gebhart/patrepeval huggingface dataset:
Substrate Transfer for GaN based LEDs grown on Silicon (2011)

This paper focuses on the substrate transfer process which is applied after the fabrication of LEDs on 4 inch Si (111) wafers comprising p and n contact formation to the GaN layer. After applying a passivation layer, a bonding metal is deposited. The wafer is then bonded to a Si carrier substrate using metallic bonding. Next, the original Si (111) substrate is completely removed by grinding and wet etching. GaN-LEDs are thus transferred to a new carrier substrate. The last step is etching of the transferred GaN layer from the back to open the contacts. A surface roughening technique on the backside of the transferred GaN layer to improve the light extraction efficiency of GaN-LEDs is also investigated. All the issues of the substrate transfer process steps such as permanent Cu/Sn bonding, thinning by grinding and wet etching will be discussed in detailed. A typical issue occurring during processing of GaN-LEDs on Si substrates is high stress and related large wafer bow originating from the GaN layer and the thick Cu/Sn metal bonding layer. Such a large wafer bow causes problems for some automatic handling tools and processes like lithography. Solutions to manage the stress and wafer bow have been investigated.
Interferon-independent STING signaling promotes resistance to HSV-1 in vivo (2020)

The Stimulator of Interferon Genes (STING) pathway initiates potent immune responses upon recognition of DNA. To initiate signaling, serine 365 (S365) in the C-terminal tail (CTT) of STING is phosphorylated, leading to induction of type I interferons (IFNs). Additionally, evolutionary conserved responses such as autophagy also occur downstream of STING, but their relative importance during in vivo infections remains unclear. Here we report that mice harboring a serine 365-to-alanine (S365A) mutation in STING are unexpectedly resistant to Herpes Simplex Virus (HSV)-1, despite lacking STING-induced type I IFN responses. By contrast, resistance to HSV-1 is abolished in mice lacking the STING CTT, suggesting that the STING CTT initiates protective responses against HSV-1, independently of type I IFNs. Interestingly, we find that STING-induced autophagy is a CTT- and TBK1-dependent but IRF3-independent process that is conserved in the STING S365A mice. Thus, interferon-independent functions of STING mediate STING-dependent antiviral responses in vivo.
Effects of the source, surface, and sensor couplings and colorimetric of laser speckle pattern on the performance of optical imaging system (2011)

Optical imaging systems are widely used in different applications include tracking for portable scanners; input pointing devices for laptop computers, cell phones, and cameras, fingerprint-identification scanners, optical navigation for target tracking, and in optical computer mouse. We presented an experimental work to measure and analyze the laser speckle pattern (LSP) produced from different optical sources (i.e. various color LEDs, 3 mW diode laser, and 10mW He-Ne laser) with different produced operating surfaces (Gabor hologram diffusers), and how they affects the performance of the optical imaging systems; speckle size and signal-to-noise ratio (signal is represented by the patches of the speckles that contain or carry information, and noise is represented by the whole remaining part of the selected image). The theoretical and experimental studies of the colorimetry (color correction is done in the color images captured by the optical imaging system to produce realistic color images which contains most of the information in the image by selecting suitable gray scale which contains most of the informative data in the image, this is done by calculating the accurate Red-Green-Blue (RGB) color components making use of the measured spectrum for light sources, and color matching functions of International Telecommunication Organization (ITU-R709) for CRT phosphorus, Tirinton-SONY Model ) for the used optical sources are investigated and introduced to present the relations between the signal-to-noise ratios with different diffusers for each light source. The source surface coupling has been discussed and concludes that the performance of the optical imaging system for certain source varies from worst to best based on the operating surface. The sensor /surface coupling has been studied and discussed for the case of He-Ne laser and concludes the speckle size is ranged from 4.59 to 4.62 μm, which are slightly different or approximately the same for all produced diffusers (which satisfies the fact that the speckle size is independent on the illuminating surface). But, the calculated value of signal-tonoise ratio takes different values ranged from 0.71 to 0.92 for different diffuser. This means that the surface texture affects the performance of the optical sensor because, all images captured for all diffusers under the same conditions [same source (He-Ne laser), same distances of the experimental set-up, and the same sensor (CCD camera)].
Extracellular Matrix Remodeling by Fibroblast-MMP14 Regulates Melanoma Growth (2021)

