gebhart/patrepeval huggingface dataset:
Solvent effects on resonant first hyperpolarizabilities and Raman and hyper-Raman spectra of DANS and a water-soluble analog (2006)

The two-photon-resonant first hyperpolarizabilities associated with hyper-Rayleigh and hyper-Raman scattering are reported for 4-dimethylamino-4-nitrostilbene in 1,4-dioxane, dichloromethane, acetonitrile, and methanol, and for an ionic analog, 4-N,N-bis(6-(N,N,N-trimethylammonium)-hexyl)amino-4-nitrostilbene dibromide in methanol and water. Resonance Raman and hyper-Raman excitation profiles are also measured and modeled. The resonance Raman and hyper-Raman spectra show very similar relative intensities which do not vary much as the excitation frequency is tuned across the lowest-energy strong linear absorption band, suggesting that a single resonant electronic state dominates the one- and two-photon absorptions in this region. The absorption, resonance Raman, and hyper-Raman profiles can be simulated reasonably well with a common set of parameters. The peak resonant (absolute value of beta)2, measured by hyper-Rayleigh scattering, varies by about 50% over the range of solvents examined and shows a weak correlation with the linear absorption maximum, with the redder-absorbing systems exhibiting larger peak hyperpolarizabilities. The experimental hyper-Rayleigh intensities are higher than those calculated, possibly reflecting contributions from nonresonant electronic states.
Delay-Optimal Distributed Resource Allocation for Device-to-Device Communications (2015)

In this paper, the resource allocation problem is investigated for Device-to-Device (D2D) communications underlaying cellular networks with bursty traffic arrival. We formulate an infinite horizon average reward constraint Markov decision process (CMDP) that aims at minimizing the average delay under the dropping propability constraint. Then, we present a reduced-state Bellman's equation with linear value function approximation to deal with the curse of dimensionality problem in solving the CMDP. A distributed resource allocation algorithm is derived with low computation complexity and signaling overhead, which consists of a subchannel bidding mechanism to obtain the optimal control action, and a distributed online stochastic learning algorithm to estimate the value function and the optimal Lagrangian Multipliers (LMs). Simulation results show that the performance of our proposed algorithm is very close to that achieved by the offline value iteration algorithm, and is better than various baselines algorithms.
Arthroscopic‐Assisted Minimally Invasive Total Knee Arthroplasty (2011)

This technical note describes an arthroscopic technique to enhance visualization during minimally invasive total knee arthroplasty. The arthroscope is used, with the aid of balloon catheter retractors, to allow intraoperative identification of potentially adverse findings, including retained bone and cement fragments. This technique has been used successfully to identify and treat knees with these findings. Although further study and refinement are needed, this technique shows promise in reducing postoperative complications and improving outcomes in total knee arthroplasty.
Magnetic Resonance Imaging of Ferumoxide-Labeled Mesenchymal Stem Cells Seeded on Collagen Scaffolds—Relevance to Tissue Engineering (2006)

Mesenchymal stem cells (MSCs) are a promising candidate cell for tissue engineering. Magnetic resonance imaging (MRI) has been proven effective in visualizing iron-labeled stem cells; however, the efficiency of this approach for visualization of cells seeded on scaffolds intended for use as tissue-engineered heart valves has not been assessed. MSCs were labeled by incubating for 48 h with ferumoxide and poly-L-lysine as transfecting agent. Any detrimental effect of iron labeling on cell viability, proliferation, and differentiation was examined using appropriate functional assays. Change in the nuclear magnetic relaxation properties of labeled cells was determined using in vitro relaxometry of cells seeded in 3-dimensional collagen gels. Images of labeled and non-labeled cells seeded onto 1% type I bovine collagen scaffolds were obtained using MRI. The presence of intracellular iron in labeled cells was demonstrated using Prussian blue staining, confocal microscopy, and electron microscopy. Cell viability, proliferation, and differentiation were comparable in labeled and non-labeled cells. The T2 relaxation time was 40% to 50% shorter in ferumoxide-labeled cells. Labeled cells seeded on scaffolds appeared as areas of reduced signal intensity in T2 weighted images. Ferumoxide labeling persisted and remained effective even on scans performed 4 weeks after the labeling procedure. Ferumoxide labeling of human MSCs seeded on collagen scaffolds is an effective, non-toxic technique for visualization of these cells using MRI. This technique appears promising for cell tracking in future tissue-engineering applications.
Ultrasoft silicon nanomembranes: thickness-dependent effective elastic modulus (2019)

