gebhart/patrepeval huggingface dataset:
Automatic Tip-Steering of Concentric Tube Robots in the Trachea Based on Visual SLAM (2020)

Concentric tube robots are continuum robots particularly well-suited for minimally-invasive surgery. Their small diameter, natural free channel and snake-like shape unlock the potential for applications that require a high degree of dexterity in confined spaces. The synthesis and planning of such robots are generally based on the patient's anatomy and the type of surgery to be performed. However, their practical deployment can be challenging. Open-loop approaches are prone to errors due to modeling accuracy or physiological motions of the patient during the procedure, and human-in-the-loop approaches require specific skills from the surgeon. In this article, we propose an automatic tip-steering approach for concentric tube robots based on visual SLAM (simultaneous localization and mapping). This allows a closed-loop control scheme to compensate for open-loop errors, and provides to the surgeon the opportunity to focus on the medical procedure, simplifying the management of the deployment. A method is proposed in the case of a robot geometry that achieves approximate follow-the-leader deployment. It is validated by performing an automatic tip-steering task in the trachea using a realistic simulator for concentric tube robots.
A Concise Asymmetric Route for the Synthesis of a Novel Class of Glucocorticoid Mimetics Containing a Trifluoromethyl‐Substituted Alcohol. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
High-bitrate visible light communication and high-quality solid-state lighting using superluminescent diode (2019)

King Abdulaziz City for Science and Technology (KACST), Grant No. KACST TIC R2-FP- 008; This work was partially supported by the King Abdullah University of Science and Technology (KAUST) baseline funding, BAS/1/1614-01-01; KAUST equipment funding KCR/1/2081-01-01; GEN/1/6607-01-01; KAUST-KFUPM Special Initiative (KKI) Program, REP/1/2878-01-01.
P3‐341: Increased membrane cholesterol may render mature hippocampal neurons more susceptible to beta‐amyloid‐induced calpain activation and tau toxicity (2008)

A primary focus of Alzheimer's disease (AD) research has been to elucidate the relationship between beta amyloid (Aβ) and neurite degeneration; yet, it remains unknown why AD affects primarily the elderly. We have previously described a process of neurite degeneration involving Aβ-dependent calpain activation, resulting in the generation of a neurotoxic 17 kDa tau fragment in mature cultured hippocampal neurons. However, the potential developmental regulation of this process has not been investigated. Therefore, we analyzed to what extent Aβ toxicity differs in neurons of different developmental stages, and whether membrane cholesterol, a potential player in AD pathology, may mediate these differences. Seven (young) and 21 (mature) days in culture hippocampal neurons were cultured in the absence or presence of 10 μM pre-aggregated Aβ1–40 for 24 hours. We used immunocytochemistry and immunoblotting to detect Aβ-induced neurodegenerative morphology and 17 kDa tau production, respectively. Aβ-dependent calpain activity in these lysates was measured by immunoblotting for cleaved spectrin as well as by a calpain activity assay. Membrane cholesterol was detected in young and mature neurons via filipin labeling and the Amplex Red cholesterol assay to assess the potential mediatory role of cholesterol in these mechanisms of Aβ toxicity. To determine whether low cholesterol in young neurons was protective against Aβ-induced calpain activation and toxicity, we repeated the aforementioned experiments in mature neurons depleted of cholesterol using methyl-β-cyclodextrin (MBCD). Aβ treatment induced neurodegenerative morphology and 17 kDa tau production only in mature neurons as compared to young ones. Our results also demonstrated that 17 kDa tau production is regulated by elevated calpain activity. These age-dependent changes in Aβ-induced calpain activity were accompanied by an age-dependent increase in neuron membrane cholesterol; thus, suggesting that mediatory components of this neurodegenerative process likely lie upstream of calpain. Concurringly, MBCD treatment of mature neurons significantly reduced their vulnerability to Aβ-induced calpain activation and 17 kDa tau production under these experimental conditions. Together, these results revealed an age-dependent increase in susceptibility of hippocampal neurons to Aβ-induced calpain-mediated 17 kDa tau production and degeneration. Furthermore, they identified membrane cholesterol as a potential mediator of these mechanisms.
Chromosome Conformation Capture (3C) in Budding Yeast (2015)