Maintaining a balanced state in remodeling the extracellular matrix is crucial for tissue homeostasis, and this process is altered during skin cancer progression. In melanoma, several proteolytic enzymes are expressed in a time and compartmentalized manner to support tumor progression by generating a permissive environment. One of these proteases is the matrix metalloproteinase 14 (MMP14). We could previously show that deletion of MMP14 in dermal fibroblasts results in the generation of a fibrotic-like skin in which melanoma growth is impaired. That was primarily due to collagen I accumulation due to lack of the collagenolytic activity of MMP14. However, as well as collagen I processing, MMP14 can also process several extracellular matrices. We investigated extracellular matrix alterations occurring in the MMP14-deleted fibroblasts that can contribute to the modulation of melanoma growth. The matrix deposited by cultured MMP14-deleted fibroblast displayed an antiproliferative and anti-migratory effect on melanoma cells in vitro. Analysis of the secreted and deposited-decellularized fibroblast's matrix identified a few altered proteins, among which the most significantly changed was collagen XIV. This collagen was increased because of post-translational events, while de novo synthesis was unchanged. Collagen XIV as a substrate was not pro-proliferative, pro-migratory, or adhesive, suggesting a negative regulatory role on melanoma cells. Consistent with that, increasing collagen XIV concentration in wild-type fibroblast-matrix led to reduced melanoma proliferation, migration, and adhesion. In support of its anti-tumor activity, enhanced accumulation of collagen XIV was detected in peritumoral areas of melanoma grown in mice with the fibroblast's deletion of MMP14. In advanced human melanoma samples, we detected reduced expression of collagen XIV compared to benign nevi, which showed a robust expression of this molecule around melanocytic nests. This study shows that loss of fibroblast-MMP14 affects melanoma growth through altering the peritumoral extracellular matrix (ECM) composition, with collagen XIV being a modulator of melanoma progression and a new proteolytic substrate to MMP14.
Direct Laser Sintering of Metals (2018)

The use of a directed laser bealn source to selectively sinter multiple layers of\nbinderless metal powder for the purposes of rapid prototyping is described. The\nwork in this paper is restricted to -325 mesh iron powder, which was sintered\nusing a C\\V 50 W Nd:YAG laser to approximately 3.5% density. A subsequent\npost-treatlnent was perfornled to achieve a fully dense saulple. It is envisioned\nthat such a system can be used to manufacture functional metallic prototypes\ndirectly from CAD without part-specific tooling.
Low-ultraviolet circular dichroism spectroscopy of sequential peptides 1-63, 64-95, 96-128, and 129-168 derived from myelin basic protein of rabbit (1985)

Four sequential peptides (sequences 1-63, 64-95, 96-128, and 129-168) derived from rabbit myelin basic protein by thrombic cleavage were examined by low-ultraviolet circular dichroism spectroscopy in 0.5 mM tris(hydroxymethyl)aminomethane hydrochloride (pH approximately 7.2) containing 0-92% trifluoroethanol (TFE). In the absence of the alcohol, all of the peptides contained a significant amount (17-29%) of beta-structure. In the presence of relatively low concentrations (up to 30%) of TFE, all of the peptides except 96-128 adopted considerable alpha-helix (16-33%). This involved a transition from the beta-structure in peptide 1-63 and transitions from the nonordered structure in peptides 1-63, 64-95, and 129-168. Furthermore, additional alpha-helix formed in peptide 1-63 between 30% and 92% TFE at the expense of nonordered structure, whereas the alpha-helix formation above 50% TFE in peptide 129-168 resulted largely from a beta-structure----alpha-helix transition. With the exception of the 129-168 peptide, approximately 65-100% of the maximum level of beta-structure persisted throughout the entire range of TFE concentration. In the case of peptide 129-168, however, most of the beta-structure was converted to alpha-helix and nonordered structure at 75% TFE. While the present results support our previous assignments of beta-structure- and alpha-helix-forming regions to specific amino acid sequences of the basic protein, they also demonstrate that the beta-structure----alpha-helix transitions evidenced at various concentrations of TFE were influenced to a considerable degree by the length of the peptide, presumably due to the presence or absence of interactions between noncontiguous portions of the myelin basic protein polypeptide chain.
MR contrast agents: Physical and pharmacologic basics (2007)

