gebhart/patrepeval huggingface dataset:
An Optimization Framework for Silicon Photonic Evanescent-Field Biosensors Using Sub-Wavelength Gratings (2022)

Silicon photonic (SiP) evanescent-field biosensors aim to combine the information-rich readouts offered by lab-scale diagnostics, at a significantly lower cost, and with the portability and rapid time to result offered by paper-based assays. While SiP biosensors fabricated with conventional strip waveguides can offer good sensitivity for label-free detection in some applications, there is still opportunity for improvement. Efforts have been made to design higher-sensitivity SiP sensors with alternative waveguide geometries, including sub-wavelength gratings (SWGs). However, SWG-based devices are fragile and prone to damage, limiting their suitability for scalable and portable sensing. Here, we investigate SiP microring resonator sensors designed with SWG waveguides that contain a "fishbone" and highlight the improved robustness offered by this design. We present a framework for optimizing fishbone-style SWG waveguide geometries based on numerical simulations, then experimentally measure the performance of ring resonator sensors fabricated with the optimized waveguides, targeting operation in the O-band and C-band. For the O-band and C-band devices, we report bulk sensitivities up to 349 nm/RIU and 438 nm/RIU, respectively, and intrinsic limits of detection as low as 5.1 × 10<sup>-4</sup> RIU and 7.1 × 10<sup>-4</sup> RIU, respectively. This performance is comparable to the state of the art in SWG-based sensors, positioning fishbone SWG resonators as an attractive, more robust, alternative to conventional SWG designs.
A Critical Appraisal of the Role of Dietary Long-Chain Polyunsaturated Fatty Acids on Neural Indices of Term Infants: A Randomized, Controlled Trial (2000)

LCPUFA supplementation did not influence VEP acuity development in these well-nourished, formula-fed infants.
Qualification of laser optics for upcoming ESA space laser missions (2018)

As a consequence of the ongoing interest for deployment of laser systems into space, suitable optical components have to be developed and must be extensively space qualified to ensure reliable, continuous, and autonomous operation. The exposure to space environment can adversely affect the longevity of optics, mainly coatings, and lead to system degradation.
Isothermal Guest Desorption from Crystalline and Amorphous Phases of Syndiotactic Polystyrene (1999)

Isothermal desorption kinetics at different temperatures of 1,2-dichloroethane (DCE) from syndiotactic polystyrene films have been studied by Fourier transform infrared spectroscopy. For β-form films, where DCE is present only into the amorphous phase, nearly equal populations of trans and gauche conformers, during the whole desorption processes, are observed. On the other hand, for clathrate films, where DCE is present in both amorphous and crystalline phases, its trans conformer becomes largely predominant, as the desorption processes proceed. In agreement with previous FTIR and X-ray diffraction studies, these results can be rationalized by assuming that essentially only the DCE trans conformer is present in the clathrate phase. In this assumption, experimental desorption kinetics from clathrate samples can be separated into faster processes from the amorphous phase and slower processes from the crystalline phase. The validity of this separation procedure is confirmed by the close similarity between the desorption kinetics observed for the amorphous phase of β-form films and calculated for the amorphous phase of clathrate films.
The Japan Multi-Institutional Collaborative Cohort Study (J-MICC Study) to detect gene-environment interactions for cancer. (2008)

The Japan Multi-institutional Collaborative Cohort Study (J-MICC Study) launched in 2005, supported by a research grant for Scientific Research on Special Priority Areas of Cancer from the Japanese Ministry of Education, Culture, Sports, Science and Technology. Although the main purpose is to confirm and detect gene-environment interactions of lifestyle-related diseases, mainly of cancer, through the cohort analyses, it includes cross-sectional analyses on lifestyle factors, biomarkers, and genotypes, as well as confirmation/ screening of new biomarkers usable for early diagnosis of cancer. The endpoints are cancer diagnosis and death. The participants diagnosed as cancer will be identified through population-based cancer registries, hospital cancer registries, mail questionnaires, questionnaires at repeated visits, death certificates, health insurance data, and second survey questionnaires. Subjects are individuals aged 35 to 69 years enrolled from respondents to study announcements in specified areas, inhabitants attending health checkup examinations by local governments, visitors at health checkup centers, and patients at a cancer hospital. The number of subjects was set to be 100,000 throughout Japan. The enrollment period is from April 2005 to March 2010. The second survey is scheduled 5 years after their enrollment. The participants will be followed until 2025. The J-MICC Central Office is placed at Nagoya University Graduate School of Medicine. Ten participating research groups (Cohort Study Executing Groups) send baseline data and blood samples (buffy coat, serum, and plasma) anonymized with an identification number (J-MICC ID) to the Central Office. The data of second survey and follow-up will be linked using J-MICC ID. This study is expected to produce many findings on lifestyle and genetic traits associated with lifestyle-related diseases including cancer among Japanese.
Identification of preferential polishing effects using broad-probe AEM (1983)