For decades, silicon (Si) has been widely used for the mass production of microelectronic circuits. Recently, as the thickness has been reduced to the nanometer scale, its application has expanded to various fields, including flexible and transparent 2D semiconductors. For the reliable and reproducible operation of such large flexible and transparent devices, obtaining precise information about the mechanical properties of low dimensional Si is crucial. Here, we demonstrate that a 2 nm-thick Si nanomembrane (NM) exhibits an extremely low Young's modulus of 3.25 GPa, a two-order smaller value than that of the bulk counterpart. Our systematic measurement of thickness-controlled Si NMs reveals the existence of significant size effect: The effective modulus rapidly changes from 180 GPa to 3.25 GPa under 25 nm to 2 nm thickness reduction. Our theoretical modeling successfully provides physical insight into the unique stiff-to-soft transition and extremely low modulus. We further demonstrate that the modulus of Si NMs can be tailored precisely via the control of surface morphology of membrane. This work therefore provides a comprehensive picture of how and why originally hard & stiff Si deforms so softly in the ultrathin 2D geometry, and proposes a new strategy to design the mechanical properties at nanoscale dimensions.
MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database (2008)

MachiBase (http://machibase.gi.k.u-tokyo.ac.jp/) provides a comprehensive and freely accessible resource regarding Drosophila melanogaster 5'-end mRNA transcription at different developmental states, supporting studies on the variabilities of promoter transcriptional activities and gene-expression profiles in the fruitfly. The data were generated in conjunction with the recently developed high-throughput genome sequencer Illumina/Solexa using a newly developed 5'-end mRNA collection method.
Modern Trends in Inductive Power Transfer for Transportation Applications (2013)

Inductive power transfer (IPT) has progressed to be a power distribution system offering significant benefits in modern automation systems and particularly so in stringent environments. Here, the same technology may be used in very dirty environments and in a clean room manufacture. This paper reviews the development of simple factory automation (FA) IPT systems for both today's complex applications and onward to a much more challenging application—IPT roadway. The underpinning of all IPT technology is two strongly coupled coils operating at resonance to transfer power efficiently. Over time the air-gap, efficiency, coupling factor, and power transfer capability have significantly improved. New magnetic concepts are introduced to allow misalignment, enabling IPT systems to migrate from overhead monorails to the floor. However, the demands of IPT roadway bring about significant challenges. Here, compared with the best FA practice, air-gaps need to be 100 times larger, power levels greater than ten times, system losses ten times lower to meet efficiency requirements, and systems from different manufacturers must be interoperable over the full range of operation. This paper describes how roadway challenges are being met and outlines the problems that still exist and the solutions designers are finding to them.
Four critical aspartic acid residues potentially involved in the catalytic mechanism ofEscherichia coliK-12 WaaR (1999)

Escherichia coli K-12 WaaR is a non-processive alpha-1,2 glucosyltransferase, involved in the synthesis of the R-core of lipopolysaccharide. WaaR possesses the four conserved structural regions I, II, III and IV, each presumably involved in the mechanistic function in catalysis. Regions I and III contain the pair of strictly conserved Asp residues. Asp-129, 131 (region I) and 215, 217 (region III) of WaaR were individually converted to Asn by the site-directed mutagenesis of the waaR gene. All mutated enzymes were inactive, supporting the model for an alpha-glycosyl transfer reaction where the pair of strictly conserved aspartic acid residues in regions I and III play a critical role in the catalytic function.
Phase 1 Study of Pandemic H1 DNA Vaccine in Healthy Adults (2015)

Clinicaltrials.gov NCT00973895.
O Meças, de Rentes de Carvalho: romance polifónico sobre Portugal (2018)