Abstract Since approval of the first magnetic resonance (MR) contrast agent was granted in 1988, there has been remarkable growth in the utilization of intravenous gadolinium (Gd)‐based agents. Currently it is estimated that nearly half of all MR studies performed are contrast‐enhanced. Despite containing a toxic heavy metal, these agents have proven to be not only an effective diagnostic adjunct to non‐enhanced MRI, but also remarkably well tolerated and safe. As a result, conventional wisdom has been that MR contrast media are “biologically inert,” a notion that is clearly false. Ultimately, it is the radiologist's responsibility to understand the potential adverse effects of Gd‐based agents and the special situations in which they are likely to occur; however, the basic pharmacology of contrast agents is generally not included in medical school curricula or formally taught in residency. The purpose of this review is to discuss the mechanism of action of MR contrast agents and relevant aspects of their clinical pharmacology, including effects on the cardiovascular and renal systems, potential laboratory errors, and special situations involving women and children. We also briefly discuss the issue of nephrogenic systemic fibrosis (NSF). J. Magn. Reson. Imaging 2007;25:884–899. © 2007 Wiley‐Liss, Inc.
Na-K-2Cl cotransport in intestinal epithelial cells. Influence of chloride efflux and F-actin on regulation of cotransporter activity and bumetanide binding. (1994)

Although cAMP-dependent epithelial chloride secretion is largely regulated via apical membrane chloride channels, cAMP also remodels basolateral F-actin and activates basolateral Na-K-2Cl cotransport. Whether activation of cotransport is a primary event or secondary to activation of chloride efflux is not established, and the basis for the cytoskeletal dependence is unknown. We studied cotransport in the intestinal line HT29 (which lacks cAMP-regulated chloride efflux) and in its subclone Cl.19A (in which this pathway is present). Cotransporter activity was enhanced by forskolin in both lines but to a considerably greater extent in subclone Cl.19A, in which the number of bumetanide binding sites was also observed to increase. The F-actin stabilizer phalloidin markedly attenuated cAMP-stimulated cotransport in Cl.19A monolayers, but the increase in bumetanide binding was preserved. These studies identify two mechanisms for activation of Na-K-2Cl cotransport by cAMP: components independent and dependent of cAMP-elicited chloride efflux. Additional Na-K-2Cl cotransporters become accessible to the cell surface coincident with the salt efflux-dependent activation of cotransport. While F-actin rearrangements influence salt efflux-dependent up-regulation of the cotransporter, this influence occurs independently of increases in bumetanide-accessible cotransporters.
Phenol‐Soluble‐Modulin‐Inspired Amphipathic Peptides Have Bactericidal Activity against Multidrug‐Resistant Bacteria (2019)

Phenol-soluble modulins (PSMs) are a large family of cytolytic peptide toxins produced by Staphylococcus aureus. Based on their amino acid sequences, we have constructed a small library of cationic isoleucine-rich peptides for antimicrobial evaluation. Relative to the parent PSMs, peptide zp3 (GIIAGIIIKIKK-NH<sub>2</sub> ) was found to possess greatly improved physicochemical properties (soluble in water) and antibacterial activity (MIC=8 μm for E. coli, B. subtilis, and C. freundii) while maintaining low hemolytic activity (<5 % at 256 μm) and cytotoxicity (HEK293 cells IC<sub>50</sub> >80 μm). We reasoned that the selective activity of zp3 toward bacterial cells is due to its amphiphilic nature and positive net charge. Moreover, it is difficult for bacteria to develop resistance against zp3. Through microscopic studies of E. coli, we demonstrated that zp3 can penetrate the bacterial membrane, thereby causing leakage of the bacterial cytoplasm. Our findings present a promising antimicrobial peptide lead, which has great potential for further chemical modification.
New and emerging technologies for genetic toxicity testing (2010)

