.
Active vibration control in automotive chassis systems (1993)

For over 100 years, comfort in road vehicles has been linked to the introduction of passive components that isolate passenger compartments from mechanical vibration. Near-optimal performance has been achieved by years of experimentation and testing, careful selection and shaping of individual component characteristics, and the development of ingenious mechanisms intended to minimise the effect of inherent design constraints associated with passive systems. It is now apparently the case that only a technological leap can significantly improve vibration suppression in automotive chassis systems over that achieved to date. This article considers the analysis and design of active control solutions for two automotive chassis subsystems susceptible to mechanical vibration phenomena.
Real-Time Multi-UAV Task Assignment in Dynamic and Uncertain Environments (2009)

This paper analyzes task assignment for heterogeneous air vehicles using a guaranteed conflict-free assignment algorithm, the Consensus Based Bundle Algorithm (CBBA). We extend this recently proposed algorithm to handle two realistic multi-UAV operational complications. Our first extension accounts for obstacle regions in order to generate collision free paths for UAVs. Our second extension reduces task planner sensitivity to sensor measurement noise, and thereby minimizes churning behavior in flight paths. After integrating our enhanced CBBA module with a 3D visualization and interaction software tool, we simulate multiple aircraft servicing stationary and moving ground targets. Preliminary simulation results establish that consistent, conflict-free multi-UAV path assignments can be calculated on the order of a few seconds. The enhanced CBBA consequently demonstrates significant potential for real-time performance in stressing environments. I.
Differences in the recognition by CTL of peptides presented by the HLA‐B*4402 and the HLA‐B*4403 molecules which differ by a single amino acid (1999)

The HLA-B*4402 and B*4403 molecules differ only at residue 156, which borders the peptide binding site. Strong in vivo allogeneic reactions mediated by cytolytic T lymphocytes (CTLs) were reported in patients who received a bone marrow graft mismatched for these B44 subtypes, indicating that HLA-B*4402 and B*4403 molecules present distinct antigens. This could be due either to the presentation of different sets of antigenic peptides or to the recognition by CTLs of conformational epitopes formed by the MHC molecules alone or in association with antigenic peptides. To address this question, we compared the two B44 subtypes in their presentation to tumor-specific CTLs of three peptides, encoded by genes MAGE-3, MUM-1 and Tyrosinase. The peptides bound with similar affinities to B*4402 or B*4403 molecules, as assessed by lytic competition assays. One HLA-B*4402-restricted and one HLA-B*4403-restricted CTL clone were derived against each peptide. When tested for lysis of B*4402 and B*4403 cells incubated with the antigenic peptides, most CTLs showed a marked preference for one of the two B44 subtypes. Using variant peptides incorporating single alanine substitutions, we compared a given CTLs' recognition of its antigenic peptide presented by both B44 subtypes. Some substitutions, which had no effect on the binding of the peptide, affected its recognition by the same CTL differently on B*4402 and B*4403 molecules. These results imply that the conformations adopted by the same peptide on the two HLA-B44 subtypes are different. We conclude that the B44 subtype specificity of T cells results mostly from distinct conformations adopted by the same peptides in the two B44 molecules. This does not exclude the possibility that in some cases the B44 subtype specificity results from the selective binding of a peptide to one subtype. We found several peptides, different from the three mentioned above, that contain the canonical HLA-B44 binding motif and bind to B*4403 but not to B*4402 molecules.
TFT active image sensor with current-mode readout circuit for digital x-ray fluoroscopy (2005)

In this paper, an innovative current-programmed, current-output active TFT image sensor suitable for real time x-ray imaging (fluoroscopy) using hydrogenated amorphous silicon (a-Si:H) thin film transistor (TFT) technology coupled with a transimpedance feedback column amplifier for pixel signal readout is presented. Simulation results show that this new TFT circuit can successfully compensate for variations in a-Si:H TFT characteristics under prolonged gate voltage stress. The readout is fast enough to fulfill the timing requirements of digital fluoroscopy. Dynamic effects such as charge injection, charge feed-through and drain-source voltage variation as well as additive noise of the pixel TFTs induce error on the output current of the pixel. To explore the dependence of this error on pixel parameters, concise analytical expressions are derived which can be used to reduce the amount of the output current error by proper pixel design.
Contributions of Franz–Keldysh and Avalanche Effects to Responsivity of a Germanium Waveguide Photodiode in the $\hbox{L}$-Band (2014)

When driven with a high-voltage reverse bias of 15 V, a germanium photodiode with a silicon waveguide exhibits responsivity of over 1.14 A/W in the entire <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\hbox{C}$</tex> </formula> -and <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\hbox{L}$</tex></formula> -bands. The high responsivity in the <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\hbox{L}$</tex></formula> -band is due to Franz–Keldysh (F-K) and avalanche effects. We prove by numerical calculation that the high responsivity under high bias driving is due to both effects. For accuracy in the calculation, we consider a change in the thickness of depletion layer in the germanium mesa with bias voltage. Calculation results, considering the contributions of both effects, show good agreement with measurement results. Considering the contributions of both effects to minimum detection limit, we discuss optimization for dark current and the electric field applied to Ge.
Differential Selectivity of Natural and Synthetic Aminoglycosides towards the Eukaryotic and Prokaryotic Decoding A Sites (2007)

