gebhart/patrepeval huggingface dataset:
Transcriptional regulation of the <i>agr</i> locus and the identification of DNA binding residues of the global regulatory protein SarR in <i>Staphylococcus aureus</i> (2006)

Many members of the transcriptional regulator SarA protein family are winged-helix proteins that are involved in gene regulation essential to Staphylococcus aureus pathogenesis. Investigation of the mechanism by which this family of genes acts at the molecular level will likely contribute to the understanding of the pathogenesis process and enhance the potential for the development of inhibitors capable of controlling S. aureus infections. Our previously published studies demonstrate that SarR is a repressor of sarA expression. Here, we show that SarR (a member of the SarA protein family) in part regulates agr expression by direct binding to the agr intergenic promoter region as determined by gel shift and DNase I footprinting assays. Analysis of the double sarA/sarR mutant in the early phase of growth reveals its significant role in regulating agr expression as compared with single mutants. Based on the previously reported crystal structure of SarR, we conducted site-specific mutagenesis and demonstrate that K52 residues within helix-turn-helix (HTH), K80, R82 and R88 (in the wing) and L105 (in the alpha5 helix) are important for DNA binding. Interestingly, SarR and SarA binding sites on the agr promoter are confined within the same region of DNA. Additional gel shift studies with SarR and SarA suggest that these two proteins may bind the same region of the agr promoter.
Wireless RFID-Based Thermal Bubble Type Accelerometer and Monitor System Design (2010)

This research proposes a wireless RFID-based thermal bubble accelerometer design, and relates more particularly for the technology to manufacture it on a flexible substrate. The key technology is to integrate both a thermal bubble accelerometer and a wireless RFID antenna on the same substrate, such that the accelerometer is very convenient for usage. In this paper we use xenon inert gas in the chamber with heavier molecular weight to increase the acceleration sensitivity instead of traditional air or carbon dioxide. On the other hand, the specific heat of xenon gas is also lower so that the bandwidth of the proposed accelerometer is larger and the power consumption is lower. In addition, the inner shape of the chamber is changed as hemisphere instead of rectangular type, comparisons are also made. We have seen that the sensitivity of the proposed design is better.
Nanotube x-ray for cancer therapy: a compact microbeam radiation therapy system for brain tumor treatment (2014)

Microbeam radiation therapy (MRT) is a promising preclinical modality for cancer treatment, with remarkable preferential tumoricidal effects, that is, tumor eradication without damaging normal tissue functions. Significant lifespan extension has been demonstrated in brain tumor-bearing small animals treated with MRT. So far, MRT experiments can only be performed in a few synchrotron facilities around the world. Limited access to MRT facilities prevents this enormously promising radiotherapy technology from reaching the broader biomedical research community and hinders its potential clinical translation. We recently demonstrated, for the first time, the feasibility of generating microbeam radiation in a laboratory environment using a carbon nanotube x-ray source array and performed initial small animal studies with various brain tumor models. This new nanotechnology-enabled microbeam delivery method, although still in its infancy, has shown promise for achieving comparable therapeutic effects to synchrotron MRT and has offered a potential pathway for clinical translation.
Time-varying continuous-time optimisation with pre-defined finite-time stability (2020)

In this paper, we propose a new family of continuous-time optimisation algorithms based on discontinuous second-order gradient optimisation flows, with finite-time convergence guarantees to local optima, for locally strongly convex (time-varying) cost functions. To analyse our flows, we first extend a well-know Lyapunov inequality condition for finite-time stability, to the case of (time-varying) differential inclusions. We then prove the convergence of these second-order flows in finite-time. In some particular cases, we can show that the finite-time convergence can be pre-defined by the user. We propose a robustification of the flows to bounded additive uncertainties and extend some of the results to the case of constrained optimisation. We show the performance of these flows on well-known optimisation benchmarks, namely, the Rosenbrock function, and the Rastringin function.
MicroRNA Directs mRNA Cleavage of the Transcription Factor <i>NAC1</i> to Downregulate Auxin Signals for Arabidopsis Lateral Root Development (2005)