Chromosome conformation capture (3C) is a method for studying chromosomal organization that takes advantage of formaldehyde cross-linking to measure the spatial association of two pieces of chromatin. The 3C method begins with whole-cell formaldehyde fixation of chromatin. After cell lysis, solubilized chromatin is digested with a type II restriction endonuclease, and cross-linked DNA fragments are ligated together. Cross-links are reversed by degradation with proteinase K, and chimeric DNA molecules are purified by standard phenol:chloroform extraction. The resulting 3C library represents chromatin fragments that may be separated by large genomic distances or located on different chromosomes, but are close enough in three-dimensional space for cross-linking. Locus-specific oligonucleotide primers are used to detect interactions of interest in the 3C library using end-point polymerase chain reaction (PCR).
Analysis of the N‐terminal DNA binding domain of the IS<i>30</i> transposase (2004)

IS30 is the founding member of a large family of widely spread bacterial insertion sequences with closely related transposases. The N-terminal end of the IS30 transposase had been shown to retain sequence-specific DNA binding activity and to protect the IS30 terminal inverted repeats. Structural predictions revealed the presence of a helix-helix-turn-helix motif (H-HTH2) which, in the case of IS30, is preceded by an additional helix-turn-helix motif (HTH1). Analysis of deletion and point mutants in this region revealed that both motifs are important for IS30 transposition. IS30 exhibits two types of insertion specificity preferring either a 24 bp palindromic hot-spot (GOHS) or sequences resembling its ends [left and right terminal inverted repeat (IRL and IRR)]. Results are presented suggesting that the HTH1 region is required for GOHS targeting and interferes with the inverted repeat (IR) targeting. On the other hand, H-HTH2 appears to be required for both. The binding activities of the mutant proteins to the terminal IS30 IRs as measured by gel retardation correlated well with these results. Furthermore, close inspection of the H-HTH2 region revealed significant amino acid identity with a similar predicted secondary structure carried by the transcriptional regulator FixJ of Sinorhizobium meliloti and involved in FixJ binding to its target sequence. This suggests that FixJ and IS30 transposase share similar sequence-specific DNA binding mechanisms.
Cracking in a Cristobalite-Containing Mullite Body during Cooling. (2000)

Cracking of a cristobalite-containing mullite body at the middle stage of crystallization during cooling was investigated by acoustic emission (AE) and the crack formation was discussed. The specimen was composed of an outside layer of crystalline cristobalite and the inner part remaining as a glass phase. There are two kinds of cracks, of which the one is almost parallel to the surface of specimen at the boundary between the outside layer and the inner part and the other is perpendicular to the surface. AE signals indicated that the cracks occurred in two stages, the first stage at the temperature range 750-650°C and the second stage below 250°C. Cracks parallel to the surface were formed at the first stage due to a mismatch in thermal expansion coefficient between the outside layer and the inner part. Those perpendicular to the surface were generated at the second stage under a tensile stress developed in the outside layer, which was caused by the β-α phase transition of cristobalite, in the direction parallel to the surface
A 57–63 GHz quadrature VCO in CMOS 65 nm (2009)

A 60 GHz I-Q VCO covering the frequency range from 57.5 to 63.1 GHz is presented. It exhibits a phase noise of − 95.3 dBc/Hz at 1 MHz offset from a 57.5 GHz carrier. Fabricated in a 65 nm bulk CMOS process, the two VCO-cores consume 30 mA in total from a 1.2 V supply.
Backscattered electrons from X-ray target (2014)

X-rays are radiated from a target when an electron beam is accelerated and collides it. When high energy electrons struck a metal target, significant backscattered electrons could be generated and reduce the image sharpness. This paper will describe the Monte Carlo algorithm to analyze backscattered electrons in Beam Optics Analyzer (BOA) and present simulation results of an X-ray tube. The results will be compared with experimental data.
Inflammation and cancer: interweaving microRNA, free radical, cytokine and p53 pathways (2009)

Chronic inflammation and infection are major causes of cancer. There are continued improvements to our understanding of the molecular connections between inflammation and cancer. Key mediators of inflammation-induced cancer include nuclear factor kappa B, reactive oxygen and nitrogen species, inflammatory cytokines, prostaglandins and specific microRNAs. The collective activity of these mediators is largely responsible for either a pro-tumorigenic or anti-tumorigenic inflammatory response through changes in cell proliferation, cell death, cellular senescence, DNA mutation rates, DNA methylation and angiogenesis. As our understanding grows, inflammatory mediators will provide opportunities to develop novel diagnostic and therapeutic strategies. In this review, we provide a general overview of the connection between inflammation, microRNAs and cancer and highlight how our improved understanding of these connections may provide novel preventive, diagnostic and therapeutic strategies to reduce the health burden of cancer.
Investigation of New HPCMP CREATETM-AV Kestrel Capabilities for Simulation of Extraction Parachutes (2022)

