gebhart/patrepeval huggingface dataset:
Development and validation of a treatment planning model for magnetic nanoparticle hyperthermia cancer therapy (2014)

The use of magnetic nanoparticles (mNPs) to induce local hyperthermia has been emerging in recent years as a promising cancer therapy, in both a stand-alone and combination treatment setting, including surgery radiation and chemotherapy. The mNP solution can be injected either directly into the tumor, or administered intravenously. Studies have shown that some cancer cells associate with, internalize, and aggregate mNPs more preferentially than normal cells, with and without antibody targeting. Once the mNPs are delivered inside the cells, a low frequency (30-300kHz) alternating electromagnetic field is used to activate the mNPs. The nanoparticles absorb the applied field and provide localized heat generation at nano-micron scales. Treatment planning models have been shown to improve treatment efficacy in radiation therapy by limiting normal tissue damage while maximizing dose to the tumor. To date, there does not exist a clinical treatment planning model for magnetic nanoparticle hyperthermia which is robust, validated, and commercially available. The focus of this research is on the development and experimental validation of a treatment planning model, consisting of a coupled electromagnetic and thermal model that predicts dynamic thermal distributions during treatment. When allowed to incubate, the mNPs are often sequestered by cancer cells and packed into endosomes. The proximity of the mNPs has a strong influence on their ability to heat due to interparticle magnetic interaction effects. A model of mNP heating which takes into account the effects of magnetic interaction was developed, and validated against experimental data. An animal study in mice was conducted to determine the effects of mNP solution injection duration and PEGylation on macroscale mNP distribution within the tumor, in order to further inform the treatment planning model and future experimental technique. In clinical applications, a critical limiting factor for the maximum applied field is the heating caused by eddy currents, which are induced in the noncancerous tissue. Phantom studies were conducted to validate the ability of the model to accurately predict eddy current heating in the case of zero blood perfusion, and preliminary data was collected to show the validity of the model in live mice to incorporate blood perfusion.
Information extraction to improve cross-lingual document retrieval (2007)

We present a filtering mechanism using two cross-lingual information extraction (CLIE) systems for improving document relevance of cross-lingual information retrieval (CLIR) for queries conforming to predefined templates. Experiments on retrieving Chinese documents in response to English GALE arrest queries show that this approach can obtain a 12.7% absolute improvement in relevance (representing a 24.8% relative error reduction) for the top 25 retrieved documents. We also demonstrate that Chinese IE can provide a valuable supplement to English IE to enhance retrieval performance.
4:1 Silicon Photonic Serializer for Data Center Interconnects Demonstrating 104 Gbaud OOK and PAM4 Transmission (2019)

With next-generation optical interconnects for data centers aiming for 0.8 Tb/s or 1.6 Tb/s, 100 Gbaud capable transmitters from a single-laser source will become indispensable. However, these lane rates would require bandwidths of 70 GHz or more, doubling the bandwidth requirements of the electrical and optical components with respect to the fastest current generation of optical interconnects running at 53 Gbaud pulse-amplitude modulation (PAM-4). In this paper, we propose an integrated 4:1 optical serializer topology to achieve 104 Gbaud On-Off Keying (OOK) and PAM-4 transmission using only quarter rate components at the transmitter. We show 104 (208) Gbit/s OOK (PAM4) transmission using four GeSi electro-absorption modulators (EAMs) over 1 km of single-mode fiber (SMF). For 104 Gbaud OOK, clearly open eyes are obtained, while for PAM-4 the performance is limited by the nonlinear E/O-transfer function of the EAM. However, adding pre-emphasis in the electrical driver or replacing the single EAM with our previously demonstrated optical DAC topology-consisting of two EAMs in parallel with a 90° phase difference between each-could substantially improve these results. Additionally, we discuss the possibility of a four channel transmitter (4 × 208 Gb/s) from a single mode locked laser, amounting to a 832 Gb/s rate based on the current demonstrator.
Solvent-free microwave extraction: an eco-friendly and rapid process for green isolation of essential oil from lemongrass (2020)