The International Life Sciences Institute (ILSI) Health and Environmental Sciences Institute (HESI) Project Committee on the Relevance and Follow-up of Positive Results in In Vitro Genetic Toxicity (IVGT) Testing established an Emerging Technologies and New Strategies Workgroup to review the current State of the Art in genetic toxicology testing. The aim of the workgroup was to identify promising technologies that will improve genotoxicity testing and assessment of in vivo hazard and risk, and that have the potential to help meet the objectives of the IVGT. As part of this initiative, HESI convened a workshop in Washington, DC in May 2008 to discuss mature, maturing, and emerging technologies in genetic toxicology. This article collates the abstracts of the New and Emerging Technologies Workshop together with some additional technologies subsequently considered by the workgroup. Each abstract (available in the online version of the article) includes a section addressed specifically to the strengths, weaknesses, opportunities, and threats associated with the respective technology. Importantly, an overview of the technologies and an indication of how their use might be aligned with the objectives of IVGT are presented. In particular, consideration was given with regard to follow-up testing of positive results in the standard IVGT tests (i.e., Salmonella Ames test, chromosome aberration assay, and mouse lymphoma assay) to add weight of evidence and/or provide mechanism of action for improved genetic toxicity risk assessments in humans.
Sobol' Indices and Shapley Value (2014)

Global sensitivity analysis measures the importance of some input variables to a function $f$ by looking at the impact on $f$ of making large random perturbations to subsets of those variables. Using measures like those of Sobol' we can attribute importance to input variables based on the extent to which they help predict the target function $f$. There is a longstanding literature in economics and game theory that considers how to attribute the value of a team effort to individual members of that team. The primary result, known as the Shapley value, is the unique method satisfying some intuitively necessary criteria. In this paper we find the Shapley value of individual variables when we take “variance explained” as their combined value. The result does not match either of the usual Sobol' indices. It is instead bracketed between them for variance explained or indeed any totally monotone game. Because those indices are comparatively easy to compute, Sobol' indices provide effectively computable bounds for the Shapley value.
Differential effects of nitrogen mustard<i>in vivo</i>on the cancer and host cells in MCa‐11 tumours (1995)

We analysed the effects of nitrogen mustard (HN2) on the growth, cell cycle distributions, and ratios of tumour cells to host cells for MCa-11 tumours grown in vivo. Treatment of tumour-bearing BALB/c mice with 3 mg/kg of HN2 produced a significant slowing of MCa-11 tumour growth. Seventy-two hours after treatment in vivo with either 3 or 4 mg/kg of HN2, the host cells in the treated tumours showed a significantly decreased G0/G1 peak and an increased G2/M peak (P < 0.01), whereas the cancer cells in the treated tumours showed significant increases in the G0/G1 peak coupled with relatively decreased proportions of S and G2/M tumour cells (P < 0.001). The ratio of the total number of cancer cells to the total number of host cells in the tumours was significantly increased 72 h after HN2 administration (P < 0.01). Thirty-two days after treatment with HN2, the cell cycle distributions of the host and tumour cells in the treatment and control tumours had returned to being identical, but the ratio of the total number of cancer cells to the total number of host cells remained increased in the treated tumours (P < 0.01). These results show that the administration in vivo of HN2 can lead to entirely different cell cycle effects for the host and cancer cells in the same tumour, and that the partial growth arrest of MCa-11 tumours from HN2 treatment may be due in part to the preferential destruction of host cells rather than solely to a direct cytotoxic effect on the cancer cells.
Shape, culture and environment: a lesson of urban design from Dakhleh oasis, Egypt (2006)

The paper is based on an ongoing research project regarding traditional architecture in the New Valley (Egypt), funded by the Italian and Egyptian Ministries of Foreign Affairs, between the Politecnico di Torino (Italy), and the Assyut University (Egypt). This research studies the mud brick settlements built between the XII - XIII century a.c. in Dakhleh (25°30' N, 29°07' E) Egyptian oasis (Al Qasr, Balat, Mushiya, Qalamun, Bashandi, Tineida, Mut), 250km W of Luxor and 800km SSE of Cairo. In the western Libyan desert, it is evident that urban morphology and building typology are not the result of accidental layered events, but an acquainted effect of a strong interaction of local, cultural, social and religious values, bioclimatic design knowledge elements and an extreme attention to the local resources. These factors all together have contributed to the realization of a sustainable urban model ante litteram. On-site survey, research and conducted comparing the Coranic prescriptions with the technological aspects, show connections between urban shape, environmental quality and socially shared values. This paper aims to consider the ancient Egyptian approach to sustainable urban design and rehabilitation.
Fault tolerant distributed shared memory algorithms (2002)