Many applications of AEM (XEDS or EELS) in multiphase alloys demand the highest spatial resolution microanalysis, hence minimum probe size and thin (50-75 nm) foils. The quantitative elemental analyses, however, can be misleading if preferential polishing has occurred causing exaggeration or even removal of microstructural/microcompositional features. In this study, a large probe or “broad-beam” XEDS technique was employed to detect and identify preferential polishing effects. The broad-beam technique yields a “bulk” analysis, which, ideally, should be equivalent to the bulk chemical analysis. The XEDS analyses were performed with a JEM 120CX AEM equipped with a Kevex detector. Spectra were quantified with an ORTEC-EEDSII computer/multichannel analyzer employing the standardless technique and absorption correction (where necessary, following Tixier and Philibert) with programs developed by Zaluzec. Matrix analysis were made in a spot mode and “bulk” analyses were made with a broad, elliptically stigmated probe (∼10μm major axis), with the major axis parallel to the foil edge to minimize thickness variations in the analyzed volume.
Response of chondrocytes to shear stress: antagonistic effects of the binding partners Toll‐like receptor 4 and caveolin‐1 (2011)

Osteoarthritis (OA) is often a consequence of excessive mechanical loading of cartilage, which produces hydrostatic stress, tensile strain, and fluid flow. Application of high fluid shear to chondrocytes recapitulates the earmarks of OA, as evidenced by the induction of cyclooxygenase-2, prostaglandins (PGs), and interleukin-6 (IL-6). Here, we delineated the signaling pathway by which high fluid shear mediates the temporal regulation of IL-6 synthesis in human chondrocytes. We determined that Toll-like receptor 4 (TLR4) and caveolin-1 are binding partners in chondrocytes. Their expression is temporally regulated by fluid shear via the sequential up-regulation of microsomal PGE synthase-1 (mPGES-1) and L-PGDS. High shear stress rapidly induces an 8-fold up-regulation of TLR4 expression via an mPGES-1-dependent pathway, whereas prolonged shear exposure concurrently down-regulates TLR4 by >4-fold and up-regulates caveolin-1 expression by > 2.5-fold in an L-PGDS-dependent manner. TLR4 and caveolin-1 exert opposing effects on the activation of ERK1/2, PI3-K and PKA signaling pathways, which, in turn, regulate the NF-κB-dependent IL-6 synthesis in a time-dependent fashion. Reconstructing the signaling network regulating shear-induced IL-6 expression in chondrocytes may provide insights for developing therapeutic strategies to combat osteoarthritis.
Adaptive Scheduling in MCMC and Probabilistic Programming (2015)

We introduce an adaptive output-sensitive inference algorithm for MCMC and probabilistic programming, Adaptive Random Database. The algorithm is based on a single-site updating Metropolis-Hasting sampler, the Random Database (RDB) algorithm. Adaptive RDB (ARDB) differs from the original RDB in that the schedule of selecting variables proposed for modification is adapted based on the output of of the probabilistic program, rather than being fixed and uniform. We show that ARDB still converges to the correct distribution. We compare ARDB to RDB on several test problems highlighting different aspects of the adaptation scheme.
Supplementary Figure 1 from The Interplay Between Neutrophils and CD8&lt;sup&gt;+&lt;/sup&gt; T Cells Improves Survival in Human Colorectal Cancer (2023)