The extraction of lemongrass essential oil (LGEO) using large quantities of solvents makes this extraction a hazardous and environmentally unfriendly procedure. Our aim was to find a suitable method for the improvement of its extraction and its quality. Solvent-Free Microwave Extraction (SFME) is a combination of dry distillation and microwave heating. SFME of LGEO was compared with conventional extraction hydrodistillation (HD). SFME is quicker than conventional HD. An extraction time of 15 min with SFME provided a yield of 0.6% comparable with that obtained after 120 min using HD. The composition of these oils revealed that the main components obtained with HD and SFME were both geranial (59.93% vs 44.59%, respectively). The quality of lemongrass is determined by its citral content, and a higher amount of citral was present in SFME oil (74%) in comparison with HD oil (60%). SFME is a green and a promising technology for the extraction of essential oils.
20 Watt CW TEM00 intracavity doubled optically pumped semiconductor laser at 532 nm (2012)

Optically-pumped semiconductor (OPS) lasers are power-scalable, wavelength-flexible, infrared brightness converters. Adding intra-cavity frequency doubling turns them into efficient, low noise, high power visible laser sources. We report on a laser combining an InGaAs gain medium with an LBO nonlinear crystal to produce more than 20 Watt CW in single transverse mode at 532 nm. Efficient cooling of the single gain chip using advanced mounting techniques is the key to making the laser reliable at high CW powers. A rugged and compact package withstands significant environmental excursions. The laser's low noise makes it suitable for demanding Ti:Sapphire pumping applications.
Coming close and then pulling away (2007)

Interventional cardiologists have focused great interest and resources on vascular healing. The obvious reasons for this interest relate to what happens after vascular segments have been manipulated—expanded, stretched, cracked, or otherwise broken—during percutaneous intervention. The earliest energies focused on what happened after balloon dilatation alone. There were four possibilities: (i) a significant dissection developed which disrupted flow and resulted in acute or threatened closure, (ii) the artery was initially stretched but then recoiled within the first 24 h, (iii) the artery healed after the initial injury but then developed neointimal hyperplasia which often resulted in significant stenosis or ischaemia which required treatment, and (iv) the artery healed and did not develop significant neointimal hyperplasia but instead became inert and resistant to subsequent instability.

With the introduction of stents, the situation became more complex because a foreign body was placed and became part of the enduring landscape. This development either eliminated or greatly decreased the above-mentioned issues of acute or threatened closure and recoil. However, the longer term … 

Corresponding author. Tel: +1 507 255 2504; fax: +1 507 255 2550. E-mail address : dholmes{at}mayo.edu/hughes.karyn{at}mayo.edu
David Sassoli: por uma Europa mais livre, mais justa e mais próspera (2023)

This essay aims to reflect on the political and ecological future of Europe, starting with the figure and the democratic values of David Sassoli.
The Role of Shewanella Oneidensis MR-1 Structural Proteins in Electrochemical Performance and Biofilm Development (2016)