View Video Presentation: https://doi.org/10.2514/6.2022-3898.vid The recent efforts towards realistic simulation of extraction parachutes from a C-17 in airdrop configurations are presented. The problem considers the stability and control analysis of rigid models, single and cluster of three ring-slot chutes with zero and 20% geometric porosity, in the freestream and behind the C-17 aircraft with an open cargo door and extended flaps. Specifically, this study uses the new capabilities of the CREATE-AV Kestrel simulation software. This includes: 1) prescribed-body motions to determine the chute stability and control characteristics over a wide range of angles of attack , 2) an adaptive mesh refinement method for capturing the wakes behind chutes, 3) a responding-body motion to study the stability of a chute cluster in free-stream and behind C-17 aircraft, 4) and finally a Catenary utility for modeling static lines attached to extraction chutes. Angle-of-attack sweep motions are used to generate the continues plots of aerodynamic over a wide range of angles of attack and to investigate the static stability characteristics. For responding-body motions, the weight and balance data of chutes were estimated; the chute then responds to aerodynamic forces and its weight. A ``ball" constraint was defined to keep the distance to the suspension line confluence point constant during the motion. The positions and Euler angles were then extracted and compared for these simulations. These motions determine dynamic stability characteristics of chutes. A Catenary capability is tested to include static and suspension lines during the responding-body motions. The results show that decreasing geometric porosity will increase the drag coefficient but makes the rigid chute model less stable. A rigid chute model positioned behind C-17 aircraft with open cargo ramp is less stable than a chute in freestream as well. Responding-body motions confirm that an extraction chute with 20% geometry is statically and dynamically stable in pitch direction. A rigid chute model with 0\% porosity undergoes large pitch angle oscillations with no damping seen during the simulated time.
Speed of Sound Measurement in Solids Using Polyvinylidene Fluoride (PVDF) Sensors (2013)

Piezoelectric film sensors such as polyvinylidene flouride (PVDF) generate an electrical voltage in response to an applied mechanical stress with a remarkably high sensitivity. They provide very fast response times and do not require extensive signal conditioning. This paper presents a straightforward method of measuring the speed of sound in solid materials and structures using commercial PVDF sensors. PVDF sensors are most commonly used to measure stresses applied in the sensors’ thickness direction. However, this requires that the sensors be located in the load path, which may result in damage to the sensor or affect the response of the system. In this paper, two PVDF sensors are bonded to the side of a structure and a small impact is applied to one end. The sensors are used to measure the time for the impact-induced plane stress wave to travel between the sensors. The observed speed of the propagating stress wave is shown to be in good agreement with the theoretical speed of sound for the material and finite element calculations. In addition, the finite element simulations confirm the validity of the plane wave assumption for non-ideal and non-uniform impact inputs.
ZrB<sub>2</sub>Substrate for Nitride Semiconductors (2003)

Zirconium diboride (ZrB2) has excellent properties as an electrically conductive substrate for nitride semiconductors. In this paper, the bulk growth of ZrB2 by a floating-zone method and some properties of ZrB2, together with a brief summary of heteroepitaxial growth of gallium nitride (GaN) by molecular beam epitaxy (MBE) and metalorganic vapor phase epitaxy (MOVPE), are presented. By optimizing the bulk growth conditions, a 20-mm-diameter ZrB2 single crystal was obtained. The cleavage direction of the ZrB2 (0001) substrate was confirmed to be parallel to [1120], which is parallel to that of GaN (0001). Epitaxial growth by both MBE and MOVPE was demonstrated. The grown n-type GaN/ZrB2 structure exhibited ohmic-like current–voltage behavior. These results indicate that ZrB2 has potential for application to the substrate for nitride semiconductors.
Tumor Necrosis Factor Receptor Superfamily 12 may Destabilize Atherosclerotic Plaques by Inducing Matrix Metalloproteinases (2001)