&lt;p&gt;Comparative phenotypic analysis of peripheral blood neutrophils from healthy donors and patients with CRC.&lt;/p&gt;
The necessity for standardization of glioma stem cell culture: a systematic review (2020)

Here, we review the most commonly used serum-free media and added components for glioma stem cell culture while highlighting the function of each component used in the media. We emphasize the necessity for standardization of glioma stem cell culture and propose a standard culture medium to prevent bias in glioma stem cell research.
First-principles theory of electron-spin fluctuation coupling and superconducting instabilities in iron selenide (2015)

We present first-principles calculations of the coupling of quasiparticles to spin fluctuations in iron selenide and discuss which types of superconducting instabilities this coupling gives rise to. We find that strong antiferromagnetic stripe-phase spin fluctuations lead to large coupling constants for superconducting gaps with ${s}_{\ifmmode\pm\else\textpm\fi{}}$ symmetry, but these coupling constants are significantly reduced by other spin fluctuations with small wave vectors. An accurate description of this competition and an inclusion of band-structure and Stoner parameter renormalization effects lead to a value of the coupling constant for an ${s}_{\ifmmode\pm\else\textpm\fi{}}$-symmetric gap which can produce a superconducting transition temperature consistent with experimental measurements.
Characterization of GaAs self-aligned refractory-gate metal-semiconductor field-effect transistor (MESFET) integrated circuits (1987)

GaAs metal-semiconductor field-effect transistors (MESFETs) and other integrated-circuit elements were characterized by including extensive process test sites on wafers with digital logic and memory circuits. A self-aligned, refractory-gate enhancement/depletion (E/D) process was employed which included 47SiF+ channel and source/drain implants, capless arsenic overpressure furnace annealing, WSi0.11 gate metal with in situ sputter cleaning, Ni-Au-Ge ohmic contacts, Si3N4 or SiO2 insulation, and Ni-Au wiring. On-water threshold voltage standard deviations as low as 31 mV for 1-μm E-FETs and 49 mV for 1-μm D-FETs were measured using 51-mm standard semi-insulating liquid-encapsulated Czochralski GaAs substrates. Threshold voltage control from wafer to wafer was of order 100 mV. Schottky diode barrier height was about 0.73 eV with an ideality of 1.2, although small self-aligned Schottky gates often showed excess conduction believed to occur at the gate edges. FET square-law coefficient, subthreshold leakage, gate capacitance, backgating, contact resistance, and wiring and insulation characteristics were also measured and found satisfactory. Fully functional 1-μm gate E/D MESFET circuits including a 4×4 bit multiplier, a 4×4 crosspoint switch, a 448-bit static RAM, and an integrated photodiode amplifier were demonstrated.
Performance of low loss, high speed interconnects for multi-GHz digital systems (2003)

Preliminary frequency-, time-, and digital-domain testing and electromagnetic simulations indicate that the striplines and microstrip lines of Honeywell's thin-film multilayer (TFML) technology are suitable for high-performance digital systems that require operation at frequencies greater than 1 GHz. The return loss was typically -20 dB, which indicates the ability to design and fabricate controlled impedance lines with Honeywell's TFML technology. The 1- and 2-GHz digital-domain test measurements did not appear to be affected significantly by the reflections. The insertion loss of approximately -2.5 dB/in. at 9 GHz is acceptable for relatively short signal interconnect lines which, in any event, are required to minimize interchip propagation delays in a functioning system. Predictions from the Mayo electromagnetic modeling package show excellent agreement with measured signal and crosstalk waveforms. The crosstalk between adjacent lines is less than -20 dB even when the coupled line length is very long (>6 in.). Vias and via pads show negligible effects on insertion and return losses up to a frequency of 9 GHz. Large impedance mismatches severely affect the return losses, and therefore should be avoided. Stubs in the interconnect must be kept smaller than 1/4 of the smallest wavelength within the signal bandwidth.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
PfCRT and PfMDR1 modulate interactions of artemisinin derivatives and ion channel blockers (2016)