Distributed shared memory (DSM) has received increased attention as a mechanism for interprocess communication in loosely-coupled distributed systems because of its perceived advantages over direct use of message passing or remote procedure calls. One problem with most DSM algorithms proposed to date, however, is that they do not tolerate faults. The paper extends four basic DSM algorithms to tolerate single host failures and argues that this degree of fault tolerance is sufficient for most applications. It analyzes the performance behavior of the fault tolerant DSM algorithms and shows that for some algorithms the additional overhead for fault tolerance is quite small, but that for other algorithms the extra overhead can be substantial and even unpredictable.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
In-room transmission BER performance of anti-multipath modulation PSK-VP (1993)

The BER (bit error rate) performance of an anti-multipath modulation pi /4-QPSK-VP is evaluated in comparison to a conventional differential pi /4-QPSK, when applied to high-speed digital radio transmission within a room where both transmitting and receiving antennas are set up, using a transmission experiment and a BER calculation. Through this transmission experiment at about 3 and 6 Mb/s, pi /4-QPSK-VP was confirmed to improve the BER significantly for both data rates in two test rooms. A delay profile measurement was additionally carried out to characterize the propagation channels of the test rooms and to find out an appropriate channel model. The BER calculation based on the above channel model, which was confirmed to estimate the upper bound of a floor error rate sufficiently in comparison to the transmission experiment, reveals the relationship between the data rate and the BER and indicates an optimum and a maximum data rate for pi /4-QPSK-VP with respect to the maximum delay spread of the room. The results show that pi /4-QPSK-VP is estimated to raise the available data rate up to about 20 times over that of pi /4-QPSK for a BER of 10/sup -4/, although pi /4-APSK-VP requires twice the transmission bandwidth.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Screening of Antibiotics That Interact with Organic Anion-Transporting Polypeptides 1B1 and 1B3 Using Fluorescent Probes (2011)

Hepatic organic anion transporters OATP1B1 and OATP1B3 are expressed at the sinusoidal membrane of hepatocytes and contribute to the hepatic uptake of a wide variety of clinically used drugs. To identify the antibiotics that interact with the human organic anion transporters OATP1B1 and OATP1B3, we applied a screening system using fluorescent probes. Twenty-six antibiotics with a variety of mechanisms of action were examined. The screening demonstrated that four antibiotics inhibited OATP1B1-mediated transport and 11 antibiotics inhibited OATP1B3-mediated transport in a concentration-dependent manner. Antibiotics that inhibited OATP1B3-mediated transport tended to exhibit higher affinity than those that inhibited OATP1B1-mediated transport. To clarify whether the antibiotics that interacted with OATP1B1 and/or OATP1B3 were substrates for these transporters, an uptake study was performed. Rifampicin and penicillin were transported by both OATP1B1 and OATP1B3. Moreover, OATP1B3 was involved in the transport of ceftriaxone, cefmetazole, cefoperazone, and cefotaxime. Macrolides were not significantly transported by either transporter. In conclusion, the results demonstrated that our system is a useful method for the rapid screening of transporter-antibiotic interaction, and we found novel substrates. Our results indicate that OATP1B1 and/or OATP1B3 contribute to the transport process of some antibiotics, and that drug-drug interactions associated with these transporters could occur after the administration of antibiotics.
A perceptual visibility metric for banding artifacts (2016)

Banding is a common video artifact caused by compressing low texture regions with coarse quantization. Relatively few previous attempts exist to address banding and none incorporate subjective testing for calibrating the measurement. In this paper, we propose a novel metric that incorporates both edge length and contrast across the edge to measure video banding. We further introduce both reference and non-reference metrics. Our results demonstrate that the new metrics have a very high correlation with subjective assessment and certainly outperforms PSNR, SSIM, and VQM.
DOPAMINE TRANSPORTER AS A COCAINE RECEPTOR (1992)

BOJA, J W; CARROLL, F I; WONG, D; DANNALS, R; SCHEFFEL, U; VAUGHAN, R; CLINE, E; PATEL, A; KUHAR, M J Author Information