Immunohistochemical staining of human atherosclerotic plaques revealed expression of the tumor necrosis factor receptor superfamily (TNFRSF) 12 in regions rich in macrophage/foam cells. The role of TNFRSF12 in the functioning of monocytes in relation to atherogenesis was investigated by analysis of cellular events after stimulation of TNFRSF12 in a human macrophage-like cell line, THP-1. Activation of the THP-1 cells on plates coated with monoclonal antibody against TNFRSF12 induced the expression of matrix metalloproteinases (MMPs) -1, -9, and -13. Furthermore, the expression patterns of TNFRSF12 and the MMPs overlapped in atherosclerotic plaques. Signaling of TNFRSF12 may thus contribute to the induction of extracellular matrix degrading enzymes in macrophages.
Level of agreement among Latin American glaucoma subspecialists on the diagnosis and treatment of glaucoma: results of an online survey (2013)

This survey shows a high level of agreement on most aspects of glaucoma diagnosis and treatment among Latin American glaucoma experts. Areas of disagreement highlight the need for further evidence or education. These findings will be useful for guiding future efforts to optimize glaucoma practice by clinicians in Latin America.
A Simple and Low-Cost Method for the Preparation of Monodisperse Hollow Silica Spheres (2008)

This paper presents a simple and low-cost method to prepare hollow silica spheres. This method is just based on a PVP-involved emulsion polymerization and subsequent sol−gel process. PVP first participated in the polymerization reaction as a stabilizer or surfactant and then played a coupling agent role in the latter process. The polystyrene particles were dissolved subsequently or simultaneously during the sol−gel coating process to form hollow silica spheres. The influence of some parameters, such as the amount of PVP, the amount of NH4OH, and the amount of TEOS on the morphology of the hollow spheres was investigated. The parameters to control over the formation of all hollow spheres were also studied.
Automatic hotspot classification using pattern-based clustering (2008)

This paper proposes a new design check system that works in three steps. First, hotspots such as pinching/bridging are recognized in a product layout based on thorough process simulations. Small layout snippets centered on hotspots are clipped from the layout and similarities between these snippets are calculated by computing their overlapping areas. This is accomplished using an efficient, rectangle-based algorithm. The snippet overlapping areas can be weighted by a function derived from the optical parameters of the lithography process. Second, these hotspots are clustered using a hierarchical clustering algorithm. Finally, each cluster is analyzed in order to identify the common cause of failure for all the hotspots in that cluster, and its representative pattern is fed to a pattern-matching tool for detecting similar hotspots in new design layouts. Thus, the long list of hotspots is reduced to a small number of meaningful clusters and a library of characterized hotspot types is produced. This could lead to automated hotspot corrections that exploit the similarities of hotspots occupying the same cluster. Such an application will be the subject of a future publication.
A monoclonal antibody (12G5) directed against CXCR-4 inhibits infection with the dual-tropic human immunodeficiency virus type 1 isolate HIV-1(89.6) but not the T-tropic isolate HIV-1(HxB) (1997)

We used a monoclonal antibody (12G5) directed against an extracellular domain of CXCR-4 to investigate the role of this receptor in infection of immortalized lymphoid cell lines, peripheral blood mononuclear cells (PBMCs), and primary brain microglia with a dual-tropic strain of human immunodeficiency virus (HIV-1(89.6)) and a T-tropic strain (HIV-1(IIIB)). Addition of antibody 12G5 to cells prior to and during infection with HIV-1(89.6) inhibited p24 production 100- to 10,000-fold in CEMx174 and 174-CD4 cells and about 10-fold in PBMC cultures but had no activity against infection of either monocyte-derived macrophages or brain microglia. In contrast, 12G5 had little or no effect on infection of CEMx174 cells with HIV-1(IIIB) or HIV-1(HxB). To identify the region of the HIV-1(89.6) envelope that confers sensitivity to 12G5, we used chimeric molecular clones. Chimeras containing the V3 loop region of HIV-1(89.6) were inhibited by 12G5 to the same degree as wild-type HIV-1(89.6) whereas replication of those viruses containing the V3 loop of HIV-1(HxB) was not inhibited by the antibody. A similar pattern was seen in infections of a U87 glioblastoma line that coexpresses CD4 and CXCR-4. Antibody 12G5 was also able to block fusion between HeLa-CD4 cells and CEMx174 cells chronically infected with HIV-1(89.6) but had no effect on fusion mediated by cells chronically infected with HIV-1(IIIB). Taken together, these results suggest that different strains of HIV-1 may interact with different sites on CXCR-4 or may have different binding affinities for the coreceptor.
Killing of myeloid APCs via HLA class I, CD2 and CD226 defines a novel mechanism of suppression by human Tr1 cells (2011)