Esta resenha faz parte dos trabalhos da Catedra Internacional Jose Saramago (Universidade de Vigo), projeto POEPOLIT (FFI2016-77584-P, Ministerio de Economia e Competitividade da Espanha) e do Programa Estrategico UID/ELT/00500/2013 da FCT (Portugal).
Ketorolac modulates Rac-1/HIF-1α/DDX3/β-catenin signalling via a tumor suppressor prostate apoptosis response-4 (Par-4) in renal cell carcinoma (2023)

Renal cell carcinoma (RCC) is the most difficult-to-treat form of kidney cancer with a median 5-year survival of 10% under metastatic setting. In RCC, although cytoreductive nephrectomy is common, approximately 20-30% of patients will develop recurrent cancer after surgery, which highlights the need for an effective therapy. Rho-GTPases viz, Rac-1 and Cdc42 are the central regulators of cancer cell migration and invasion and thus metastasis in multiple cancer types. Hence, we elucidated the role of Ketorolac, a modulator Rho-GTPases against RCC through potentiation of tumor suppressor Par-4. The effect of Ketorolac alone and in combination on proliferation, apoptosis, cell-cycle progression, migration, tumor inhibition and their related markers were studied. Moreover, Ketorolac's impact on metastasis by influencing Rac-1/HIF-1α/DDX3/β-catenin signalling was studied with respect to its ability to modulate the expression of tumor suppressor Par-4, and this mechanism was confirmed by siRNA knockdown studies. Ketorolac induced cytotoxicity in a panel of renal cells including patient derived tumor cells with IC<sub>50</sub> 2.8 to 9.02 mM and 0.28 to 3.8 mM in monolayer and anchorage independent clonogenic assays respectively. Ketorolac caused significant down regulation of proliferation (Ki-67, Cyclin D1, pRB and DDX3), migration/invasion (Rac-1, Cdc42, and Tiam1), and angiogenesis (HIF-1α and VEGF) markers as studied by gene and protein expression. Moreover, it caused a significant upregulation of tumor suppressor Par-4 known to be downregulated in RCC. This mechanism was further confirmed by using siRNA knockdown studies where we could demonstrate a negative relation between the expression of Par-4 and Rac-1/Cdc42. Importantly, Ketorolac alone and in combination with Sunitinib showed tumor growth inhibition (TGI) of 73% and 86% respectively in xenograft model. This anti-tumor activity was further corroborated by down regulation of Rac-1/Cdc42/HIF-1α/DDX3/β-catenin signalling. This is the first report which implicates the role of Ketorolac against RCC by acting as a small molecule secretagogue causing upregulation of Par-4 in autocrine and paracrine manner. Consequently, these findings suggest that Par-4 can serve as a valuable therapeutic target and a prognostic marker for the treatment of RCC.
PCF11 links alternative polyadenylation to formation and spontaneous regression of neuroblastoma (2018)

Abstract Diversification at the transcriptome 3’end is an important and evolutionarily conserved layer of gene regulation associated with differentiation and dedifferentiation processes. However the underlying mechanisms and functional consequences are poorly defined. Here, we identify extensive transcriptome-3’end-alterations in neuroblastoma, a tumour entity with a paucity of recurrent somatic mutations and an unusually high frequency of spontaneous regression. Utilising extensive RNAi-screening we reveal the landscape and drivers of transcriptome-3’end-diversification, discovering PCF11 as critical regulator, directing alternative polyadenylation (APA) of hundreds of transcripts including a differentiation RNA-operon. PCF11 shapes inputs converging on WNT-signalling, and governs cell cycle, proliferation, apoptosis and neurodifferentiation. Postnatal PCF11 down-regulation induces a neurodifferentiation program, and low-level PCF11 in neuroblastoma associates with favourable outcome and spontaneous tumour regression. Our findings document a critical role for APA in tumourigenesis and describe a novel mechanism for cell fate reprogramming in neuroblastoma with important clinical implications. An interactive data repository of transcriptome-wide APA covering &gt;170 RNAis, and an APA-network map with regulatory hubs is provided.
2D sound source position estimation using microphone arrays and its application to a VR-based bird song analysis system (2019)