Microbial exoelectrogens present promising avenues for the development of bioremediation, biofuel cells and synthetic biology. Our research interests are focused on achieving efficient electron transfer from these organisms embedded in biohybrid constructs while reducing ohmic loses in the system. A crucial aspect for attaining this goal is to fully understand bacterial motility and attachment to the solid support of interest in which respiration occurs. Therefore, biofilm formation is of central interest in anode respiring microorganisms relying on extracellular electron transfer (EET). Microbial appendages have been proposed to be involved in cell attachment as well as in different modes of cell motility prior to the biofilm formation process as observed in select microorganisms [1]. Amongst them, Shewanella oneidensis has been thoroughly used as a model for further understanding microbial electrochemical phenomena. A crucial area of study contributing to the development of microbial electrochemical systems consists in identifying key components involved in the assembly and functionality of pili and flagella in this organism. Therefore, in this study we utilized motility mutants of S. oneidensis MR-1 that lack key proteins involved in the secretion of type IV pili and flagella. Electrochemical techniques were explored to compare the performance and current generation from microbial fuel cells containing motility-impaired mutants as well as wild type S. oneidensis. Furthermore, we studied and quantified the anodic biofilm morphological characteristics based on microscopic techniques. We found that type IV pili mutants exhibited the highest deficiencies in electrochemical performance and current production based on chronoamperometric studies. Specifically, these deficiencies were more pronounced on PilD and PilT protein-lacking mutants. These complexes are essential inner membrane proteins responsible for pili assembly and contraction [2]. On the other hand, flagella-lacking S. oneidensis mutants did not present significant restrains in current output and biofilm formation. We conclude that the discussed structural protein assemblies present relevant roles in bacterial surface attachment. Our findings present direct implications in the development of fully engineered biohybrid assemblies, bacteria-anode interactions, and bacterial electron transfer quantification. Figure 1. SEM images of wild type, pili-lacking and flagella-lacking mutants of S. oneidensis attachedto carbon felt fibers. References: 1. K.M. Thormann, R.M. Saville, S. Shukla, D.A. Pelletier, A.M. Spormann, Initial phases of biofilm formation in Shewanella oneidensis MR-1. J Bacteriol, 2004. 186: 8096–8104. 2. R.M Saville, N. Dieckmann , A.M. Spormann, Spatiotemporal activity of the mshA gene system in Shewanella oneidensis MR-1 biofilms. FEMS Microbiol Lett. 2010 . 308:76–83. Figure 1
Probing the Role of Glycol Chain Lengths in π-Donor–Acceptor [2]Pseudorotaxanes Based on Monopyrrolo-Tetrathiafulvalene and Cyclobis(paraquat-p-phenylene) (2016)

We have investigated and quantified the role that the glycol chain length has on the strength of the noncovalent bonding interactions taking place between cyclobis(paraquat-p-phenylene) (CBPQT<sup>4+</sup>) and five different monopyrrolo-tetrathiafulvalene (MPTTF) derivatives that only differ in the length of the N-substituted glycol chain. The MPTTF derivatives were used to form [2]pseudorotaxanes by mixing them with CBPQT<sup>4+</sup>. The binding constants (K<sub>a</sub>) associated with the complexation process leading to the formation of the [2]pseudorotaxanes were obtained using the UV-vis-NIR dilution method and the [2]pseudorotaxanes were characterized structurally using <sup>1</sup>H NMR spectroscopy. These experimental investigations clearly indicate that the glycol chains provide additional stability to the [2]pseudorotaxanes findings that were further supported by density functional theory (DFT) studies. The DFT calculated superstructure of the [2]pseudorotaxane 3⊂CBPQT<sup>4+</sup> reveal that [C-H···O] hydrogen bonding interactions between the acidic α-H protons in CBPQT<sup>4+</sup> and the oxygen atoms present in the glycol chain can take place on the exterior of the [2]pseudorotaxane. However, the length of the glycol chain is of paramount importance and the present studies show that the first and second oxygen atom in the [2]pseudorotaxanes 2-5⊂CBPQT<sup>4+</sup> are engaged in [C-H···O] hydrogen bonding interactions with CBPQT<sup>4+</sup>, whereas the third and fourth oxygen atoms are not.
ChemInform Abstract: AN UNUSUALLY FACILE DIELS‐ALDER REACTION WITH NOVEL 6‐ALKYLTHIO DERIVATIVES OF 1,2,4‐TRIAZINE (1985)

Abstract Aus den Aminosäuren (I) werden über (II) die Triazinone (III) hergestellt und zu (IV) oxidiert.
Simulation of intermodulation distortion in passive CMOS FET mixers (2009)

The simulation of third-order intermodulation distortion in a passive CMOS FET mixer will typically predict a fictitious 2:1 slope using the industry standard EKV, BSIM3 and BSIM4 models. This phenomenon has been attributed to the discontinuity in the second-order derivatives of the drain-current and the terminal charge model. This paper establishes the connection between the discontinuous derivatives and the resulting intermodulation distortion slope and provides experimental verification.
Lithium Perchlorate (2007)