Although several plant microRNAs (miRNAs) have been shown to play a role in plant development, no phenotype has yet been associated with a reduction or loss of expression of any plant miRNA. Arabidopsis thaliana miR164 was predicted to target five NAM/ATAF/CUC (NAC) domain-encoding mRNAs, including NAC1, which transduces auxin signals for lateral root emergence. Here, we show that miR164 guides the cleavage of endogenous and transgenic NAC1 mRNA, producing 3'-specific fragments. Cleavage was blocked by NAC1 mutations that disrupt base pairing with miR164. Compared with wild-type plants, Arabidopsis mir164a and mir164b mutant plants expressed less miR164 and more NAC1 mRNA and produced more lateral roots. These mutant phenotypes can be complemented by expression of the appropriate MIR164a and MIR164b genomic sequences. By contrast, inducible expression of miR164 in wild-type plants led to decreased NAC1 mRNA levels and reduced lateral root emergence. Auxin induction of miR164 was mirrored by an increase in the NAC1 mRNA 3' fragment, which was not observed in the auxin-insensitive mutants auxin resistant1 (axr1-12), axr2-1, and transport inhibitor response1. Moreover, the cleavage-resistant form of NAC1 mRNA was unaffected by auxin treatment. Our results indicate that auxin induction of miR164 provides a homeostatic mechanism to clear NAC1 mRNA to downregulate auxin signals.
An Enhanced Approach to Cloud-based Privacy-preserving Benchmarking (2019)

Benchmarking is an important measure for companies to investigate their performance and to increase efficiency. As companies usually are reluctant to provide their key performance indicators (KPIs) for public benchmarks, privacy-preserving benchmarking systems are required. In this paper, we present an enhanced privacy-preserving benchmarking protocol, which we implemented and evaluated based on the real-world scenario of product cost optimisation. It is based on homomorphic encryption and enables cloud-based KPI comparison, providing a variety of statistical measures. The theoretical and empirical evaluation of our benchmarking system underlines its practicability.
Costimulation through ICAM-1 induces the differentiation of human naive CD4+ T cells to regulatory T cells: acquisition of distinct signaling and homing profiles during differentiation (89.39) (2009)

Abstract Inducible regulatory T (Treg) cells are important mediators of peripheral tolerance that arise by mechanisms not fully defined. We have previously shown that a subset of human naïve CD4+ T cells that are costimulated through Intercellular Adhesion Molecule-1 (ICAM-1) will differentiate into cells with a Foxp3+CD25+CD127(-) phenotype and suppressive function characteristic of inducible Treg cells. Our present work identifies some of the signaling pathways that are activated during this differentiation process. We also characterize some of the chemokine receptors and other homing markers that are displayed on these Treg cells, including CCR7, CD62L, and specific integrins. These results help clarify the signaling requirements for in vitro differentiation of human naïve CD4+ T cells to Treg cells after costimulation through ICAM-1 and suggest possible microenvironments in which these cells could migrate and function during immune responses in vivo. This work was supported by the National Institute on Aging/NIH.
Digital Topological Analysis of In Vivo Magnetic Resonance Microimages of Trabecular Bone Reveals Structural Implications of Osteoporosis (2001)

Osteoporosis is a disease characterized by bone volume loss and architectural deterioration. The majority of work aimed at evaluating the structural implications of the disease has been performed based on stereologic analysis of histomorphometric sections. Only recently noninvasive imaging methods have emerged that provide sufficient resolution to resolve individual trabeculae. In this article, we apply digital topological analysis (DTA) to magnetic resonance microimages (mu-MRI) of the radius obtained at 137 x 137 x 350 microm3 voxel size in a cohort of 79 women of widely varying bone mineral density (BMD) and vertebral deformity status. DTA is a new method that allows unambiguous determination of the three-dimensional (3D) topology of each voxel in a trabecular bone network. The analysis involves generation of a bone volume fraction map, which is subjected to subvoxel processing to alleviate partial volume blurring, followed by thresholding and skeletonization. The skeletonized images contain only surfaces, profiles, curves, and their mutual junctions as the remnants of trabecular plates and rods after skeletonization. DTA parameters were compared with integral BMD in the lumbar spine and femur as well as MR-derived bone volume fraction (BV/TV). Vertebral deformities were determined based on sagittal MRIs of the spine with a semiautomatic method and the number of deformities counted after threshold setting. DTA structural indices were found the strongest discriminators of subjects with deformities from those without deformities. Subjects with deformities (n = 29) had lower topological surface (SURF) density (p < 0.0005) and surface-to-curve ratio (SCR; a measure of the ratio of platelike to rodlike trabeculae; p < 0.0005) than those without. Profile interior (PI) density, a measure of intact trabecular rods, was also lower in the deformity group (p < 0.0001). These data provide the first in vivo evidence for the structural implications inherent in postmenopausal osteoporosis accompanying bone loss, that is, the conversion of trabecular plates to rods and disruption of rods due to repeated osteoclastic resorption.
26-Hydroxycholesterol. Identification and quantitation in human serum. (1981)