This paper addresses the problem of 2D sound source localization using multiple microphone arrays in an outdoor environment. Two main issues exist in such localization. Since the localization performance depends on a variety of parameters, the lack of knowledge about how to design the system is one of those issues. A thorough analysis in respect to the accuracy of the localization results with different simulation conditions has been performed. Obtained characteristics lead to a discussion on limitations and applicability of the system. The distinction between multiple simultaneous sound sources is another problem. This is directly related to the appearance of outliers in the localization process. To solve this issue, an outlier removal method is proposed, which takes the properties of the observed sounds into consideration. In this paper a VR-based visualization method of the obtained results is also introduced. As the application scenario, we selected bird song analysis, which provides a challenging environment in terms of constantly changing signal-to-noise ratio and relative sensor-to-target position. A prototype system has been established using the proposed method. Several simulation results have been presented followed by a discussion on the issues. This leads to establishing system design guidelines that ensure a predictable performance.
TGF-β and atherosclerosis in man (2007)

The transforming growth factor type-beta (TGF-beta) superfamily of ligands, receptors, binding proteins and ligand traps together plays a key role in the maintenance of normal blood vessel wall structure. Specific defects in genes encoding superfamily members have now been linked to a range of cardiovascular syndromes involving loss of healthy vessel architecture, including hypertension and aneurysm. However the contribution of TGF-beta to the development of atherosclerosis is simultaneously more subtle and more complex. TGF-beta ligands are produced by a range of different cell types, which also regulate release of the active cytokine that, in turn, signals through multiple receptor complexes on different cell types. Recent evidence suggests that the T cell may be both a key source of TGF-beta1 and a key target for its effects during atherogenesis, as in other chronic inflammatory disorders. Here we review the evidence for the role of TGF-beta in the human vasculature during atherogenesis, and evaluate the available data in the context of our knowledge from animal models of the disease.
Corrosion of Heritage Objects: Collagen‐Like Triple Helix Found in the Calcium Acetate Hemihydrate Crystal Structure (2020)

Helical motifs are common in nature, for example, the DNA double or the collagen triple helix. In the latter proteins, the helical motif originates from glycine, the smallest amino acid, whose molecular confirmation is closely related to acetic acid. The combination of acetic acid with calcium and water, which are also omnipresent in nature, materializing as calcium acetate hemihydrate, was now revealed to exhibit a collagen-like triple helix structure. This calcium salt is observed as efflorescence phase on calcareous heritage objects, like historic Mollusca shells, pottery or marble reliefs. In a model experiment pure calcium acetate hemihydrate was crystallized on the surface of a terracotta vessel. Calcium acetate hemihydrate crystallizes in a surprisingly large unit cell with a volume of 11,794.5(3) Å<sup>3</sup> at ambient conditions. Acetate ions bridge neighboring calcium cations forming spiral chains, which are arranged in a triple helix motif.
Blue light inhibits proliferation of melanoma cells (2016)

Photobiomodulation with blue light is used for several treatment paradigms such as neonatal jaundice, psoriasis and back pain. However, little is known about possible side effects concerning melanoma cells in the skin. The aim of this study was to assess the safety of blue LED irradiation with respect to proliferation of melanoma cells. For that purpose we used the human malignant melanoma cell line SK-MEL28. Cell proliferation was decreased in blue light irradiated cells where the effect size depended on light irradiation dosage. Furthermore, with a repeated irradiation of the melanoma cells on two consecutive days the effect could be intensified. Fluorescence-activated cell sorting with Annexin V and Propidium iodide labeling did not show a higher number of dead cells after blue light irradiation compared to non-irradiated cells. Gene expression analysis revealed down-regulated genes in pathways connected to anti-inflammatory response, like B cell signaling and phagosome. Most prominent pathways with up-regulation of genes were cytochrome P450, steroid hormone biosynthesis. Furthermore, even though cells showed a decrease in proliferation, genes connected to the cell cycle were up-regulated after 24h. This result is concordant with XTT test 48h after irradiation, where irradiated cells showed the same proliferation as the no light negative control. In summary, proliferation of melanoma cells can be decreased using blue light irradiation. Nevertheless, the gene expression analysis has to be further evaluated and more studies, such as in-vivo experiments, are warranted to further assess the safety of blue light treatment.
ChemInform Abstract: Two New 3‐Methoxy‐4‐quinolone Alkaloids from the Bark of Sarcomelicope megistophylla. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
High Daytime Temperature Responsive MicroRNA Profiles in Developing Grains of Rice Varieties with Contrasting Chalkiness (2023)