Treatment of the symptomatic asexual stage of Plasmodium falciparum relies almost exclusively on artemisinin (ART) combination therapies (ACTs) in endemic regions. ACTs combine ART or its derivative with a long-acting partner drug to maximize efficacy during the typical three-day regimen. Both laboratory and clinical studies have previously demonstrated that the common drug resistance determinants P. falciparum chloroquine resistance transporter (PfCRT) and multidrug resistance transporter (PfMDR1) can modulate the susceptibility to many current antimalarial drugs and chemical compounds. Here we investigated the parasite responses to dihydroartemisinin (DHA) and various Ca(2+) and Na(+) channel blockers and showed positively correlated responses between DHA and several channel blockers, suggesting potential shared transport pathways or mode of action. Additionally, we demonstrated that PfCRT and PfMDR1 could also significantly modulate the pharmacodynamic interactions of the compounds and that the interactions were influenced by the parasite genetic backgrounds. These results provide important information for better understanding of drug resistance and for assessing the overall impact of drug resistance markers on parasite response to ACTs.
Palladium hetero‐di(N‐heterocyclic carbene) complexes and their catalytic activities in direct C–H arylation of heteroarenes (2022)

A library of neutral and cationic palladium complexes of cis ‐chelating hetero‐dicarbene ligands have been prepared. These ligands contain two different NHC donors allowing for a wider degree of variation, and the impact of the distinct NHC units has been compared using various spectroscopic means. In addition, the catalytic activities of these complexes in the direct C‐H arylation of thiophenes with aryl halides were studied leading to the finding that the neutral dibromido complexes of the type [PdBr 2 (diNHC)] generally outperformed their cationic [Pd (NCMe) 2 (diNHC)](OTf) 2 counterparts. More importantly, complexes containing more distinct NHC units give rise to superior catalysts due to an amplified “stereoelectronic asymmetry” within the complex. A preliminary photophysical study of some selected thiophene reaction products has been conducted as well. The ability to individually change each NHC donor in such dicarbene ligands allows for a better fine‐tuning of complex properties in search for superior catalysts.
Uncertainty Quantification, Rare Events and Mission Optimization: Stochastic Variations of Metal Temperature During a Transient (2014)

Gas turbines are designed to follow specific missions and the metal temperature is usually predicted with deterministic methods. However, in real life the mission is subjected to strong variations which can affect the thermal response of the components. This paper presents a stochastic analysis of the metal temperature variations during a gas turbine transient. A Monte Carlo Method (MCM) with Meta Model is used to evaluate the probability distribution of the stator disk temperature. The MCM is applied to a series of CFD simulations of a stator well, whose geometry is modified according to the deformations predicted during the engine cycle by a coupled thermo-mechanical analysis of the metal components. It is shown that even considering a narrow band for the stochastic output, +/− σ, the transient thermal gradients can be up to two orders of magnitude greater than those obtained with a standard deterministic analysis. Moreover, a small variation in the tail of the input probability density function, a rare event, can have serious consequences on the uncertainty level of the temperature. Rare events although inevitable they are not usually considered during the design phase. In this paper it is shown for the first time that is possible to mitigate their effect, minimizing the maximum standard deviation induced by the tail of the input PDF. The mission optimization reduces the maximum standard deviation by 15% and the mean standard deviation of about 12%. The maximum thermal gradients are also reduced by 10%, although this was not the parameter used as the goal in the optimisation study.
Expression of hypoxia-inducible protein 2 in renal cell carcinoma: A promising candidate for molecular targeting therapy (2010)