Using isotope dilution mass spectrometry, 26-hydroxycholesterol was identified in the serum of normal adults. Total values ranged from 9.2 to 25.6 micrograms/100 ml of which 31-35% was free sterol. Density gradient ultracentrifugation indicates that the steroid is distributed among the low and high density lipoproteins.
Antigenic Variation of the Dengue Virus 2 Genotypes Impacts the Neutralization Activity of Human Antibodies in Vaccinees (2020)

Dengue virus (DENV) infects an estimated 390 million people each year worldwide. As tetravalent DENV vaccines have variable efficacy against DENV serotype 2 (DENV2), we evaluated the role of genetic diversity within the pre-membrane (prM) and envelope (E) proteins of DENV2 on vaccine performance. We generated a recombinant DENV2 genotype variant panel with contemporary prM and E isolates that are representative of global genetic diversity. The DENV2 genotype variants differ in growth kinetics, morphology, and virion stability. Importantly, the DENV2 genotypic variants are differentially neutralized by monoclonal antibodies, polyclonal serum neutralizing antibodies from DENV2-infected human subjects, and vaccine-elicited antibody responses from the TV003 NIH DENV2 monovalent and DENV tetravalent vaccines. We conclude that DENV2 prM and E genetic diversity significantly modulates antibody neutralization activity. These findings have important implications for dengue vaccines, which are being developed under the assumption that intraserotype variation has minimal impact on neutralizing antibodies.
Antibodies targeting hepatoma-derived growth factor as a novel strategy in treating lung cancer (2009)

Hepatoma-derived growth factor (HDGF) is overexpressed in lung cancer and the overexpression correlates with aggressive biological behaviors and poor clinical outcomes. We developed anti-HDGF monoclonal antibodies and tested their antitumor activity in lung cancer xenograft models. We also determined biological effects in tumors treated with the antibody alone or in combination with bevacizumab/avastin (an anti-vascular endothelial growth factor antibody) and/or gemcitabine (a chemotherapeutic agent). We found the anti-HDGF was effective to inhibit tumor growth in non-small cell lung cancer xenograft models. In the A549 model, compared with control IgG, tumor growth was substantially inhibited in animals treated with anti-HDGF antibodies, particularly HDGF-C1 (P = 0.002) and HDGF-H3 (P = 0.005). When HDGF-H3 was combined with either bevacizumab or gemcitabine, we observed enhanced tumor growth inhibition, particularly when the three agents were used together. HDGF-H3-treated tumors exhibited significant reduction of microvessel density with a pattern distinctive from the microvessel reduction pattern observed in bevacizumab-treated tumors. HDGF-H3-treated but not bevacizumab-treated tumors also showed a significant increase of apoptosis. Interestingly, many of the apoptotic cells in HDGF-H3-treated tumors are stroma cells, suggesting that the mechanism of the antitumor activity is, at least in part, through disrupting formation of tumor-stroma structures. Our results show that HDGF is a novel therapeutic target for lung cancer and can be effectively targeted by an antibody-based approach.
Correction of ECG variations due to non-standard electrode positions (2002)