[7791-03-9] ClLiO4 (MW 106.39) InChI = 1S/ClHO4.Li/c2-1(3,4)5;/h(H,2,3,4,5);/q;+1/p-1 InChIKey = MHCFAGZWMAWTNR-UHFFFAOYSA-M (mild Lewis acid1 for cycloaddition reactions,2 conjugate additions,3 ring opening of epoxides,4 and ring expansion of cyclopropanes5) Physical Data: mp 236 °C; bp 430 °C (dec); d 2.428 g cm−3. Solubility: 60 g/100 mL H2O (25 °C); 150 g/100 mL H2O (89 °C); 152 g/100 mL EtOH (25 °C); 137 g/100 mL acetone (25 °C); 182 g/100 mL MeOH (25 °C); 114 g/100 mL ether. Form Supplied in: white solid; widely available in anhydrous form or as the trihydrate; it is usually used in solution in ether or MeOH. Purification: anhydrous lithium perchlorate is prepared by heating the commercially available anhydrous material or its trihydrate at 160 °C for 48 h under high vacuum (P2O5 trap). Handling, Storage, and Precautions: the anhydrous material should be used as prepared for best results. The decomposition of lithium perchlorate starts at about 400 °C and becomes rapid at 430 °C, yielding lithium chloride and oxygen. Perchlorates are potentially explosive and should be handled with caution.
Extracellular Calcium Modulates Actions of Orthosteric and Allosteric Ligands on Metabotropic Glutamate Receptor 1α (2013)

Metabotropic glutamate receptor 1α (mGluR1α), a member of the family C G protein-coupled receptors, is emerging as a potential drug target for various disorders, including chronic neuronal degenerative diseases. In addition to being activated by glutamate, mGluR1α is also modulated by extracellular Ca(2+). However, the underlying mechanism is unknown. Moreover, it has long been challenging to develop receptor-specific agonists due to homologies within the mGluR family, and the Ca(2+)-binding site(s) on mGluR1α may provide an opportunity for receptor-selective targeting by therapeutics. In the present study, we show that our previously predicted Ca(2+)-binding site in the hinge region of mGluR1α is adjacent to the site where orthosteric agonists and antagonists bind on the extracellular domain of the receptor. Moreover, we found that extracellular Ca(2+) enhanced mGluR1α-mediated intracellular Ca(2+) responses evoked by the orthosteric agonist l-quisqualate. Conversely, extracellular Ca(2+) diminished the inhibitory effect of the mGluR1α orthosteric antagonist (S)-α-methyl-4-carboxyphenylglycine. In addition, selective positive (Ro 67-4853) and negative (7-(hydroxyimino)cyclopropa[b]chromen-1a-carboxylate ethyl ester) allosteric modulators of mGluR1α potentiated and inhibited responses to extracellular Ca(2+), respectively, in a manner similar to their effects on the response of mGluR1α to glutamate. Mutations at residues predicted to be involved in Ca(2+) binding, including E325I, had significant effects on the modulation of responses to the orthosteric agonist l-quisqualate and the allosteric modulator Ro 67-4853 by extracellular Ca(2+). These studies reveal that binding of extracellular Ca(2+) to the predicted Ca(2+)-binding site in the extracellular domain of mGluR1α modulates not only glutamate-evoked signaling but also the actions of both orthosteric ligands and allosteric modulators on mGluR1α.
Insight into the removal and reapplication of small inhibitor molecules during area-selective atomic layer deposition of SiO2 (2020)