This study investigated the expression of hypoxia-inducible protein 2 (HIG2), a novel renal cell carcinoma (RCC)-associated molecule and an essential growth factor for RCC, in kidneys to elucidate its clinical significance in RCC. An immunohistochemical study of HIG2 was conducted in 93 surgical samples of RCC tissues and 10 samples of normal kidney tissues obtained after nephrectomies for localized RCC. HIG2 expression was also correlated with clinicopathological characteristics and survival. Only faint or weak immunostaining for HIG2 was observed in normal kidney samples. HIG2 expression was found in 86% of RCC tissues (80/93). When analyzed by histological type, positive staining for HIG2 was detected in all papillary (7/7), chromophobe (1/1) and cyst-associated (3/3) RCC. In contrast, the HIG2 expression was observed in 85% of clear cell (68/80) and 50% of spindle cell (1/2) RCC. Labeling indices were 74.1, 45.4, 39, 24.8 and 12.1% in papillary, spindle, clear cell, cyst-associated and chromophobe RCC, respectively. A significant increase in HIG2 expression was noted in RCC tissues obtained from patients with high stage RCC, lymph node metastasis and high nuclear grade (p<0.001, p<0.02 and p<0.006, respectively). RCC patients with a negative HIG2 staining had prolonged 5-year cancer-specific survival. In conclusion, HIG2 expression was extensively observed in RCC tissues and was higher in advanced RCC, suggesting that HIG2 is a candidate for the development of molecular targeting therapy.
Clinical application and technical challenges for intracardiac ultrasound imaging - catheter based ICE imaging with EP mapping (2005)

A 9F combination intracardiac imaging and electrophysiology mapping catheter has been developed and tested to help guide diagnostic and therapeutic intracardiac electrophysiology procedures. A 7.5 MHz, 64 element, side looking phased array was used for sector scanning from the tip of the catheter. Multiple electrophysiology (EP) mapping sensors were mounted as ring electrodes just proximal to the array for electrocardiographic synchronization of ultrasound images. The catheter has been used in vivo in a porcine animal model and has demonstrated useful intracardiac echocardiographic (ICE) visualization of both cardiac tissue and electrophysiology catheters in the right atrium. The catheter performed well in high frame rate imaging, color flow imaging, and strain rate imaging of atrial and ventricular structures.
Opportunities and challenges for the development of antisense treatment in neuromuscular disorders (2011)

A lot of progress has been made in the development of antisense-mediated approaches during recent years and they may become clinically applicable in the near future.
Haplotypes of the endothelial protein C receptor (EPCR) gene are not associated with severe malaria in Tanzania (2015)

Frequencies of SNPs determining PROCR haplotypes were in concordance with other African studies. The PROCR H3 allele was associated with higher levels of sEPCR, confirming earlier findings, however, in this Tanzanian population; neither PROCR haplotype nor level of sEPCR was associated with severe malaria, however, larger studies are needed to confirm these findings.
Synthese totale de structures polypyridiniques helicoidales et synthese de molecules polypyridiniques comportant des unites 1,3-pyrimidiniques (1996)

Ce manuscrit presente la synthese totale de macrostructures polypyridiniques helicoidales et la synthese de molecules polypyridiniques comportant des unites 1,3-pyrimidiniques. Le premier chapitre est consacre a une breve presentation generale du probleme concernant les applications des structures de type polypyridiniques et polypyrimidiniques. Dans le deuxieme chapitre, nous presenterons, tout d'abord, une etude bibliographique detaillee sur les methodes de synthese des pyridines et polypyridines. Ensuite, nous decrirons les strategies envisagees pour la synthese des macrostructures polypyridiniques helicoidales. Apres la presentation de la synthese de l'octahydroacridine substituee en position 9 par une chaine hydrocarbonee, nous presenterons les differents amenagements fonctionnels realises sur ce synthon essentiel. Partant de ces derives de l'octahydroacridine, nous decrirons la synthese de ces homologues superieurs penta et heptacycliques, qui constituent les intermediaires cles pour acceder aux macrostructures polypyridiniques a 11 cycles et a 15 cycles adjacents. Au cours de ce travail, deux nouvelles methodes synthetiques ont ete mises au point: le rearrangement de boekelheide dans l'anhydride trifluoroacetique et l'alkylation des enaminones par les organomagnesiens. Le troisieme chapitre sera consacre a la presentation d'une methode simple et efficace de synthese des differentes structures polypyridiniques comportant des unites 1,3-pyrimidiniques. La methode est entierement basee sur la condensation d'une enaminone avec une amidine et permet d'aboutir avec d'excellents rendements a plusieurs composes polypyridiniques. Nous presenterons egalement, une etude preliminaire des proprietes de complexation de ces structures vis-a-vis du ruthenium