Electrode positions for continuous monitoring of 12-lead ECG are different from those for recording a standard 12-lead ECG. To reduce noise and to minimize false alarms, proximal placement of the limb leads is preferred over the standard location at the wrists and ankles. These differences are often associated with apparent frontal QRS-axis shifts, disappearing Q-waves in the inferior leads and marked changes of R-amplitudes in leads I and II. These changes make it difficult to compare ECGs. This study presents a general and patient-specific method to correct for these changes.
Free-breathing T2* mapping using respiratory motion corrected averaging (2015)

A free-breathing approach to T2* mapping is demonstrated to produce consistently good quality maps in the presence of respiratory motion and arrhythmias.
Antibiotic–cell‐penetrating peptide conjugates targeting challenging drug‐resistant and intracellular pathogenic bacteria (2021)

The failure to treat everyday bacterial infections is a current threat as pathogens are finding new ways to thwart antibiotics through mechanisms of resistance and intracellular refuge, thus rendering current antibiotic strategies ineffective. Cell-penetrating peptides (CPPs) are providing a means to improve antibiotics that are already approved for use. Through coadministration and conjugation of antibiotics with CPPs, improved accumulation and selectivity with alternative and/or additional modes of action against infections have been observed. Herein, we review the recent progress of this antibiotic-cell-penetrating peptide strategy in combatting sensitive and drug-resistant pathogens. We take a closer look into the specific antibiotics that have been enhanced, and in some cases repurposed as broad-spectrum drugs. Through the addition and conjugation of cell-penetrating peptides to antibiotics, increased permeation across mammalian and/or bacterial membranes and a broader range in bacterial selectivity have been achieved.
Real-time Embedded Panorama Mosaic System for Digital Camera (2008)

We propose an embedded image panorama mosaic system which can operate in real-time in digital cameras or cellphone cameras. The users can check the panorama result as soon as all the images are acquired by the camera. The proposed system shows comparable performance to other PC-based methods.
New insights into the ORF2 capsid protein, a key player of the hepatitis E virus lifecycle (2019)

Hepatitis E Virus (HEV) genome encodes three proteins including the ORF2 capsid protein. Recently, we demonstrated that HEV produces three different forms of ORF2: (i) the ORF2i form (infectious ORF2) which is the component of infectious particles, (ii) the secreted ORF2g (glycosylated ORF2) and ORF2c (cleaved ORF2) forms that are not associated with infectious particles, but are the major antigens in HEV-infected patient sera. The ORF2 protein sequence contains three highly conserved potential N-glycosylation sites (N1, N2 and N3). The status and biological relevance of ORF2 N-glycosylation in HEV lifecycle remain to be elucidated. Here, we generated and extensively characterized a series of ORF2 mutants in which the three N-glycosylation sites were mutated individually or in combination. We demonstrated that the ORF2g/c protein is N-glycosylated on N1 and N3 sites but not on the N2 site. We showed that N-glycosylation of ORF2 protein does not play any role in replication and assembly of infectious HEV particles. We found that glycosylated ORF2g/c forms are very stable proteins which are targeted by patient antibodies. We also demonstrated that the ORF2i protein is translocated into the nucleus of infected cells. Hence, our study led to new insights into the molecular mechanisms of ORF2 expression.
Creasing of Multilayer Polymer Films (2014)

A soft elastic material placed under compressive stress can undergo a surface creasing instability in which the free interface becomes directly unstable to the formation of sharp self-contacting features. The resulting changes in contact between neighboring surface regions, and the non-affine in-plane displacement of material elements, provide unique opportunities for designing shape-programmable materials. This presentation will highlight several recent advances related to the formation of creases on the surfaces of multilayer polymer films. In one example, we study the influence of pre-compression of the substrate in a soft elastic bilayer as a means to tune hysteresis between crease onset and disappearance, yielding well-defined bistability. In another example, we consider the behavior of patterned stiff films on soft substrates, wherein the interplay between wrinkling and creasing modes offers promise for the design of new types of electronic switches with potential applications in flexible electronics.
<title>True-time-delay transmit/receive optical beam-forming system for phased arrays and other signal processing applications</title> (1994)