The lack of absolute prokaryotic selectivity of natural antibiotics is widespread and is a significant clinical problem. The use of this disadvantage of aminoglycoside antibiotics for the possible treatment of human genetic diseases is extremely challenging. Here, we have used a combination of biochemical and structural analysis to compare and contrast the molecular mechanisms of action and the structure-activity relationships of a new synthetic aminoglycoside, NB33, and a structurally similar natural aminoglycoside apramycin. The data presented herein demonstrate the general molecular principles that determine the decreased selectivity of apramycin for the prokaryotic decoding site, and the increased selectivity of NB33 for the eukaryotic decoding site. These results are therefore extremely beneficial for further research on both the design of new aminoglycoside-based antibiotics with diminished deleterious effects on humans, as well as the design of new aminoglycoside-based structures that selectively target the eukaryotic ribosome.
A novel hot-hole injection degradation model for lateral nDMOS transistors (2002)

For the first time, the degradation of a DMOS transistor is shown to be due to hot hole injection in the drift region field oxide. The saturation effects observed in the parameter shifts are reproduced by a new degradation model using the bulk current as the driving force. A very good agreement with experimental data is obtained for various stressing conditions.
All-trans retinoic acid upregulates VEGF expression in glioma cells in vitro (2013)

All-trans retinoid 酸(ATRA ) 是大多数之一有势力和导致 glioma 房间的区别和 apoptosis 的最彻底地学习的区别 inducers。然而， glioma 遗体的 angiogenesis 上的 ATRA 的效果糟糕理解。我们在不同 glioma 房间线在脉管的 endothelial 生长因素(VEGF ) 的表示上检验了 ATRA 的效果并且调查了内在的机制，打算部分揭示 glioma 的 angiogenesis 上的 ATRA 的效果。Glioma 房间被 ATRA 在 5 和 10 &#x000b5 对待； mol/L。VEGF mRNA 抄本层次被即时 RT-PCR 和 VEGF 的蛋白质层次在 glioma 房间决定被西方的弄污评估试金。而且，组织缺氧可诱导的 factor-1&#x003b1；(HIF-1&#x003b1；) mRNA 表示被使用即时 RT-PCR 分析。在有 5 和 10 &#x000b5 的处理以后； mol/L ATRA，在 glioma 房间的 VEGF mRNA 抄本层次显著地增加了，与那相比，在控制组，和相对蛋白质， VEGF 的表示也是起来调整的。同时， HIF-1&#x003b1；mRNA 表示也增加了。ATRA 在 transcriptional 和翻译层次在 glioma 房间增加 VEGF 的表示。
Ribonucleotide reductase subunits M1 and M2 mRNA expression levels and clinical outcome of lung adenocarcinoma patients treated with docetaxel/gemcitabine (2008)

Ribonucleotide reductase subunits M1 (RRM1) and M2 (RRM2) are involved in the metabolism of gemcitabine (2',2'-difluorodeoxycytidine), which is used for the treatment of nonsmall cell lung cancer. The mRNA expression of RRM1 and RRM2 in tumours from lung adenocarcinoma patients treated with docetaxel/gemcitabine was assessed and the results correlated with clinical outcome. RMM1 and RMM2 mRNA levels were determined by quantitative real-time PCR in primary tumours of previously untreated patients with advanced lung adenocarcinoma who were subsequently treated with docetaxel/gemcitabine. Amplification was successful in 42 (79%) of 53 enrolled patients. Low levels of RRM2 mRNA were associated with response to treatment (P< 0.001). Patients with the lowest expression levels of RRM1 had a significantly longer time to progression (P=0.044) and overall survival (P=0.02) than patients with the highest levels. Patients with low levels of both RRM1 and RRM2 had a significantly higher response rate (60 vs 14.2%; P=0.049), time to progression (9.9 vs 2.3 months; P=0.003) and overall survival (15.4 vs 3.6; P=0.031) than patients with high levels of both RRM1 and RRM2. Ribonucleotide reductase subunit M1 and RRM2 mRNA expression in lung adenocarcinoma tumours is associated with clinical outcome to docetaxel/gemcitabine. Prospective studies are warranted to evaluate the role of these markers in tailoring chemotherapy.
L-lactate transport in Ehrlich ascites-tumour cells (1976)