IL-10-producing CD4(+) type 1 regulatory T (Tr1) cells, defined based on their ability to produce high levels of IL-10 in the absence of IL-4, are major players in the induction and maintenance of peripheral tolerance. Tr1 cells inhibit T-cell responses mainly via cytokine-dependent mechanisms. The cellular and molecular mechanisms underlying the suppression of APC by Tr1 cells are still not completely elucidated. Here, we defined that Tr1 cells specifically lyse myeloid APC through a granzyme B (GZB)- and perforin (PRF)-dependent mechanism that requires HLA class I recognition, CD54/lymphocyte function-associated antigen (LFA)-1 adhesion, and activation via killer cell Ig-like receptors (KIRs) and CD2. Notably, interaction between CD226 on Tr1 cells and their ligands on myeloid cells, leading to Tr1-cell activation, is necessary for defining Tr1-cell target specificity. We also showed that high frequency of GZB-expressing CD4(+) T cells is detected in tolerant patients and correlates with elevated occurrence of IL-10-producing CD4(+) T cells. In conclusion, the modulatory activities of Tr1 cells are not only due to suppressive cytokines but also to specific cell-to-cell interactions that lead to selective killing of myeloid cells and possibly bystander suppression.
Role of the Angiotensin AT <sub>1</sub> Receptor in Rat Aortic and Cardiac PAI-1 Gene Expression (2000)

Although the renin-angiotensin system has been implicated in increasing plasminogen activator inhibitor-1 (PAI-1) expression, the role of the angiotensin type 1 (AT(1)) receptor is controversial. This report examines the effects of angiotensin peptides, angiotensin-converting enzyme inhibition, and AT(1) antagonism on rat aortic and cardiac PAI-1 gene expression. In vitro, angiotensin (Ang) I, Ang II, and angiotensin Arg(2)-Phe(8) (Ang III) were potent agonists of PAI-1 mRNA expression in rat aortic smooth muscle cells (RASMCs), and stimulation of PAI-1 by these peptides was blocked by the AT(1) antagonist candesartan. Angiotensin Val(3)-Phe(8) (Ang IV) and angiotensin Asp(1)-Pro(7) (Ang [1-7]) did not affect PAI-1 expression in RASMCs. In neonatal rat cardiomyocytes, Ang II increased PAI-1 mRNA expression by 4-fold (P<0.01), and this response was completely blocked by AT(1) receptor antagonism. Continuous intrajugular infusion of Ang II into Sprague-Dawley rats for 3 hours increased aortic and cardiac PAI-1 mRNA expression by 17- and 9 fold, respectively, and these Ang II responses were completely blocked by coinfusion with candesartan. Aortic and cardiac PAI-1 expressions were compared in spontaneously hypertensive rats and Wistar-Kyoto rats. PAI-1 expression in the aorta and heart from spontaneously hypertensive rats was 5.8-fold and 2-fold higher, respectively, than in control Wistar-Kyoto rats (P<0.05). Candesartan treatment for 1 week reduced aortic and cardiac PAI-1 expression in spontaneously hypertensive rats by 94% and 72%, respectively (P<0.05), but did not affect vascular PAI-1 levels in Wistar-Kyoto rats. These results demonstrate a role for the AT(1) receptor in mediating the effects of Ang II on aortic and cardiac PAI-1 gene expression.
Low Complexity Receiver Structures for Space-Time Coded Multiple-Access Systems (2002)

Multiuser detection for space-time coded synchronous multiple-access systems in the presence of independent Rayleigh fading is considered. Under the assumption of quasi-static fading, it is shown that optimal (full diversity achieving) space-time codes designed for single-user channels, can still provide full diversity in the multiuser channel. The joint optimal maximum likelihood multiuser detector, which can be implemented with a Viterbi-type algorithm, is derived for such space-time coded systems. Low complexity, partitioned detector structures that separate the multiuser detection and space-time decoding into two stages are also developed. Both linear and nonlinear multiuser detection schemes are considered for the first stage of these partitioned space-time multiuser receivers. Simulation results show that these latter methods achieve performance competitive with the single-user bound for space-time coded systems.