This paper addresses the problem of dynamic optical processing for the control of phased array antennas. The significant result presented is the demonstration of a continuously variable photonic RF/microwave delay line. Specifically, it is shown that by applying spatial frequency dependent optical phase compensation in an optical heterodyne process, variable RF delay can be achieved over a prescribed frequency band. Experimental results which demonstrate the performance of the delay line with regard to both maximum delay and resolution over a broad bandwidth are presented. Additionally, a spatially integrated optical system is proposed for control of phased array antennas. The integrated system provides mechanical stability, essentially eliminates the drift problems associated with free space optical systems, and can provide high packing density. This approach uses a class of spatial light modulator known as a deformable mirror device and leads to a steerable arbitrary antenna radiation pattern of the true time delay type. Also considered is the ability to utilize the delay line as a general photonic signal processing element in an adaptive (reconfigurable) transversal frequency filter configuration. Such systems are widely applicable in jammer/noise canceling systems, broadband ISDN, spread spectrum secure communications and the like.
Methods for the Construction and Propagation of Recombinant Adeno-Associated Virus Vectors (2003)

The development of gene transfer vectors from the human parvovirus, adeno-associated virus (AAV), has provided scientists with an efficient and effective way of delivering genes into mammalian cells. This chapter aims to explore the various practical aspects of the AAV vector system, and in consequence, to highlight particular difficulties that may be encountered by workers new to the field. However, before describing the methodology involved in the generation of recombinant AAV vectors, it is of value to briefly discuss the structure and life cycle of this unique virus. Detailed and more extensive reviews that describe the biology of adeno-associated virus are also available (1-3).
GPU Instruction Hotspots Detection Based on Binary Instrumentation Approach (2019)

The problem of profiling a compute kernel running on the CPU is mostly solved with the help of technologies that explore a code behavior in detail. But with a last decade trend when computation spreads to other devices, more power and performance efficient, we face a high need for fine-grain code profiling on such devices. Traditional methods are not always sufficient: program counter sampling requires special hardware support, and performance simulation works slowly. In this paper, we introduce a novel method for instruction hotspots detection based on the binary instrumentation approach and demonstrate it on Intel® Graphics. This method relies on three key principles: measurement with instruction block granularity, conscious placement of probes, and combination of static and runtime information. We demonstrate its ability to highlight the hottest instructions and lines of code, and its relatively low runtime overhead comparable to a native run. The method is applicable to GPUs and accelerators with in-order architecture, and could be used in a rapidly growing segment of accelerator solutions for computer vision and artificial intelligence.
Synthesis and Characterization of Metal Aluminophosphate Molecular Sieves (1989)

Novel metal aluminophosphate molecular sieves (MeAPO-n) have been synthesized, where Me can be the divalent form of Co, Fe, Mg, Mn, or Zn, or trivalent Fe. These MeAPO molecular sieves have tetrahedral frameworks containing metal, aluminum, and phosphorus, and exhibit a wide range of compositions within the general formula 0 - 0.3 R : (MexAlyPz)O2 where x, y, and z represent normalized mole fractions with x = 0.01-0.25, y = 0.15-0.52 and z = 0.35-0.6 and R refers to the organic template, an amine or quaternary ammonium salt. The structures can be envisioned as hypothetical AlPO4 frameworks with metal incorporated into some of the Al sites. The anionic framework charge generated by such substitution leads to Bronsted acidity. The 18 reported MeAPO structure-types include structures topologically related to zeolites, AlPO4, and SAPO molecular sieves as well as novel structures. The catalytic properties of MeAPO's are both metal and structure dependent, and as acidic catalysts they range in activity from low to high.
A Technique to Enhance the Frequency Bandwidth of Contactless Magnetoresistive Current Sensors (2016)

Isolated wideband current measurement is required in many power electronic converters when the switching frequency is above 1 MHz. Typically current passing through a printed circuit board trace induces a highly nonuniform magnetic field which varies as a function of frequency and position relative to the trace. This paper proposes a technique to increase the frequency bandwidth of anisotropic magnetoresistive (AMR) current sensors and simultaneously to intensify and normalize the field detected by the sensor in the frequency range of interest, i.e., DC-5 MHz. We demonstrate experimentally that the proposed technique yields significant enhancement in detection bandwidth of AMR current sensors.