Ehrlich ascites-tumour cells were investigated with regard to their stability to transport L-lactate by measuring either the distribution of [14C]lactate or concomitant H+ ion movements. The movement of lactate was dependent on the pH difference across the cell membrane and was electroneutral, as evidenced by an observed 1:1 antiport for OH- ions or 1:1 symport with H+ ions. 2. Kinetic experiments showed that lactate transport was saturable, with an apparent Km of approx. 4.68 mM and a Vmax. as high as 680 nmol/min per mg of protein at pH 6.2 and 37°C. 3. Lactate transport exhibited a high temperature dependence (activation energy = 139 kJ/mol). 4. Lactate transport was inhibited competitively by (a) a variety of other substituted monocarboxylic acids (e.g. pyruvate, Ki = 6.3 mM), which were themselves transported, (b) the non-transportable analogues α-cyano-4-hydroxycinnamate (Ki = 0.5 mM), α-cyano-3-hydroxycinnamate (Ki = 2mM) and DL-p-hydroxyphenyl-lactate (Ki = 3.6 mM) and (c) the thiol-group reagent mersalyl (Ki = 125 muM). 5. Transport of simple monocarboxylic acids, including acetate and propionate, was insensitive to these inhibitors; they presumably cross the membrane by means of a different mechanism. 6. Experiments using saturating amounts of mersalyl as an “inhibitor stop” allowed measurements of the initial rates of net influx and of net efflux of [14C]lactate. Influx and efflux of lactate were judged to be symmetrical reactions in that they exhibited similar concentration dependence. 7. It is concluded that lactate transport in Ehrlich ascites-tumour cells is mediated by a carrier capable of transporting a number of other substituted monocarboxylic acids, but not unsubstituted short-chain aliphatic acids.
Expression of antigenic crossreactivity to RD114 p 30 protein in a human fibrosarcoma cell line. (1977)

An antigen crossreacting with the 30,000-molecular-weight protein (p30) of the feline endogenous oncornavirus (RD114) was detected in a well-characterized human fibrosarcoma cell line, HT1080, by indirect immunofluorescence. Three antisera against RD114 p30 gave similar positive results, while two antisera prepared against simian sarcoma virus p30, one antiserum prepared against murine leukemia virus p30, and one antiserum prepared against feline leukemia virus p30 gave no immunofluorescence. The reactivity observed with the antiserum against RD114 p30 was detected in 10-40% of the cells at early passages and was no longer expressed by the forty-first subculture. The reactivity could be removed by adsorption of the antiserum with RD114-infected dog or human cells, but not by uninfected cells or by cells infected with an antigenically unrelated oncornavirus, feline leukemia virus. Neither complete virus particles nor reverse transcriptase (RNA-dependent DNA nucleotidyltransferase) activity was detected in the culture. These experiments suggest that the fibrosarcoma cell line is expressing an antigen related to the p30 protein of RD114 baboon endogenous virus group of oncornaviruses without producing complete virions.
Cellular Traction Stresses Increase with Increasing Metastatic Potential (2012)

Cancer cells exist in a mechanically and chemically heterogeneous microenvironment which undergoes dynamic changes throughout neoplastic progression. During metastasis, cells from a primary tumor acquire characteristics that enable them to escape from the primary tumor and migrate through the heterogeneous stromal environment to establish secondary tumors. Despite being linked to poor prognosis, there are no direct clinical tests available to diagnose the likelihood of metastasis. Moreover, the physical mechanisms employed by metastatic cancer cells to migrate are poorly understood. Because metastasis of most solid tumors requires cells to exert force to reorganize and navigate through dense stroma, we investigated differences in cellular force generation between metastatic and non-metastatic cells. Using traction force microscopy, we found that in human metastatic breast, prostate and lung cancer cell lines, traction stresses were significantly increased compared to non-metastatic counterparts. This trend was recapitulated in the isogenic MCF10AT series of breast cancer cells. Our data also indicate that increased matrix stiffness and collagen density promote increased traction forces, and that metastatic cells generate higher forces than non-metastatic cells across all matrix properties studied. Additionally, we found that cell spreading for these cell lines has a direct relationship with collagen density, but a biphasic relationship with substrate stiffness, indicating that cell area alone does not dictate the magnitude of traction stress generation. Together, these data suggest that cellular contractile force may play an important role in metastasis, and that the physical properties of the stromal environment may regulate cellular force generation. These findings are critical for understanding the physical mechanisms of metastasis and the role of the extracellular microenvironment in metastatic progression.
Topological Kondo Effect with Majorana Fermions (2012)

The Kondo effect is a striking consequence of the coupling of itinerant electrons to a quantum spin with degenerate energy levels. While degeneracies are commonly thought to arise from symmetries or fine-tuning of parameters, the recent emergence of Majorana fermions has brought to the fore an entirely different possibility: a topological degeneracy that arises from the nonlocal character of Majorana fermions. Here we show that nonlocal quantum spins formed from these degrees of freedom give rise to a novel topological Kondo effect. This leads to a robust non-Fermi liquid behavior, known to be difficult to achieve in the conventional Kondo context. Focusing on mesoscopic superconductor devices, we predict several unique transport signatures of this Kondo effect, which would demonstrate the nonlocal quantum dynamics of Majorana fermions and validate their potential for topological quantum computation.
Preoperative Delays in the US Medicare Population With Breast Cancer (2012)

Waiting times for breast cancer surgery have increased in Medicare patients, and measurable delays are associated with demographics and preoperative evaluation components. If such increases continue, periodic assessment may be required to rule out detrimental effects on outcomes.