As the semiconductor industry progresses toward more complex multilayered devices with ever smaller features, accurately aligning these layers with respect to each other has become a bottleneck in the advancement to smaller transistor nodes. To avoid alignment issues, area-selective atomic layer deposition (ALD) can be employed to deposit material in a self-aligned fashion. Previously, we demonstrated area-selective ALD of SiO2 using three-step (i.e., ABC-type) ALD cycles comprising an acetylacetone (Hacac) dose (step A), a bis(diethylamino)silane precursor dose (step B), and an O2 plasma exposure (step C). In this work, the mechanisms of the removal and reapplication of the inhibitor molecules during area-selective ALD were studied, with the aim of enhancing the selectivity of the process. In situ infrared spectroscopy shows that the O2 plasma exposure does not completely remove the adsorbed Hacac species (i.e., acac adsorbates) at the end of the cycle. The persisting species were found to contain fragments of Hacac molecules, which hinder subsequent inhibitor adsorption in the next ALD cycle, and thereby contribute to a loss in selectivity. Alternatively, it was found that an H2 plasma is able to completely remove all acac species from the surface. An improvement in selectivity was achieved by using a four-step ALD cycle that includes an H2 plasma step, allowing the nucleation delay to be prolonged from 18 ± 2 to 30 ± 3 ALD cycles. As a result, 2.7 ± 0.3 nm SiO2 can be deposited with a selectivity of 0.9, whereas only 1.6 ± 0.2 nm can be achieved without the H2 plasma step. This work shows that the addition of a dedicated inhibitor removal step before the reapplication of the inhibitors can significantly improve the selectivity.
A Study of Joints Suitable for Lamina Emergent Mechanisms (2008)

One way to save space and reduce cost in a competitive environment is to use ortho-planar compliant mechanisms which can be made from sheets of material, or lamina emergent mechanisms (LEMs). One major challenge associated with LEM design, however, is creating joints with the desired motion characteristics, especially where complex spatial mechanism topologies are required. This paper presents some important considerations for designing joints for LEMs. A technique commonly used in robotics, using serial chains of revolute and prismatic joints to approximate the motion of complex joints, is presented for use in lamina emergent mechanisms. Important considerations such as linkage configuration and simple prototyping are also discussed.
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome (2007)

A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization.
An adequate theory for the shear strength of reinforced concrete structures (2008)

Traditional shear design procedures for concrete structures rely on empirical equations derived from laboratory experiments and lack the type of adequate theory that forms the basis of flexural design. As shear resistance depends on so many variables and because laboratory tests do not cover the full practical range of parameters, empirical shear design equations can result in structures with inadequate shear strength. Recent failures of such structures have highlighted the need for shear design provisions solidly based on an adequate theory. This paper introduces such a theory and explains the simple design models derived from the theory, which include a strut-and-tie model for disturbed regions and a sectional model for flexural regions. These models form the basis of the shear provisions on the 2004 Canadian standard for the design of concrete structures. In the current paper, results from nine major experimental series are compared with predictions from the new shear provisions and with predictions from the shear provisions of the Eurocode and the American Concrete Institute code. It is demonstrated that the new shear design provisions are capable of predicting the shear strength of reinforced concrete members and prestressed concrete members with considerably greater reliability.
In vitro selection of RNAs with increased tertiary structure stability (1999)

An in vitro selection system was devised to select RNAs based on their tertiary structural stability, independent of RNA activity. Selection studies were conducted on the P4-P6 domain from the Tetrahymena thermophila group I intron, an autonomous self-folding unit that contains several important tertiary folding motifs including the tetraloop receptor and the A-rich bulge. Partially randomized P4-P6 molecules were selected based on their ability to fold into compact structures using native gel electrophoresis in the presence of decreasing concentrations of MgCl2. After 10 rounds of the selection process, a number of sequence alterations were identified that stabilized the P4-P6 RNA. One of these, a single base deletion of C209 within the P4 helix, significantly stabilized the P4-P6 molecule and would not have been identified by an activity-based selection because of its essential role for ribozyme function. Additionally, the sequence analysis provided evidence that stabilization of secondary structure may contribute to overall tertiary stability for RNAs. This system for probing RNA structure irrespective of RNA activity allows analysis of RNA structure/function relationships by identifying nucleotides or motifs important for folding and then comparing them with RNA sequences required for function.