High temperature impairs starch biosynthesis in developing rice grains and thereby increases chalkiness, affecting the grain quality. Genome encoded microRNAs (miRNAs) fine-tune target transcript abundances in a spatio-temporal specific manner, and this mode of gene regulation is critical for a myriad of developmental processes as well as stress responses. However, the role of miRNAs in maintaining rice grain quality/chalkiness during high daytime temperature (HDT) stress is relatively unknown. To uncover the role of miRNAs in this process, we used five contrasting rice genotypes (low chalky lines Cyp, Ben, and KB and high chalky lines LaGrue and NB) and compared the miRNA profiles in the R6 stage caryopsis samples from plants subjected to prolonged HDT (from the onset of fertilization through R6 stage of caryopsis development). Our small RNA analysis has identified approximately 744 miRNAs that can be grouped into 291 families. Of these, 186 miRNAs belonging to 103 families are differentially regulated under HDT. Only two miRNAs, Osa-miR444f and Osa-miR1866-5p, were upregulated in all genotypes, implying that the regulations greatly varied between the genotypes. Furthermore, not even a single miRNA was commonly up/down regulated specifically in the three tolerant genotypes. However, three miRNAs (Osa-miR1866-3p, Osa-miR5150-3p and canH-miR9774a,b-3p) were commonly upregulated and onemiRNA (Osa-miR393b-5p) was commonly downregulated specifically in the sensitive genotypes (LaGrue and NB). These observations suggest that few similarities exist within the low chalky or high chalky genotypes, possibly due to high genetic variation. Among the five genotypes used, Cypress and LaGrue are genetically closely related, but exhibit contrasting chalkiness under HDT, and thus, a comparison between them is most relevant. This comparison revealed a general tendency for Cypress to display miRNA regulations that could decrease chalkiness under HDT compared with LaGrue. This study suggests that miRNAs could play an important role in maintaining grain quality in HDT-stressed rice.
[Asynchronus rejection of intrathoracic heart-lung transplantation rats]. (1990)

We have reported intrathoracic heart-lung transplantation in rats could be made easily by using Internal Shunt Method as described elsewhere. In this study, we examined the rejection of intrathoracic heart-lung allografts in this model to determine whether acute pulmonary rejection precedes cardiac rejection following heart-lung transplantation or not. Ten heart-lung allografts (no immunosuppressive agent was given) and four isografts were examined pathologically. There was no pathologic change except perivascular or peribronchiolar edema in isografts, which was attributed to operative damage. Acute pulmonary rejection apparent pathologically 3 days after transplantation and lung allografts lost its function 6 days after transplantation. Otherwise, acute cardiac rejection first became apparent pathologically 5 days after transplantation. And their pulsation appeared well 6 days after it. It is concluded that pulmonary rejection precedes cardiac rejection following heart-lung transplantation.
Optimization of CMP defect detection schemes [VLSI manufacture] (2002)

In this paper, the use of Fourier filtering in dark field defect detection is investigated for the post chemical mechanical polishing (CMP) inspection application using a simulation tool, METRO. Advanced detection techniques have been studied to determine methods of increasing capture rates in densely patterned arrays. Two critical CMP process defects, microscratches and particles, are evaluated. The results illustrate that Fourier filtering will improve the defect signal relative to the background signal. Additionally, color variation, underlying grain and pattern noise will be minimized using Fourier filtering.
Overview of MPEG-4 audio and its applications in mobile communications (2000)

MPEG-4 is a member of the well-known family of ISO/MPEG coding standards, and provides an integrated set of audio coders with attractive novel capabilities, including bitrate and bandwidth scalability. The paper gives an introduction into the underlying design concepts of MPEG-4 and provide an overview of MPEG-4 audio coding technology and its features. In particular, it discusses the technical provisions which make MPEG-4 audio very well suited for applications in the domain of mobile communications.